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Thanh TN, Tien ST, Van PN, Thai SD, Cong TL, Le TD, Nguyen ST, Van TT, Duong HH, Bui TM, Nguyen KT. Optimization of Multiplex-PCR Technique To Determine Azf Deletions in infertility Male Patients. Int J Gen Med 2024; 17:1579-1589. [PMID: 38690198 PMCID: PMC11059631 DOI: 10.2147/ijgm.s455513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Background To optimize the multiplex polymerase chain reaction (M-PCR) technique to diagnose microdeletions of azoospermia factors (AZF) on the Y chromosome and initially apply the technique to diagnose male patients with sperm density less than 5×106 million sperm/mL was assigned to do a test to check for AZF microdeletions on the Y chromosome. Methods Based on the positive control samples which belong to male subjects who have had 2 healthy children without any assisted reproductive technologies, the M-PCR method was developed to detect simultaneously and accurately AZF microdeletions on 32 male patients with sperm densities below 5×106 million sperm/mL of semen at the Department of Biology and Medical Genetics - Vietnam Military Medical University. Results Successful optimization of the M-PCR technique including 7 reactions arranged according to each AZFabc region using 24 STS/gene on the Y chromosome. Initial application to diagnose AZF deletion on 32 azoospermic and oligospermic men reveals that AZFa deletion accounts for 6.25% (2/32); deletion of all 3 regions AZFa,b,c with 18.75% (6/32 cases); The combined deletion rate of AZFb,c is highest, accounting for 56.24% (18/32 patients). Conclusion Successfully optimized the M-PCR technique in identifying AZF microdeletions using 24 sequence tagged sites (STS)/gene for azoospermic and oligozoospermic men. The M-PCR technique has great potential in the application of AZF deletion diagnosis.
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Affiliation(s)
- Tung Nguyen Thanh
- Military Institute of Clinical Embryology and Histology, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Sang Trieu Tien
- Department of Biology and Medical Genetics, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Phong Nguyen Van
- Department of Biology and Medical Genetics, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Son Dang Thai
- Institute of Biological and Food Technology, Hanoi Open University, Hanoi, 100000, Vietnam
| | - Thuc Luong Cong
- Cardiovascular Center, Military Hospital 103, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Tuan Dinh Le
- Department of Rheumatology and Endocrinology, Military Hospital 103, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Son Tien Nguyen
- Department of Rheumatology and Endocrinology, Military Hospital 103, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Tuan Tran Van
- Military Institute of Clinical Embryology and Histology, Vietnam Military Medical University, Hanoi, 100000, Vietnam
| | - Hoang Huy Duong
- Department of Neurology, Thai Binh University of Medicine and Pharmacy, Thai Binh, 410000, Vietnam
| | - Tien Minh Bui
- Department of Obstetrics and Gynecology, Thai Binh University of Medicine and Pharmacy, Thai Binh, 410000, Vietnam
| | - Kien Trung Nguyen
- Department of Obstetrics and Gynecology, Thai Binh University of Medicine and Pharmacy, Thai Binh, 410000, Vietnam
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Pavia AT, Cohen DM, Leber AL, Daly JA, Jackson JT, Selvarangan R, Kanwar N, Bender JM, Dien Bard J, Festekjian A, Duffy S, Larsen C, Holmberg KM, Bardsley T, Haaland B, Bourzac KM, Stockmann C, Chapin KC, Leung DT. Clinical Impact of Multiplex Molecular Diagnostic Testing in Children With Acute Gastroenteritis Presenting to an Emergency Department: A Multicenter Prospective Study. Clin Infect Dis 2024; 78:573-581. [PMID: 38097379 PMCID: PMC10954335 DOI: 10.1093/cid/ciad710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Multiplex molecular diagnostic panels have greatly enhanced detection of gastrointestinal pathogens. However, data on the impact of these tests on clinical and patient-centered outcomes are limited. METHODS We conducted a prospective, multicenter, stepped-wedge trial to determine the impact of multiplex molecular testing at 5 academic children's hospitals on children presenting to the emergency department with acute gastroenteritis. Caregivers were interviewed on enrollment and 7-10 days after enrollment to determine symptoms, risk factors, subsequent medical visits, and impact on family members. During the pre-intervention period, diagnostic testing was performed at the clinician's discretion . During the intervention period, multiplex molecular testing was performed on all children, with results available to clinicians. The primary outcome was return visits to a healthcare provider within 10 days of enrollment. RESULTS Potential pathogens were identified by clinician-ordered tests in 19 of 571 (3.3%) in the pre-intervention period compared with 434 of 586 (74%) in the intervention period; clinically relevant pathogens were detected in 2.1% and 15%, respectively. In the multivariate model, the intervention was associated with a 21% reduction in the odds of any return visit (odds ratio, 0.79; 95% confidence interval, .70-.90) after adjusting for potential confounders. Appropriate treatment was prescribed in 11.3% compared with 19.6% during the intervention period (P = .22). CONCLUSIONS Routine molecular multiplex testing for all children who presented to the ED with acute gastroenteritis detected more clinically relevant pathogens and led to a 21% decrease in return visits. Additional research is needed to define patients most likely to benefit from testing. Clinical Trials Registration. NCT02248285.
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Affiliation(s)
- Andrew T Pavia
- Departments of Pediatrics and Internal Medicine, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Daniel M Cohen
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Amy L Leber
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Judy A Daly
- Department of Pathology, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | | | | | - Neena Kanwar
- Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Jeffrey M Bender
- Children's Hospital of Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jennifer Dien Bard
- Children's Hospital of Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ara Festekjian
- Children's Hospital of Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Susan Duffy
- Department of Emergency Medicine, Hasbro Children's Hospital, Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Chari Larsen
- Departments of Pediatrics and Internal Medicine, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | | | - Tyler Bardsley
- Department of Population Health Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Benjamin Haaland
- Department of Population Health Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | | | - Christopher Stockmann
- Departments of Pediatrics and Internal Medicine, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Kimberle C Chapin
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Daniel T Leung
- Departments of Pediatrics and Internal Medicine, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, Utah, USA
- Department of Pathology, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, Utah, USA
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del Rosal T, Bote-Gascón P, Falces-Romero I, Sainz T, Baquero-Artigao F, Rodríguez-Molino P, Méndez-Echevarría A, Bravo-Queipo-de-Llano B, Alonso LA, Calvo C. Multiplex PCR and Antibiotic Use in Children with Community-Acquired Pneumonia. Children (Basel) 2024; 11:245. [PMID: 38397359 PMCID: PMC10887858 DOI: 10.3390/children11020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
Antibiotics are frequently prescribed to children with pneumonia, although viruses are responsible for most cases. We aimed to evaluate the impact of multiplex polymerase chain reaction (mPCR) on antibiotic use. We conducted a prospective study of children under 14 years of age admitted for suspected viral pneumonia, from October 2019 to June 2022 (except March-November 2020). A mPCR respiratory panel (FilmArray® 2plus, bioMérieux, Marcy-l'Étoile, France) was performed within 72 h of admission. Patients with positive reverse transcription PCR for respiratory syncytial virus, influenza, or SARS-CoV-2 were excluded. We compared the patients with historical controls (2017-2018) who had suspected viral pneumonia but did not undergo an aetiological study. We included 64 patients and 50 controls, with a median age of 26 months. The respiratory panel detected viral pathogens in 55 patients (88%), including 17 (31%) with co-infections. Rhinovirus/enterovirus (n = 26) and human metapneumovirus (n = 22) were the most common pathogens, followed by adenovirus and parainfluenza (n = 10). There were no statistically significant differences in the total antibiotic consumption (83% of cases and 86% of controls) or antibiotics given for ≥72 h (58% vs. 66%). Antibiotics were prescribed in 41% of the cases and 72% of the controls at discharge (p = 0.001). Ampicillin was the most commonly prescribed antibiotic among the patients (44% vs. 18% for controls, p = 0.004), while azithromycin was the most commonly prescribed among the controls (19% vs. 48% for patients and controls, respectively; p = 0.001). Our findings underscore the need for additional interventions alongside molecular diagnosis to reduce antibiotic usage in paediatric community-acquired pneumonia.
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Affiliation(s)
- Teresa del Rosal
- Pediatrics and Infectious Diseases Department, Institute for Health Research IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (P.B.-G.); (T.S.); (F.B.-A.); (P.R.-M.); (A.M.-E.); (L.A.A.); (C.C.)
- Translational Research Network in Pediatric Infectious Diseases (RITIP), 28046 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER U767, Instituto de Salud Carlos III), 28029 Madrid, Spain
| | - Patricia Bote-Gascón
- Pediatrics and Infectious Diseases Department, Institute for Health Research IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (P.B.-G.); (T.S.); (F.B.-A.); (P.R.-M.); (A.M.-E.); (L.A.A.); (C.C.)
- Translational Research Network in Pediatric Infectious Diseases (RITIP), 28046 Madrid, Spain
- Pediatric Emergency Department, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Iker Falces-Romero
- Microbiology Department, Hospital Universitario La Paz, 28046 Madrid, Spain;
- Center for Biomedical Network Research on Infectious Diseases (CIBERINFEC, Instituto de Salud Carlos III), 28029 Madrid, Spain
| | - Talía Sainz
- Pediatrics and Infectious Diseases Department, Institute for Health Research IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (P.B.-G.); (T.S.); (F.B.-A.); (P.R.-M.); (A.M.-E.); (L.A.A.); (C.C.)
- Translational Research Network in Pediatric Infectious Diseases (RITIP), 28046 Madrid, Spain
- Center for Biomedical Network Research on Infectious Diseases (CIBERINFEC, Instituto de Salud Carlos III), 28029 Madrid, Spain
- Department of Pediatrics, Faculty of Medicine, Universidad Autónoma de Madrid, 28029 Madrid, Spain
| | - Fernando Baquero-Artigao
- Pediatrics and Infectious Diseases Department, Institute for Health Research IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (P.B.-G.); (T.S.); (F.B.-A.); (P.R.-M.); (A.M.-E.); (L.A.A.); (C.C.)
- Translational Research Network in Pediatric Infectious Diseases (RITIP), 28046 Madrid, Spain
- Center for Biomedical Network Research on Infectious Diseases (CIBERINFEC, Instituto de Salud Carlos III), 28029 Madrid, Spain
| | - Paula Rodríguez-Molino
- Pediatrics and Infectious Diseases Department, Institute for Health Research IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (P.B.-G.); (T.S.); (F.B.-A.); (P.R.-M.); (A.M.-E.); (L.A.A.); (C.C.)
- Translational Research Network in Pediatric Infectious Diseases (RITIP), 28046 Madrid, Spain
- Center for Biomedical Network Research on Infectious Diseases (CIBERINFEC, Instituto de Salud Carlos III), 28029 Madrid, Spain
| | - Ana Méndez-Echevarría
- Pediatrics and Infectious Diseases Department, Institute for Health Research IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (P.B.-G.); (T.S.); (F.B.-A.); (P.R.-M.); (A.M.-E.); (L.A.A.); (C.C.)
- Translational Research Network in Pediatric Infectious Diseases (RITIP), 28046 Madrid, Spain
- Center for Biomedical Network Research on Infectious Diseases (CIBERINFEC, Instituto de Salud Carlos III), 28029 Madrid, Spain
- Department of Pediatrics, Faculty of Medicine, Universidad Autónoma de Madrid, 28029 Madrid, Spain
| | - Blanca Bravo-Queipo-de-Llano
- Pediatrics and Infectious Diseases Department, Institute for Health Research IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (P.B.-G.); (T.S.); (F.B.-A.); (P.R.-M.); (A.M.-E.); (L.A.A.); (C.C.)
- Translational Research Network in Pediatric Infectious Diseases (RITIP), 28046 Madrid, Spain
| | - Luis A. Alonso
- Pediatrics and Infectious Diseases Department, Institute for Health Research IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (P.B.-G.); (T.S.); (F.B.-A.); (P.R.-M.); (A.M.-E.); (L.A.A.); (C.C.)
- Translational Research Network in Pediatric Infectious Diseases (RITIP), 28046 Madrid, Spain
| | - Cristina Calvo
- Pediatrics and Infectious Diseases Department, Institute for Health Research IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (P.B.-G.); (T.S.); (F.B.-A.); (P.R.-M.); (A.M.-E.); (L.A.A.); (C.C.)
- Translational Research Network in Pediatric Infectious Diseases (RITIP), 28046 Madrid, Spain
- Center for Biomedical Network Research on Infectious Diseases (CIBERINFEC, Instituto de Salud Carlos III), 28029 Madrid, Spain
- Department of Pediatrics, Faculty of Medicine, Universidad Autónoma de Madrid, 28029 Madrid, Spain
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Wang D, Haley E, Luke N, Mathur M, Festa RA, Zhao X, Anderson LA, Allison JL, Stebbins KL, Diaz MJ, Baunoch D. Emerging and Fastidious Uropathogens Were Detected by M-PCR with Similar Prevalence and Cell Density in Catheter and Midstream Voided Urine Indicating the Importance of These Microbes in Causing UTIs. Infect Drug Resist 2023; 16:7775-7795. [PMID: 38148772 PMCID: PMC10750486 DOI: 10.2147/idr.s429990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Introduction This study compared microbial compositions of midstream and catheter urine specimens from patients with suspected complicated urinary tract infections to determine if emerging and fastidious uropathogens are infecting the bladder or are contaminants. Methods Urine was collected by in-and-out catheter (n = 1000) or midstream voiding (n = 1000) from 2000 adult patients (≥60 years of age) at 17 DispatchHealth sites across 11 states. The two groups were matched by age (mean 81 years), sex (62.1% female, 37.9% male), and ICD-10-CM codes. Microbial detection was performed with multiplex polymerase chain reaction (M-PCR) with a threshold for "positive detection" ≥ 10,000 cells/mL for bacteria or any detection for yeast. Results were divided by sex. Results In females, 28 of 30 microorganisms/groups were found by both collection methods, while in males 26 of 30 were found by both. There were significant overlaps in the detection and densities of classical uropathogens including Escherichia coli, Enterococcus faecalis, and Klebsiella pneumoniae, as well as emerging uropathogens including Actinotignum schaalii and Aerococcus urinae. In females, detection rates were slightly higher in midstream voided compared to catheter-collected (p = 0.0005) urine samples, while males showed the opposite trend (p < 0.0001). More polymicrobial infections were detected in midstream voided compared to catheter-collected samples (64.4% vs 45.7%, p < 0.0001) in females but the opposite in males (35.6% vs 47.0%, p = 0.002). Discussion In-and-out catheter-collected and midstream voided urine specimens shared significant similarities in microbial detections by M-PCR, with some differences found for a small subset of organisms and between sexes. Conclusion Non-invasive midstream voided collection of urine specimens for microbial detection and identification in cases of presumed UTI does not result in significantly more contamination compared to in-and-out catheter-collected specimens. Additionally, organisms long regarded as contaminants should be reconsidered as potential uropathogens.
