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Yang H, Liu A, Ma F, Gao X, Wang K, Wang Y. Establishment of portable Pseudomonas aeruginosa detection platform based on one-tube CRISPR/Cas12a combined with recombinase polymerase amplification technology. Clin Chim Acta 2024; 554:117760. [PMID: 38176521 DOI: 10.1016/j.cca.2024.117760] [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: 11/01/2023] [Revised: 12/07/2023] [Accepted: 01/01/2024] [Indexed: 01/06/2024]
Abstract
Pseudomonas aeruginosa, a common Gram-negative bacterium, is associated with diverse diseases. Its increasing resistance to antibiotics presents challenges in clinical treatment. The predominant diagnostic approach involves conventional biochemical cultures, known for their time and labor intensiveness. Despite progress in isothermal amplification studies, limitations persist, including reliance on specialized equipment, intricate primer design, and aerosol contamination. Therefore, there is a demand for enhanced clinical assays. This study successfully combined RPA and CRISPR/Cas12a techniques. Through a series of experiments involving the design and screening of lasB crRNA, the creation of lasB RPA primers, and the establishment of a streamlined RPA-CRISPR/Cas12a assay, the study developed a one-tube detection method targeting P. aeruginosa's lasB gene. The assay demonstrated inclusive behavior across standard and 21 isolates, while specifically discerning P. aeruginosa from diverse strains. Sensitivity reached 15.9 CFU/reaction. Clinical validation revealed a 97.62% concordance with traditional methods. The one-tube assay's protocol mitigated aerosol contamination. Offering precision, specificity, and sensitivity, this method shows promise for field applications in resource-scarce regions, enabling early detection and improved management of P. aeruginosa infections.
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Affiliation(s)
- Haitao Yang
- Department of Medicine Laboratory, The Second People's Hospital of Lianyungang Affiliated to Kangda College of Nanjing Medical University, The Second People's Hospital of Lianyungang City, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Aibo Liu
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Fenfen Ma
- Department of Medicine Laboratory, The Second People's Hospital of Lianyungang Affiliated to Kangda College of Nanjing Medical University, The Second People's Hospital of Lianyungang City, Lianyungang 222000, China
| | - Xuzhu Gao
- Department of Medicine Laboratory, The Second People's Hospital of Lianyungang Affiliated to Kangda College of Nanjing Medical University, The Second People's Hospital of Lianyungang City, Lianyungang 222000, China
| | - Kun Wang
- Department of Medicine Laboratory, The Second People's Hospital of Lianyungang Affiliated to Kangda College of Nanjing Medical University, The Second People's Hospital of Lianyungang City, Lianyungang 222000, China
| | - Yan Wang
- Department of Medicine Laboratory, The Second People's Hospital of Lianyungang Affiliated to Kangda College of Nanjing Medical University, The Second People's Hospital of Lianyungang City, Lianyungang 222000, China.
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Chowdhury G, Das B, Kumar S, Pant A, Mukherjee P, Ghosh D, Koley H, Miyoshi SI, Okamoto K, Paul A, Dutta S, Ramamurthy T, Mukhopadyay AK. Genomic insights into extensively drug-resistant Pseudomonas aeruginosa isolated from a diarrhea case in Kolkata, India. Future Microbiol 2023; 18:173-186. [PMID: 36916516 DOI: 10.2217/fmb-2022-0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Aim: To characterize extensively drug-resistant Pseudomonas aeruginosa from a patient with diarrhea. Materials & methods: Antimicrobial susceptibility was tested by the disk diffusion method. The P. aeruginosa genome was sequenced to identify virulence, antibiotic resistance and prophages encoding genes. Results: P. aeruginosa had a wide spectrum of resistance to antibiotics. Genomic analysis of P. aeruginosa revealed 76 genes associated with antimicrobial resistance, xenobiotic degradation and the type three secretion system. Conclusion: This is the first report on diarrhea associated with P. aeruginosa. Since no other organism was identified, the authors assume that the patient had dysbiosis due to antibiotic exposure, leading to antibiotic-associated diarrhea. The in vivo toxicity expressed by the pathogen may be associated with T3SS.
