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Zhang Q, Wen D, Liu Q, Opriessnig T, Yu X, Jiang Y. Universal primer multiplex PCR assay for detection and genotyping of porcine astroviruses. J Virol Methods 2023; 322:114822. [PMID: 37729969 DOI: 10.1016/j.jviromet.2023.114822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/03/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
Porcine astroviruses (PAstV) are members of the family Astroviridae, Mamastravirus genus and have been identified to have five genotypes (PAstV1-5). These viruses are highly prevalent in pigs and can cause enteric disease as well as neurological or respiratory symptoms depending on their genotypes. At present, the epidemiological impacts of some PAstV genotypes on pigs are largely unknown and hence continuously monitoring of these PAstVs may be needed. The purpose of this research was to develop an improved and efficient detection tool for PAstVs and to evaluate the developed method using clinical samples. Initially, a set of five chimeric primers (CP), each comprising genotype specific primer pairs with an identical universal adapter at the 5' end, and a universal primer (UP) that is identical to universal adapter sequence, were designed. With these tools in place, a novel multiplex PCR system with universal primer was established for the simultaneous detection of the five types of PAstV. This method can specifically detect PAstV genotypes, with a limit of detection (LOD) of 5 copies/μL for each genotype irrespective of single or mixed target template. Using this new assay, 273 pig fecal samples were investigated for further assay evaluation. Among all samples, the positive rate was 70.0% with PAstV4 in 56.8% of the samples, PAstV2 in 38.8%, PAstV1 in 16.8%, and PAstV5 in 11.0%. More than one PAstV in a sample were detected in 39.2% of the samples. The consistency rate between the novel multiplex PCR and singleplex PCRs was 96.4-100%. Given its rapidity, specificity and sensitivity, the novel multiplex PCR is a useful approach for demonstrating single or mixed genotype infections of PAstV.
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Affiliation(s)
- Qiuya Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Dan Wen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Qin Liu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Tanja Opriessnig
- Vaccines and Diagnostics Department, Moredun Research Institute, Penicuik, Midlothian, UK; Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Xiaoya Yu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yonghou Jiang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China.
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Ghorbani G, Rahimi E, Shakerian A. Antibiotic resistance's Genotypic and Phenotypic Characteristics and the Frequency of Virulence Factors in P. aeruginosa Isolates Isolated from Water Samples in Iran. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7076433. [PMID: 36246982 PMCID: PMC9553504 DOI: 10.1155/2022/7076433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/22/2022] [Accepted: 09/23/2022] [Indexed: 11/18/2022]
Abstract
Pseudomonas aeruginosa is a pathogenic bacterium that can contaminate water. In this study, 430 water samples were evaluated for P. aeruginosa, antibiotic resistance, and the abundance of virulence factors. P. aeruginosa was isolated from 28 (6.51%) water samples. Among the types of water, well and spring water showed the highest P. aeruginosa with, respectively, 20 (15.6%) and 5 (8.06%) positive samples per type of samples. Drinking water and mineral water showed minor contamination with P. aeruginosa. The prevalence of antibiotic resistance against meropenem, imipenem, erythromycin, gentamicin, chloramphenicol, and enrofloxacin was zero. The lowest and highest prevalence of antibiotic resistance was observed in drinking water and well water, respectively. The most abundant genes encoding antibiotic resistance in the P. aeruginosa were blaTEM , blaCTX-M , and blaSHV . This study also showed that the most abundant virulence genes in the Pseudomonas aeruginosa strain isolated from water were algD (15 = 3.49%), lasB (11 = 2.56%), toxA (10 = 2.32%), and exoS (7 = 1.63%). This study suggests that water may be a source of P. aeruginosa and contribute to releasing resistance genes through the food chain. Cross-contamination is the water transfer process that can cause contamination with P. aeruginosa in water. Therefore, hygienic principles can be effective in reducing water contamination.