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Affiliation(s)
- Dakun Wang
- Department of Writing, Stat4Ward, Pittsburgh, PA, USA
| | - Emery Haley
- Department of Clinical Research, Pathnostics, Irvine, CA, USA
| | - Natalie Luke
- Department of Clinical Research, Pathnostics, Irvine, CA, USA
| | - Mohit Mathur
- Department of Medical Affairs, Pathnostics, Irvine, CA, USA
| | | | - Xinhua Zhao
- Department of Statistical Analysis, Stat4Ward, Pittsburgh, PA, USA
| | - Lori A Anderson
- L. Anderson Diagnostic Market Access Consulting, San Diego, CA, USA
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Mattila S, Honkila M, Paalanne N, Mäki-Koivisto V, Halt K, Jartti T, Ruuskanen O, Waris M, Pokka T, Tapiainen T. Clinical Outcomes of Acutely Ill Children According to Cycle Threshold Values of Respiratory Viruses Detected by Multiplex PCR Testing. J Pediatric Infect Dis Soc 2023; 12:549-552. [PMID: 37738173 DOI: 10.1093/jpids/piad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
In this cohort study of 800 children attending a pediatric emergency department at Oulu University Hospital, Finland with fever or respiratory symptoms, the cycle threshold values of point-of-care multiplex polymerase chain reaction testing for respiratory viruses were not associated with hospitalization, respiratory support, or need for intensive care.
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Affiliation(s)
- Suvi Mattila
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Minna Honkila
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Niko Paalanne
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | | | - Kimmo Halt
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Tuomas Jartti
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Olli Ruuskanen
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Matti Waris
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tytti Pokka
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Research Service Unit, Oulu University Hospital, Oulu, Finland
| | - Terhi Tapiainen
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
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Rajan R. A Study on Glycopeptide-Resistant Genotypes among Clinical Isolates of Enterococcus with Van B Phenotype. Adv Biomed Res 2023; 12:196. [PMID: 37694237 PMCID: PMC10492609 DOI: 10.4103/abr.abr_133_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 02/13/2022] [Accepted: 02/17/2022] [Indexed: 09/12/2023] Open
Abstract
Background Enterococci, although remarked as harmless commensals of the intestinal tract of humans and animals, have become a significant source of infection in hospitalized patients worldwide.The present study aimed to isolate and identify enterococci from clinical samples and to determine the genotypic characteristics of vancomycin-resistant enterococcus isolates. Materials and Methods A total of 774 isolates of enterococci from clinical samples were identified to the species level, and their anti-microbial susceptibility pattern was determined by Kirby Bauer Disk Diffusion method and Vitek 2 automated system. Screening for vancomycin resistance was performed by using brain heart infusion agar containing 6 micrograms/ml of vancomycin. The minimum inhibitory concentration (MIC) of vancomycin was determined by the agar dilution method and Epsilometer test (E test). Genotyping was carried out for resistant isolates by multiplex polymerase chain reaction. Results Thirty (3.88%) isolates were resistant to vancomycin by agar screen method. Five isolates showed intermediate resistance with anMIC of 8-16 micrograms/ml for vancomycin by agar dilution. By the E test, two isolates displayed an MIC of ≥32 micrograms/ml for vancomycin and one isolate showed an MICof ≥32 micrograms/ml for teicoplanin.Van A was the common genotype isolated. The present study reports isolates of Enterococcus faecalis with a susceptible MIC for glycopeptide and the presence of the Van A gene. Conclusion Heterogeneous resistance among clinical isolates of Enterococcus faecalis was observed in our study. The predominant phenotype and genotype detected among clinical isolates were Van A.
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Affiliation(s)
- Reena Rajan
- Department of Microbiology, Vinayaka Mission's Kirupananda Variyar Medical College, Salem, Tamil Nadu, India
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Keomoungkhoun B, Arjentinia IPGY, Sangmaneedet S, Taweenan W. First report on the molecular prevalence and associated risk factors of Eimeria spp. in dairy cattle in Khon Kaen, Thailand. Vet World 2023; 16:1489-1495. [PMID: 37621543 PMCID: PMC10446723 DOI: 10.14202/vetworld.2023.1489-1495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/09/2023] [Indexed: 08/26/2023] Open
Abstract
Background and Aim Bovine coccidiosis, caused by the protozoa Eimeria, is an important parasitic cattle disease that affects animal health and has economic impact worldwide. This study was conducted to report the first molecular prevalence and genetic diversity of Eimeria spp. in dairy cattle in Khon Kaen province, Thailand, and to identify the risk factors associated with Eimeria spp. infection. Materials and Methods From July 2020 to October 2021, 296 fecal samples were collected from dairy cattle divided into three age groups, including <3-month-old calves, 3-month-old to 1-year-old calves, and >1-year-old cattle. Eimeria spp. were identified by multiplex polymerase chain reaction (PCR) amplifying 18S RNA gene and confirmed by DNA sequencing. Information regarding all associated risk factors was collected using questionnaires and analyzed using logistic regression tests in the Statistical Package for the Social Sciences program. Results Polymerase chain reaction results showed that 104 (35.13%) of 296 samples were positive for Eimeria spp. The <3-month-old calves (46.51%) had the highest infection rate. Moreover, multiplex PCR identified five species of Eimeria, namely, Eimeria bovis (32.69%), Eimeria zuernii (18.26%), Eimeria alabamensis (5.76%), Eimeria ellipsoidalis (3.84%), and Eimeria cylindrica (2.88%). An association was observed between risk factors and Eimeria spp. incidence (p < 0.05). DNA sequencing revealed the similarity of each Eimeria spp. with 91%-100% nucleotide identity. Phylogenetic tree analysis demonstrated the close relationships of clusters of E. bovis and E. zuernii, E. ellipsoidalis, and E. cylindrica and another cluster of E. alabamensis. Conclusion The results confirm that Eimeria spp. are commonly found in dairy cattle, especially calves. The molecular test could be powerful for species identification. This study also provides epidemiological information for developing future strategies to control bovine coccidiosis.
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Affiliation(s)
- Bamphen Keomoungkhoun
- Division of Pathobiology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | | | - Somboon Sangmaneedet
- Division of Pathobiology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Weerapol Taweenan
- Division of Pathobiology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
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Sueda A, Otake S, Kasai M, Kagawa T. The usefulness of a nasopharyngeal multiplex polymerase chain reaction system to screen pediatric patients with preoperative fever. Acta Anaesthesiol Scand 2023; 67:724-729. [PMID: 36866976 DOI: 10.1111/aas.14226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 03/04/2023]
Abstract
BACKGROUND When children have a preoperative fever, anesthesiologists must help determine whether to postpone or proceed with surgery, as fever may be a sign of upper respiratory tract infection (URTI). Such infections are a known risk factor for perioperative respiratory adverse events (PRAEs), which are still one of the prime causes of anesthetic mortality and morbidity in pediatric patients. Since the COVID-19 pandemic, preoperative assessments have become drastically more complex as hospitals strive to balance practicality and safety. In our facility, if pediatric patients presented with preoperative fever, we used the FilmArray® Respiratory Panel 2.1 to determine whether to postpone or proceed with surgery. METHODS This is a single-center retrospective observational study evaluating the efficacy of the FilmArray® Respiratory Panel 2.1 as a preoperative screening test. This study included pediatric patients scheduled for elective surgeries between March 2021 and February 2022. FilmArray was used if a patient had a preoperative fever (determined by axillary temperature, ≥38°C for <1-year-old, ≥37.5°C for ≥1-year-old) between hospital admission and before surgery. We excluded patients if they had apparent symptoms of URTI. RESULTS In the FilmArray positive group, 11 of 25 (44%) cases developed subsequent symptoms after surgery was canceled. No patients in the negative group developed symptoms. The proportion of the development of subsequent symptoms between the FilmArray positive and negative groups was statistically significant (p < .001, odds ratio: 29.6, 95% confidence interval: [3.80-1356.01]). CONCLUSIONS Our retrospective observational study revealed that 44% of the FilmArray positive group subsequently developed symptoms, and no PRAEs were observed in the FilmArray negative group. We suggest that FilmArray could be useful as a screening test for pediatric patients with preoperative fever.
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Affiliation(s)
- Aya Sueda
- Department of Anesthesiology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
| | - Shogo Otake
- Division of Infectious Diseases, Department of Pediatrics, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Masashi Kasai
- Division of Infectious Diseases, Department of Pediatrics, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
| | - Tetsuro Kagawa
- Department of Anesthesiology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
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Kottrashetti VS, Bhat KG, Kugaji MS, Naik SS, Tanakanti P. Simultaneous detection and evaluation of Prevotella intermedia, Prevotella nigrescens, Prevotella loescheii, and Prevotella melaninogenica in subgingival plaque samples of chronic periodontitis and healthy individuals through multiplex polymerase chain reaction. J Indian Soc Periodontol 2023; 27:283-289. [PMID: 37346862 PMCID: PMC10281318 DOI: 10.4103/jisp.jisp_154_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/25/2022] [Accepted: 11/27/2022] [Indexed: 06/23/2023] Open
Abstract
Background Prevotella is a Gram-negative anaerobic bacilli. The phenotypic characteristics of the various species of Prevotella are similar, which often makes it difficult in routine differentiation and identification of all the species. Aim The purpose of the study was to detect and compare presence of Prevotella intermedia, Prevotella nigrescens, Prevotella melaninogenica, and Prevotella loescheii in subgingival plaque samples of chronic periodontitis and healthy individuals. Materials and Methods Two hundred and thirty-six subjects were considered consisting of chronic periodontitis (128) and healthy (108) individuals. Subgingival plaque sample was collected in reduced transport fluid and analyzed. DNA extraction and polymerase chain reaction (PCR) were performed for genus Prevotella followed by positive samples were considered for the detection of selected species through multiplex PCR using specific primers. Results Out of 236 samples, 94.1% were positive for genus Prevotella. Out of 222 cases P. nigrescens showed the highest number of cases positive (59.5%) followed by P. melaninogenica (57.2%), P. intermedia (55.4%), and P. loescheii (40.1%). Species were analyzed individually between chronic periodontitis and healthy, P. intermedia, P. nigrescens, and P. loescheii showed greater positivity in healthy compared to chronic periodontitis. Positivity for P. melaninogenica was high in chronic periodontitis compared to healthy. Conclusion The number of positive cases for species, when correlated with clinical parameters showed an increase in mean score for all clinical parameters assessed, suggesting the presence of variation in the prevalence of Prevotella species and geographic variation do exist in oral microflora. Findings suggest that they can be normal commensals and opportunistic.
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Affiliation(s)
- Vijaylakshmi S Kottrashetti
- Department of Oral Pathology and Microbiology, Maratha Mandal’s Nathajirao G. Halgekar Institute of Dental Sciences and Research Centre, Belagavi, Karnataka, India
| | - Kishore G Bhat
- Central Research Laboratory, Maratha Mandal’s Nathajirao G. Halgekar Institute of Dental Sciences and Research Centre, Belagavi, Karnataka, India
| | - Manohar S Kugaji
- Central Research Laboratory, Maratha Mandal’s Nathajirao G. Halgekar Institute of Dental Sciences and Research Centre, Belagavi, Karnataka, India
| | - Sachita Shrikant Naik
- Department of Periodontology, Maratha Mandal’s Nathajirao G. Halgekar Institute of Dental Sciences and Research Centre, Belagavi, Karnataka, India
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Owusu W, van Vliet AHM, Riddell NE, Stewart G, Akwani WC, Aryeetey S, Arthur RA, Sylverken AA, Hingley-Wilson SM. A multiplex PCR assay for the differentiation of Mycobacterium tuberculosis complex reveals high rates of mixed-lineage tuberculosis infections among patients in Ghana. Front Cell Infect Microbiol 2023; 13:1125079. [PMID: 37077529 PMCID: PMC10108843 DOI: 10.3389/fcimb.2023.1125079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
In low-resource settings with high tuberculosis (TB) burdens, lack of rapid diagnostic methods for detection and differentiation of Mycobacterium tuberculosis complex (MTBC) is a major challenge affecting TB management. This study utilized comparative genomic analyses of MTBC lineages; M. tuberculosis, M. africanum Lineages 5/6 and M. bovis to identify lineage-specific genes. Primers were designed for the development of a Multiplex PCR assay which was successful in differentiating the MTBC lineages. There was no cross-reaction with other respiratory pathogens tested. Validation of the assay using clinical samples was performed with sputum DNA extracts from 341 clinically confirmed active TB patients. It was observed that 24.9% of cases were caused by M. tuberculosis, while M. africanum L5 & L6 reported 9.0% and 14.4%, respectively. M. bovis infection was the least frequently detected lineage with 1.8%. Also, 27.0% and 17.0% of the cases were PCR negative and unspeciated, respectively. However, mixed-lineage TB infections were recorded at a surprising 5.9%. This multiplex PCR assay will allow speciation of MTBC lineages in low-resource regions, providing rapid differentiation of TB infections to select appropriate medication at the earliest possible time point. It will also be useful in epidemiological surveillance studies providing reliable information on the prevalence of TB lineages as well as identifying difficult to treat cases of mixed-lineage tuberculosis infections.
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Affiliation(s)
- Wellington Owusu
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Arnoud H. M. van Vliet
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Natalie E. Riddell
- Department of Biochemical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Graham Stewart
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Winifred C. Akwani
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Rejoice Agyeiwaa Arthur
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Suzanne M. Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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11
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Mattila S, Sarlin S, Heikkilä R, Leinonen E, Nurmi V, Riikonen J, Paalanne N, Honkila M, Huhtamäki H, Pokka T, Koskela U, Renko M, Tapiainen T. Nasopharyngeal detection of atypical bacteria by multiplex polymerase chain reaction panel in acutely ill children was associated with an increased risk of pneumonia. Acta Paediatr 2023; 112:830-836. [PMID: 36644932 DOI: 10.1111/apa.16672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/17/2023]
Abstract
AIM We aimed to assess whether detection of respiratory bacteria by multiplex polymerase chain reaction (PCR) testing associates with clinical outcomes in acutely ill children. METHODS This cross-sectional study enrolled children under the age of 18 with a suspected respiratory infection treated in a paediatric emergency department of Oulu University Hospital, Finland from January 2015 through December 2015. Nasopharyngeal samples were routinely analysed for 16 respiratory viruses and later, after storage, analysed with a multiplex PCR panel for seven respiratory bacteria. RESULTS At least one bacterial pathogen was detected in 600 out of the 1195 children (50%). The mean age was 3.3 (SD 3.7) years and 54% were boys. Atypical bacteria were associated with a risk of pneumonia (adjusted odds ratio [aOR] 14.1, 95% CI 3.98-50.1). Co-detection of rhinovirus with Streptococcus pneumoniae was not associated with risk of pneumonia (aOR 2.39, 95% CI 0.78-7.30). Detection of Streptococcus pneumoniae, Haemophilus influenzae or both was not associated with the risk of hospital admission or prescription of antibiotics. CONCLUSION Nasopharyngeal detection of atypical bacteria in acutely ill children was associated with a markedly increased risk of pneumonia. The clinical utility of wide testing for other respiratory bacteria needs further evaluation.
