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Cuesta G, Puerta-Alcalde P, Vergara A, Roses E, Bosch J, Casals-Pascual C, Soriano A, Marcos MÁ, Sanz S, Vila J. An Assessment of a New Rapid Multiplex PCR Assay for the Diagnosis of Meningoencephalitis. Diagnostics (Basel) 2024; 14:802. [PMID: 38667448 DOI: 10.3390/diagnostics14080802] [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: 03/01/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
The rapid and broad microbiological diagnosis of meningoencephalitis (ME) has been possible thanks to the development of multiplex PCR tests applied to cerebrospinal fluid (CSF). We aimed to assess a new multiplex PCR panel (the QIAstat-Dx ME panel), which we compared to conventional diagnostic tools and the Biofire FilmArray ME Panel. The pathogens analyzed using both methods were Escherichia coli K1, Haemophilus influenzae, Listeria monocytogenes, Neisseria meningitidis, Streptococcus agalactiae, Streptococcus pneumoniae, Enterovirus, herpes simplex virus 1-2, human herpesvirus 6, human parechovirus, varicella zoster virus, and Cryptococcus neoformans/gattii. We used sensitivity, specificity, PPV, NPV, and kappa correlation index parameters to achieve our objective. Fifty CSF samples from patients with suspected ME were included. When conventional methods were used, 28 CSF samples (56%) were positive. The sensitivity and specificity for QIAstat-Dx/ME were 96.43% (CI95%, 79.8-99.8) and 95.24% (75.2-99.7), respectively, whereas the PPV and NPV were 96.43% (79.8-99.8) and 95.24% (75.1-99.7), respectively. The kappa value was 91.67%. Conclusions: A high correlation of the QIAstat-Dx ME panel with reference methods was shown. QIAstat-Dx ME is a rapid-PCR technique to be applied in patients with suspected ME with a high accuracy.
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Affiliation(s)
- Genoveva Cuesta
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain
| | - Pedro Puerta-Alcalde
- Department of Infectious Diseases, Hospital Clínic-IDIBAPS, University of Barcelona, 08007 Barcelona, Spain
| | - Andrea Vergara
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain
- Department of Basic Clinical Practice, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
| | - Enric Roses
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain
| | - Jordi Bosch
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
| | - Climent Casals-Pascual
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain
- Department of Basic Clinical Practice, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
| | - Alex Soriano
- Department of Infectious Diseases, Hospital Clínic-IDIBAPS, University of Barcelona, 08007 Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Mª Ángeles Marcos
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain
- Department of Basic Clinical Practice, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
| | - Sergi Sanz
- Department of Basic Clinical Practice, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jordi Vila
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain
- Department of Basic Clinical Practice, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
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Meng Z, Wang S, Yu L, Zhao K, Wu T, Zhu X, Yang N, Qiao Q, Ma J, Wu B, Ge Y, Cui L. A novel fast hybrid capture sequencing method for high-efficiency common human coronavirus whole-genome acquisition. mSystems 2024:e0122223. [PMID: 38564711 DOI: 10.1128/msystems.01222-23] [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: 12/05/2023] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Rapid and accurate sequencing of the entire viral genome, coupled with continuous monitoring of genetic changes, is crucial for understanding the epidemiology of coronaviruses. We designed a novel method called micro target hybrid capture system (MT-Capture) to enable whole-genome sequencing in a timely manner. The novel design of probes used in target binding exhibits a unique and synergistic "hand-in-hand" conjugation effect. The entire hybrid capture process is within 2.5 hours, overcoming the time-consuming and complex operation characteristics of the traditional liquid-phase hybrid capture (T-Capture) system. By designing specific probes for these coronaviruses, MT-Capture effectively enriched isolated strains and 112 clinical samples of coronaviruses with cycle threshold values below 37. Compared to multiplex PCR sequencing, it does not require frequent primer updates and has higher compatibility. MT-Capture is highly sensitive and capable of tracking variants.IMPORTANCEMT-Capture is meticulously designed to enable the efficient acquisition of the target genome of the common human coronavirus. Coronavirus is a kind of virus that people are generally susceptible to and is epidemic and infectious, and it is the virus with the longest genome among known RNA viruses. Therefore, common human coronavirus samples are selected to evaluate the accuracy and sensitivity of MT-Capture. This method utilizes innovative probe designs optimized through probe conjugation techniques, greatly shortening the time and simplifying the handwork compared with traditional hybridization capture processes. Our results demonstrate that MT-Capture surpasses multiplex PCR in terms of sensitivity, exhibiting a thousandfold increase. Moreover, MT-Capture excels in the identification of mutation sites. This method not only is used to target the coronaviruses but also may be used to diagnose other diseases, including various infectious diseases, genetic diseases, or tumors.
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Affiliation(s)
- Zixinrong Meng
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuo Wang
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Liping Yu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Kangchen Zhao
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Tao Wu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xiaojuan Zhu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Ning Yang
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiao Qiao
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Junyan Ma
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bin Wu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yiyue Ge
- School of Public Health, Nanjing Medical University, Nanjing, China
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Lunbiao Cui
- School of Public Health, Nanjing Medical University, Nanjing, China
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
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3
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Hong YJ, Jung BK, Kim JK. Epidemiological Characterization of Respiratory Pathogens Using the Multiplex PCR FilmArray™ Respiratory Panel. Diagnostics (Basel) 2024; 14:734. [PMID: 38611647 PMCID: PMC11011807 DOI: 10.3390/diagnostics14070734] [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: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Various pathogens can cause upper respiratory tract infections, presenting challenges in accurate diagnosis due to similar symptomatology. Therefore, rapid and precise diagnostic tests are crucial for effective treatment planning. Traditional culture-based methods for diagnosis are limited by their reliance on skilled personnel and lengthy processing times. In contrast, multiplex polymerase chain reaction (PCR) techniques offer enhanced accuracy and speed in identifying respiratory pathogens. In this study, we aimed to assess the efficacy of the FilmArray™ Respiratory Panel (RP), a multiplex PCR test capable of simultaneously screening 20 pathogens. This retrospective analysis was conducted at Dankook University Hospital, South Korea, between January 2018 and December 2022. Samples from patients with upper respiratory tract infections were analyzed. Results revealed adenovirus as the most prevalent pathogen (18.9%), followed by influenza virus A (16.5%), among others. Notably, a 22.5% co-infection rate was observed. The FilmArray™ RP method successfully identified 20 pathogens within 2 h, facilitating prompt treatment decisions and mitigating unnecessary antibiotic prescriptions. This study underscores the utility of multiplex PCR in respiratory pathogen identification, offering valuable insights for epidemiological surveillance and diagnosis.
