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Adewusi OO, Waldner CL, Hanington PC, Hill JE, Freeman CN, Otto SJG. Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review. J Vet Diagn Invest 2024; 36:400-417. [PMID: 38456288 PMCID: PMC11110769 DOI: 10.1177/10406387241235968] [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] [Indexed: 03/09/2024] Open
Abstract
Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.
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Affiliation(s)
- Olufunto O. Adewusi
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Janet E. Hill
- Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
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Gorina LG, Krylova NA, Rakovskaya IV, Geppe NA, Gamova NA, Barkhatova OI. Mechanisms of Long-Term Persistence of Mycoplasmas in Children with Asthma. Microorganisms 2023; 11:1683. [PMID: 37512855 PMCID: PMC10383847 DOI: 10.3390/microorganisms11071683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Improving the management of children with asthma associated with mycoplasma infection is important. Aim: To study the duration of the persistence of antigens, and DNA in a free state, in the structures of circulating immune complexes (CICs) and living cells of Mycoplasma pneumoniae (Mpn) and Mycoplasma hominis (Mh) in children with asthma. In total, 205 children with asthma from 1 to 14 years were observed. The reaction of aggregate-hemagglutination (AHAA), the direct immunofluorescence reaction (DIF), the reaction of the polymerase chain reaction (PCR), and the culture method were used. In addition, 47 children were re-examined 1.5 months after the treatment of mycoplasma infection with azithromycin. The number of samples positive for antigens and DNA in the free state and in the structures of CICs significantly decreased. Then, 50 blood serum samples containing Mh antigens, and 50 samples containing Mpn antigens were analyzed by culture method. Mh was isolated in 21 (65.5%) of 32 samples containing DNA. Mpn was isolated from antigen-positive samples in nine cases. The presented data indicate the long-term persistence of antigens, and DNA of mycoplasma cells in the free state, in the structure of CICs, as well as in the form of "microcolonies". A high level of CICs can be used to predict the course of the disease and the response to therapy.
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Affiliation(s)
- Luisa G Gorina
- Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Natalya A Krylova
- Department of Childhood Diseases Sechenov, First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Irina V Rakovskaya
- Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Natalia A Geppe
- Department of Childhood Diseases Sechenov, First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Natalia A Gamova
- Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Olga I Barkhatova
- Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
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Lin C, Zeng Y, Zhu Z, Liao J, Yang T, Liu Y, Wei H, Li J, Ma J, Wu X, Lin G, Lin L, Chen L, Huang H, Chen W, Wang J, Wen F, Lin M. A Rapid Antimicrobial Resistance Diagnostic Platform for Staphylococcus aureus Using Recombinase Polymerase Amplification. Microbiol Spectr 2023; 11:e0447622. [PMID: 36975799 PMCID: PMC10100846 DOI: 10.1128/spectrum.04476-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/24/2023] [Indexed: 03/29/2023] Open
Abstract
Antimicrobial resistance (AMR) has posed a global threat to public health. The Staphylococcus aureus strains have especially developed AMR to practically all antimicrobial medications. There is an unmet need for rapid and accurate detection of the S. aureus AMR. In this study, we developed two versions of recombinase polymerase amplification (RPA), the fluorescent signal monitoring and lateral flow dipstick, for detecting the clinically relevant AMR genes retained by S. aureus isolates and simultaneously identifying such isolates at the species level. The sensitivity and specificity were validated with clinical samples. Our results showed that this RPA tool was able to detect antibiotic resistance for all the 54 collected S. aureus isolates with high sensitivity, specificity, and accuracy (all higher than 92%). Moreover, results of the RPA tool are 100% consistent with that of PCR. In sum, we successfully developed a rapid and accurate AMR diagnostic platform for S. aureus. The RPA might be used as an effective diagnostic test in clinical microbiology laboratories to improve the design and application of antibiotic therapy. IMPORTANCE Staphylococcus aureus is a species of Staphylococcus and belongs to Gram-positive. Meanwhile, S. aureus remains one of the most common nosocomial and community-acquired infections, causing blood flow, skin, soft tissue, and lower respiratory tract infections. The identification of the particular nuc gene and the other eight genes of drug-resistant S. aureus can reliably and quickly diagnose the illness, allowing doctors to prescribe treatment regimens sooner. The detection target in this work is a particular gene of S. aureus, and a POCT is built to simultaneously recognize S. aureus and analyze genes representing four common antibiotic families. We developed and assessed a rapid and on-site diagnostic platform for the specific and sensitive detection of S. aureus. This method allows the determination of S. aureus infection and 10 different AMR genes representing four different families of antibiotics within 40 min. It was easily adaptable in low-resource circumstances and professional-lacking circumstances. It should be supported in overcoming the continuous difficulty of drug-resistant S. aureus infections, which is a shortage of diagnostic tools that can swiftly detect infectious bacteria and numerous antibiotic resistance indicators.