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Affiliation(s)
- Suvi Mattila
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Suvi Sarlin
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Reetta Heikkilä
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Emilia Leinonen
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Violetta Nurmi
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Jonni Riikonen
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Niko Paalanne
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Minna Honkila
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Heikki Huhtamäki
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Tytti Pokka
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Ulla Koskela
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Marjo Renko
- Department of Pediatrics and Adolescent Medicine, Kuopio University Hospital, Kuopio, Finland.,University of Eastern Finland, Kuopio, Finland
| | - Terhi Tapiainen
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
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12
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de Nattes T, Beadle J, Toulza F, Candon E, Ruminy P, François A, Bertrand D, Guerrot D, Drieux F, Roufosse C, Candon S. A Simple Molecular Tool for the Assessment of Kidney Transplant Biopsies. Clin J Am Soc Nephrol 2023; 18:499-509. [PMID: 36723289 PMCID: PMC10103338 DOI: 10.2215/cjn.0000000000000100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/17/2023] [Indexed: 02/02/2023]
Abstract
BACKGROUND The Banff Classification for Allograft Pathology recommendations for the diagnosis of kidney transplant rejection includes molecular assessment of the transplant biopsy. However, implementation of molecular tools in clinical practice is still limited, partly due to the required expertise and financial investment. The reverse transcriptase multiplex ligation-dependent probe amplification (RT-MLPA) assay is a simple, rapid, and inexpensive assay that permits simultaneous evaluation of a restricted gene panel using paraffin-embedded tissue blocks. The aim of this study was to develop and validate a RT-MLPA assay for diagnosis and classification of rejection. METHODS A retrospective cohort of 220 kidney transplant biopsies from two centers, which included 52 antibody-mediated rejection, 51 T-cell-mediated rejection, and 117 no-rejection controls, was assessed. A 17-gene panel was identified on the basis of relevant pathophysiological pathways. A support vector machine classifier was developed. A subset of 109 biopsies was also assessed using the Nanostring Banff Human Organ Transplant panel to compare the two assays. RESULTS The support vector machine classifier train and test accuracy scores were 0.84 and 0.83, respectively. In the test cohort, the F1 score for antibody-mediated rejection, T-cell-mediated rejection, and control were 0.88, 0.86, and 0.69, respectively. Using receiver-operating characteristic curves, the area under the curve for class predictions was 0.96, 0.89, and 0.91, respectively, with a weighted average at 0.94. Classifiers' performances were highest for antibody-mediated rejection diagnosis with 94% correct predictions, compared with 88% correct predictions for control biopsies and 60% for T-cell-mediated rejection biopsies. Gene expression levels assessed by RT-MLPA and Nanostring were correlated: r = 0.68, P < 0.001. Equivalent gene expression profiles were obtained with both assays in 81% of the samples. CONCLUSIONS The 17-gene panel RT-MLPA assay, developed here for formalin-fixed paraffin-embedded kidney transplant biopsies, classified kidney transplant rejection with an overall accurate prediction ratio of 0.83. PODCAST This article contains a podcast at https://dts.podtrac.com/redirect.mp3/www.asn-online.org/media/podcast/CJASN/2023_04_10_CJN10100822.mp3.
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Affiliation(s)
- Tristan de Nattes
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
- Univ Rouen Normandie, INSERM U1234, Rouen, France
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Jack Beadle
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Frederic Toulza
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Edvin Candon
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Philippe Ruminy
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, Rouen, France
| | - Arnaud François
- Pathology Department, Rouen University Hospital, Rouen, France
| | - Dominique Bertrand
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Dominique Guerrot
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Fanny Drieux
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, Rouen, France
- Pathology Department, Rouen University Hospital, Rouen, France
| | - Candice Roufosse
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
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Gu X, Ma X, Wu Q, Tao Q, Chai Y, Zhou X, Han M, Li J, Huang X, Wu T, Zhang X, Zhong F, Cao Y, Zhang L. Isolation, identification, molecular typing, and drug resistance of Escherichia coli from infected cattle and sheep in Xinjiang, China. Vet Med Sci 2023; 9:1359-1368. [PMID: 36977209 DOI: 10.1002/vms3.1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Escherichia coli infections are common in Xinjiang, a major region of cattle and sheep breeding in China. Therefore, strategies are required to control E. coli. The aim of this study was to investigate the phylogenetic groups, virulence genes, and antibiotic resistance characteristics of E. coli isolates. METHODS In this study, 116 tissue samples were collected from the organs of cattle and sheep that were suspected of having E. coli infections between 2015 and 2019. Bacteria in the samples were identified using a biochemical identification system and amplification of 16S rRNA, and the phylogenetic groupings of E. coli isolates were determined by multiplex polymerase chain reactions. In addition, PCR detection and analysis of virulence factors, antibiotic resistance genes, and drug-resistant phenotypes of E. coli isolates were performed. RESULTS A total of 116 pathogenic E. coli strains belonging to seven phylogenetic groups were isolated, with the majority of isolates in groups A and B1. Among the virulence genes, curli-encoding crl had the highest detection rate of 97.4%, followed by hemolysin-encoding hlyE with the detection rate of 94.82%. Antimicrobial susceptibility test results indicated that the isolates had the highest rates of resistance against streptomycin (81.9%). CONCLUSION These characteristics complicate the prevention and treatment of E. coli-related diseases in Xinjiang.
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Affiliation(s)
- Xiaoxiao Gu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xue Ma
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Qin Wu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Qiaoxiaoci Tao
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yingjin Chai
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xia Zhou
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Mengli Han
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Jie Li
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xin Huang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Tongzhong Wu
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xingxing Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Fagang Zhong
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Yiheng Cao
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Liyuan Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
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Pedace CS, Gonçalves MG, Souza AR, Dos Santos Simeão FC, de Carvalho NFG, Gallo JF, Chimara E. Development of multiplex real-time PCR for detection of clarithromycin resistance genes for the Mycobacterium abscessus group. J Med Microbiol 2023; 72. [PMID: 36920844 DOI: 10.1099/jmm.0.001670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Introduction. The M. abscessus molecular identification and its drug-resistance profile are important to choose the correct therapy.Aim. This work developed a multiplex real-time PCR (mqPCR) for detection of clarithromycin resistance genes for the Mycobacterium abscessus group.Methodology. Isolates received by Adolfo Lutz Institute from 2010 to 2012, identified by PCR restriction enzyme analysis of a fragment of the hsp65 gene (PRA-hsp65) as M. abscessus type 1 (n=135) and 2 (n=71) were used. Drug susceptibility test (DST) for CLA were performed with reading on days 3 and 14. Subespecies identification by hsp65 and rpoB genes sequencing and erm(41) and rrl genes for mutation detection and primer design were performed. erm(41) gene deletion was detected by conventional PCR. Primers and probes were designed for five detections: erm(41) gene full size and with deletion; erm(41) gene T28 and C28; rrl gene A2058.Results. In total, 191/206 (92.7 %) isolates were concordant by all methods and 13/206 (6.3 %) were concordant only between molecular methods. Two isolates (1.0 %) were discordant by mqPCR compared to rrl gene sequencing. The mqPCR obtained 204/206 (99.0 %) isolates in agreement with the gold standard, with sensitivity and specificity of 98 and 100 %, respectively, considering the gold standard method and 92 and 93 % regarding DST.Conclusion. The mqPCR developed by us proved to be an easy-to-apply tool, minimizing time, errors and contamination.
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Affiliation(s)
- Carolina Salgado Pedace
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Maria Gisele Gonçalves
- Immunology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 10th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Andréia Rodrigues Souza
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Fernanda Cristina Dos Santos Simeão
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Natalia Fernandes Garcia de Carvalho
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Juliana Failde Gallo
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Erica Chimara
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
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Lee SJ, Jang TS, Kim JK. A retrospective study on the status of sexually transmitted co-infections in university hospitals in Korea from 2017 to 2021. Ther Adv Infect Dis 2023; 10:20499361231220154. [PMID: 38145192 PMCID: PMC10748651 DOI: 10.1177/20499361231220154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023] Open
Abstract
Background The prevalence of sexually transmitted infections (STIs) remains high worldwide. Despite the worldwide increase in the incidence of STIs every year, there are few reports on the frequency of STIs with different pathogens according to age and gender. Accordingly, a study was conducted to determine trends in co-infection with STIs by age and gender in Cheonan, South Korea from 2017 to 2021. Objectives To identify trends by age or sex in co-infection of STIs in this region. Design A retrospective study was conducted on clinical samples examined at Dankook University Hospital from January 2017 to November 2021. A total of 3297 specimens were collected from patients visiting Dankook University Hospital (Cheonan, Korea), and statistical analysis was performed on patients ranging in age from 1 day to 93 years. Methods Multiplex polymerase chain reaction, the most efficient method to diagnose a bacterial infection, was performed using an MJ Research PTC-200 Thermal Cycler (Marshall Scientific, Richmond, VA, USA) and a Seeplex STD Detection Kit (Seegene, Seoul, Republic of Korea). The co-infection rate with STI pathogens was analyzed according to age and sex. Results Of the 3297 clinical samples, 1017 (30.9%) tested positive for sexually transmitted pathogens, ranging from one to six co-infections. Analysis of the co-infection rate by age revealed that the average age gradually decreased as the total number of co-infection pathogens increased. The co-infection percentage and age distribution of STIs differed according to sex. Co-infection was more prevalent in female patients. Furthermore, co-infection in male patients occurred frequently in the 30-39-year-old group, while those in female patients occurred in the 20-29- and 30-39-year-old groups. Conclusion Our statistical analysis showed that STI co-infections were more common among younger than older people. Therefore, it helps in recognizing STIs at a young age and provides possible indicator data to prevent STIs at a young age. In addition, further research is needed on co-infection in other regions.
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Affiliation(s)
- Sun Jung Lee
- Department of Biomedical Laboratory Science, Dankook University College of Health Sciences, Chungnam, Republic of Korea
| | - Tae Su Jang
- Department of Health Administration, Dankook University College of Health Sciences, Chungnam, Republic of Korea
| | - Jae Kyung Kim
- Department of Biomedical Laboratory Science, Dankook University College of Health Sciences, 119, Dandae-ro, Dongnam-gu, Cheonan-si, Chungnam 31116, Republic of Korea
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Gómez de la Torre Pretell JC, Hueda-Zavaleta M, Cáceres-DelAguila JA, Barletta-Carrillo C, Copaja-Corzo C, Poccorpachi MDPS, Delgado MSV, Sanchez GMML, Benites-Zapata VA. Clinical Characteristics Associated with Detected Respiratory Microorganism Employing Multiplex Nested PCR in Patients with Presumptive COVID-19 but Negative Molecular Results in Lima, Peru. Trop Med Infect Dis 2022; 7:340. [PMID: 36355882 PMCID: PMC9692319 DOI: 10.3390/tropicalmed7110340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/15/2023] Open
Abstract
The COVID-19 pandemic circumstances have varied the pathogens related to acute respiratory infections (ARI), and most specialists have ignored them due to SARS-CoV-2's similar symptomatology. We identify respiratory pathogens with multiplex PCR in samples with presumptive SARS-CoV-2 but negative RT-qPCR results. We performed a retrospective transversal study employing clinical data and nasopharyngeal swab samples from patients with suspected clinical SARS-CoV-2 infection and a negative PCR result in a private laboratory in Lima, Peru. The samples were analyzed using the FilmArray™ respiratory panel. Of 342 samples, we detected at least one pathogen in 50% of the samples. The main ones were rhinovirus (54.38%), influenza A(H3N2) (22.80%), and respiratory syncytial virus (RSV) (14.04%). The clinical characteristics were sore throat (70.18%), cough (58.48%), nasal congestion (56.43%), and fever (40.06%). Only 41.46% and 48.78% of patients with influenza met the definition of influenza-like illness (ILI) by the World Health Organization (WHO) (characterized by cough and fever) and the Centers for Disease Control and Prevention (CDC) (characterized by fever and cough and sore throat), respectively. A higher prevalence of influenza was associated with ILI by WHO (aPR: 2.331) and ILI by CDC (aPR: 1.892), which was not observed with other respiratory viruses. The clinical characteristic associated with the increased prevalence of rhinovirus was nasal congestion (aPR: 1.84). For patients with ARI and negative PCR results, the leading respiratory pathogens detected were rhinovirus, influenza, and RSV. Less than half of patients with influenza presented ILI, although its presence was specific to the disease.
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Affiliation(s)
| | - Miguel Hueda-Zavaleta
- Facultad de Ciencias de la Salud, Universidad Privada de Tacna, Tacna 23003, Peru
- Hospital III Daniel Alcides Carrión-Essalud Tacna, Tacna 23000, Peru
| | | | | | - Cesar Copaja-Corzo
- Facultad de Ciencias de la Salud, Universidad Privada de Tacna, Tacna 23003, Peru
- Red Asistencial Ucayali EsSalud, Pucallpa 25003, Peru
| | | | | | | | - Vicente A. Benites-Zapata
- Unidad de Investigación para la Generación y Síntesis de Evidencias en Salud, Universidad San Ignacio de Loyola, Lima 15024, Peru
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Hara M, Ishihara M, Nakajima H. Use of the FilmArray® Meningitis/Encephalitis panel to detect pathogenic microorganisms in cerebrospinal fluid specimens: a single-center retrospective study. J Int Med Res 2022; 50:3000605221129561. [PMID: 36214109 PMCID: PMC9551344 DOI: 10.1177/03000605221129561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Meningitis and encephalitis are neurological emergencies requiring rapid diagnosis and treatment. The performance of the FilmArray® Meningitis/Encephalitis (ME) panel, a multiplex polymerase chain reaction test, and conventional methods for diagnosing meningitis and encephalitis was compared. METHODS This retrospective study assessed 20 patients diagnosed with meningitis or encephalitis according to clinical symptoms and laboratory examination findings between January 2018 and December 2019. The results of the FilmArray® ME panel were compared with those of conventional methods. RESULTS Pathogens were identified in 11 (55%) patients using the FilmArray® ME panel and in nine (45%) patients using conventional methods. The test identified herpes simplex virus type 1 in two patients, herpes simplex virus type 2 in one, varicella-zoster virus in four, Streptococcus pneumoniae in three, and Cryptococcus neoformans in one. Furthermore, additional pathogens were detected (n = 1, S. pneumoniae and n = 1, varicella-zoster virus). The median times to pathogen identification were 2 hours using the FilmArray® ME panel and 96 hours with conventional methods. CONCLUSIONS The sensitivity of the FilmArray® ME panel for rapidly detecting the most common pathogens was similar to that of conventional methods. Hence, this method could decrease the time to definitive diagnosis and treatment initiation.
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Affiliation(s)
| | | | - Hideto Nakajima
- Hideto Nakajima, Division of Neurology,
Department of Medicine, Nihon University School of Medicine, 30-1
Oyaguchikamicho, Itabashi, Tokyo 173-8610, Japan.
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Mohd Hanafiah N, Cheng A, Lim PE, Sethuraman G, Mohd Zain NA, Baisakh N, Mispan MS. Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice. Life (Basel) 2022; 12:life12101542. [PMID: 36294977 PMCID: PMC9604669 DOI: 10.3390/life12101542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Simple Summary Rice, the staple food for more than half of humanity, is grown predominantly in Asia, the world’s most populous continent with the fastest-growing economy. The present-day rice industry must not only meet increasing demand but also changing consumer demands, with a strong emphasis placed on producing high-quality rice. While the rapid development of advanced genotyping methods can be useful for modern rice breeding programs, some methods (such as capillary electrophoresis or sequencing) can be costly to apply in laboratories with limited resources. To address this issue, we developed six novel multiplex polymerase chain reaction (PCR) assays that employ a standard agarose-based gel electrophoresis system to simultaneously detect at least two major grain quality (amylose content and fragrance) and biotic stress (blast, sheath blight, and bacterial leaf blight) genes in rice. One of these assays, which can detect all three targeted biotic stresses, was found to be useful in screening Malaysian weedy rice that may contain novel sources of disease resistance. The universal protocol described in this study can be used in routine molecular laboratories to aid rice breeding initiatives in Malaysia and other resource-constrained countries. Abstract While previous research has demonstrated that multiplex polymerase chain reaction (PCR) can be a cost-effective approach to detect various genes in crops, the availability of multiplex assays to simultaneously screen both grain quality and biotic stress resistance traits in rice (Oryza sativa) is limited. In this work, we report six novel multiplex assays that use a universal protocol to detect major rice grain quality (amylose content and fragrance) and biotic stress (blast, sheath blight, and bacterial leaf blight) traits with amplified products consisting of up to four primer pairs that can be analyzed using a standard agarose-based gel electrophoresis system. Recent studies have suggested that weedy rice has novel sources of disease resistance. However, an intensive screening of weedy biotypes has not been reported in Malaysia. Accordingly, we employed one of the developed multiplex assays to screen reported genes or quantitative trait loci (QTLs) associated with blast, sheath blight, and bacterial leaf blight diseases in 100 weedy rice biotypes collected from five local fields, with phenotyping performed to validate the genotyping results. In conclusion, our universal multiplex protocol is effective for the large-scale genotyping of rice genetic resources, and it can be employed in routine molecular laboratories with limited resources.