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Affiliation(s)
- Ghasem Ghorbani
- Department of Food Hygiene, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Ebrahim Rahimi
- Department of Food Hygiene, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Amir Shakerian
- Research Center of Nutrition and Organic Products, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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3
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Bakht M, Alizadeh SA, Rahimi S, Kazemzadeh Anari R, Rostamani M, Javadi A, Peymani A, Marashi SMA, Nikkhahi F. Phenotype and genetic determination of resistance to common disinfectants among biofilm-producing and non-producing Pseudomonas aeruginosa strains from clinical specimens in Iran. BMC Microbiol 2022; 22:124. [PMID: 35525944 PMCID: PMC9078005 DOI: 10.1186/s12866-022-02524-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 04/11/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is a common pathogen in Hospitalized patients, and its various resistance mechanisms contribute to patient morbidity and mortality. The main aims of the present study were to assess the susceptibility of biofilm-producing and non-producing P. aeruginosa isolates to the five commonly used Hospital disinfectants, to evaluate the synergistic effect of selected disinfectants and Ethylene-diamine-tetra acetic acid (EDTA), and the effect of exposure to sub-inhibitory concentrations of Sodium hypochlorite on antimicrobial susceptibility test. RESULTS The results showed that sodium hypochlorite 5% and Ethanol 70% were the most and least effective disinfectants against P. aeruginosa, respectively. The addition of EDTA significantly increased the effectiveness of the selected disinfectants. The changes in the antibiotic-resistance profiles after exposure to sub-inhibitory concentrations of disinfectants were observed for different classes of antibiotics (Carbapenems, Aminoglycosides, Cephalosporins, Fluoroquinolones). As well as near the all isolates harbored efflux pump genes and 117 (97.5%) of isolates produced biofilm. CONCLUSION In the current study, the mixture of disinfectant and EDTA were the most suitable selection to disinfect Hospital surfaces and instruments. Also, it was clear that exposure to sub-inhibitory concentrations of Sodium hypochlorite results in resistance to some antibiotics in P. aeruginosa species. Strong and intermediate biofilm formers belonged to MDR/XDR strains. Future studies should include more complex microbial communities residing in the Hospitals, and more disinfectants use in Hospitals.
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Affiliation(s)
- Mehdi Bakht
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Safar Ali Alizadeh
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Sara Rahimi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Raana Kazemzadeh Anari
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohammad Rostamani
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amir Javadi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
- Department of Community Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amir Peymani
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Farhad Nikkhahi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran.
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Fakhkhari P, Tajeddin E, Azimirad M, Salmanzadeh-Ahrabi S, Abdi-Ali A, Nikmanesh B, Eshrati B, Gouya MM, Owlia P, Zali MR, Alebouyeh M. Involvement of Pseudomonas aeruginosa in the occurrence of community and hospital acquired diarrhea, and its virulence diversity among the stool and the environmental samples. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:61-71. [PMID: 32073302 DOI: 10.1080/09603123.2020.1726300] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
Transmission of Pseudomonas aeruginosa along the food chain could cause gastrointestinal infections. To show this involvement, the prevalence, putative virulence genotype, and antibiotic resistance phenotype of P. aeruginosa isolates from stool of 1482 patients with community and hospital acquired diarrhea were compared with 87 isolates from the environmental samples. The results showed infection with P. aeruginosa in 3.4% of the cases, while 57.4% of vegetable samples were contaminated. Significantly higher frequency of lasB (98%), aprA (98%), exoY (98%), and exoS (90%), but lower rate of exoT (39.2%), was detected among the stool isolates. Multi-drug resistance (MDR) phenotype was detected in 25.5% and 4% of the stool and vegetable isolates, respectively. A higher rate of studied virulence genes was detected among the MDR strains vs non-MDR strains. These results indicate P. aeruginosa as a causative agent of diarrhea either among the hospitalized patients and those with community-acquired diarrhea.
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Affiliation(s)
- Parisa Fakhkhari
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Elahe Tajeddin
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- National Nutrition and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Ahya Abdi-Ali
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Bahram Nikmanesh
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Eshrati
- Center for Communicable Disease Control, Ministry of Health and Medical Education, Tehran, Iran
| | - Mohammad Mehdi Gouya
- Center for Communicable Disease Control, Ministry of Health and Medical Education, Tehran, Iran
| | - Parviz Owlia
- Molecular Microbiology Research Center (MMRC), Shahed University, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Alebouyeh
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Ramos JF, Leite G, Martins RCR, Rizek C, Al Sanabani SS, Rossi F, Guimarães T, Levin AS, Rocha V, Costa SF. Clinical outcome from hematopoietic cell transplant patients with bloodstream infection caused by carbapenem-resistant P. aeruginosa and the impact of antimicrobial combination in vitro. Eur J Clin Microbiol Infect Dis 2021; 41:313-317. [PMID: 34651217 DOI: 10.1007/s10096-021-04361-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/01/2021] [Indexed: 11/25/2022]
Abstract
Bloodstream infection (BSI) caused by carbapenem-resistant P. aeruginosa (CRPA) has high mortality in hematopoietic stem cell transplant (HSCT) recipients. We performed MIC, checkerboard, time-kill assay, PFGE, PCR, and whole genome sequence and described the clinical outcome through Epi Info comparing the antimicrobial combination in vitro. Mortality was higher in BSI caused by CRPA carrying the lasB virulence gene. The isolates were 97% resistant to meropenem displaying synergistic effect to 57% in combination with colistin. Seventy-three percent of the isolates harbored blaSPM-1 and Tn4371 and belonged to ST277. The synergistic effect in vitro with meropenem with colistin appeared to be a better therapeutic option.