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Affiliation(s)
- Young Jun Hong
- Department of Biomedical Laboratory Science, College of Health Sciences, Dankook University, Cheonan 31116, Republic of Korea;
| | - Bo Kyeung Jung
- Department of Laboratory Medicine, College of Medicine, Dankook University, Cheonan 31116, Republic of Korea;
| | - Jae Kyung Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Dankook University, Cheonan 31116, Republic of Korea;
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Cuadrado García B, Madueño Alonso A, Martín Bermúdez A, Romero-Acevedo L, Pérez Orán P, Lecuona Fernández M. [Rapid diagnosis of a case of post-surgical meningitis with BioFire® Joint Infection Panel]. Rev Esp Quimioter 2024:cuadrado27mar2024. [PMID: 38533781 DOI: 10.37201/req/009.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Affiliation(s)
- B Cuadrado García
- Belén Cuadrado García, Servicio de Microbiología y Control de la Infección. Hospital Universitario de Canarias. Ctra. Ofra S/N La Cuesta 38320, San Cristóbal de La Laguna. Spain.
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Lu M, Sun X, Zhao Y, Zheng L, Lin J, Tang C, Chao K, Chen Y, Li K, Zhou Y, Xiao J. Low cycle number multiplex PCR: A novel strategy for the construction of amplicon libraries for next-generation sequencing. Electrophoresis 2024. [PMID: 38533931 DOI: 10.1002/elps.202300160] [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] [Received: 03/14/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/28/2024]
Abstract
Multiplex PCR is a critical step when preparing amplicon library for next-generation sequencing. However, there are several challenges related to multiplex PCR including poor uniformity, nonspecific amplification, and primer-dimers. To address these issues, we propose a novel solution strategy that involves using a low cycle number (<10 cycles) in multiplex PCR and then employing carrier DNAs and magnetic beads for the selection of targeted products. This technique improves the amplicon uniformity while also reducing primer-dimers and PCR artifacts. To evaluate our technique, we initially utilized 120 DNA fragments from mouse genome containing single nucleotide polymorphism (SNP) sites. Sequencing results demonstrated that with only 7 cycles of multiplex PCR, 95.8% of the targeted SNP sites were mapped, with a coverage of at least 1×. The average sequencing depth of all amplicons was 1705.79 ± 1205.30×; 87% of them reached a coverage depth that exceeded 0.2-fold of the average sequencing depth. Our method had a greater uniformity (87%) when compared to Hi-Plex PCR (53.3%). Furthermore, we validated our strategy by randomly selecting 90 primer pairs twice from the initial set of 120 primer-pairs. Next, we used the same protocol to prepare amplicon libraries. The two groups had an average sequencing depth of 1013.30 ± 585.57× and 219.10 ± 158.27×, respectively; over 84% of the amplicons had a sequencing depth that exceeded 0.2-fold of average depth. These results suggest that the use of a low cycle number in multiplex PCR is a cost-effective and efficient approach for the preparation of amplicon libraries.
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Affiliation(s)
- Meng Lu
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Xiuxiu Sun
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Yuxin Zhao
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Linlin Zheng
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Junjie Lin
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Chen Tang
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Kaiyue Chao
- Shanghai Biowing Biotechnology Application Co., Ltd, Shanghai, P. R. China
| | - Ye Chen
- Shanghai Biowing Biotechnology Application Co., Ltd, Shanghai, P. R. China
| | - Kai Li
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Yuxun Zhou
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Junhua Xiao
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
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6
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Seto J, Takahashi J, Sampei M, Ikeda T, Mizuta K. A Case of Legionella pneumophila Serogroup 13 Pneumonia Based on the Detection of Serogroup-Specific Genes in Culture-Negative Sputum. Jpn J Infect Dis 2024; 77:118-120. [PMID: 38030269 DOI: 10.7883/yoken.jjid.2023.302] [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] [Indexed: 12/01/2023]
Abstract
Legionella pneumophila serogroup (SG) 1, the main cause of Legionnaires' disease, can be diagnosed using urinary antigen testing kits. However, lower respiratory tract specimen cultures are required to identify L. pneumophila SG 2-15. We attempted to detect L. pneumophila SG-specific genes in a culture-negative sputum specimen from a patient with pneumonia who was suspected to have Legionnaires' disease. Two multiplex PCR methods targeting L. pneumophila were modified and amplicons considered to be SG13 specific were detected. Direct sequencing revealed that the amplicons were identical to the nucleotide sequence of L. pneumophila SG13. Based on the presentation and clinical course (fever, muscle pain, disturbance of consciousness, high C-reactive protein titer, rhabdomyolysis, hypophosphatemia, and symptomatic improvement with levofloxacin treatment), in combination with the detection of L. pneumophila SG-specific genes, we suspected L. pneumophila SG13 pneumonia. L. pneumophila non-SG1 pneumonia is thought to be underestimated because of its difficult laboratory diagnosis. The modified multiplex PCR system for lower respiratory tract specimens revealed in this study is likely to improve the diagnosis of Legionnaires' disease caused by L. pneumophila SG13 and other SGs.
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Affiliation(s)
- Junji Seto
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Japan
| | - Jun Takahashi
- Department of General Medicine, Okitama Public General Hospital, Japan
| | - Mika Sampei
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Japan
| | - Tatsuya Ikeda
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Japan
| | - Katsumi Mizuta
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Japan
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7
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Knoth C, Humphries R, Johnson JK, Patel A, Lima A, Silbert S, Vinjé J. Multicenter evaluation of BioCode GPP for syndromic molecular detection of gastrointestinal pathogens from stool specimens. J Clin Microbiol 2024; 62:e0154523. [PMID: 38329337 PMCID: PMC10935640 DOI: 10.1128/jcm.01545-23] [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: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Acute gastroenteritis (AGE) is a leading cause of morbidity and mortality worldwide across all age groups that disproportionally affects young children in low- and middle-income countries and immunocompromised patients in high-income countries. Regional outbreaks of AGE are typically detected by traditional microbiological detection methods that target limited organisms and are associated with low sensitivity and lengthy time-to-results. Combined, these may result in repeat testing, imprecise or delayed treatment, and delayed recognition of outbreaks. We conducted a multi-site prospective study comparing the BioCode Gastrointestinal Pathogen Panel (BioCode GPP) for the detection of 17 common bacterial, viral, and protozoan causes of gastroenteritis with reference methods, including stool culture, enzyme immunoassays, pathogen-specific PCR assays, and sequencing. One thousand five hundred fifty-eight residual, de-identified stool samples (unpreserved stool and stool in Cary-Blair transport medium) were enrolled and tested for 11 bacterial, 3 viral, and 3 protozoan pathogens. BioCode GPP and reference methods were positive for 392 (25.2%) and 283 (18.2%) samples, respectively (P < 0.0001). In this study, the BioCode GPP and reference methods detected 69 and 65 specimens positive for Clostridioides difficile, 51 and 48 for enteroaggregative Escherichia coli, 33 and 27 for enterotoxigenic E. coli, 50 and 47 for norovirus GI/GII, and 30 and 22 for rotavirus A, respectively. The BioCode GPP showed good positive and negative agreements for each pathogen ranging from 89.5% to 100%, with overall sensitivity and specificity of 96.1% and 99.7%, post adjudication. The BioCode GPP detected >1 pathogens in 49 samples, representing 12.5% of the total 392 positive specimens. IMPORTANCE This study highlights performance of a novel technology for timely and accurate detection and differentiation of 17 common bacterial, viral, and protozoan causes of gastroenteritis. Utilizing molecular tests such as the BioCode Gastrointestinal Pathogen Panel may improve the detection of gastrointestinal pathogens and provide actionable results, particularly for patient populations at most risk.