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Affiliation(s)
- Noraikim Mohd Hanafiah
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Acga Cheng
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (A.C.); (M.S.M.)
| | - Phaik-Eem Lim
- Institute of Ocean and Earth Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Gomathy Sethuraman
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Nurul Amalina Mohd Zain
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Niranjan Baisakh
- School of Plant, Environmental and Soil Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Muhamad Shakirin Mispan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (A.C.); (M.S.M.)
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19
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Lee SJ, Jang TS, Jeon JS, Kim JK. Coinfections with multiple sexually transmitted pathogens in Republic of Korea, 2018-2020. J Clin Lab Anal 2022; 36:e24682. [PMID: 36036770 PMCID: PMC9550954 DOI: 10.1002/jcla.24682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Sexually transmitted infections (STIs) can have serious consequences, and the global STI incidence remains high. However, there is little information on the frequency of STIs with multiple pathogens according to age. Accordingly, we conducted a study to determine the trends of coinfection with sexually transmitted pathogens according to age in the Republic of Korea from 2018 to 2020. METHODS From January 2018 to December 2020, 65,191 samples of swab, urine, and other types submitted for STI screening were obtained from U2Bio Co. Ltd. (Seoul, Republic of Korea). Multiplex polymerase chain reaction, a sensitive and rapid method for simultaneous detection of STIs caused by multiple different pathogens, was performed using an AccuPower STI4C-Plex Real-Time PCR kit, AccuPower STI8A-Plex Real-Time PCR kit, and AccuPower STI8B-Plex Real-Time PCR kit with an Exicycler 96 Real-Time Quantitative Thermal Block. RESULTS Of the 65,191 samples tested, 35,366 (54.3%) tested positive for one or more sexually transmitted pathogens. The prevalence of coinfections with two or more sexually transmitted pathogens was inversely proportional to age. Furthermore, the rates of coinfection with sexually transmitted pathogens and age distribution differed according to sex and the sexually transmitted pathogen type. CONCLUSION This study confirmed that a significant proportion of patients with STIs are coinfected with multiple pathogens. Public health managers could use these results to recognize and prevent STIs according to age.
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Affiliation(s)
- Sun Jung Lee
- Department of Biomedical Laboratory Science, Dankook University College of Health Sciences, Chungnam, Korea
| | - Tae Su Jang
- Department of Health Administration, Dankook University College of Health Sciences, Chungnam, Korea
| | - Jae-Sik Jeon
- Department of Biomedical Laboratory Science, Dankook University College of Health Sciences, Chungnam, Korea
| | - Jae Kyung Kim
- Department of Biomedical Laboratory Science, Dankook University College of Health Sciences, Chungnam, Korea
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20
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Liao YC, Wu HC, Liou CH, Lauderdale TLY, Huang IW, Lai JF, Chen FJ. Rapid and Routine Molecular Typing Using Multiplex Polymerase Chain Reaction and MinION Sequencer. Front Microbiol 2022; 13:875347. [PMID: 35422786 PMCID: PMC9002326 DOI: 10.3389/fmicb.2022.875347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/09/2022] [Indexed: 11/26/2022] Open
Abstract
Molecular typing is an essential tool that has been extensively applied in laboratories as well as in clinical settings. Next-generation sequencing technologies promise high-throughput and cost-effective molecular applications; however, the accessibility of these technologies is limited due to the high capital cost. Oxford Nanopore Technologies (ONT) offers a MinION device with the advantages of real-time data analysis, rapid library preparation, and low cost per test. However, the advantages of the MinION device are often overshadowed by its lower raw accuracy. Herein, we present a concise multilocus sequence typing protocol of Staphylococcus aureus using multiplex polymerase chain reaction and Rapid Barcoding Kit for barcoding and MinION device for sequencing. Moreover, to clarify the effects of carryover DNA on tasks that require high sequence accuracy, we used the MinION flow cell in successive runs of washing and reusing. Our results revealed that the MinION flow cell could achieve accurate typing of a total of 467 samples with 3,269 kilobase-long genes within a total of 5 runs. This thus demonstrates the effectiveness of a portable nanopore MinION sequencer in providing accurate, rapid, and routine molecular typing.
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Affiliation(s)
- Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Ci-Hong Liou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Tsai-Ling Yang Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - I-Wen Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Jui-Fen Lai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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21
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Akwani WC, van Vliet AH, Joel JO, Andres S, Diricks M, Maurer FP, Chambers MA, Hingley-Wilson SM. The Use of Comparative Genomic Analysis for the Development of Subspecies-Specific PCR Assays for Mycobacterium abscessus. Front Cell Infect Microbiol 2022; 12:816615. [PMID: 35419298 PMCID: PMC8995789 DOI: 10.3389/fcimb.2022.816615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/07/2022] [Indexed: 01/21/2023] Open
Abstract
Mycobacterium abscessus complex (MABC) is an important pathogen of immunocompromised patients. Accurate and rapid determination of MABC at the subspecies level is vital for optimal antibiotic therapy. Here we have used comparative genomics to design MABC subspecies-specific PCR assays. Analysis of single nucleotide polymorphisms and core genome multilocus sequence typing showed clustering of genomes into three distinct clusters representing the MABC subspecies M. abscessus, M. bolletii and M. massiliense. Pangenome analysis of 318 MABC genomes from the three subspecies allowed for the identification of 15 MABC subspecies-specific genes. In silico testing of primer sets against 1,663 publicly available MABC genomes and 66 other closely related Mycobacterium genomes showed that all assays had >97% sensitivity and >98% specificity. Subsequent experimental validation of two subspecies-specific genes each showed the PCR assays worked well in individual and multiplex format with no false-positivity with 5 other mycobacteria of clinical importance. In conclusion, we have developed a rapid, accurate, multiplex PCR-assay for discriminating MABC subspecies that could improve their detection, diagnosis and inform correct treatment choice.
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Affiliation(s)
- Winifred C. Akwani
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Arnoud H.M. van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Jordan O. Joel
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Sönke Andres
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Margo Diricks
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Florian P. Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark A. Chambers
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Suzanne M. Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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22
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Lee GY, Kim WK, Cho S, Park K, Kim J, Lee SH, Lee J, Lee YS, Kim JH, Byun KS, Song JW. Genotyping and Molecular Diagnosis of Hepatitis A Virus in Human Clinical Samples Using Multiplex PCR-Based Next-Generation Sequencing. Microorganisms 2022; 10:100. [PMID: 35056549 DOI: 10.3390/microorganisms10010100] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 02/04/2023] Open
Abstract
Hepatitis A virus (HAV) is a serious threat to public health worldwide. We used multiplex polymerase chain reaction (PCR)-based next-generation sequencing (NGS) to derive information on viral genetic diversity and conduct precise phylogenetic analysis. Four HAV genome sequences were obtained using multiplex PCR-based NGS. HAV whole-genome sequence of one sample was obtained by conventional Sanger sequencing. The HAV strains demonstrated a geographic cluster with sub-genotype IA strains in the Republic of Korea. The phylogenetic pattern of HAV viral protein (VP) 3 region showed no phylogenetic conflict between the whole-genome and partial-genome sequences. The VP3 region in serum and stool samples showed sensitive detection of HAV with differences of quantification that did not exceed <10 copies/μL than the consensus VP4 region using quantitative PCR (qPCR). In conclusion, multiplex PCR-based NGS was implemented to define HAV genotypes using nearly whole-genome sequences obtained directly from hepatitis A patients. The VP3 region might be a potential candidate for tracking the genotypic origin of emerging HAV outbreaks. VP3-specific qPCR was developed for the molecular diagnosis of HAV infection. This study may be useful to predict for the disease management and subsequent development of hepatitis A infection at high risk of severe illness.
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23
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Jo KJ, Choi SH, Oh CE, Kim H, Choi BS, Jo DS, Park SE. Epidemiology and Clinical Characteristics of Human Coronaviruses-Associated Infections in Children: A Multi-Center Study. Front Pediatr 2022; 10:877759. [PMID: 35498812 PMCID: PMC9039334 DOI: 10.3389/fped.2022.877759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Human coronaviruses (HCoVs) are associated with upper respiratory tract infections. Although studies have analyzed the clinical and epidemiological characteristics of HCoV-associated infections, no multi-center studies have been conducted in Korean children. We aimed to describe the epidemiology and clinical characteristics of HCoV-associated infection in children. METHODS We retrospectively reviewed medical records of children in whom HCoVs were detected using multiplex reverse transcriptase-polymerase chain reaction amplification in five centers from January 2015 to December 2019. RESULTS Overall, 1,096 patients were enrolled. Among them, 654 (59.7%) patients were male. The median age was 1 year [interquartile range (IQR), 0-2 years]. HCoVs were identified mainly in winter (55.9%). HCoV-229E, HCoV-OC43, and HCoOV-NL63 were detected mainly in winter (70.9, 55.8, and 57.4%, respectively), but HCoV-HKU1 was mainly identified in spring (69.7%). HCoV-OC43 (66.0%) was detected most frequently, followed by HCoV-NL63 (33.3%), and HCoV-229E (7.7%). Two different types of HCoVs were co-detected in 18 samples, namely. Alphacoronavirus-betacoronavirus co-infection (n = 13) and, alphacoronavirus-alphacoronavirus co-infection (n = 5). No betacoronavirus-betacoronavirus co-infection was detected. Patients were diagnosed with upper respiratory tract infection (41.4%), pneumonia (16.6%), acute bronchiolitis (15.5%), non-specific febrile illness (13.1%), croup (7.3%), and acute gastroenteritis (5.1%). There were 832 (75.9%) hospitalized patients with a median duration of hospitalization of 4 days (IQR, 3-5 days); 108 (9.9%) patients needed supplemental oxygen with 37 (3.4%) needing high-flow nasal cannula or mechanical ventilation. There were no deaths. CONCLUSION HCoV-associated infections exhibit marked seasonality with peaks in winter. Patients with lower respiratory tract infection, a history of prematurity, or underlying chronic diseases may progress to a severe course and may need oxygen therapy.
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Affiliation(s)
- Kyo Jin Jo
- Department of Pediatrics, Pusan National University Children's Hospital, Yangsan, South Korea
| | - Soo-Han Choi
- Department of Pediatrics, Pusan National University Hospital, Busan, South Korea
| | - Chi Eun Oh
- Department of Pediatrics, Kosin University College of Medicine, Busan, South Korea
| | - HyeonA Kim
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Bong Seok Choi
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Dae Sun Jo
- Department of Pediatrics, Jeonbuk National University Medical School, Jeonju, South Korea
| | - Su Eun Park
- Department of Pediatrics, Pusan National University Children's Hospital, Yangsan, South Korea
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24
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Berenger BM, Chui L, Ferrato C, Lloyd T, Li V, Pillai DR. Performance of four commercial real-time PCR assays for the detection of bacterial enteric pathogens in clinical samples. Int J Infect Dis 2021; 114:195-201. [PMID: 34700003 DOI: 10.1016/j.ijid.2021.10.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022] Open
Abstract
OBJECTIVES Many laboratories use culture-independent diagnostic tests for bacterial gastroenteritis (ie. real-time polymerase chain reaction [RT-PCR]) instead of culture because of better sensitivity, automation, and faster turnaround times. To address some gaps in initial evaluations and lack of intraassay comparisons for many commercial RT-PCRs we compared the ability of four commercially available RT-PCR tests (Ridagene, Fast Track Diagnostics, BD Max, and Prodesse Progastro) to detect five major bacterial enteric pathogens: Campylobacter, Salmonella, Shiga-toxin producing E. coli (STEC), Shigella and Yersinia. METHODS Clinical stool specimens and contrived samples comprising commonly circulating species, serotypes, biovars and/or toxin subtypes were used for the comparison. RESULTS Concordance rates for RT-PCR and culture using culture positive and negative clinical stools were greater than 90% for Campylobacter (97.5-100%), Salmonella (97.5-100%), Shigella (100%) and STEC (90-100%). However, the agreement between RT-PCR and culture for Y. enteroccolitica ranged from 70-90%. For the contrived sample set, stx2f was detected by only 1 of 4 assays. Of note, no assay could detect Yersinia non-enterocolitica and C. upsaliensis. CONCLUSIONS Depending on the prevalence of certain stx sub-types, Yersinia and Campylobacter species in a laboratory's jurisdiction, culture methods remain critical for the detection of these pathogens without further improvement in PCR assays.
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Affiliation(s)
- Byron M Berenger
- South Sector Microbiology, Alberta Precision Laboratories, 3535 Research Road, Calgary, AB, Canada T2L 1Y1; Alberta Public Health Laboratory, Alberta Precision Laboratories, 3300 Hospital Drive NW, Calgary, AB, T2N 4W4; Department of Pathology and Laboratory Medicine, University of Calgary, 3535 Research Road, Calgary, AB, Canada T2L 1Y1.
| | - Linda Chui
- Alberta Public Health Laboratory, Alberta Precision Laboratories, 3300 Hospital Drive NW, Calgary, AB, T2N 4W4; Department of Laboratory Medicine and Pathology, University of Alberta, 116 St. and 85 Ave Edmonton, AB, Canada T6G 2R3.
| | - Christina Ferrato
- Alberta Public Health Laboratory, Alberta Precision Laboratories, 3300 Hospital Drive NW, Calgary, AB, T2N 4W4.
| | - Tracie Lloyd
- South Sector Microbiology, Alberta Precision Laboratories, 3535 Research Road, Calgary, AB, Canada T2L 1Y1.
| | - Vincent Li
- Alberta Public Health Laboratory, Alberta Precision Laboratories, 3300 Hospital Drive NW, Calgary, AB, T2N 4W4.
| | - Dylan R Pillai
- South Sector Microbiology, Alberta Precision Laboratories, 3535 Research Road, Calgary, AB, Canada T2L 1Y1; Department of Pathology and Laboratory Medicine, University of Calgary, 3535 Research Road, Calgary, AB, Canada T2L 1Y1; Department of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1.