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Affiliation(s)
- Chuangxing Lin
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Pediatric Hematology and Oncology, Shenzhen Children's Hospital, China Medical University, Shenzhen, Guangdong, China
| | - Yongmei Zeng
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zhihong Zhu
- Department of Endocrinology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Jiayu Liao
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Tiandan Yang
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yaqun Liu
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
| | - Huagui Wei
- School of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Jiamin Li
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Jibin Ma
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Xiaoqing Wu
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Guangyu Lin
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Liyun Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
| | - Liying Chen
- School of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Huiying Huang
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
| | - Weizhong Chen
- Department of Medical Laboratory, Chaozhou People’s Hospital Affiliated to Shantou University Medical College, Chaozhou, Guangdong, China
| | - Junli Wang
- School of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Feiqiu Wen
- Department of Pediatric Hematology and Oncology, Shenzhen Children's Hospital, China Medical University, Shenzhen, Guangdong, China
| | - Min Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
- School of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
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Hara Y, Nakamura K, Tanno D, Toyokawa M, Suzuki H, Ohashi K, Harada R, Hidaka T, Nagano T, Torii K, Kanemitsu K. Detection of Clostridioides difficile toxin B gene in clinical stool specimens using rapid diagnostic quenching probe-polymerase chain reaction assay. J Microbiol Methods 2023; 205:106666. [PMID: 36608708 DOI: 10.1016/j.mimet.2022.106666] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023]
Abstract
We tested the accuracy of quenching probe-polymerase chain reaction (QP-PCR) for detecting Clostridioides difficile toxin B gene (tcdB) in stools from inpatients with suspected C. difficile infection and compared the results with other nucleic acid amplification tests (NAATs). Toxigenic culture results were used as reference for comparison. QP-PCR had comparable diagnostic accuracy with other NAATs and prior bead-beating enabled detection of tcdB in specimens judged as negative, without bead-beating. Taken together, the QP-PCR either with or without bead-beating showed sufficient effectiveness for detecting tcdB in stool specimens.
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Affiliation(s)
- Yasuka Hara
- Department of Infection Control, Fukushima Medical University, Fukushima, Japan.
| | - Kiwamu Nakamura
- Department of Infection Control, Fukushima Medical University, Fukushima, Japan
| | - Daiki Tanno
- Department of Infection Control, Fukushima Medical University, Fukushima, Japan; Department of Clinical Laboratory Sciences, School of Health Sciences, Fukushima Medical University, Fukushima, Japan
| | - Masahiro Toyokawa
- Department of Clinical Laboratory Sciences, School of Health Sciences, Fukushima Medical University, Fukushima, Japan
| | - Hiroko Suzuki
- Clinical Microbiology Laboratory, Ohta-Nishinouchi Hospital, Koriyama, Japan
| | - Kazutaka Ohashi
- Clinical Microbiology Laboratory, Fukushima Medical University Hospital, Fukushima, Japan
| | - Rie Harada
- Clinical Microbiology Laboratory, Fukushima Medical University Hospital, Fukushima, Japan
| | - Tomoo Hidaka
- Department of Hygiene and Preventive Medicine, Fukushima Medical University, Fukushima, Japan
| | | | | | - Keiji Kanemitsu
- Department of Infection Control, Fukushima Medical University, Fukushima, Japan
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Tsuda M, Watanabe Y, Oikawa R, Watanabe R, Higashino M, Kubo K, Yamamoto H, Itoh F, Kato M. Clinical evaluation of a novel molecular diagnosis kit for detecting Helicobacter pylori and clarithromycin-resistant using intragastric fluid. Helicobacter 2022; 27:e12933. [PMID: 36263754 PMCID: PMC9788249 DOI: 10.1111/hel.12933] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Although there are many Helicobacter pylori (H. pylori) diagnostic methods, the culture and antibiotic susceptibility test is an important method for selecting the most effective H. pylori eradication regimen. However, this diagnostic method is complicated and takes several days; therefore, the development of a rapid and simple diagnostic method is required. Eradication failure due to clarithromycin (CAM) resistance should also be considered. In this study, we report the clinical evaluation of point-of-care testing (POCT) kit using intragastric fluid, a novel kit for detecting H. pylori and CAM resistance. MATERIALS AND METHODS The study participants were 143 patients suspected of H. pylori infection and had an endoscopic examination. The novel diagnostic kit diagnosed H. pylori infection and CAM resistance-associated mutation using intragastric fluid. To diagnose H. pylori infection, the relationship between the diagnostic kit and conventional diagnostic methods (urea breath test, stool antigen test, culture test, and real-time polymerase chain reaction [PCR]) was evaluated. For CAM resistance-associated mutation detection, the concordance between the diagnostic kit and antibiotic susceptibility test was evaluated. RESULTS The diagnosis of H. pylori infection with the novel molecular diagnostic kit using intragastric fluid showed significant relationship with conventional diagnostic methods. Especially when the culture was control, the sensitivity was 100% (67/67), the specificity was 95.9% (71/74), and the overall concordance was 97.9% (138/141). The detection of CAM resistance-associated mutations had a concordance rate of 97.0% (65/67) when compared with the antibiotic susceptibility test. CONCLUSIONS The H. pylori molecular POCT kit uses intragastric fluid as a sample and can diagnose H. pylori infection and detect CAM resistance-associated mutations within an hour. This novel kit is expected to prove useful in selecting the most effective eradication regimen for H. pylori.