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Affiliation(s)
| | - Romney Humphries
- University of California Los Angeles Medical Center, Los Angeles, California, USA
| | - J. Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Anami Patel
- Le Bonheur Children’s Hospital, Memphis, Tennessee, USA
| | | | | | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Pflüger LS, Nörz D, Grunwald M, Pfefferle S, Giersch K, Christner M, Weber B, Aepfelbacher M, Rohde H, Lütgehetmann M. Analytical and clinical validation of a multiplex PCR assay for detection of Neisseria gonorrhoeae and Chlamydia trachomatis including simultaneous LGV serotyping on an automated high-throughput PCR system. Microbiol Spectr 2024; 12:e0275623. [PMID: 38345391 PMCID: PMC10913481 DOI: 10.1128/spectrum.02756-23] [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: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 03/06/2024] Open
Abstract
For effective infection control measures for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG), a reliable tool for screening and diagnosis is essential. Here, we aimed to establish and validate a multiplex PCR assay on an automated system using a dual-target approach for the detection of CT/NG and differentiation between lymphogranuloma venereum (LGV) and non-LGV from genital and extra-genital specimens. Published primer/probe sets (CT: pmpH, cryptic plasmid; NG: porA, opa) were modified for the cobas 5800/6800/8800. Standards quantified by digital PCR were used to determine linearity and lower limit of detection (LLoD; eSwab, urine). For clinical validation, prospective samples (n = 319) were compared with a CE-marked in vitro diagnostics (CE-IVD) assay. LLoDs ranged from 21.8 to 244 digital copies (dcp)/mL and 10.8 to 277 dcp/mL in swab and urine, respectively. A simple linear regression analysis yielded slopes ranging from -4.338 to -2.834 and Pearson correlation coefficients from 0.956 to 0.994. Inter- and intra-run variability was <0.5 and <1 cycle threshold (ct), respectively. No cross-reactivity was observed (n = 42). Clinical validation showed a sensitivity of 94.74% (95% confidence interval (CI): 87.23%-97.93%) and 95.51% (95% CI: 89.01%-98.24%), a specificity of 99.59% (95% CI: 97.71%-99.98%) and 99.57% (95% CI: 97.58%-99.98%), positive predictive values of 89.91% (estimated prevalence: 3.7%; 95% CI: 80.91%-95.6%) and 88.61% (estimated prevalence: 3.4%; 95% CI: 80.18%-94.34%), and negative predictive values of 99.81% (95% CI: 98.14%-100%) and 99.85% (95% CI: 98.14%-100%) for the detection of CT and NG, respectively. In conclusion, we established a dual-target, internally controlled PCR on an automated system for the detectiwon of CT/NG from genital and extra-genital specimens. Depending on local regulations, the assay can be used as a screening or a confirmatory/typing assay.IMPORTANCEChlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) represent a major global health burden, with the World Health Organization estimating that >128 million and >82 million people, respectively, were newly infected in 2020. For effective infection control measures, a reliable tool for sensitive diagnosis and screening of CT/NG is essential. We established a multiplex PCR assay for the detection of CT/NG and simultaneous discrimination between lymphogranuloma venereum (LGV) and non-LGV strains, which has been validated for genital and extra-genital specimens on a fully automated system. To increase assay sensitivity, a dual-target approach has been chosen for both pathogens. This strategy reduces false-positive results in oropharyngeal swabs due to the detection of commensal N. species that may harbor NG DNA fragments targeted in the PCR due to horizontal gene transmission following previous infection. In sum, the established assay provides a powerful tool for use as either a screening/diagnostic or a typing/confirmatory assay.
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Affiliation(s)
- Lisa Sophie Pflüger
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Dominik Nörz
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Moritz Grunwald
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Susanne Pfefferle
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Katja Giersch
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Martin Christner
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Beatrice Weber
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Martin Aepfelbacher
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Holger Rohde
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, Hamburg, Germany
| | - Marc Lütgehetmann
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, Hamburg, Germany
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Sheikh AA, Schneiderman D, Sykes EME, Kumar A, Chen W, Lapen DR, Khan IUH. Three novel multiplex PCR assays for rapid detection of virulence, antimicrobial resistance, and toxin genes in Acinetobacter calcoaceticus-baumannii complex species. Lett Appl Microbiol 2024; 77:ovae027. [PMID: 38460955 DOI: 10.1093/lambio/ovae027] [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: 01/18/2024] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/11/2024]
Abstract
The Acinetobacter calcoaceticus-baumannii (ACB) complex is an often-overlooked group of nosocomial pathogens with a significant environmental presence. Rapid molecular screening methods for virulence, antimicrobial resistance, and toxin (VAT) genes are required to investigate the potential pathogenicity of environmental isolates. This study aimed to develop and apply novel ACB complex-specific multiplex PCR (mPCR) primers and protocols for the rapid detection of eight VAT genes. We optimized three single-tube mPCR assays using reference DNA from ACB complex and other Acinetobacter species. These assays were then applied to detect VAT genes in cultured ACB complex isolates recovered from clinical and environmental sources. Widespread detection of VAT genes in environmental isolates confirmed the validity, functionality, and applicability of these novel assays. Overall, the three newly developed ACB complex species-specific mPCR assays are rapid and simple tools that can be adopted in diagnostic and clinical lab settings. The detection of VAT genes in environmental isolates suggests that environmental niches could serve as a reservoir for potentially pathogenic ACB complex and warrants further investigation. The newly developed mPCR assays are specific, sensitive, and efficient, making them well-suited for high-throughput screening in epidemiological studies and evaluating the potential pathogenicity of ACB complex recovered from various sources.