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Affiliation(s)
- Goutam Chowdhury
- Division of Bacteriology, Indian Council of Medical Research - National Institute of Cholera & Enteric Diseases, Kolkata, 700010, India.,Collaborative Research Center of Okayama University for Infectious Diseases, Indian Council of Medical Research - National Institute of Cholera & Enteric Diseases, Kolkata, 700010, India
| | - Bhabatosh Das
- Infection & Immunology Division, Translational Health Science & Technology Institute, Faridabad, 121001, India
| | - Shakti Kumar
- Infection & Immunology Division, Translational Health Science & Technology Institute, Faridabad, 121001, India
| | - Archana Pant
- Infection & Immunology Division, Translational Health Science & Technology Institute, Faridabad, 121001, India
| | - Priyadarshini Mukherjee
- Division of Bacteriology, Indian Council of Medical Research - National Institute of Cholera & Enteric Diseases, Kolkata, 700010, India
| | - Debjani Ghosh
- Division of Bacteriology, Indian Council of Medical Research - National Institute of Cholera & Enteric Diseases, Kolkata, 700010, India
| | - Hemanta Koley
- Division of Bacteriology, Indian Council of Medical Research - National Institute of Cholera & Enteric Diseases, Kolkata, 700010, India
| | - Shin-Ichi Miyoshi
- Collaborative Research Center of Okayama University for Infectious Diseases, Indian Council of Medical Research - National Institute of Cholera & Enteric Diseases, Kolkata, 700010, India.,Graduate School of Medicine, Dentistry & Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Keinosuke Okamoto
- Collaborative Research Center of Okayama University for Infectious Diseases, Indian Council of Medical Research - National Institute of Cholera & Enteric Diseases, Kolkata, 700010, India
| | - Alapan Paul
- Department of Medicine, Nil Ratan Sircar Medical College & Hospital, Kolkata, 700014, India
| | - Shanta Dutta
- Division of Bacteriology, Indian Council of Medical Research - National Institute of Cholera & Enteric Diseases, Kolkata, 700010, India
| | - Thandavarayan Ramamurthy
- Division of Bacteriology, Indian Council of Medical Research - National Institute of Cholera & Enteric Diseases, Kolkata, 700010, India.,Infection & Immunology Division, Translational Health Science & Technology Institute, Faridabad, 121001, India
| | - Asish K Mukhopadyay
- Division of Bacteriology, Indian Council of Medical Research - National Institute of Cholera & Enteric Diseases, Kolkata, 700010, India
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Soonthornsit J, Pimwaraluck K, Kongmuang N, Pratya P, Phumthanakorn N. Molecular epidemiology of antimicrobial-resistant Pseudomonas aeruginosa in a veterinary teaching hospital environment. Vet Res Commun 2023; 47:73-86. [PMID: 35449493 DOI: 10.1007/s11259-022-09929-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 04/17/2022] [Indexed: 01/27/2023]
Abstract
This study aimed to investigate sites for colonization and molecular epidemiology of antimicrobial-resistant Pseudomonas aeruginosa in a veterinary teaching hospital. Bacterial specimens from surface and liquid samples (n = 165) located in five rooms were collected three times every 2 months, and antimicrobial susceptibility was subsequently determined by minimum inhibitory concentrations. The genomes of resistant strains were further analyzed using whole-genome sequencing. Among 19 P. aeruginosa isolates (11.5%, 19/165), sinks were the most frequent colonization site (53.3%), followed by rubber tubes (44.4%), and anesthesia-breathing circuit (33.3%). The highest resistance to gentamicin (47.4%), followed by piperacillin/tazobactam (36.8%), levofloxacin (36.8%), and ciprofloxacin (36.8%), was observed from 19 P. aeruginosa isolates, of which 10 were resistant strains. Of these 10 antimicrobial-resistant isolates, five were multidrug-resistant isolates, including carbapenem. From the multilocus sequence typing (MLST) analysis, five sequence types (STs), including a high-risk clone of human ST235 (n = 3), and ST244 (n = 3), ST606 (n = 2), ST485 (n = 1), and ST3405 (n = 1) were identified in resistant strains. Multiresistant genes were identified consistent with STs, except ST235. The MLST approach and single nucleotide polymorphism analysis revealed a link between resistant strains from ward rooms and those from examination, wound care, and operating rooms. The improvement of routine cleaning, especially of sink environments, and the continued monitoring of antimicrobial resistance of P. aeruginosa in veterinary hospitals are necessary to prevent the spread of resistant clones and ensure infection control.
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Affiliation(s)
- Jeerawat Soonthornsit
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Salaya Campus, 999 Phutthamonthon Sai 4 Road Salaya, Phutthamonthon Nakhon Pathom, Thailand
| | | | | | - Ploy Pratya
- Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Nathita Phumthanakorn
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Salaya Campus, 999 Phutthamonthon Sai 4 Road Salaya, Phutthamonthon Nakhon Pathom, Thailand.
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Genotyping of Extended Spectrum Beta-Lactamase-Producing Pseudomonas aeruginosa Isolated from People with Nosocomial Infections. Jundishapur J Microbiol 2022. [DOI: 10.5812/jjm-119802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Pseudomonas aeruginosa nosocomial infections are among major problems associated with increased mortality and mobility among patients. Objectives: The aim of this research was to determine the molecular epidemiology of extended spectrum beta-lactamase (ESBL)-producing P. aeruginosa genotypes isolated from patients with nosocomial infections. Methods: One hundred forty-six clinical isolates of Pseudomonas spp. were obtained from a tertiary referral hospital. Phenotypic identification and PCR detection of gyrB were used to characterize P. aeruginosa. Extended spectrum beta-lactamases in samples were identified using the disk approximation test and the combination disk test (CDT). The blaSHV and blaTEM genes were detected by PCR. The strains were typed by the pulse field gel electrophoresis (PFGE), repetitive element sequence (Rep)-PCR, and enterobacterial repetitive intergenic consensus (ERIC)–PCR methods. Results: A total of 134 (91.78%) P. aeruginosa isolates were separated, 41.79% of whom were related to nosocomial infections. The extended spectrum beta-lactamase analysis test revealed that 5.97% and 66.41% of the isolates harbored the blaSHV and blaTEM genes, respectively. Enterobacterial repetitive intergenic consensus PCR, Rep-PCR, and PFGE each showed 56, 55, and 55 different patterns, respectively. Pulse-field gel electrophoresis indicated that pulso types C3 were dominant. Conclusions: The associations between ESBL production, blaSHV and blaTEM positivity, and ERIC, Rep-PCR, and PFGE patterns were not significant (P ≥ 0.05). Among nosocomial infections, a relatively high prevalence of ESBL-producing P. aeruginosa isolates was observed in the Kurdistan province of Iran. Periodic review of antibiotic resistance and molecular characterization of P. aeruginosa isolates is recommended to prevent the spread of nosocomial infections in hospitals.
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