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Affiliation(s)
- Jessica Fernandes Ramos
- Department of Infectious Diseases of Faculdade de Medicina, University of Sao Paulo, São Paulo, Brazil
- Department of Haematology, Hemotherapy and Cellular Therapy of Faculdade de Medicina, University of Sao Paulo, São Paulo, Brazil
| | - Gleice Leite
- Laboratory of Medical Investigation - LIM 49 - Medical Tropical Institute, University of Sao Paulo, São Paulo, Brazil.
| | | | - Camila Rizek
- Laboratory of Medical Investigation - LIM 49 - Medical Tropical Institute, University of Sao Paulo, São Paulo, Brazil
| | - Sabri Saeed Al Sanabani
- Laboratory of Medical Investigation - LIM 52 - Medical Tropical Institute, University of Sao Paulo, São Paulo, Brazil
| | - Flavia Rossi
- Laboratory of Clinical Microbiology of Hospital das Clínicas, Faculdade de Medicina, University of Sao Paulo, São Paulo, Brazil
| | - Thais Guimarães
- Department of Infectious Diseases of Faculdade de Medicina, University of Sao Paulo, São Paulo, Brazil
- Laboratory of Medical Investigation - LIM 49 - Medical Tropical Institute, University of Sao Paulo, São Paulo, Brazil
| | - Anna Sara Levin
- Department of Infectious Diseases of Faculdade de Medicina, University of Sao Paulo, São Paulo, Brazil
- Laboratory of Medical Investigation - LIM 49 - Medical Tropical Institute, University of Sao Paulo, São Paulo, Brazil
| | - Vanderson Rocha
- Department of Haematology, Hemotherapy and Cellular Therapy of Faculdade de Medicina, University of Sao Paulo, São Paulo, Brazil
- Haematology Department, NHS BT, Oxford University, Oxford, UK
| | - Silvia Figueiredo Costa
- Department of Infectious Diseases of Faculdade de Medicina, University of Sao Paulo, São Paulo, Brazil
- Laboratory of Medical Investigation - LIM 49 - Medical Tropical Institute, University of Sao Paulo, São Paulo, Brazil
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6
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Yang H, Wang Y, Yang Q, Fan H, Wang L, Zhang T, Li Z, Liu G, Zhao P, Wu H, Dong J, Liang W. A Rapid and Sensitive Detection Method for Pseudomonas aeruginosa Using Visualized Recombinase Polymerase Amplification and Lateral Flow Strip Technology. Front Cell Infect Microbiol 2021; 11:698929. [PMID: 34595129 PMCID: PMC8478171 DOI: 10.3389/fcimb.2021.698929] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
Pseudomonas aeruginosa is a common opportunistic pathogen that causes acute nosocomial necrotizing pneumonia and is the predominant source of chronic lung infections in patients with the genetic disorder cystic fibrosis. Early diagnosis in infected patients and monitoring P. aeruginosa contamination is therefore of great importance in controlling disease spread and development with timely drugs intervention treatment and cut off infection source. Traditional culture-biochemical methods are time consuming and highly dependent on technicians and expensive instruments. To address these challenges, the present study aimed to develop a rapid, sensitive, and specific, on-site detection method for P. aeruginosa based on recombinase polymerase amplification (RPA) combined with lateral flow strip (LFS) technology. The experimental process included screening and modification of primer and probe sets targeting the unique virulence gene elastase B (lasB); specificity detection in 29 strains of P. aeruginosa and 23 closely-related pathogenic bacteria; sensitivity measurements with gradient-diluted P. aeruginosa genomic DNA and probit regression analysis; and clinical application evaluation using 574 patients samples and calculating coincidence rate and kappa index value in comparison with the culture-biochemical method. The P. aeruginosa RPA-LFS assay could complete the amplification process at 37°C constant temperature within 30 min and results could be visualized by the naked eye within 10 min on LFS. The assay displayed high sensitivity with a limit of detection of 3.05 CFU/reaction. It also demonstrated high specificity by showing no cross reaction with other pathogenic bacteria, and rapidness by being completed in less than an hour. Furthermore, when used with clinical samples, the assay had a coincidence rate of 98.26% with the culture-biochemical method and a kappa index value of 0.9433. These data indicate that the RPA-LFS assay represents a major improvement for P. aeruginosa detection, especially in resource-limited areas.