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Affiliation(s)
- Alexander A Sheikh
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Danielle Schneiderman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Ellen M E Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, MB, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, MB, Canada
| | - Wen Chen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - David R Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
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Bhattarai RK, Basnet HB, Dhakal IP, Devkota B. Antimicrobial resistance of avian pathogenic Escherichia coli isolated from broiler, layer, and breeder chickens. Vet World 2024; 17:480-499. [PMID: 38595648 PMCID: PMC11000482 DOI: 10.14202/vetworld.2024.480-499] [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: 10/18/2023] [Accepted: 01/24/2024] [Indexed: 04/11/2024] Open
Abstract
Background and Aim Antimicrobials are extensively used in poultry production for growth promotion as well as for the treatment and control of diseases, including avian pathogenic Escherichia coli (APEC). Poor selection, overuse, and misuse of antimicrobial agents may promote the emergence and dissemination of antimicrobial resistance (AMR) in APEC. This study aimed to assess antimicrobial susceptibility patterns and detect antibiotic resistance genes (ARGs) in APEC isolated from clinical cases of colibacillosis in commercial broiler, layer, and breeder chickens. Materials and Methods A total of 487 APEC were isolated from 539 across 300 poultry farms in various regions of Nepal. Antimicrobial susceptibility patterns was determined using the Kirby-Bauer disk diffusion and broth microdilution methods. The index of AMR, such as multiple antibiotic resistance (MAR) index, resistance score (R-score), and multidrug resistance (MDR) profile, were determined. Polymerase chain reaction was employed to detect multiple ARGs and correlations between phenotypic and genotypic resistance were analyzed. Results The prevalence of APEC was 91% (487/539). All of these isolates were found resistant to at least one antimicrobial agent, and 41.7% of the isolates were resistant against 8-9 different antimicrobials. The antibiogram of APEC isolates overall showed the highest resistance against ampicillin (99.4%), whereas the highest intermediate resistance was observed in enrofloxacin (92%). The MAR index and R-score showed significant differences between broiler and layers, as well as between broiler breeder and layers. The number of isolates that were resistant to at least one agent in three or more antimicrobial categories tested was 446 (91.6%) and were classified as MDR-positive isolates. The ARGs were identified in 439 (90.1%) APEC isolates, including the most detected mobilized colistin resistance (mcr1) which was detected in the highest (52.6%) isolates. Overall, resistance gene of beta-lactam (blaTEM), mcr1, resistance gene of sulphonamide (sul1) and resistance gene of tetracycline (tetB) (in broiler), were detected in significantly higher than other tested genes (p < 0.001). When examining the pair-wise correlations, a significant phenotype-phenotype correlation (p < 0.001) was observed between levofloxacin and ciprofloxacin, chloramphenicol and tetracycline with doxycycline. Similarly, a significant phenotype-genotype correlation (p < 0.001) was observed between chloramphenicol and the tetB, and colistin with blaTEM and resistance gene of quinolone (qnrA). Conclusion In this study, the current state of APEC AMR in commercial chickens is revealed for the first time in Nepal. We deciphered the complex nature of AMR in APEC populations. This information of molecular surveillance is useful to combat AMR in APEC and to contribute to manage APEC associated diseases and develop policies and guidelines to enhance the commercial chicken production.
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Affiliation(s)
- Rebanta K Bhattarai
- Department of Veterinary Microbiology and Parasitology, Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Nepal
| | - Hom B Basnet
- Department of Veterinary Microbiology and Parasitology, Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Nepal
| | - Ishwari P Dhakal
- Department of Medicine and Public Health, Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Nepal
| | - Bhuminand Devkota
- Department of Theriogenology, Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Nepal
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11
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Pazoki N, Salehi M, Angaji SA, Abdollahpour‐Alitappeh M. Association of Y chromosome AZF region microdeletions with recurrent miscarriage in Iranian couples: A case-control study. Mol Genet Genomic Med 2024; 12:e2392. [PMID: 38407572 PMCID: PMC10847708 DOI: 10.1002/mgg3.2392] [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: 11/25/2023] [Revised: 01/08/2024] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND Recent studies have linked recurrent pregnancy loss (RPL) to abnormalities in the sperm genome, specifically microdeletions in the azoospermia factor (AZF) region. This study investigated the potential association between Y chromosome microdeletions in the AZF region and RPL in Iranian couples. METHODS The research presents a case-control study of 240 men: 120 whose partners experienced recurrent miscarriage, and 120 who had successful pregnancies without history of miscarriage. The study used semen parameters, hormone analyses, and microdeletion analysis via multiplex PCR and the YChromStrip kit. Thus, the sequence-tagged site (STS) markers of AZFa (sY84, sY86), AZFb (sY127, sY134), and AZFc (sY254, sY255) regions were examined. RESULTS The variations in semen parameters and sex hormone levels between cases and controls are suggest impaired testicular function in men whose partners had recurrent miscarriages (p < 0.05). Furthermore, the study revealed a negative correlation between sperm count and follicle-stimulating hormone (FSH) level, and a positive one between sperm motility and testosterone concentration. There were no microdeletions in the control group, while the RPL group showed 20 deletions in AZFb (sY134) (16.66%) and 10 deletions each in AZFb (sY127) (8.33%) and AZFc (sY254) (8.33%). CONCLUSION Microdeletions in sY134 (AZFb) were significantly associated with RPL in Iranian men (p = 0.03). AZF microdeletion screening in couples with RPL can provide valuable information for ethnical genetic counseling and management of recurrent miscarriage. Further studies on larger populations or across various ethnic groups, conclusions and the inclusion of other factors like epigenetic changes explain the role of AZF microdeletions in RPL.
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Affiliation(s)
- Nasrin Pazoki
- Department of Genetics, Faculty of Biological SciencesNorth Tehran Branch, Islamic Azad UniversityTehranIran
| | - Mitra Salehi
- Department of Biology, Faculty of Biological SciencesNorth Tehran Branch, Islamic Azad UniversityTehranIran
| | - Seyed Abdolhamid Angaji
- Department of Cell and Molecular BiologySchool of Biological Sciences, Kharazmi UniversityTehranIran
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12
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Yadav H, Pandit D, Singh S, Sharma P, Garg K, Girdhar N, Sharma K, Chopra V, Chopra S, Sharma S. GST polymorphism as a predictive biomarker for modulating the susceptibility to chronic obstructive pulmonary disease: A North Indian study. Exp Physiol 2024; 109:302-311. [PMID: 37948104 PMCID: PMC10988663 DOI: 10.1113/ep091339] [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: 06/08/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is commonly characterized by shortness of breath, coughing or expectoration. Smoking is the leading cause of COPD development, but only a small percentage of smokers develop symptoms, implying a genetic component. Glutathione S-transferase enzymes are responsible for detoxifying cigarette smoke components. The role of glutathione S-transferase T1 (GSTT1) and glutathione S-transferase M1 (GSTM1) gene polymorphism was assessed with COPD susceptibility and associated clinical parameters in the North Indian population. This was a cross-sectional study involving 200 COPD patients and 200 healthy individuals, with peripheral blood sampling and adequate questionnaires. Multiplex PCR was used for genotyping GSTT1 and GSTM1 gene polymorphism. Logistic regression was used to calculate the odds ratio and 95% confidence intervals to assess the COPD risk and GST polymorphisms. The GSTT1 gene deletion rate was higher in COPD cases (34.5%) than in healthy individuals (20.5%). A statistical relationship between the GSTT1(-) null genotype and COPD risk was observed (odds ratio = 2.04, 95% CI = 1.30-3.20, P = 0.0019). After adjusting for covariates like age, sex and smoking status, a significant association was found for GSTT1(-) null genotype and COPD risk (adjusted odds ratio = 2.90, 95% CI = 1.43-5.87, P = 0.003). The GSTT1(-) genotype was also significantly correlated with clinical parameters for COPD risk. Another primary observation was that females with the GSTT1(-) null genotype were more vulnerable to COPD than males with the same gene deletion. The GSTT1(-) null genotype strongly correlates with COPD development, while no association was observed in the GSTM1(-) null genotype in the North Indian population.