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25
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Kayser MZ, Seeliger B, Valtin C, Fuge J, Ziesing S, Welte T, Pletz MW, Chhatwal P, Gottlieb J. Clinical decision making is improved by BioFire Pneumonia Plus in suspected lower respiratory tract infection after lung transplantation: Results of the prospective DBATE-IT * study. Transpl Infect Dis 2021; 24:e13725. [PMID: 34542213 DOI: 10.1111/tid.13725] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/20/2021] [Accepted: 08/29/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality in lung transplant (LTx) recipients. Timely and precise pathogen detection is vital to successful treatment. Multiplex PCR kits with short turnover times like the BioFire Pneumonia Plus (BFPPp) (manufactured by bioMérieux) may be a valuable addition to conventional tests. METHODS We performed a prospective observational cohort study in 60 LTx recipients with suspected LRTI. All patients received BFPPp testing of bronchoalveolar lavage fluid in addition to conventional tests including microbiological cultures and conventional diagnostics for respiratory viruses. Primary outcome was time-to-test-result; secondary outcomes included time-to-clinical-decision and BFPPp test accuracy compared to conventional tests. RESULTS BFPPp provided results faster than conventional tests (2.3 h [2-2.8] vs. 23.4 h [21-62], p < 0.001), allowing for faster clinical decisions (2.8 [2.2-44] vs. virology 28.1 h [23.1-70.6] and microbiology 32.6 h [4.6-70.9], both p < 0.001). Based on all available diagnostic modalities, 26 (43%) patients were diagnosed with viral LRTI, nine (15 %) with non-viral LRTI, and five (8 %) with combined viral and non-viral LRTI. These diagnoses were established by BFPPp in 92%, 78%, and 100%, respectively. The remaining 20 patients (33 %) received a diagnosis other than LRTI. Preliminary therapies based on BFPPp results were upheld in 90% of cases. There were six treatment modifications based on pathogen-isolation by conventional testing missed by BFPPp, including three due to fungal pathogens not covered by the BFPPp. CONCLUSION BFPPp offered faster test results compared to conventional tests with good concordance. The absence of fungal pathogens from the panel is a potential weakness in a severely immunosuppressed population.
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Affiliation(s)
- Moritz Z Kayser
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Benjamin Seeliger
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
| | - Christina Valtin
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Jan Fuge
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
| | - Stefan Ziesing
- Department of Microbiology and Hospital Hygiene, Hannover Medical School, Hannover, Germany
| | - Tobias Welte
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
| | - Mathias W Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Patrick Chhatwal
- Department of Microbiology and Hospital Hygiene, Hannover Medical School, Hannover, Germany.,Department of Microbiology, MVZ Medical Laboratory Hannover, Hannover, Germany
| | - Jens Gottlieb
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
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26
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Liu H, Li J, Lin Y, Bo X, Song H, Li K, Li P, Ni M. Assessment of two-pool multiplex long-amplicon nanopore sequencing of SARS-CoV-2. J Med Virol 2021; 94:327-334. [PMID: 34524690 PMCID: PMC8662006 DOI: 10.1002/jmv.27336] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/12/2021] [Indexed: 01/28/2023]
Abstract
Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) plays an important role in COVID‐19 pandemic control and elimination efforts, especially by elucidating its global transmission network and illustrating its viral evolution. The deployment of multiplex PCR assays that target SARS‐CoV‐2 followed by either massively parallel or nanopore sequencing is a widely‐used strategy to obtain genome sequences from primary samples. However, multiplex PCR‐based sequencing carries an inherent bias of sequencing depth among different amplicons, which may cause uneven coverage. Here we developed a two‐pool, long‐amplicon 36‐plex PCR primer panel with ~1000‐bp amplicon lengths for full‐genome sequencing of SARS‐CoV‐2. We validated the panel by assessing nasopharyngeal swab samples with a <30 quantitative reverse transcription PCR cycle threshold value and found that ≥90% of viral genomes could be covered with high sequencing depths (≥20% mean depth). In comparison, the widely‐used ARTIC panel yielded 79%–88% high‐depth genome regions. We estimated that ~5 Mbp nanopore sequencing data may ensure a >95% viral genome coverage with a ≥10‐fold depth and may generate reliable genomes at consensus sequence levels. Nanopore sequencing yielded false‐positive variations with frequencies of supporting reads <0.8, and the sequencing errors mostly occurred on the 5′ or 3′ ends of reads. Thus, nanopore sequencing could not elucidate intra‐host viral diversity.
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Affiliation(s)
- Hongjie Liu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jinhui Li
- Department of Bio-security, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yanfeng Lin
- Department of Bio-security, Chinese PLA Center for Disease Control and Prevention, Beijing, China.,Graduate School, Academy of Military Medical Sciences, Beijing, China
| | - Xiaochen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Hongbin Song
- Department of Bio-security, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kuibiao Li
- Laboratory of Clinical Microbiology, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Peng Li
- Department of Bio-security, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ming Ni
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
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Feng Y, Li X, Ma Q, Zhang S, Zhu M, Li S, Fang L, Tian J, Sun L. Intercellular Adhesion Molecule-1 Gene Polymorphisms and Susceptibility to Cervical Cancer in the Northern Chinese Han Population. Front Genet 2021; 12:668539. [PMID: 34386034 PMCID: PMC8353393 DOI: 10.3389/fgene.2021.668539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Many epidemiological studies have confirmed that ICAM-1 gene single-nucleotide polymorphisms (SNPs) are associated with susceptibility of various cancers, but there are relatively few studies on the relationship between ICAM-1 gene polymorphisms and the risk of cervical cancer. Therefore, we aimed to explore the potential role of ICAM-1 gene polymorphisms and the combined effect of SNPs in the pathogenesis of cervical cancer in Han women in northern China. This case–control group includes 488 cases of cervical cancer, 684 cases of cervical precancerous lesions, and 510 healthy females. Multiplex polymerase chain reaction (PCR) combined with the next-generation sequencing method was used for the determination of gene polymorphisms (rs5498, rs3093030, and rs281432). In our study, we divide cervical cancer into two subgroups: cervical squamous cell carcinoma (CSCC) group and cervical adenocarcinoma (CAC) group. We analyzed the alleles and genotypes of all research subjects using multivariate logistic regression analysis combined with 10,000 permutation tests. In addition, we also analyzed the distribution of haplotypes of the three SNPs in cervical cancer and cervical precancerous lesions. We found that the T allele and the dominant model of rs3093030 were associated with the susceptibility of cervical cancer (p = 0.042, p = 0.040, respectively). However, the significance disappeared after the Bonferroni correction for multiple testing (p > 0.05). For rs5498, its mutant gene G, the codominant model, and the dominant model could reduce the risk of CAC (p = 0.009, p = 0.028, p = 0.011, respectively). Significant differences remained after Bonferroni correction (p < 0.05, all). In addition, the frequency of haplotype “CTG” was significantly lower in the CAC group than in the controls. In conclusion, the study suggested that ICAM-1 gene polymorphisms may have a potential role in the pathogenesis of cervical cancer in the northern Chinese Han population.
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Affiliation(s)
- Yanan Feng
- Department of Ultrasound, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoying Li
- Department of Ultrasound, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qi Ma
- Department of Ultrasound, Harbin Red Cross Central Hospital, Harbin, China
| | - Shuang Zhang
- Department of Ultrasound, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Manning Zhu
- Department of Ultrasound, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Songxue Li
- Department of Ultrasound, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lei Fang
- Department of Ultrasound, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiawei Tian
- Department of Ultrasound, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Litao Sun
- Department of Ultrasound, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Ultrasound, People's Hospital of Zhejiang Province, Hangzhou, China
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Joji RM, Al-Mahameed AE, Jishi TA, Fatani DI, Saeed NK, Jaradat A, Ezzat H, Bindayna KM. Molecular detection of plasmid-derived AmpC β-lactamase among clinical strains of Enterobacteriaceae in Bahrain. Ann Thorac Med 2021; 16:287-293. [PMID: 34484445 PMCID: PMC8388573 DOI: 10.4103/atm.atm_523_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Enterobacteriaceae with AmpC β-lactamase are multidrug-resistant organisms and represent a significant challenge to patient care. This study aims to determine the prevalence of plasmid-derived AmpC β-lactamase among extended spectrum β-lactamases (ESBL)-producing Enterobacteriaceae strains in Bahrain. METHODS It was a cross-sectional study. A total of 185 ESBL-producing Enterobacteriaceae isolates were recovered from clinically significant specimens from January 2018 to December 2019. The samples underwent initial screen for cefoxitin resistance by disc diffusion test and subsequent phenotypic confirmation of AmpC production with phenyl boronic acid assays as well as genotypic analysis by multiplex polymerase chain reactions for AmpC subtypes. Drug-resistant features of these clinical isolates were also examined. RESULTS Twenty-nine ESBL-producing Enterobacteriaceae isolates were cefoxitin resistant. Phenotypic and genotypic analyses confirmed that 8 and 12 cefoxitin-resistant isolates are AmpC positive, respectively. These AmpC producers are multidrug resistant, and Escherichia coli is the dominant strain among them. CONCLUSIONS Plasmid-mediated spread of AmpC is present in clinically relevant Enterobacteriaceae species in Bahrain. Rational antimicrobial therapy against these multidrug-resistant organisms and continued surveillance of antimicrobial resistance mechanisms among the clinical isolates are recommended for optimal patient care.
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Affiliation(s)
- Ronni Mol Joji
- Departments of Microbiology, Immunology and Infectious Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Ali Ebrahim Al-Mahameed
- Departments of Microbiology, Immunology and Infectious Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Thamer Al Jishi
- Departments of Microbiology, Immunology and Infectious Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Dania Ismail Fatani
- Departments of Microbiology, Immunology and Infectious Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Nermin K Saeed
- Department of Pathology, Salmaniya Medical Complex, Ministry of Health, Manama, Kingdom of Bahrain
| | - Ahmed Jaradat
- Department of Community Medicine, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Hicham Ezzat
- Departments of Microbiology, Immunology and Infectious Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Khalid Mubarak Bindayna
- Departments of Microbiology, Immunology and Infectious Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain
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Wagner JL, Markovich KC, Barber KE, Stover KR, Biehle LR. Optimizing rapid diagnostics and diagnostic stewardship in Gram-negative bacteremia. Pharmacotherapy 2021; 41:676-685. [PMID: 34131939 DOI: 10.1002/phar.2606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 01/05/2023]
Abstract
Antimicrobial resistance remains a high global concern, as it is associated with prolonged hospitalizations, increased morbidity and mortality, and escalating healthcare-related costs. Rapid diagnostic technology (RDT) has become the cornerstone in achieving prompt blood culture results providing a quicker initiation of optimal therapy, decreased mortality, and decreased spread of resistance. To maximize the benefits of RDTs, antimicrobial stewardship programs must implement a diagnostic stewardship (DS) subgroup to optimize communication, education, and interpretation of RDT results within the healthcare system. The DS subgroup is necessary to evaluate the technologies available, better integrate the selected technologies into the healthcare system, and develop innovative and appropriate use to improve patient outcomes.
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Affiliation(s)
- Jamie L Wagner
- University of Mississippi School of Pharmacy, Jackson, Mississippi, USA
| | | | - Katie E Barber
- University of Mississippi School of Pharmacy, Jackson, Mississippi, USA
| | - Kayla R Stover
- University of Mississippi School of Pharmacy, Jackson, Mississippi, USA.,University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Lauren R Biehle
- University of Wyoming School of Pharmacy, Laramie, Wyoming, USA
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Rivero Z, Villareal L, Bracho Á, Prieto C, Villalobos R. Molecular identification of Entamoeba histolytica, E. dispar, and E. moshkovskii in children with diarrhea from Maracaibo, Venezuela. ACTA ACUST UNITED AC 2021; 41:23-34. [PMID: 34111338 DOI: 10.7705/biomedica.5584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Indexed: 11/22/2022]
Abstract
Introducción. Las amebas no patógenas Entamoeba dispar, Entamoeba moshkovskii y Entamoeba bangladeshi son morfológicamente idénticas a Entamoeba histolytica, parásito responsable de la amebiasis, por lo cual se necesitan técnicas moleculares para diferenciarlas. Objetivo. Determinar la frecuencia de las diferentes especies de Entamoeba mediante reacción en cadena de la polimerasa (Polymerase Chain Reaction, PCR) en muestras fecales de niños menores de cinco años con diarrea, provenientes de Maracaibo (Venezuela). Materiales y métodos. Se recolectó una muestra fecal por individuo en 75 niños con diarrea (grupo de casos) y en 25 niños sin diarrea (grupo control). Las heces se evaluaron mediante examen microscópico, método de concentración de formól-éter y PCR múltiple anidada en una sola ronda para identificar E. histolytica, E. dispar y E. moshkovskii. Además, se hizo una encuesta en la que se recopilaron los datos demográficos, signos, manifestaciones clínicas y estrato socioeconómico de los niños. Resultados. El 48 % de los participantes (38 del grupo de casos y 10 del grupo de control) tenían enteroparásitos. Solo en las muestras de cuatro de los niños, se encontraron quistes del complejo Entamoeba (tres en el grupo de casos y uno en el de control). Mediante PCR se amplificaron nueve muestras (9 %) para la detección de las amebas estudiadas. En el grupo de casos se registraron tres (28,13 %) de E. histolytica, cuatro (30,50 %) de E. dispar y una (9,37 %) de E. moshkovskii, en tanto que solo una (25 %) muestra amplificó para E. dispar en el grupo de control. Conclusión. En general, predominó E. dispar; sin embargo, todos los infectados con E. histolytica se detectaron en el grupo de niños con diarrea y se detectó el primer caso de E. moshkovskii en la región.
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Jang JG, Ahn JH, Jin HJ. Incidence and Prognostic Factors of Respiratory Viral Infections in Severe Acute Exacerbation of Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2021; 16:1265-1273. [PMID: 33994783 PMCID: PMC8112874 DOI: 10.2147/copd.s306916] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/19/2021] [Indexed: 01/08/2023] Open
Abstract
Purpose Severe acute exacerbations of chronic obstructive pulmonary disease (AECOPD) that require hospitalization and emergency department visits are associated with considerable morbidity and mortality. Respiratory viral infection is an important cause of severe AECOPD. We evaluated the incidence and prognostic factors of viral infection in severe AECOPD. Patients and Methods We performed a retrospective study of 262 cases of severe AECOPD in 192 patients who required hospitalization and emergency department visits at a tertiary teaching hospital in Daegu, Korea. A multiplex polymerase chain reaction panel using a nasopharyngeal swab sample was performed to detect viral infection. Results Viral infection was detected in 108 events (41.2%) from 96 patients. The most common virus was rhinovirus/enterovirus (27.5%), followed by influenza virus (22.5%), respiratory syncytial virus (13.3%), parainfluenza virus (12.5%), coronavirus (12.5%), metapneumovirus (7.5%), and adenovirus (4.2%). Virus-positive exacerbations, compared to virus-negative exacerbations, had a higher frequency of symptoms of rhinopharyngitis, higher neutrophil count and C-reactive protein (CRP) level, and lower eosinophil count. Multivariate analysis demonstrated that elevated CRP levels (odds ratio [OR], 2.76; 95% confidence interval [CI], 1.24–6.15), symptoms of rhinopharyngitis (OR, 1.98; 95% CI, 1.03–3.78), low eosinophil count (OR, 1.74; 95% CI, 1.03–2.92), and inhaled corticosteroid (ICS) use (OR, 1.70; 95% CI 1.04–2.80) were associated with viral infection in severe AECOPD. Conclusion The incidence of viral infection in severe AECOPD was 41.2%, and the most commonly detected virus was rhinovirus/enterovirus. Increased CRP level, symptoms of rhinopharyngitis, low eosinophil count, and use of ICS were associated with viral infection in severe AECOPD.