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Affiliation(s)
- Momoko Tsuda
- Department of GastroenterologyNational Hospital Organization Hakodate National HospitalHakodateJapan
| | - Yoshiyuki Watanabe
- Department of Internal MedicineKawasaki Rinko General HospitalKawasakiJapan,Division of Gastroenterology, Department of Internal MedicineSt. Marianna University School of MedicineKawasakiJapan
| | - Ritsuko Oikawa
- Division of Gastroenterology, Department of Internal MedicineSt. Marianna University School of MedicineKawasakiJapan
| | - Ryosuke Watanabe
- Department of GastroenterologyNational Hospital Organization Hakodate National HospitalHakodateJapan
| | - Masayuki Higashino
- Department of GastroenterologyNational Hospital Organization Hakodate National HospitalHakodateJapan
| | - Kimitoshi Kubo
- Department of GastroenterologyNational Hospital Organization Hakodate National HospitalHakodateJapan
| | - Hiroyuki Yamamoto
- Division of Gastroenterology, Department of Internal MedicineSt. Marianna University School of MedicineKawasakiJapan,Department of BioinformaticsSt. Marianna University Graduate School of MedicineKawasakiJapan
| | - Fumio Itoh
- Division of Gastroenterology, Department of Internal MedicineSt. Marianna University School of MedicineKawasakiJapan
| | - Mototsugu Kato
- Department of GastroenterologyNational Hospital Organization Hakodate National HospitalHakodateJapan
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Kakiuchi T, Okuda M, Matsuo M, Fujimoto K. Smart Gene™ as an effective non-invasive point-of-care test to detect Helicobacter pylori clarithromycin-resistant mutation. J Gastroenterol Hepatol 2022; 37:1719-1725. [PMID: 35562319 DOI: 10.1111/jgh.15887] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIM Smart Gene™ was developed based on the concept of point-of-care genetic testing. We evaluated the detection performance of a reagent for Helicobacter pylori (H. pylori) clarithromycin (CAM)-resistant mutation assessment and determined the association between the results of Smart Gene™ and those of eradication therapy for H. pylori. METHODS In 2020, the present study was conducted on participants of the H. pylori test and treat project in Saga Prefecture. The submitted stool samples were measured for H. pylori gene and CAM-resistant mutation by Smart Gene™, and the results were compared with real-time polymerase chain reaction (PCR) and sequencing analysis. Finally, the results of the eradication therapy were examined for each result of Smart Gene™. RESULTS Stool samples were obtained from 139 patients who were tested positive by stool antigen test and were analyzed. The H. pylori detection rate was 95.7% by Smart Gene™, 92.8% by real-time PCR (P < 0.01), and 89.2% by sequencing analysis (P = 0.06). The overall concordance rate for CAM-resistant mutation between Smart Gene™ and sequencing analysis was 96.7%. Moreover, 35 of 48 students with CAM-resistant mutation and 33 of the 35 students with a mutation without CAM resistance succeeded in CAM-containing triple therapy, and the success rate was significantly higher for the mutation without CAM resistance (P = 0.012). CONCLUSIONS The detection performance of Smart Gene™ was comparable with that of real-time PCR and sequencing analysis. It is expected that the success rate of eradication would be further improved by using the reagent.
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Affiliation(s)
- Toshihiko Kakiuchi
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Masumi Okuda
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya, Japan
| | - Muneaki Matsuo
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Kazuma Fujimoto
- Department of Gastroenterology, Faculty of Medicine, International University of Health and Welfare, Fukuoka, Japan
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