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Affiliation(s)
- Harsh Yadav
- Department of Pulmonary Medicine Government Medical CollegeTB & Chest Diseases HospitalPatialaPunjabIndia
| | - Depanshi Pandit
- Department of BiotechnologyThapar Institute of Engineering and TechnologyPatialaPunjabIndia
| | - Sidhartha Singh
- Department of BiotechnologyThapar Institute of Engineering and TechnologyPatialaPunjabIndia
| | - Parul Sharma
- Department of BiotechnologyThapar Institute of Engineering and TechnologyPatialaPunjabIndia
| | - Kranti Garg
- Department of Pulmonary Medicine Government Medical CollegeTB & Chest Diseases HospitalPatialaPunjabIndia
| | - Nidhi Girdhar
- Department of Pulmonary Medicine Government Medical CollegeTB & Chest Diseases HospitalPatialaPunjabIndia
| | - Karan Sharma
- Department of Pulmonary Medicine Government Medical CollegeTB & Chest Diseases HospitalPatialaPunjabIndia
| | - Vishal Chopra
- Department of Pulmonary Medicine Government Medical CollegeTB & Chest Diseases HospitalPatialaPunjabIndia
| | - Siddharth Chopra
- Department of Internal MedicineSt. Joseph Mercy Oakland HospitalPontiacMichiganUSA
| | - Siddharth Sharma
- Department of BiotechnologyThapar Institute of Engineering and TechnologyPatialaPunjabIndia
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Ambrosius-Eichner J, Hogardt M, Berger A, Dultz G, Idris R, Kempf VAJ, Wichelhaus TA. Comparative evaluation of the detection rate, workflow and associated costs of a multiplex PCR panel versus conventional methods in diagnosis of infectious gastroenteritis. J Med Microbiol 2024; 73. [PMID: 38362908 DOI: 10.1099/jmm.0.001795] [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] [Indexed: 02/17/2024] Open
Abstract
Introduction. Infectious gastroenteritis is a common reason for consulting a physician. Although most cases of gastrointestinal illness are self-limiting, the identification of the etiologic pathogen by stool specimen analysis is important in cases of more severe illness and for epidemiological reasons.Due to the broad range of causative pathogens, the conventional examination of a stool specimen is labour-intensive and usually requires different diagnostic methods. Multiplex PCR tests [e.g. BioFire Gastrointestinal (GI) Panel] allow the rapid detecting of up to 22 pathogens in one test.Hypothesis. Using a multiplex PCR panel to test stool specimens for infectious gastroenteritis pathogens can improve the detection rate, reduce the time-to-result and hands-on time and lower the costs of a microbiology laboratory.Aim. This study was aimed at evaluating the detection rate, the workflow and associated costs of stool specimen management using the BioFire GI Panel versus conventional methods.Methodology. Stool specimens were evaluated prospectively during the routine operation. Pathogen detection rate, hands-on time, time-to-result and material and personnel costs were determined for the BioFire GI Panel and conventional methods-the latter based on physician request and excluding viral testing.Results. Analysing 333 specimens collected between 2019 and 2020, the detection rate of enteropathogens was significantly higher with a positivity rate of 39.9 % using the multiplex PCR panel compared with 15.0 % using the conventional methods. The BioFire GI Panel presented results in a median time of 2.2 h compared with 77.5 h for culture and 22.1 h for antigen testing, noting that no tests were performed at weekends except for toxinogenic Clostridioides difficile. Based on list prices, the BioFire GI Panel was nine times more expensive compared with conventional methods, whereas hands-on-time was significantly lower using the BioFire GI Panel.Conclusion. Multiplex PCR panels are valuable tools for laboratory identification of infectious agents causing diarrhoea. The higher costs of such a multiplex PCR panel might be outweighed by the higher detection rate, ease of handling, rapid results and most likely improved patient management. However, these panels do not provide information on antimicrobial susceptibility testing. Therefore, if this is necessary for targeted therapy or if outbreak monitoring and control is required, specimens must still be cultured.
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Affiliation(s)
- J Ambrosius-Eichner
- Institute of Medical Microbiology and Infection Control, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - M Hogardt
- Institute of Medical Microbiology and Infection Control, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - A Berger
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- Institute of Medical Virology, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - G Dultz
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- Department of Medicine I, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - R Idris
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- Department of Medicine II-Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - V A J Kempf
- Institute of Medical Microbiology and Infection Control, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
| | - T A Wichelhaus
- Institute of Medical Microbiology and Infection Control, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- University Center for Infectious Diseases, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
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Yang SM, Kim JS, Kim E, Kim HY. Rapid and Simultaneous Authentication of Six Laver Species Using Capillary Electrophoresis-Based Multiplex PCR. Foods 2024; 13:363. [PMID: 38338499 PMCID: PMC10855616 DOI: 10.3390/foods13030363] [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] [Received: 12/24/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
Lavers are typically consumed in dried or seasoned forms. However, commercially processed lavers can lead to seafood fraud because it is impossible to authenticate the original species based on morphological characteristics alone. In this study, we developed a capillary electrophoresis-based multiplex polymerase chain reaction (PCR) to authenticate six different laver species. The species-specific primer sets to target the chloroplast rbcL or rbcS genes were newly designed. We successfully established both singleplex and multiplex conditions, which resulted in specific amplicons for each species (N. dentata, 274 bp; N. yezoensis, 211 bp; N. seriata, 195 bp; N. tenera, 169 bp; N. haitanensis, 127 bp; P. suborbiculata, 117 bp). Moreover, the assays were sensitive enough to detect DNA ranging from 10 to 0.1 pg of DNA. The optimized capillary electrophoresis-based multiplex PCR was successfully applied to 40 commercial laver products. In addition to detecting the laver species as stated on the commercial label, the assay discovered cases where less expensive species were mixed in. With its advantageous properties, such as short amplicon size, high specificity, and superior sensitivity, this assay could be used for the authentication of the six laver species.
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Affiliation(s)
| | | | | | - Hae-Yeong Kim
- Institute of Life Sciences & Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea; (S.-M.Y.); (J.-S.K.); (E.K.)
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15
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Rounsville TF, Polinski MP, Marini AG, Turner SM, Vendramin N, Cuenca A, Pietrak MR, Peterson BC, Bouchard DA. Rapid differentiation of infectious salmon anemia virus avirulent (HPR0) from virulent (HPRΔ) variants using multiplex RT-qPCR. J Vet Diagn Invest 2024:10406387231223290. [PMID: 38212882 DOI: 10.1177/10406387231223290] [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: 01/13/2024] Open
Abstract
Infectious salmon anemia virus (ISAV; Isavirus salaris) causes an economically important disease of Atlantic salmon (Salmo salar L.). ISA outbreaks have resulted in significant losses of farmed salmon globally, often with a sudden onset. However, 2 phenotypically distinct variants of ISAV exist, each with divergent disease outcomes, associated regulations, and control measures. ISAV-HPRΔ, also known as ISAV-HPR deleted, is responsible for ISA outbreaks; ISAV-HPR0, is avirulent and is not known to cause fish mortality. Current detection methodology requires genetic sequencing of ISAV-positive samples to differentiate phenotypes, which may slow responses to disease management. To increase the speed of phenotypic determinations of ISAV, we developed a new, rapid multiplex RT-qPCR method capable of 1) detecting if a sample contains any form of ISAV, 2) discriminating whether positive samples contain HPRΔ or HPR0, and 3) validating RNA extractions with an internal control, all in a single reaction. Following assay development and optimization, we validated this new multiplex on 31 ISAV strains collected from North America and Europe (28 ISAV-HPRΔ, 3 ISAV-HPR0). Finally, we completed an inter-laboratory comparison of this multiplex qPCR with commercial ISAV testing and found that both methods provided equivalent results for ISAV detection.