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Affiliation(s)
- Jong Geol Jang
- Division of Pulmonology and Allergy, Department of Internal Medicine, College of Medicine, Yeungnam University and Regional Center for Respiratory Diseases, Yeungnam University Medical Center, Daegu, South Korea
| | - June Hong Ahn
- Division of Pulmonology and Allergy, Department of Internal Medicine, College of Medicine, Yeungnam University and Regional Center for Respiratory Diseases, Yeungnam University Medical Center, Daegu, South Korea
| | - Hyun Jung Jin
- Division of Pulmonology and Allergy, Department of Internal Medicine, College of Medicine, Yeungnam University and Regional Center for Respiratory Diseases, Yeungnam University Medical Center, Daegu, South Korea
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Paul P, Faruque MR, Rahman MK, Das P, Chowdhury MYE. Study on bacterial pathogens through multiplex polymerase chain reaction system and their antimicrobial resistance pattern in goats presumed with fever and/or diarrhea. Vet World 2021; 14:1080-1092. [PMID: 34220107 PMCID: PMC8243672 DOI: 10.14202/vetworld.2021.1080-1092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/16/2021] [Indexed: 12/03/2022] Open
Abstract
Background and Aim: Goat is one of the major livestock species, plays an important role in the economy of Bangladesh. However, the outbreak of different infectious diseases in goats causes high mortality and economic losses due to lack of proper diagnosis and treatment. Conventional culture-based methods for detecting specific pathogens as confirmatory diagnosis are laborious as well as time-consuming in comparison to multiplex polymerase chain reaction (mPCR), by which multiple pathogens can be detected at a time. The present study was aimed to perform faster molecular identification of bacterial pathogens from goats presumed with fever and/or diarrhea and their antimicrobial resistance (AMR) pattern. Materials and Methods: A total of 200 blood samples were collected from goats at S. A. Quaderi Teaching Veterinary Hospital (SAQTVH) in Chattogram Veterinary and Animal Sciences University for the period of July 2017-April 2018. DNA was extracted and subsequently, mPCR assay was performed for the screening of several bacterial pathogens (Salmonella spp., Listeria monocytogenes, Bacillus cereus, Yersinia enterocolitica, Campylobacter jejuni, Campylobacter coli, Clostridium perfringens, Vibrio cholerae, and Staphylococcus aureus). An antimicrobial susceptibility test against ten antimicrobials for positive samples of each organism was conducted using the Kirby–Bauer Disk-Diffusion Method on selective media. Results: S. aureus, C. perfringens, L. monocytogenes, and Salmonella spp. were detected from collected samples and their overall prevalence was 11.5%, 3.5%, 1%, and 20.5%, respectively. The most common clinical signs were mild fever, nasal discharge, dyspnea, and coughing (39.1%) for S. aureus, diarrhea, convulsion, abdominal pain, and incoordination (57.1%) for C. perfringens, fever, protrusion of tongue, and incoordination (100%) for L. monocytogenes, and fever, anorexia, dehydration with mucous feces (36.6%) for Salmonella spp. infection in goats. AntimGentamicinicrobial diagram of S. aureus showed resistance against Cefotaxime (74%), Cefixime (65%), and Tetracycline (65%); highly sensitive against Amoxicillin (48%), Ciprofloxacin (44%), and Gentamicin (44%). On the other hand, C. perfringens showed highly resistant against Ampicillin (71%), Gentamicin (71%), sensitive against Penicillin (57%), and Cefotaxime (57%). L. monocytogenes were found to be sensitive to Penicillin (100%) and Cefixime (100%) and Salmonella spp. showed resistance to Ampicillin (78%) and Amoxicillin (59%) but sensitive to Ciprofloxacin (54%). Conclusion: This study identified pathogens with their specific clinical signs in goats presumed fever and/or diarrhea through mPCR with their AMR pattern in SAQTVH, Chattogram. Potential risk factors, measuring the strength of association of disease caused by these particular pathogens, were also determined. mPCR may use as an effective tool for rapid detection of pathogens in animal.
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Affiliation(s)
- Pranab Paul
- Department of Medicine and Surgery, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Md Rayhan Faruque
- Department of Medicine and Surgery, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | | | - Priyanka Das
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
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Kim YK, Lee JH, Kim SY, Ahn JY, Choi KH, Lee YH, Jang KM, Hau YS, Lee JM. Rapid Molecular Tests for Detecting Respiratory Pathogens Reduced the Use of Antibiotics in Children. Antibiotics (Basel) 2021; 10:283. [PMID: 33801828 DOI: 10.3390/antibiotics10030283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/06/2021] [Accepted: 03/07/2021] [Indexed: 12/25/2022] Open
Abstract
Multiplex polymerase chain reaction (mPCR) is increasingly being used to diagnose infections caused by respiratory pathogens in pediatric inpatient facilities. mPCR assays detect a broader array of viruses, with higher specificity and sensitivity and faster turnaround than previous assays. We adapted the FilmArray Respiratory Panel (FA-RP) for diagnosing respiratory infections. FA-RP is an in vitro mPCR assay that simultaneously and rapidly (in about 1 h) detects 20 pathogens directly from respiratory specimens. Here, we studied the clinical efficacy of FA-RP in children who underwent testing for respiratory pathogens at Yeungnam University Hospital from November 2015 to August 2018. From November 2015 to June 2016, routine mPCR testing was performed on nasopharyngeal swabs using the routine mPCR kit. From November 2016 to July 2018, mPCR testing was performed using FA-RP. A total of 321 tests by routine mPCR and 594 tests by FA-RP were included. The positive detection rates for routine mPCR and FA-RP were 71.3% and 83.3%, respectively. FA-RP reduced the lead time, waiting time, turnaround time, intravenous (IV) antibiotic use, and length of hospital stay for pediatric patients. The decreased use of antibiotics is expected to reduce antibiotic resistance in children.
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Li F, Wang Y, Zhang Y, Shi P, Cao L, Su L, Zhu Q, Wang L, Lu R, Tan W, Shen J. Etiology of Severe Pneumonia in Children in Alveolar Lavage Fluid Using a High-Throughput Gene Targeted Amplicon Sequencing Assay. Front Pediatr 2021; 9:659164. [PMID: 34249808 PMCID: PMC8267249 DOI: 10.3389/fped.2021.659164] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Objective: To evaluate the diagnostic value of a high-throughput gene targeted amplicon sequencing (TAS) assay for detecting pathogenic microorganisms in alveolar lavage fluid (ALF) from children with severe community-acquired pneumonia (SCAP). Methods: A retrospective study was performed on 48 frozen ALF samples from 47 severe pneumonia cases admitted to Children's Hospital of Fudan University from January 1, 2019, to March 31, 2019. All samples were tested by a multiplex PCR (Multi-PCR) assay and a TAS assay. The results of the TAS panels were parallel compared with Multi-PCR and Conventional Tests (CT) including culture, direct fluorescent antibody method (DFA), and singleplex polymerase chain reaction (PCR). Results: The proportion of pathogens detection by CT was 81.2% (39/48). The 8 common respiratory viruses including respiratory syncytial virus (RSV), adenovirus (ADV), influenza A virus (FLUA), influenza B virus (FLUB), parainfluenza virus 1-3 (PIV1-3), and human Metapneumovirus (hMPV) were found in 31.2% (15/48) of the 48 samples by DFA. With the criteria of CT results used as "Golden Standard" for determing of TAS results, the proportion of pathogens detection by TAS was 70.8% (34/48). The difference of proportion of pathogens detection between TAS and CT was not statistically significant (p = 0.232). The sensitivity and specificity of TAS for pathogens detection based on CT were 87.1% (95% CI, 71.77-95.18%) and 100.0% (95% CI, 62.88-100%), the positive predictive value (PPV) and negative predictive value (NPV) were 100.0% (95% CI, 87.35-100%) and 64.2% (95% CI, 35.62-86.02%), respectively. While Multi-PCR results were used as "Golden Standard," the total pathogens detection rate of TAS was 83.3% (40/48), which had a significant difference with that of Multi-PCR (p = 0.003). The sensitivity and PPV of TAS compared with Multi-PCR were 83.3% (95% CI, 69.23-92.03%) and 100.0% (95% CI, 89.08-100%), respectively. High rates of co-infection were proved by CT, Multi-PCR, and TAS. Mycoplasma pneumoniae (MP) and ADV were the two most frequently detected pathogens in all three assays. Conclusion: Compared with the CT and Multi-PCR methods, this TAS assay had a good performance in detecting bacteriological and viral pathogens from ALF. More research is needed to establish interpretation criteria based on TAS reads or analysis platforms.
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Affiliation(s)
- Fei Li
- Infectious Disease Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yin Wang
- Clinical Trial Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yuhan Zhang
- Infectious Disease Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Peng Shi
- Statistics and Data Management Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Linfeng Cao
- Virology Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - LiYun Su
- Virology Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Qiguo Zhu
- Respiratory Department, Children's Hospital Xiamen Branch, Xiamen, China
| | - Libo Wang
- Respiratory Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Roujian Lu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Wenjie Tan
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Jun Shen
- Infectious Disease Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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Abooj J, Varma SA. Prevalence of herpes virus in chronic periodontitis patients with and without type 2 diabetes mellitus: A clinico-microbiological study. J Oral Maxillofac Pathol 2021; 25:141-146. [PMID: 34349425 PMCID: PMC8272489 DOI: 10.4103/jomfp.jomfp_154_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/26/2020] [Accepted: 10/05/2020] [Indexed: 12/01/2022] Open
Abstract
Background: Unfavorable modifications of tooth and its surrounding structures result in periodontal complications. Viruses, in specific herpes virus, are known to increase disease severity in periodontal patients. Periodontitis is known to be more established in type 2 diabetes mellitus (DM2) patients. Hence, the detection of the viral load, its effect on the prevalence of periodontitis and the glycemic control status of patients are to be evidenced. The study aimed to reveal the association of herpes virus with periodontal parameters and its prevalence in DM2 patients. Materials and Methods: The cross-sectional study involved a total of 120 patients falling into three groups; Group I (healthy), Group II (periodontitis without DM2) and Group III (periodontitis with DM2) were subjected for sampling. Subgingival samples of periodontitis patients were tested for clinical parameters, and DNA extraction was performed. The presence of herpes virus (Epstein–Barr virus [EBV-1] and human Cytomegalovirus [HCMV]) was detected using multiplex polymerase chain reaction primers. Glycemic status of patients was recorded as glycosylated hemoglobin and scored accordingly. Chi-square test was performed to analyze the association between the categorical variables, and t-test/Mann–Whitney U-test/analysis of variance/Kruskal–Wallis test was used for continuous data. Results: Significant levels of EBV-1 were detected in Group III (n = 21, 52.5%), followed by Group II (n = 16, 40%) and Group I (n = 2, 5%) (P < 0.0001). HCMV was not detected. A significant association of EBV-1 to periodontal site-specific parameters was observed in Group II patients (P < 0.05). EBV-1 was predominant with poor glycemic status patients. Conclusion: This study revealed that the incidence of herpes virus infection in periodontal patients was higher in diabetic patients and the examined patients were prone to EBV-1 infections.
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Affiliation(s)
- Jai Abooj
- Department of Periodontology, School of Dental Sciences, Krishna Institute of Medical Sciences "Deemed to be University," Karad, Maharashtra, India
| | - Siddhartha A Varma
- Department of Periodontology, School of Dental Sciences, Krishna Institute of Medical Sciences "Deemed to be University," Karad, Maharashtra, India
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Dehority W, Janowski AB, Messacar K, Polgreen PM, Beekmann SE. Variability in the Use of Novel Diagnostic Technology in Children With Suspected Encephalitis and in the Management of Emerging Encephalitides by Pediatric Infectious Disease Providers. J Pediatric Infect Dis Soc 2020; 10:529-532. [PMID: 33347568 PMCID: PMC8087119 DOI: 10.1093/jpids/piaa149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/18/2020] [Indexed: 11/14/2022]
Abstract
We surveyed pediatric infectious disease physicians through the Infectious Disease Society of America's Emerging Infections Network regarding the diagnosis and management of encephalitis. We identified practice variations, particularly with the use of new diagnostic modalities and management of autoimmune encephalitides. These findings may inform the creation of updated management guidelines.
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Affiliation(s)
- Walter Dehority
- Department of Pediatrics, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA,Corresponding Author: Walter Dehority, MD, MSc, Department of Pediatrics, Division of Infectious Diseases, The University of New Mexico School of Medicine, MSC10 5590. Albuquerque, NM 87131-0001, USA. E-mail:
| | - Andrew B Janowski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kevin Messacar
- Department of Pediatrics, University of Colorado, Aurora, Colorado, USA,Department of Pediatrics, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Philip M Polgreen
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Susan E Beekmann
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
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Li Q, Xie G, Wang Y, Aguilar ZP, Xu H. Vancomycin-modified poly-l-lysine magnetic separation combined with multiplex polymerase chain reaction assay for efficient detection of Bacillus cereus in milk. J Dairy Sci 2020; 104:1465-1473. [PMID: 33272582 DOI: 10.3168/jds.2020-18962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/26/2020] [Indexed: 12/19/2022]
Abstract
In this study, a new vancomycin (Van)-modified poly-l-lysine (PLL) magnetic bead (MB) technique was developed for isolation of gram-positive bacteria. The method combines magnetic separation with a multiplex PCR (mPCR) assay and gel electrophoresis for easy and rapid detection of Bacillus cereus. Vancomycin was used as a molecular ligand between the MB and the d-alanyl-d-alanine moieties on the cell wall surface of B. cereus. The PLL served as a flexible molecular tether between the MB and Van that reduced steric hindrance maintaining the biological activity of Van. The MB-PLL-Van capture nanoprobes exhibited excellent capture and isolation efficiency for B. cereus in spiked milk matrix samples without interference from the complex food matrix. The subsequent mPCR assay showed high specificity for the 4 target genes in B. cereus, the entFM, cesB, cer, and 16S rRNA genes, that were used to achieve efficient genotyping and detection. Under optimum conditions, the limit of detection reached 103 cfu/mL, with a dynamic range of detection at 103 to 107 cfu/mL in pure culture. Application of the MB-PLL-Van mediated mPCR assay for B. cereus in milk matrix samples achieved results similar to those of the pure culture. In addition, with a 6-h pre-enrichment of B. cereus that was spiked in milk matrix samples, the limit of detection reached 101 cfu/mL. The MB-PLL-Van mediated mPCR assay developed in this study could be used as a universal technology platform for the efficient enrichment and genotyping of gram-positive bacteria.
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Affiliation(s)
- Qianying Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Guoyang Xie
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Yutong Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | | | - Hengyi Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China.