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Affiliation(s)
- Haitao Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Yan Wang
- Department of Laboratory Medicine, The Second People's Hospital of Lianyungangg City, Lianyungangg, China
| | - Qiankun Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Hui Fan
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Lei Wang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China.,Department of Laboratory Medicine, The Second People's Hospital of Lianyungangg City, Lianyungangg, China
| | - Tianmeng Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Zhixing Li
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Gang Liu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Panpan Zhao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Huahua Wu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Jingquan Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Wei Liang
- Laboratory Department of Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, China
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Dual-mode aptasensor for simultaneous detection of multiple food-borne pathogenic bacteria based on colorimetry and microfluidic chip using stir bar sorptive extraction. Mikrochim Acta 2021; 188:244. [PMID: 34231048 DOI: 10.1007/s00604-021-04902-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023]
Abstract
A dual-mode aptasensor using colorimetry and microfluidic chip (MC) together with stir bar sorptive extraction (SBSE) has been developed for firstly qualifying samples contaminated with Vibrio parahaemolyticus (V.P) and Salmonella typhimurium (S.T), then precisely determine both of them in positive samples. For this purpose, the aptamer-streptavidin encoded probes (Apt-SAEs) corresponding to different bacteria were prepared in advance. Then, a stir bar modified with 4-mercaptophenylboronic acid (MPBA) was made to extract bacteria together with Apt-SAE probes. The binding event of aptamer and target triggered the formation of two sandwich structures containing Apt-SAE, V.P or S.T. The concentration of bacteria could be enriched by 1000 times within 15 min to avoid long-time enrichment process. Finally, the stir bar was immersed in the 3,3',5,5'-Tetramethylbenzidine (TMB)-H2O2 solution for color development. The color could be observed by naked eyes to judge whether the analytes were present. The colorless samples were judged to be negative. For the positive samples, the adsorbed encoded probes corresponding to different bacteria would be eluted from the stir bar and rapidly analyzed by the MC. Under the optimized conditions, 100 CFU/mL of V.P or S.T or both of them could be observed by colorimetry and 35 CFU/mL of them could be detected (S/N = 3) by the MC. The assay has significant application value for on-site screening and multiple detection of food-borne pathogenic bacteria.
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8
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Nan P, Wen D, Opriessnig T, Zhang Q, Yu X, Jiang Y. Novel universal primer-pentaplex PCR assay based on chimeric primers for simultaneous detection of five common pig viruses associated with diarrhea. Mol Cell Probes 2021; 58:101747. [PMID: 34116142 DOI: 10.1016/j.mcp.2021.101747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 11/18/2022]
Abstract
Viral pathogens associated with diarrhea in pigs include porcine circovirus 2 (PCV2), porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine rotavirus A (RVA) and C (RVC) among others. In this study, a novel universal primer-based pentaplex PCR (UP-M-PCR) assay was developed for simultaneous detection and differentiation of these five viruses. The assay uses a short-cycle multiplex amplification by chimeric primers (CP), which are virus specific, with a tail added at the 5' end of the universal primer (UP), followed by universal amplification using UPs and a regular cycle amplification. Five universal primers with CPs (UP1-5) were designed and evaluated in an UP-based single PCR (UP-S-PCR). All five UPs were found to work efficiently and UP2 exhibited the best performance. After system optimizations, the analytical sensitivity of the UP-M-PCR, using plasmids containing the specific viral target fragments, was 5 copies/reaction for each of the five viruses irrespective of presence of a single or multiple viruses in the reaction. No cross-reaction was observed with other non-target viruses. When 273 fecal samples from clinically healthy pigs were tested, the assay sensitivity was 90.9-100%, the specificity was 98.0-100%, and the agreement rate with the UP-S-PCR was 98.5-99.6% with a Kappa value being 0.95-0.98. In summary, the UP-M-PCR developed here is a rapid and highly sensitive and specific detection method that can be used to demonstrate mixed infections in pigs with diarrhea.
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Affiliation(s)
- Pei Nan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Dan Wen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Tanja Opriessnig
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK; Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Qiuya Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xiaoya Yu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yonghou Jiang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China.
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9
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Lin Z, Li H, He L, Jing Y, Pistolozzi M, Wang T, Ye Y. Efficient genome editing for Pseudomonas aeruginosa using CRISPR-Cas12a. Gene 2021; 790:145693. [PMID: 33961975 DOI: 10.1016/j.gene.2021.145693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/29/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
The CRISPR-Cas12a system has been demonstrated as an attractive tool for bacterial genome engineering. In particular, FnCas12a recognizes protospacer-adjacent motif (PAM) sites with medium or low GC content, which complements the Cas9-based systems. Here we explored Francisella novicida Cas12a (FnCas12a) for genome editing in Pseudomonas aeruginosa. By using a two-plasmid system expressing the constitutive FnCas12a nuclease, the inducible λRed recombinase, a CRISPR RNA (crRNA), we achieved gene deletion, insertion and replacement with high efficiency (in most cases > 75%), including the deletion of large DNA fragments up to 15 kb and the serial deletion of duplicate gene clusters. This work should provide a useful and complementary addition to the genome engineering toolbox for the study of P. aeruginosa biology and physiology.