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Affiliation(s)
- Thomas F Rounsville
- Pest Management Unit, University of Maine Cooperative Extension Diagnostic and Research Laboratory, Orono, ME, USA
| | - Mark P Polinski
- National Cold Water Marine Aquaculture Center, U.S. Department of Agriculture-Agricultural Research Service, Franklin, ME, USA
| | - Alyssa G Marini
- Pest Management Unit, University of Maine Cooperative Extension Diagnostic and Research Laboratory, Orono, ME, USA
- University of Maine School of Biology and Ecology, Orono, ME, USA
| | - Sarah M Turner
- Aquatic Animal Health Laboratory, University of Maine Cooperative Extension Diagnostic and Research Laboratory, Orono, ME, USA
| | - Niccolò Vendramin
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Argelia Cuenca
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael R Pietrak
- National Cold Water Marine Aquaculture Center, U.S. Department of Agriculture-Agricultural Research Service, Franklin, ME, USA
| | - Brian C Peterson
- National Cold Water Marine Aquaculture Center, U.S. Department of Agriculture-Agricultural Research Service, Franklin, ME, USA
| | - Deborah A Bouchard
- Aquatic Animal Health Laboratory, University of Maine Cooperative Extension Diagnostic and Research Laboratory, Orono, ME, USA
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Kamarinou CS, Kiousi DE, Repanas P, Argyri AA, Chorianopoulos NG, Galanis A. Dissecting the Genetic Basis of the Technological, Functional, and Safety Characteristics of Lacticaseibacillus paracasei SRX10. Microorganisms 2024; 12:93. [PMID: 38257920 PMCID: PMC10820299 DOI: 10.3390/microorganisms12010093] [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] [Received: 12/09/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/24/2024] Open
Abstract
Nonstarter lactic acid bacteria (NSLAB) are major contributors to the unique characteristics (e.g., aroma, flavor, texture) of dairy and nondairy fermented products. Lc. paracasei SRX10 is an NSLAB strain originally isolated from a traditional Greek cheese and previously shown to exhibit favorable biotechnological characteristics. More specifically, the strain showed tolerance to simulated gastrointestinal conditions, exopolysaccharide (EPS) biosynthetic capacity, and lack of hemolytic activity and was used in the production of yoghurt and feta cheese with distinct organoleptic characteristics. The aim of the present study was to investigate these traits at the genome level through whole-genome sequencing (WGS), annotation, and comparative genomics. Functional annotation of the genome revealed that Lc. paracasei SRX10 can utilize different carbon sources, leading to the generation of flavor compounds, including lactic acid, acetate, ethanol, and acetoin. Similarly, full clusters for fatty acid biosynthesis, protein and peptide degradation, as well as genes related to survival under extreme temperatures, osmotic shock, and oxidative stress were annotated. Importantly, no transferable antibiotic resistance genes or virulence factors were identified. Finally, strain-specific primers based on genome-wide polymorphisms were designed for the efficient and rapid identification of Lc. paracasei SRX10 via multiplex PCR in fermented products.
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Affiliation(s)
- Christina S. Kamarinou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, 14123 Lycovrissi, Greece;
| | - Despoina E. Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
| | - Panagiotis Repanas
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, 14123 Lycovrissi, Greece;
| | - Nikos G. Chorianopoulos
- Laboratory of Microbiology and Biotechnology of Foods, School of Food and Nutritional Sciences, Department of Food Science and Human Nutrition, Agricultural University of Athens, 11855 Athens, Greece;
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
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Choi EJ, Baek IC, Park S, Kim HJ, Kim TG. Development of cost-effective and fast KIR genotyping by multiplex PCR-SSP. HLA 2024; 103:e15191. [PMID: 37688498 DOI: 10.1111/tan.15191] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 09/11/2023]
Abstract
Killer-cell immunoglobulin-like receptors (KIR) control natural killer (NK) cell functions by recognizing HLA molecules and modulating the activity of NK cells. The KIR gene cluster contains polymorphic and highly homologous genes. Diversity of the KIR region is achieved through differences in gene content, allelic polymorphism, and gene copy number, which result in unrelated individuals having different KIR genotypes and individualized immune responses that are relevant to multiple aspects of human health and disease. Therefore, KIR genotyping is increasingly used in epidemiological studies. Here, we developed multiplex polymerase chain reaction with sequence-specific primers (PCR-SSP) to compensate for the shortcomings of the conventional PCR-SSP method, which is most commonly used for KIR analysis. Multiplex PCR-SSP method involves six multiplex reactions that detect 16 KIR genes and distinguish variant types of some KIR genes by adding two reactions. The assay was evaluated in a blind survey using a panel of 40 reference DNA standards from the UCLA KIR Exchange Program. The results are 100% concordant with the genotype determined using Luminex-based reverse sequence-specific oligonucleotide typing systems. Additionally, we investigated the currently known 16 KIR genes and their common variants in 120 unrelated Korean individuals. The results were consistent with the KIR genotype previously reported by Hwang et al. This multiplex PCR-SSP is an efficient method for analyzing KIR genotypes in both small- and large-scale studies with minimal labor, reagents, and DNA. Furthermore, by providing a better definition of KIR polymorphisms it can contribute to developments in immunogenetics.
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Affiliation(s)
- Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - In-Cheol Baek
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Silvia Park
- Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hee-Je Kim
- Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Tai-Gyu Kim
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Lee YJ, Jun LJ, Kim YJ, Han JE, Ko YJ, Oh YE, Lee EJ, Lee J, Jeong JB. Comparison of specificity and sensitivity of diagnostic methods for Enteromyxum leei and Enteromyxum fugu detected from cultured tiger puffer, Takifugu rubripes in Korea. J Fish Dis 2024; 47:e13865. [PMID: 37731267 DOI: 10.1111/jfd.13865] [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] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023]
Abstract
Enteromyxum leei and Enteromyxum fugu, which are myxosporean parasites, were first found in cultured tiger puffer Takifugu rubripes in Korea. We collected four tiger puffers that showed severe emaciation signs for our experiments. DNA sequencing was confirmed that the tiger puffers were coinfected with E. leei and E. fugu. Furthermore, similar amounts of E. leei and E. fugu were confirmed using real-time PCR in the intestine. To the best of our knowledge, there have been no reports of E. fugu infection in the olive flounder Paralichthys olivaceus. However, the diagnosis of inflowing water, discharged water and olive flounder samples using highly sensitive diagnostic methods confirmed the presence of E. fugu in water and fish samples from olive flounder farms near the tiger puffer farm. Therefore, the present study aimed to develop highly sensitive diagnostic methods such as real-time and two-step PCR for early diagnosis and follow-up of the emaciation disease and multiplex PCR for rapid diagnosis. The multiplex PCR method exhibited the same sensitivity as the one-step PCR method developed in this study, demonstrating its efficacy for rapid diagnosis. Therefore, the suggested methods can be utilized for the early diagnosis and rapid diagnosis of emaciation diseases and reduction of economic losses through rapid disease control.