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Bryant S, Almahmoud I, Pierre I, Bardet J, Touati S, Maubon D, Cornet M, Richarme C, Maurin M, Pavese P, Caspar Y. Evaluation of Microbiological Performance and the Potential Clinical Impact of the ePlex ® Blood Culture Identification Panels for the Rapid Diagnosis of Bacteremia and Fungemia. Front Cell Infect Microbiol 2020; 10:594951. [PMID: 33324578 PMCID: PMC7726344 DOI: 10.3389/fcimb.2020.594951] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/29/2020] [Indexed: 12/18/2022] Open
Abstract
Molecular rapid diagnostic assays associated with antimicrobial stewardship have proven effective for the early adaptation of empiric therapy in bloodstream infections. The ePlex® BCID (GenMark Diagnostics) Panels allow identification of 56 bacteria and fungi and 10 resistance genes in 90 min directly from positive blood cultures. We prospectively evaluated 187 sepsis episodes at Grenoble University Hospital and retrospectively analyzed the cases to measure the potential clinical impact of the ePlex BCID results. Identification of all pathogens was obtained for 164/187 (88%) bloodstream infections with 100% detection of antimicrobial resistance genes (17 blaCTX-M , 1 vanA, and 17 mecA genes). Only 15/209 (7%) strains were not covered by the panels. Sensitivity for detection of micro-organisms targeted by the RUO BCID-GP, BCID-GN, and BCID-FP Panels was respectively 84/84 (100%), 103/107 (96%), and 14/14 (100%). Interestingly, accurate identification of all pathogens was achieved in 15/17 (88%) polymicrobial samples. Retrospective analysis of medical records showed that a modification of antimicrobial treatment would have been done in 45% of the patients. Treatment modifications would have been an optimization of empiric therapy, a de-escalation or an escalation in respectively 16, 17, and 11% of the patients. Moreover, 11% of the samples were classified as contaminants or not clinically relevant and would have led to early de-escalation or withdrawal of any antibiotic. Detection of resistance genes in addition to identification alone increased escalation rate from 4 to 11% of the patients. Absence of the ePlex result was considered a lost opportunity for therapy modification in 28% of patients.
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Affiliation(s)
- Sabrina Bryant
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Iyad Almahmoud
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Isabelle Pierre
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Julie Bardet
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Saber Touati
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Daniele Maubon
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Muriel Cornet
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Claire Richarme
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Max Maurin
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France.,Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Patricia Pavese
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Yvan Caspar
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France.,Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
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Abstract
We compared the clinical, radiological and microbial profile in children suffering from community-acquired pneumonia in rural populations of north India. A total of 125 such children were divided into two age groups of 2-12 months (Group A) and 13-60 months (Group B). After taking a history and clinical examination, routine investigations including full blood count, blood, urine, and nasopharyngeal swab culture and radiology were performed. Multiplex polymerase chain reaction for Streptococcus pneumoniae, Mycoplasma pneumoniae, Chlamydia pneumoniae and Haemophilus influenzae was carried out. Failure to eat or drink was more common (40.9%) in Group A, than Group B (18.7%). Lung consolidation was more common in Group B. Blood and urine culture were found to be more positive in Group A while combined nasopharyngeal culture and multiplex polymerase chain reaction favoured more bacterial growth in Group B.
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Affiliation(s)
- Rajesh Kumar Yadav
- Professor and Head, Department of Pediatrics, Uttar Pradesh University of Medical Sciences, Etawah, India
| | - Dinesh Kumar
- Associate Professor, Department of Pediatrics, Uttar Pradesh University of Medical Sciences, Etawah, India
| | - Amit Singh
- Professor, Department of Microbiology, Uttar Pradesh University of Medical Sciences, Etawah, India
| | - Mohd Ziauddin
- Assistant Professor, Department of Pediatrics, Hind Institute of Medical Science, Sitapur, India
| | - Dinesh Kumar Singh
- Professor, Department of Pediatrics, FH Medical College and Hospital, Firozabad, India
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Choi JU, Lee JB, Kim KH, Kim S, Seol YJ, Lee YM, Rhyu IC. Comparison of Periodontopathic Bacterial Profiles of Different Periodontal Disease Severity Using Multiplex Real-Time Polymerase Chain Reaction. Diagnostics (Basel) 2020; 10:E965. [PMID: 33213109 PMCID: PMC7698795 DOI: 10.3390/diagnostics10110965] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/17/2022] Open
Abstract
Periodontopathic bacteria are known to have a pivotal role in the pathogenesis of periodontitis. The aim of the study was to quantitatively compare bacterial profile of patients with different severity of periodontal disease using samples from mouthwash and the subgingival area. Further analysis was performed to evaluate the correlation between mouthwash and two subgingival sampling methods: paperpoint and gingival retraction cord; 114 subjects enrolled in the study, and were divided equally into three groups according to disease severity. Mouthwash and subgingival sampling were conducted, and the samples were quantitatively analyzed for 11 target periodontopathic bacteria using multiplex real-time PCR. There were statistically significant differences in bacterial counts and prevalence of several species between the study groups. Mouthwash sampling showed significant correlations with two different subgingival sampling methods in regard to the detection of several bacteria (e.g., ρ = 0.793 for Porphyromonas gingivalis in severe periodontitis), implying that mouthwash sampling can reflect subgingival microbiota. However, the correlation was more prominent as disease severity increased. Although bacteria in mouthwash have potential to become a biomarker, it may be more suitable for the diagnosis of severe periodontitis, rather than early diagnosis. Further research is required for the discovery of biomarkers for early diagnosis of periodontitis.
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Affiliation(s)
- Jin Uk Choi
- Department of Periodontology and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Korea; (J.U.C.); (K.-H.K.); (S.K.); (Y.-J.S.); (Y.-M.L.)
- Department of Periodontics, Seoul National University Dental Hospital, Seoul 03080, Korea;
| | - Jun-Beom Lee
- Department of Periodontics, Seoul National University Dental Hospital, Seoul 03080, Korea;
| | - Kyoung-Hwa Kim
- Department of Periodontology and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Korea; (J.U.C.); (K.-H.K.); (S.K.); (Y.-J.S.); (Y.-M.L.)
| | - Sungtae Kim
- Department of Periodontology and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Korea; (J.U.C.); (K.-H.K.); (S.K.); (Y.-J.S.); (Y.-M.L.)
- Department of Periodontics, Seoul National University Dental Hospital, Seoul 03080, Korea;
| | - Yang-Jo Seol
- Department of Periodontology and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Korea; (J.U.C.); (K.-H.K.); (S.K.); (Y.-J.S.); (Y.-M.L.)
- Department of Periodontics, Seoul National University Dental Hospital, Seoul 03080, Korea;
| | - Yong-Moo Lee
- Department of Periodontology and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Korea; (J.U.C.); (K.-H.K.); (S.K.); (Y.-J.S.); (Y.-M.L.)
- Department of Periodontics, Seoul National University Dental Hospital, Seoul 03080, Korea;
| | - In-Chul Rhyu
- Department of Periodontology and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Korea; (J.U.C.); (K.-H.K.); (S.K.); (Y.-J.S.); (Y.-M.L.)
- Department of Periodontics, Seoul National University Dental Hospital, Seoul 03080, Korea;
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Modgil V, Kaur H, Mohan B, Taneja N. Molecular, phylogenetic and antibiotic resistance analysis of enteroaggregative escherichia coli/uropathogenic Escherichia coli hybrid genotypes causing urinary tract infections. Indian J Med Microbiol 2020; 38:421-429. [PMID: 33154257 DOI: 10.4103/ijmm.ijmm_20_365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Horizontal gene transfer of virulence genes (VGs) from different Escherichia coli pathotypes results in the evolution of hybrid strains. Hybrid genotypes of enteroaggregative E. coli and uropathogenic E. coli (EAEC/UPEC) have been reported in sporadic infections and outbreaks of extraintestinal origin. Yet, their association with routine infections is still underrated. Materials and Methods In this study, we analysed 163 isolates of E. coli from cases of urinary tract infection seeking hybrid (EAEC/UPEC) strains. Using multiplex polymerase chain reaction, we investigated VGs (adhesive and toxin genes) of UPEC along with EAEC marker genes (aap and agg R), ast A (toxin genes) and serine protease autotransporters of Enterobacteriaceae, pet (plasmid-encoded toxin) and pic (mucinase gene). Those UPEC strains which had characteristic defining genes of EAEC (agg R/aap or their combination) were considered UPEC/EAEC hybrids. Results Molecular predictors of EAEC (aap and aggR) were detected in 20.2% (33/163) of the strains. The pap C was also detected in 36% of the EAEC/UPEC hybrid strains. Phylogenetic analysis revealed that hybrid strains belonged to Group D (60.6%). Nearly 73.8% of UPEC and 75.7% of UPEC/EAEC hybrid strains were multidrug-resistant. Among UPEC isolates, 72.3% and in hybrid UPEC/EAEC, 78.7% isolates were able to produce biofilm. Conclusions Our results indicated a closer relationship among EAEC and UPEC, which suggested that some EAEC strains can be potential uropathogens. Ours is a first study documenting the existence of EAEC pathotypes VGs in UPEC strains of nosocomial origin; further studies are required to understand the diarrhoeagenic potential of these hybrids.
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Affiliation(s)
- Vinay Modgil
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Harpreet Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Balvinder Mohan
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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O'Neal M, Murray H, Dash S, Al-Hasan MN, Justo JA, Bookstaver PB. Evaluating appropriateness and diagnostic stewardship opportunities of multiplex polymerase chain reaction gastrointestinal testing within a hospital system. Ther Adv Infect Dis 2020; 7:2049936120959561. [PMID: 33014363 PMCID: PMC7513010 DOI: 10.1177/2049936120959561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/27/2020] [Indexed: 12/31/2022] Open
Abstract
Objective: This single-center, retrospective, observational cohort study evaluates the
appropriateness of the BioFire® FilmArray® Gastrointestinal (GI) multiplex
PCR panel testing at a community-teaching hospital. Methods: All adult, hospitalized patients at Prisma Health Richland Hospital with a
documented GI multiplex PCR panel from 1 April 2015 through 28 February 2018
were included in the analysis. Inappropriate use of the GI panel was defined
as a test obtained without documented diarrhea, greater than 2 days of
hospitalization, redundant use with other diagnostic tests (e.g.
Clostridioides difficile PCR), or laxative use in the
preceding 48 h. Antibiotic use and host variables were compared between
groups with positive and negative results. Results: During the study period, 442 GI panels were obtained, among which 268 (61%)
were deemed inappropriate. Primary reasons for inappropriate testing were
lack of documented diarrhea (n = 92), greater than 2 days
of hospitalization (n = 116), having a duplicate C.
difficile PCR test ordered (n = 118), or
laxative use in the 48 h before testing (n = 36). A total
of 141 (32%) GI panels were positive. The most frequently identified
pathogens were C. difficile (51.1%,
n = 72), Enteropathogenic Escherichia coli
(17.7%, n = 25), and Norovirus GI/GII (12.1%,
n = 17). Patients with negative GI panel results were
initiated on antibiotics significantly less frequently than those with
positive GI panels (62.5% versus 80.2%,
p < 0.00001). Conclusion: Stewardship opportunities exist to optimize the diagnostic application of the
GI multiplex PCR panel.
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Affiliation(s)
- Melissa O'Neal
- University of South Carolina College of Pharmacy, 715 Sumter Street, Columbia, SC 29208, USA
| | - Hanna Murray
- University of South Carolina College of Pharmacy, Columbia, SC, USA
| | - Sangita Dash
- University of South Carolina School of Medicine, Columbia, SC, USA
| | - Majdi N Al-Hasan
- University of South Carolina School of Medicine, Columbia, SC, USA
| | - Julie Ann Justo
- University of South Carolina College of Pharmacy, Columbia, SC, USA
| | - P Brandon Bookstaver
- University of South Carolina College of Pharmacy, 715 Sumter Street, Columbia, SC 29208, USA
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Nguyen TT, Vu-Khac H, Nguyen TD. Isolation and characterization of Clostridium perfringens strains isolated from ostriches ( Struthio camelus) in Vietnam. Vet World 2020; 13:1679-1684. [PMID: 33061245 PMCID: PMC7522951 DOI: 10.14202/vetworld.2020.1679-1684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/30/2020] [Indexed: 12/05/2022] Open
Abstract
Background and Aim: Clostridium perfringens can cause enteritis in ostriches. The toxin release is believed to play a major role in determining pathogenesis properties of these pathogenic bacteria. This study was conducted to isolate and characterize C. perfringens strains from ostriches in Vietnam for identifying if particular virulence factors of these pathogenic bacteria are associated with enteritis progress in ostriches. Materials and Methods: The prevalence of cpa, cpb, iA, etx, cpe, and cpb2 genes among C. perfringens isolates was determined by a multiplex polymerase chain reaction (PCR) method. The NetB toxin-encoding gene was detected by PCR and then sequenced to observe their variation. The expression of NetB toxin was checked by SDS-PAGE. Results: A total of 116 C. perfringens isolates were obtained from 318 fecal samples and 105 intestinal organs. Of 80 isolates from fecal samples, 33 isolates were from healthy and 47 isolates were from diseased ostriches. The results of multiplex PCR showed that all 116 C. perfringens strains from healthy and enteric disordered ostriches were positive for the alpha toxin-encoding gene (cpa). The cpe and cpb2 genes were found in only one and five diseased ostriches, respectively. The netB gene was detected in 1/33 (3.03%) C. perfringens isolates from healthy ostriches, in 8/47 (17.05%) isolates from feces, and in 7/36 (19.44%) intestinal contents of diseased ostriches. The full-length sequences of 5 out of 15 netB-positive isolates from diseased ostriches showed 100% identity to each other as well as to the netB sequences available in GenBank. All of these five isolates produced NetB toxin in vitro. Conclusion: Type A is the most prevalent among C. perfringens isolates from ostriches in Vietnam. Especially, the study provides data emphasizing the role of NetB toxin in causing necrotic enteritis by C. perfringens in ostriches.