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Affiliation(s)
- Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
| | - Huanhuan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Lan He
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yanyun Jing
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Marco Pistolozzi
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Tingting Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
| | - Yanrui Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
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10
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Virulence genotyping of drug resistant Pseudomonas aeruginosa clinical isolates in Egypt using multiplex PCR. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2020.101000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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Shanon MR, Al-Marzoqi AH, Hussein HJ. Prototheca spp. co-infections and their virulence factors in human protothecosis in Hillah city, Iraq. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2020.101009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Wei L, Wu Q, Zhang J, Guo W, Gu Q, Wu H, Wang J, Lei T, Xue L, Zhang Y, Wei X, Zeng X. Prevalence, Virulence, Antimicrobial Resistance, and Molecular Characterization of Pseudomonas aeruginosa Isolates From Drinking Water in China. Front Microbiol 2020; 11:544653. [PMID: 33343513 PMCID: PMC7744469 DOI: 10.3389/fmicb.2020.544653] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 11/02/2020] [Indexed: 01/26/2023] Open
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen and remains a major threat to the microbial safety of drinking water. There is a lack of comprehensive data on P. aeruginosa contamination in drinking water in China. Therefore, this study aimed to determine the prevalence, genetic diversity, virulence genes, and antimicrobial resistance of P. aeruginosa isolated from mineral water and spring water in China. From January 2013 to January 2014, 314 drinking water samples were collected from 23 cities in China. Of the collected samples, 77 (24.5%) were contaminated with P. aeruginosa, and these comprised 34 raw water (30.4%), 39 activated carbon-filtered water (30.6%), and four final water product (3.9%). A total of 132 P. aeruginosa isolates were obtained, and all of them showed the presence of virulence genes, with the detection rates of ExoU, ExoS, phzM, toxA, and lasB genes being 7.6, 86.3, 95.5, 89.4, and 100%, respectively. All isolates were sensitive to the 14 antibiotics (ciprofloxacin, levofloxacin, ofloxacin, norfloxacin, gentamicin, tobramycin, amikacin, polymyxin B, imipenem, meropenem, aztreonam, ceftazidime, cefepime, and piperacillin/tazobactam) tested. The 132 isolates were categorized into 42 sequence types according to multilocus sequence typing, and ST235 accounted for 8.3% (11) of the total isolates. Thus, this study provides comprehensive data on the prevalence and characteristics of P. aeruginosa in drinking water in China and can aid in developing preventive measures against contamination during the drinking water treatment process.
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Affiliation(s)
- Lei Wei
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Weipeng Guo
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Huiqing Wu
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Tao Lei
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Youxiong Zhang
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xianhu Wei
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaocong Zeng
- Biological Testing and Analysis Department, Guangdong Provincial Institute of Food Inspection, Guangzhou, China
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13
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Shang Y, Xu Y, Huang K, Luo Y, Xu W. Multiplex pyrosequencing quantitative detection combined with universal primer-multiplex-PCR for genetically modified organisms. Food Chem 2020; 320:126634. [PMID: 32208182 DOI: 10.1016/j.foodchem.2020.126634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/27/2020] [Accepted: 03/16/2020] [Indexed: 10/24/2022]
Abstract
A multiplex pyrosequencing quantitative detection technique combined with universal primer-multiplex-PCR (UP-M-PCR) was established. In this study, a pyrosequencing results analysis software was first self-compiled, which realized the DNA sequences degeneration, and converted the pyrosequencing results and base composition of the target sequences into mathematic relations. Five calculation models were put forward based on the actual situation, which adjusted the values smaller than zero or the detection limit. By applying this method, samples containing five genetically modified (GM) lines mixed in random ratio were quantified, it showed that the quantification was very close to the actual value, and the detection sensitivity was as low as 1.47% of a single component, which satisfied most labeling policies. This novel method is realized without fluorescent group labeling, hence the number of targets is not limited by factors inherent in method or equipment, and is proven to be a reliable tool for the quantitative detection.
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Affiliation(s)
- Ying Shang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Faulty of Agriculture and Food, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yuancong Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China.