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Affiliation(s)
- Young Juhn Lee
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Lyu Jin Jun
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Ye Ji Kim
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Ji Eun Han
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Ye Jin Ko
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Yeong Eun Oh
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Eung Joon Lee
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Joon Bum Jeong
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
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19
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Naeimi B, Safari F, Ahmadikia K, Ahmadipour MJ, Sadeghzadeh F, Kondori N, Ahmadi B. Screening Candida auris through a multiplex stepwise PCR algorithm directly from clinical samples of patients suspected of otomycosis in south of Iran; Detection of five cases. Mycoses 2024; 67:e13686. [PMID: 38214363 DOI: 10.1111/myc.13686] [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: 08/10/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Otomycosis is an infection of the external auditory canal caused by molds and yeasts with descending frequency. Laboratory diagnosis is usually confirmed by microscopy and culture. However, they are not specific enough to reliably differentiate the causative agents, especially for rare pathogens such as Candida auris. The purpose of the current study was to the molecular screening of C. auris species from direct clinical samples of patients with suspected otomycosis in Southern of Iran. MATERIALS AND METHODS A total of 221 ear aspirates collected from 221 patients with suspected otomycosis over a four-year period. All the ear aspirations were examined with pan-fungal primers, then those with a positive result was included in two separate reaction mixtures simultaneously to identify the most clinically relevant Aspergillus and Candida species. The validity of positive samples for C. auris was assessed by sequencing. RESULTS Of the 189 pan-fungal positive PCRs, 78 and 39 specimens contained Aspergillus spp. and Candida spp., respectively. Furthermore, 65 specimens showed simultaneous positive bands in both Candida and Aspergillus species-specific multiplex PCR including five samples/patients with positive result for C. auris (5/189; 2.6%). Four out of five cases with C. auris species-specific PCR were reconfirmed by sequencing, while none were positive for C. auris in culture. CONCLUSION Unfortunately, due to high treatment failure rates of antifungal classes against C. auris species, rapid and accurate identification of patients colonised with C. auris is critical to overcome the challenge of preventing transmission. This PCR assay can be successfully applied for rapid and accurate detection of C. auris directly in patient samples and is able to differentiate C. auris from closely related Candida species.
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Affiliation(s)
- Behrouz Naeimi
- Department of Medical Laboratory Sciences, Faculty of Paramedical, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Fatemeh Safari
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Kazem Ahmadikia
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Farzaneh Sadeghzadeh
- Department of Medical Laboratory Sciences, Faculty of Paramedical, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Nahid Kondori
- Department of Infectious Diseases, Institution of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bahram Ahmadi
- Department of Medical Laboratory Sciences, Faculty of Paramedical, Bushehr University of Medical Sciences, Bushehr, Iran
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20
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Jańczak D, Górecki P, Maj AK. PCR-based methods in detection and identification of dermatophytes in dogs and cats with suspected dermatophytosis in 2021 in Poland. Pol J Vet Sci 2023; 26:629-634. [PMID: 38088306 DOI: 10.24425/pjvs.2023.148282] [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] [Indexed: 12/18/2023]
Abstract
Dermatophytes from Microsporum, Trichophyton and Epidermophyton genera are divided into geophilic, zoophilic and anthropophilic species which cause skin infection in humans and wide group of animals, mainly mammals. Main species causing dermatophytosis in dogs and cats are Microsporum and Trichophyton. Conventional mycological diagnostic technique includes Saburaud Dextrose Agar (SAD) and others medium cultures, 10% KOH mount and direct microscopy of hairs and scraping. Molecular diagnostic become more frequent in veterinary practice due to shortening of waiting time. In this study we based on two PCR methods. The nested PCR amplified CHS1 gene for dermatophytes detection, and multiplex PCR coding ITS1 and ITS2 fragments for species identification of detected derpatophytes. Most frequently detected species was Microsporum canis, mainly in young cats. Geophilic Microsporum gypseum and anthropophilic Trichophyton rubrum was found primarily in dogs. Molecular methods in dermatophytosis identification are rapid in contrast to routinely, long lasting culture.
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Affiliation(s)
- Dawid Jańczak
- Animallab Veterinary Laboratory, Środkowa 2/4, 03-430 Warsaw, Poland
| | - Piotr Górecki
- Animallab Veterinary Laboratory, Środkowa 2/4, 03-430 Warsaw, Poland
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21
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Yan T, Zheng R, Li Y, Sun S, Zeng X, Yue Z, Liao Y, Hu Q, Xu Y, Li Q. Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants. Viruses 2023; 15:2397. [PMID: 38140638 PMCID: PMC10748191 DOI: 10.3390/v15122397] [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: 11/02/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
The prolonged course of the COVID-19 pandemic necessitates sustained surveillance of emerging variants. This study aimed to develop a multiplex real-time polymerase chain reaction (rt-PCR) suitable for the real-time tracking of Omicron subvariants in clinical and wastewater samples. Plasmids containing variant-specific mutations were used to develop a MeltArray assay. After a comprehensive evaluation of both analytical and clinical performance, the established assay was used to detect Omicron variants in clinical and wastewater samples, and the results were compared with those of next-generation sequencing (NGS) and droplet digital PCR (ddPCR). The MeltArray assay identified 14 variant-specific mutations, enabling the detection of five Omicron sublineages (BA.2*, BA.5.2*, BA.2.75*, BQ.1*, and XBB.1*) and eight subvariants (BF.7, BN.1, BR.2, BQ.1.1, XBB.1.5, XBB.1.16, XBB.1.9, and BA.4.6). The limit of detection (LOD) of the assay was 50 copies/reaction, and no cross-reactivity was observed with 15 other respiratory viruses. Using NGS as the reference method, the clinical evaluation of 232 swab samples exhibited a clinical sensitivity of > 95.12% (95% CI 89.77-97.75%) and a specificity of > 95.21% (95% CI, 91.15-97.46%). When used to evaluate the Omicron outbreak from late 2022 to early 2023, the MeltArray assay performed on 1408 samples revealed that the epidemic was driven by BA.5.2* (883, 62.71%) and BF.7 (525, 37.29%). Additionally, the MeltArray assay demonstrated potential for estimating variant abundance in wastewater samples. The MeltArray assay is a rapid and scalable method for identifying SARS-CoV-2 variants. Integrating this approach with NGS and ddPCR will improve variant surveillance capabilities and ensure preparedness for future variants.