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Affiliation(s)
- Tham Thi Nguyen
- Department of Technology and Development Product, Institute of Veterinary Research and Development of Central Vietnam, Nha Trang City, Vietnam
| | - Hung Vu-Khac
- Department of Biotechnology, Institute of Veterinary Research and Development of Central Vietnam, Nha Trang City, Vietnam
| | - Tan Duc Nguyen
- Department of Technology and Development Product, Institute of Veterinary Research and Development of Central Vietnam, Nha Trang City, Vietnam
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Tian J, Pinto JM, Li L, Zhang S, Sun Z, Wei Y. Identification of Viruses in Patients With Postviral Olfactory Dysfunction by Multiplex Reverse-Transcription Polymerase Chain Reaction. Laryngoscope 2020; 131:158-164. [PMID: 32786080 PMCID: PMC7436707 DOI: 10.1002/lary.28997] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 12/29/2022]
Abstract
Objectives/Hypothesis To investigate causative viruses in patients with postviral olfactory disorders (PVOD). Study Design Case‐control study. Methods One hundred fifty‐one consecutive patients diagnosed with PVOD were enrolled, and samples from 38 patients who visited the doctor within 3 months of symptom onset were collected and analyzed. Thirty‐two individuals who underwent surgery for nasal septal deviation during the same time period were collected as the control group. The Sniffin' Sticks psychophysical olfactory test was used to evaluate olfactory function. Olfactory cleft specimens were collected using nasopharyngeal flocked swabs (COPAN FLOQSwabs). Eighteen viruses were tested for with the Luminex xTAG RVP FAST v2 Assay Kit. Results Out of the 38 patients with PVOD, rhinoviruses were detected in 13 patients, and coronavirus OC43 was detected in one patient. The frequency of positive virus detection in the patients with anosmia was higher than in those with hyposmia (58.8% vs. 19.0%, P = 0.018). In control group, rhinovirus was identified in one patient (3.1%). Nasal obstruction was the most common symptom and was experienced by 71.0% of patients. Conclusions Rhinovirus and coronavirus are more commonly identified in PVOD. Our methods represent an approach to screen for viruses that may be involved in PVOD. Level of Evidence 4 Laryngoscope, 131:158–164, 2021
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Affiliation(s)
- Jun Tian
- Department of Otolaryngology-Head and Neck Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jayant M Pinto
- Section of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Chicago, Chicago, Illinois, U.S.A
| | - Li Li
- Department of Otolaryngology-Head and Neck Surgery, Hospital of Renmin University of China, Beijing, China
| | - Sanmei Zhang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhifu Sun
- Department of Otolaryngology-Head and Neck Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Yongxiang Wei
- Department of Otolaryngology-Head and Neck Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
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Nair RR, Nayak M, Prasada LK, Nair AV, Soman D, Krishnan RH. PCR-based detection of three anaerobic bacteria associated with endodontic-periodontic lesions in type-2 diabetic and nondiabetic subjects. J Conserv Dent 2020; 22:430-435. [PMID: 33082657 PMCID: PMC7537750 DOI: 10.4103/jcd.jcd_326_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 06/29/2020] [Accepted: 07/04/2020] [Indexed: 01/01/2023] Open
Abstract
Aim: The aim of this study is to clinically isolate and detect three anaerobic bacteria associated with endodontic-periodontal lesions in type-2 diabetic and nondiabetic patients using polymerase chain reaction (PCR). Materials and Methods: Sixty patients presenting endodontic-periodontal lesions were divided into two groups. Thirty patients with type-2 diabetics (Group 1) and 30 nondiabetic patients (Group 2) were evaluated for the presence of three anaerobic bacteria. Clinical examinations, periapical radiographs, and microbiological sampling from the canal system and periodontal pockets were performed. Qualitative evaluation of bacteria was performed using a multiplex PCR for Porphyromonas gingivalis and Prevotella intermedia. Statistical analysis was performed using Pearson's Chi-square test and Fischer's exact test. Results: Enterococcus faecalis (73.3%) was the predominant bacteria isolated from the root canal in type 2 diabetic patients, followed by P. gingivalis (70%) and P. intermedia (36%) compared to 53.3%, 43.3%, and 23.3%, respectively, among nondiabetic patients. P. gingivalis (73.3%) was the predominant bacteria isolated from periodontal pockets in type II diabetic patients followed by P. intermedia 50% and E. faecalis 30% compared to 36.6%, 33.3%, and 30%, respectively, among nondiabetics. P. gingivalis was detected in the root canal and periodontal pocket in almost similar numbers (70% and 73%), respectively, among type-2 diabetics. Conclusion: Detection of P. gingivalis, P. intermedia, and E. faecalis in both root canal and periodontal pocket samples confirm a viable pathway for the spread of infection through dual sites. Since in the present study, P. gingivalis was found to be present in similar numbers in dual sites among type 2 diabetic patients, importance should be given in treating such anaerobic bacteria in immune-compromised patients.
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Affiliation(s)
- Rakesh Rajeevan Nair
- Department of Conservative Dentistry and Endodontics, KVG Dental College and Hospital, Sullia, Karnataka, India
| | - Moksha Nayak
- Principal, KVG Dental College and Hospital, Sullia, Karnataka, India
| | - L Krishna Prasada
- Department of Conservative Dentistry and Endodontics, KVG Dental College and Hospital, Sullia, Karnataka, India
| | - Anoop V Nair
- Consultant Endodontist, Trivandrum, Kerala, India
| | - Drisya Soman
- Department of Conservative Dentistry and Endodontics, Azeezia College of Dental Sciences and Research, Kollam, Kerala, India
| | - R Hari Krishnan
- Department of Periodontics, PMS College of Dental Science and Research, Trivandrum, Kerala, India
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Barakat AMA, El-Razik KAA, Elfadaly HA, Rabie NS, Sadek SAS, Almuzaini AM. Prevalence, molecular detection, and virulence gene profiles of Campylobacter species in humans and foods of animal origin. Vet World 2020; 13:1430-1438. [PMID: 32848321 PMCID: PMC7429388 DOI: 10.14202/vetworld.2020.1430-1438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/29/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND AND AIM Campylobacteriosis is one of the most well-characterized bacterial foodborne infections worldwide that arise chiefly due to the consumption of foods of animal origin such as poultry, milk, and their products. The disease is caused by numerous species within the genus Campylobacter, but Campylobacter jejuni is the most commonly isolated species from established cases of human campylobacteriosis. This study was conducted to determine the prevalence and virulence of Campylobacter isolates from human, chicken, and milk and milk products in Egypt. MATERIALS AND METHODS A total of 1299 samples (547 chicken intestine and liver, 647 milk and milk products, and 105 human stool) were collected and microbiologically investigated, confirmed by multiplex polymerase chain reaction (PCR) targeting the 23S rRNA, hipO, and glyA genes specific for Campylobacter spp., C. jejuni, and Campylobacter Coli, respectively, followed by virulence genes (Campylobacter adhesion to fibronectin F [cadF] and cdtB) detection using PCR. RESULTS About 38.09%, 37.84%, and 8.5% of human stool, chicken, and milk and milk product samples, respectively, were bacteriologically positive, with a total of 302 Campylobacter isolates. All isolates were molecularly confirmed as Campylobacter spp. (100%) where 285 isolates (94.37%) were identified as C. jejuni and 17 isolates (5.62%) as C. coli. Regarding the virulence pattern, all isolates (100%) carried cadF gene while cytolethal distending toxin B gene was definite in 284/302 isolates (94%), concisely, 282/285 (98.94%) C. jejuni isolates, and in 2/17 (11.76%) C. coli isolates. CONCLUSION The widespread presence of these highly virulent Campylobacter, especially C. jejuni, proofs the urgent need for the implementation of stringent control, public health, and food protection strategies to protect consumers from this zoonotic pathogen. The availability of information about pathogen virulence will enable enhanced local policy drafting by food safety and public health officials.
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Affiliation(s)
| | | | - Hassan A. Elfadaly
- Department of Zoonotic Diseases, National Research Centre, Dokki, Giza, Egypt
| | - Nagwa S. Rabie
- Department of Poultry Diseases, National Research Centre, Dokki, Giza, Egypt
| | - Sabry A. S. Sadek
- Department of Zoonotic Diseases, National Research Centre, Dokki, Giza, Egypt
| | - Abdulaziz M. Almuzaini
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
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Dussault‐Benoit C, Arsenault‐Labrecque G, Sonah H, Belzile F, Bélanger RR. Discriminant haplotypes of avirulence genes of Phytophthora sojae lead to a molecular assay to predict phenotypes. Mol Plant Pathol 2020; 21:318-329. [PMID: 31908142 PMCID: PMC7036360 DOI: 10.1111/mpp.12898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
The soybean-Phytophthora sojae interaction operates on a gene-for-gene relationship, where the product of a resistance gene (Rps) in the host recognizes that of an avirulence gene (Avr) in the pathogen to generate an incompatible reaction. To exploit this form of resistance, one must match with precision the appropriate Rps gene with the corresponding Avr gene. Currently, this association is evaluated by phenotyping assays that are labour-intensive and often imprecise. To circumvent this limitation, we sought to develop a molecular assay that would reveal the avirulence allele of the seven main Avr genes (Avr1a, Avr1b, Avr1c, Avr1d, Avr1k, Avr3a, and Avr6) in order to diagnose with precision the pathotypes of P. sojae isolates. For this purpose, we analysed the genomic regions of these Avr genes in 31 recently sequenced isolates with different virulence profiles and identified discriminant mutations between avirulence and virulence alleles. Specific primers were designed to generate amplicons of a distinct size, and polymerase chain reaction conditions were optimized in a final assay of two parallel runs. When tested on the 31 isolates of known virulence, the assay accurately revealed all avirulence alleles. The test was further assessed and compared to a phenotyping assay on 25 isolates of unknown virulence. The two assays matched in 97% (170/175) of the interactions studied. Interestingly, the sole cases of discrepancy were obtained with Avr3a, which suggests a possible imperfect interaction with Rps3a. This molecular assay offers a powerful and reliable tool to exploit and study with greater precision soybean resistance against P. sojae.
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Affiliation(s)
| | | | - Humira Sonah
- Department of PhytologyUniversité LavalQuébecQCCanada
- National Agri‐Food Biotechnology Institute (NABI)MohaliIndia
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Carreno JJ, Eaton R, Itro L, Babowicz F, Falvo J, Tobin E, Mitchell C, George M. Time to clinical response in sepsis associated with an algorithm for blood-culture pathogen identification using matrix-assisted laser desorption ionization time-of-flight mass spectroscopy. Am J Health Syst Pharm 2020; 76:460-469. [PMID: 31361820 DOI: 10.1093/ajhp/zxy087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
PURPOSE Antimicrobial stewardship programs (ASPs) can be aided by using rapid diagnostics (RDT). However, there are limited data evaluating the impact of ASPs and RDT on sepsis outcomes in the setting of the new Sepsis-3 guidelines. This study evaluates the impact of a low-resource method for ASPs with RDT on sepsis outcomes. METHODS This was a prospective, quasi-experimental study with a retrospective double pretest. Patients ≥ 18 years old with sepsis and concurrent bacteremia or fungemia were included; patients who were pregnant, had polymicrobial septicemia or who were transferred from an outside hospital were excluded. In the first pretest (O1), polymerase chain reaction was used to identify Staphylococcal species from positive blood cultures, and traditional laboratory techniques were used to identify other species. Matrix-assisted laser desorption ionization time-of-flight mass spectroscopy and FilmArray were implemented in the second pretest (O2), and twice daily blood culture review was implemented in the posttest (O3). RESULTS A total of 394 patients (157 in O1, 176 in O2, 61 in O3) were enrolled. Clinical response was 73.2%, 83.5%, and 88.5% in O1, O2, and O3, respectively, p = 0.013. By Cox regression, the O3 was associated with improved time to clinical response (hazard ratio, 1.388; 95% confidence interval, 1.004-1.919) as compared with O1. Mortality, hospital length of stay, and intensive care unit length of stay were unchanged between groups. CONCLUSION Twice-daily blood culture review may be useful for implementing rapid diagnostics within low-resource ASPs. Further research is needed to identify the optimal method of blood culture follow-up within low-resource settings.
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Affiliation(s)
- Joseph J Carreno
- Department of Pharmacy Practice, Albany College of Pharmacy and Health Sciences, Albany, NY
| | - Rachael Eaton
- Albany College of Pharmacy and Health Sciences, Albany, NY
| | - Lindsay Itro
- Albany College of Pharmacy and Health Sciences, Albany, NY
| | - Faith Babowicz
- Albany College of Pharmacy and Health Sciences, Albany, NY
| | - Jane Falvo
- Department of Nursing, Albany Medical Center Hospital, Albany, NY
| | - Ellis Tobin
- Upstate Infectious Disease Associates, Albany, NY
| | - Colby Mitchell
- Department of Pharmacy, Albany Medical Center Hospital, Albany, NY
| | - Mary George
- Department of Microbiology, Albany Medical Center Hospital, Albany, NY
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Garg A, Garg J, Kumar S, Bhattacharya A, Agarwal S, Upadhyay GC. Molecular epidemiology & therapeutic options of carbapenem-resistant Gram-negative bacteria. Indian J Med Res 2019; 149:285-289. [PMID: 31219096 PMCID: PMC6563745 DOI: 10.4103/ijmr.ijmr_36_18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background & objectives: The growing incidence and the wide diversity of carbapenemase-producing bacterial strains is a major concern as only a few antimicrobial agents are active on carbapenem-resistant bacteria. This study was designed to study molecular epidemiology of carbapenem-resistant Gram-negative bacterial (GNB) isolates from the community and hospital settings. Methods: In this study, non-duplicate GNB were isolated from clinical specimens, and phenotypic test such as modified Hodge test, metallo β-lactamase E-strip test, etc. were performed on carbapenem-resistant bacteria. Multiplex PCR was performed to identify the presence of blaIMP, blaVIM, blaKPC, blaOXA48, blaOXA23, blaSPM, blaGIM, blaSIM and blaNDM. Minimum inhibitory concentration (MIC) of colistin, fosfomycin, minocycline, chloramphenicol and tigecycline was also determined. Results: Of the 3414 GNB studied, carbapenem resistance was 9.20 per cent and maximum resistance (11.2%) was present at tertiary care centre, followed by secondary care (4%) and primary centre (2.1%). Among the carbapenem-resistant bacteria, overall, the most common isolate was Pseudomonas aeruginosa (24%). On multiplex PCR 90.3 per cent carbapenem-resistant isolates were positive for carbapenemase gene. The blaNDM (63%) was the most prevalent gene followed by blaVIM (18.4%). MIC results showed that 88 per cent carbapenem-resistant Enterobacteriaceae were sensitive to fosfomycin, whereas 78 per cent of P. aeruginosa and 85 per cent Acinetobacter spp. were sensitive to colistin. Interpretation & conclusions: Carbapenem resistance in GNB isolates from the community and hospital settings was found to be on the rise and should be closely monitored. In the absence of new antibiotics in pipeline and limited therapeutic options, prudent use of antibiotics and strict infection control practices should be followed in hospital to limit the emergence and spread of multidrug-resistant bacteria.
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Affiliation(s)
- Atul Garg
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Jaya Garg
- Department of Microbiology, Ram Manohar Lohia Institute of Medical Sciences, Lucknow, India
| | - Sachin Kumar
- Department of Pharmacy, Ganesh Shankar Vidyarthi Memorial Medical College, Kanpur, India
| | | | - Saurabh Agarwal
- Department of Medicine, Ganesh Shankar Vidyarthi Memorial Medical College, Kanpur, India
| | - G C Upadhyay
- Department of Microbiology, Ganesh Shankar Vidyarthi Memorial Medical College, Kanpur, India
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Schrimpf C, Ziesing S, Michelmann P, Rustum S, Teebken OE, Haverich A, Wilhelmi M. Conventional culture diagnostics vs. multiplex PCR for the detection of causative agents of vascular graft infections - results of a single centre observational pilot study. VASA 2019; 49:43-49. [PMID: 31755826 DOI: 10.1024/0301-1526/a000827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Background: Timely diagnosis of vascular graft infections is of major importance in vascular surgery. The detection of causative microorganisms is needed for specific medical treatment, but conventional culture is often slow, insensitive and inconclusive due to antibiotic pre-treatment. Detection of bacterial DNA by polymerase chain reaction (PCR) might bypass these problems. We hypothesised that multiplex PCR (mPCR) is feasible, fast and sensitive to detect causative microorganisms in vascular graft infections. Patients and methods: We performed a pilot observational prospective study comparing conventional culture and a commercial mPCR. Inclusion criteria were: confirmed graft infection, suspicious imaging, clinical suspicion, anastomotic aneurysm and repeated graft occlusion. Diagnostic methods were performed using identical samples. Time to result, microorganisms and antibiotic resistance in both groups were compared using Student's t-test or nonparametric tests. Results: 22 samples from 13 patients were assessed and 11 samples were negative for bacteria. Some showed multiple germs. In total, we found 15 different organisms. 13 samples matched, 9 had non-concordant results. Out of the mismatches 3 microorganisms identified in PCR were not detected by culture. Time to result with PCR was shorter (median 5 h vs. 72 h, p < 0.001) than with culture. No resistance genes were detected by mPCR, but conventional culture allowed susceptibility testing and revealed resistance in 5 samples. Conclusions: mPCR seems to be a feasible and quick tool to detect causes of vascular graft infections within 24 h and might be helpful in antibiotic pre-treated patients. The detection of antibiotic resistance with mPCR needs improvement for clinical practice.
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