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14
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Luo F, Li Z, Dai G, Lu Y, He P, Wang Q. Simultaneous detection of different bacteria by microchip electrophoresis combined with universal primer-duplex polymerase chain reaction. J Chromatogr A 2020; 1615:460734. [DOI: 10.1016/j.chroma.2019.460734] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022]
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15
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Ghazalibina M, Morshedi K, Farahani RK, Babadi M, Khaledi A. Study of virulence genes and related with biofilm formation in Pseudomonas aeruginosa isolated from clinical samples of Iranian patients; A systematic review. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Dapgh AN, Hakim AS, Abouelhag HA, Abdou AM, Elgabry EA. Detection of virulence and multidrug resistance operons in Pseudomonas aeruginosa isolated from Egyptian Baladi sheep and goat. Vet World 2019; 12:1524-1528. [PMID: 31849411 PMCID: PMC6868267 DOI: 10.14202/vetworld.2019.1524-1528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/26/2019] [Indexed: 11/24/2022] Open
Abstract
Background: Pseudomonas aeruginosa is a pit of an enormous group of free-living bacteria that are able to live everywhere and suggested to be the causative agent of great scope of acute and chronic animal infections. Aim: The current study was carried out to illustrate the prevalence of P. aeruginosa in small ruminants and existence of some virulence operons as well as its antimicrobial resistance. Materials and Methods: A total of 155 samples from sheep and 105 samples from goats (mouth abscesses, fecal swabs, nasal, tracheal swabs, and lung tissue) were collected for bacteriological study, existence of some virulence expression operons with the study of their sensitivity to the antimicrobials using disc diffusion and presence of mexR operon which is responsible for multidrug resistance (MDR). Results: The bacteriological examination revealed that P. aeruginosa was isolated from nine out of 155 samples from sheep (5.8%) and four isolates out of 105 samples from goat (3.8%). It is found that 12 (92.3%), 10 (76.9 %), and 8 (61.5%) of P. aeruginosa isolates harbored hemolysin phospholipase gene (pcl H), gene (exo S), and enterotoxin gene (tox A), respectively. The results of antibiotic sensitivity test showed that all tested isolates were resistant to ampicillin, bacitracin, erythromycin, streptomycin, tetracycline, trimethoprim-sulfamethoxazole, and tobramycin but sensitive to ciprofloxacin and norfloxacin. The MDR (mex R) operon was existed in all isolates. Conclusion: There is a growing risk for isolation of virulent MDR P. aeruginosa from sheep and goat illness cases, and this should be regarded in the efficient control programs.
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Affiliation(s)
- A N Dapgh
- Department of Bacteriology, Animal Health Research Institute, Dokki, Giza, Egypt
| | - A S Hakim
- Department of Microbiology and Immunology, National Research Centre, 33 Bohouth Street, 12622 Dokki, Cairo, Egypt
| | - H A Abouelhag
- Department of Microbiology and Immunology, National Research Centre, 33 Bohouth Street, 12622 Dokki, Cairo, Egypt
| | - A M Abdou
- Department of Microbiology and Immunology, National Research Centre, 33 Bohouth Street, 12622 Dokki, Cairo, Egypt
| | - E A Elgabry
- Department of Microbiology and Immunology, National Research Centre, 33 Bohouth Street, 12622 Dokki, Cairo, Egypt
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17
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Mangiaterra G, Amiri M, Di Cesare A, Pasquaroli S, Manso E, Cirilli N, Citterio B, Vignaroli C, Biavasco F. Detection of viable but non-culturable Pseudomonas aeruginosa in cystic fibrosis by qPCR: a validation study. BMC Infect Dis 2018; 18:701. [PMID: 30587160 PMCID: PMC6307279 DOI: 10.1186/s12879-018-3612-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/10/2018] [Indexed: 12/29/2022] Open
Abstract
Background Routine culture-based diagnosis of Pseudomonas aeruginosa lung infection in Cystic Fibrosis (CF) patients can be hampered by the phenotypic variability of the microorganism, including its transition to a Viable But Non-Culturable (VBNC) state. The aim of this study was to validate an ecfX-targeting qPCR protocol developed to detect all viable P. aeruginosa bacteria and to identify VBNC forms in CF sputum samples. Methods The study involved 115 P. aeruginosa strains of different origins and 10 non-P. aeruginosa strains and 88 CF sputum samples, 41 Culture-Positive (CP) and 47 Culture-Negative (CN). Spiking assays were performed using scalar dilutions of a mixture of live and dead P. aeruginosa ATCC 9027 and a pooled P. aeruginosa-free sputum batch. Total DNA from sputum samples was extracted by a commercial kit, whereas a crude extract was obtained from the broth cultures. Extracellular DNA (eDNA) interference was evaluated by comparing the qPCR counts obtained from DNase-treated and untreated aliquots of the same samples. The statistical significance of the results was assessed by the Wilcoxon test and Student’s t test. Results The newly-developed qPCR protocol identified 96.6% of the P. aeruginosa isolates; no amplification was obtained with strains belonging to different species. Spiking assays supported protocol reliability, since counts always matched the amount of live bacteria, thus excluding the interference of dead cells and eDNA. The protocol sensitivity threshold was 70 cells/ml of the original sample. Moreover, qPCR detected P. aeruginosa in 9/47 CN samples and showed higher bacterial counts compared with the culture method in 10/41 CP samples. Conclusions Our findings demonstrate the reliability of the newly-developed qPCR protocol and further highlight the need for harnessing a non-culture approach to achieve an accurate microbiological diagnosis of P. aeruginosa CF lung infection and a greater understanding of its evolution. Electronic supplementary material The online version of this article (10.1186/s12879-018-3612-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gianmarco Mangiaterra
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy.
| | - Mehdi Amiri
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Andrea Di Cesare
- Department of Earth, Environmental and Life Sciences, University of Genoa, Corso Europa, 26, 16132, Genoa, Italy
| | - Sonia Pasquaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Esther Manso
- Microbiology Laboratory, Azienda Ospedaliero-Universitaria, Ospedali Riuniti Umberto I°- G.M. Lancisi - G. Salesi, Ancona, Italy
| | - Natalia Cirilli
- Mother-Child Department, Cystic Fibrosis Referral Care Center, United Hospitals, Ancona, Italy
| | - Barbara Citterio
- Department of Biomolecular Sciences sect. Biotechnology, University of Urbino "Carlo Bo", Urbino, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Francesca Biavasco
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
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18
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Zhong Z, Gao X, Gao R, Jia L. Selective capture and sensitive fluorometric determination of Pseudomonas aeruginosa by using aptamer modified magnetic nanoparticles. Mikrochim Acta 2018; 185:377. [PMID: 30014163 DOI: 10.1007/s00604-018-2914-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
Abstract
A fluorometric assay is described for the detection of the food pathogen Pseudomonas aeruginosa (P. aeruginosa). It is based on the hybridization of aptamer and fluorescein-labeled complementary DNA (FAM-cDNA) in combination with magnetic separation. In the absence of P. aeruginosa, FAM-cDNA is assembled on the surface of aptamer modified magnetic particles (MNPs) via hybridization between aptamer and cDNA. Upon addition of P. aeruginosa, FAM-cDNA is replaced by the bacteria and released from the MNPs since the aptamer preferentially binds to bacteria. After magnetic separation, the amount of bacteria can be quantified by determination of the fluorescence intensity (λexc/em = 494/525 nm) of the supernatant containing the released FAM-cDNA. This kind of assay allows for both selective enrichment and sensitive fluorometric determination of bacteria in a single step. The assay has a response to the logarithm of P. aeruginosa concentration that is linear in the range between 10 and 108 cfu·mL-1, with a detection limit as low as 1 cfu·mL-1. The detection process can be finished within <1.5 h. The feasibility of the assay was verified by detecting P. aeruginosa in spiked food samples. Graphical abstract Hybridization of aptamer and carboxyfluorescein labeled complementary DNA is combined with magnetic separation for detection of as low as 1 cfu·mL-1 Pseudomonas aeruginosa. This kind of assay allows for both selective enrichment and sensitive fluorometric determination of bacteria in a single step.
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Affiliation(s)
- Zitao Zhong
- Ministry of Education Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Xiaomei Gao
- Ministry of Education Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Ran Gao
- Ministry of Education Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Li Jia
- Ministry of Education Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
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19
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Sequence Analysis of Novel Genes in Clinical and Environmental Pseudomonas aeruginosa Iraqi Isolates. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.1.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Raja B, Goux HJ, Marapadaga A, Rajagopalan S, Kourentzi K, Willson RC. Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens. J Appl Microbiol 2017; 123:544-555. [PMID: 28510991 DOI: 10.1111/jam.13493] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 01/17/2017] [Accepted: 04/20/2017] [Indexed: 01/19/2023]
Abstract
AIMS To develop and evaluate the performance of a panel of isothermal real-time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens. METHODS AND RESULTS The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Enterococcus faecalis. All five RPAs required reaction times of under 12 min to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross-react with high concentrations of nontarget bacterial genomic DNA. In a 50-sample retrospective clinical study, the five-RPA assay panel was found to have a specificity of 100% (95% CI, 78-100%) and a sensitivity of 89% (95% CI, 75-96%) for UTI detection. CONCLUSIONS The analytical and clinical validity of RPA for the rapid and sensitive detection of common UTI pathogens was established. SIGNIFICANCE AND IMPACT OF THE STUDY Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48-72-h turnaround time. The routine and widespread use of RPA to supplement or replace culture-based methods could profoundly impact UTI management and the emergence of multidrug-resistant pathogens.
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Affiliation(s)
- B Raja
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - H J Goux
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - A Marapadaga
- Medical Center Laboratories, Houston, TX, USA.,De Novo Diagnostics, Houston, TX, USA
| | - S Rajagopalan
- Medical Center Laboratories, Houston, TX, USA.,De Novo Diagnostics, Houston, TX, USA
| | - K Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - R C Willson
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.,Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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21
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Comparison of biofilm formation and antibiotic resistance pattern of Pseudomonas aeruginosa in human and environmental isolates. Microb Pathog 2017; 109:94-98. [DOI: 10.1016/j.micpath.2017.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/30/2017] [Accepted: 05/02/2017] [Indexed: 11/24/2022]
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22
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Kaiser SJ, Mutters NT, DeRosa A, Ewers C, Frank U, Günther F. Determinants for persistence of Pseudomonas aeruginosa in hospitals: interplay between resistance, virulence and biofilm formation. Eur J Clin Microbiol Infect Dis 2016; 36:243-253. [PMID: 27734161 DOI: 10.1007/s10096-016-2792-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/14/2016] [Indexed: 12/27/2022]
Abstract
Pseudomonas aeruginosa (Pa) is one of the major bacterial pathogens causing nosocomial infections. During the past few decades, multidrug-resistant (MDR) and extensively drug-resistant (XDR) lineages of Pa have emerged in hospital settings with increasing numbers. However, it remains unclear which determinants of Pa facilitated this spread. A total of 211 clinical XDR and 38 susceptible clinical Pa isolates (nonXDR), as well as 47 environmental isolates (EI), were collected at the Heidelberg University Hospital. We used RAPD PCR to identify genetic clusters. Carriage of carbapenamases (CPM) and virulence genes were analyzed by PCR, biofilm formation capacity was assessed, in vitro fitness was evaluated using competitive growth assays, and interaction with the host's immune system was analyzed using serum killing and neutrophil killing assays. XDR isolates showed significantly elevated biofilm formation (p < 0.05) and higher competitive fitness compared to nonXDR and EI isolates. Thirty percent (62/205) of the XDR isolates carried a CPM. Similarities in distribution of virulence factors, as well as biofilm formation properties, between CPM+ Pa isolates and EI and between CPM- and nonXDR isolates were detected. Molecular typing revealed two distinct genetic clusters within the XDR population, which were characterized by even higher biofilm formation. In contrast, XDR isolates were more susceptible to the immune response than nonXDR isolates. Our study provides evidence that the ability to form biofilms is an outstanding determinant for persistence and endemic spread of Pa in the hospital setting.
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Affiliation(s)
- S J Kaiser
- Department of Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - N T Mutters
- Department of Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - A DeRosa
- Department of Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - C Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - U Frank
- Department of Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - F Günther
- Department of Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.
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23
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Wu Q, Ye Y, Li F, Zhang J, Guo W. Prevalence and genetic characterization of Pseudomonas aeruginosa in drinking water in Guangdong Province of China. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2016.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Shi H, Chen Z, Kan J. Development of loop-mediated isothermal amplification assays for genotyping of Type III Secretion System in Pseudomonas aeruginosa. Lett Appl Microbiol 2016. [PMID: 26219625 DOI: 10.1111/lam.12469] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
UNLABELLED Pseudomonas aeruginosa is a well-known environmental bacterium capable of causing a variety of life-threatening human infections, with a Type III Secretion System (T3SS) as the most significant virulence determinant. P. aeruginosa strains exhibit unique T3SS virulence genotypes defined by the presence of either exoS or exoU. In this study, loop-mediated isothermal amplification (LAMP) assays for rapid detection of exoS and exoU in P. aeruginosa have been developed and evaluated. Set of four primers were designed for LAMP-based amplification of exoS and exoU respectively. The LAMP reactions were performed at 63°C for 40 min, with detection limits of 100 fg purified DNA. In 107 river water isolates, exoS and exoU were detected in 10 (9%) and 89 (83%) isolates, respectively, and in 38 soil isolates, they were detected in 7 (18%) and 31 (82%) cases respectively. In conclusion, the LAMP assays are rapid, simple and cost-effective tools for detection of the exoU- and exoS-types of P. aeruginosa strains. SIGNIFICANCE AND IMPACT OF THE STUDY This method can be used for the rapid, sensitive and low-cost detection of genes (exoS and exoU) encoding proteins that are part of Type III Secretion System of Pseudomonas aeruginosa. It can serve as an efficient method in outbreak situations or in routine surveillance studies to judge virulence potential and to investigate pathogenesis of P. aeruginosa.
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Affiliation(s)
- H Shi
- College of Food Science, Southwest University, Chongqing, China
| | - Z Chen
- College of Food Science, Southwest University, Chongqing, China
| | - J Kan
- College of Food Science, Southwest University, Chongqing, China
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25
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Cui Z, Ojaghian M, Tao Z, Kakar K, Zeng J, Zhao W, Duan Y, Vera Cruz C, Li B, Zhu B, Xie G. Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice. J Appl Microbiol 2016; 120:1357-67. [DOI: 10.1111/jam.13094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 02/04/2016] [Accepted: 02/04/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Z. Cui
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - M.R. Ojaghian
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - Z. Tao
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - K.U. Kakar
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - J. Zeng
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - W. Zhao
- Chinese Academy of Inspection and Quarantine; Beijing China
| | - Y. Duan
- USDA-ARS-USHRL; Fort Pierce FL USA
| | - C.M. Vera Cruz
- Plant Breeding, Genetics and Biotechnology Division; International Rice Research Institute; Metro Manila Philippines
| | - B. Li
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - B. Zhu
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation; College of Life Science; Zhejiang Sci-Tech University; Hangzhou China
| | - G. Xie
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
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