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Affiliation(s)
- Ting Yan
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (T.Y.); (S.S.); (Y.L.)
| | - Rongrong Zheng
- Xiamen Centre for Disease Control and Prevention, Xiamen 361021, China; (R.Z.); (X.Z.)
| | - Yinghui Li
- Shenzhen Centre for Disease Control and Prevention, Shenzhen 518055, China; (Y.L.); (Z.Y.); (Q.H.)
| | - Siyang Sun
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (T.Y.); (S.S.); (Y.L.)
| | - Xiaohong Zeng
- Xiamen Centre for Disease Control and Prevention, Xiamen 361021, China; (R.Z.); (X.Z.)
| | - Zhijiao Yue
- Shenzhen Centre for Disease Control and Prevention, Shenzhen 518055, China; (Y.L.); (Z.Y.); (Q.H.)
| | - Yiqun Liao
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (T.Y.); (S.S.); (Y.L.)
| | - Qinghua Hu
- Shenzhen Centre for Disease Control and Prevention, Shenzhen 518055, China; (Y.L.); (Z.Y.); (Q.H.)
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (T.Y.); (S.S.); (Y.L.)
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (T.Y.); (S.S.); (Y.L.)
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Xiahou ZY, Wambulwa MC, Xu ZC, Ye LJ, Fan PZ, Magige EA, Luo YH, Liu J. A Multiplex PCR System of Novel Microsatellite Loci for Population Genetic Application in Walnuts. Plants (Basel) 2023; 12:4101. [PMID: 38140428 PMCID: PMC10747719 DOI: 10.3390/plants12244101] [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: 10/28/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
Multiplex polymerase chain reaction (PCR) of microsatellite loci allows for simultaneous amplification of two or more pairs of primers in a single PCR reaction; hence, it is cost and time effective. However, very few attempts have been reported in non-model species. In this study, by combining a genome-based de novo development and cross-species application approach, a multiplex PCR system comprising 5 PCR reactions of 33 microsatellites consisting of 26 novel genomic and 7 literature-sourced loci was tested for polymorphisms, cross-species transferability, and the ability to assess genetic diversity and population structure of three walnut species (Juglans spp.). We found that the genome-based approach is more efficient than other methods. An allelic ladder was developed for each locus to enhance consistent genotyping among laboratories. The population genetic analysis results showed that all 33 loci were successfully transferred across the three species, showing high polymorphism and a strong genetic structure. Hence, the multiplex PCR system is highly applicable in walnut species. Furthermore, we propose an efficient pipeline to characterize and genotype polymorphic microsatellite loci. The novel toolbox developed here will aid future ecology and evolution studies in walnut and could serve as a model for other plant species.
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Affiliation(s)
- Zuo-Ying Xiahou
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Moses C. Wambulwa
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui 170-90200, Kenya
| | - Zu-Chang Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Lin-Jiang Ye
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Key Laboratory of Plant Resources and Biodiversity of Jiangxi Province, Jingdezhen University, Jingdezhen 333400, China
| | - Peng-Zhen Fan
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ephie A. Magige
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
| | - Jie Liu
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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23
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Sahoo M, Singh R, Kumar P, Kumar Mariappan A, Munnuswamy P, Singh K, Mani S, Dhama K, Kondabattula G, Das T, Thakor JC, Kashyap G, Sahoo NR. Novel pathologic findings and viral antigen distribution in cattle and buffalo calves naturally infected with Foot-and-Mouth disease virus. Vet Q 2023; 43:1-13. [PMID: 37733477 PMCID: PMC10548843 DOI: 10.1080/01652176.2023.2260435] [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: 01/05/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023] Open
Abstract
The Foot-and-Mouth disease is highly contagious acute viral disease of livestock inflicting huge economic loss to the farmers. The limited knowledge regarding the pathological lesions vis-a-vis distribution of the FMDV in lesser explored endocrine glands and important vital organs other than the target organs of infected calves prompted us to take the present investigation to have detailed insight into the pathogenesis. The systematic necropsy of 37 dead calves (cattle-28 and buffalo-9) was conducted, and thin representative tissue pieces from the affected organs were collected in 10% neutral buffered formalin (NBF) for pathological and immunohistochemical investigations. The genomic detection and its serotyping were done by RT-PCR and multiplex-PCR, respectively. Necropsy examination in all cases showed myocardial lesions resembling 'tigroid heart appearance'. Other organ specific lesions include vesiculo-ulcerative stomatitis, edema of the lungs, petechial hemorrhages, edema of the endocrines, and gastroenteritis. Histopathological examination showed varying sizes of vesicles and ulcerations in stratified squamous epithelium of the tongue, acute necrotizing myocarditis, lymphoid depletion in lymphoid tissues, hepatitis, pancreatitis, thymic hyperplasia, thyroiditis, adrenitis, and enteritis. Positive immunolabeling for viral antigens was observed in endocrine glands, lymphoid organs, lungs, liver, kidneys, and intestine, in addition to other typical locations. The thyroid, adrenal glands, and pancreas, in addition to the tongue and heart, are the tissue of choice for sampling in the field during epidemics. Further, the viral genome and serotype A was confirmed in the affected tissues. This study provides insights into novel tissue tropism and pathogenesis in young calves naturally infected with FMDV.
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Affiliation(s)
- Monalisa Sahoo
- ICAR-National Institute on Foot-and-Mouth Disease (NIFMD), Bhubaneswar, India
- Division of Pathology, ICAR- Indian veterinary Research Institute (IVRI), Izatnagar, India
| | - Rajendra Singh
- Veterinary Pathology, Institute of Veterinary Science and Animal Husbandry, Siksha "O" Anusandhan, Bhubaneswar, India
| | - Pawan Kumar
- Division of Pathology, ICAR- Indian veterinary Research Institute (IVRI), Izatnagar, India
| | - Asok Kumar Mariappan
- Division of Pathology, ICAR- Indian veterinary Research Institute (IVRI), Izatnagar, India
| | - Palanivelu Munnuswamy
- Division of Pathology, ICAR- Indian veterinary Research Institute (IVRI), Izatnagar, India
| | - Karampal Singh
- CADRAD, ICAR- Indian Veterinary Research Institute (IVRI), Izatnagar, India
| | - Saminathan Mani
- CADRAD, ICAR- Indian Veterinary Research Institute (IVRI), Izatnagar, India
| | - Kuldeep Dhama
- Veterinary Pathology, Institute of Veterinary Science and Animal Husbandry, Siksha "O" Anusandhan, Bhubaneswar, India
| | - Ganesh Kondabattula
- Quality control & Quality Assurance unit, ICAR-Indian Veterinary Research Institute (IVRI), Hebbal, India
| | - Tareni Das
- ICAR-National Institute on Foot-and-Mouth Disease (NIFMD), Bhubaneswar, India
| | | | - Gayatri Kashyap
- Division of Pathology, ICAR- Indian veterinary Research Institute (IVRI), Izatnagar, India
| | - Nihar Ranjan Sahoo
- ICAR-National Institute on Foot-and-Mouth Disease (NIFMD), Bhubaneswar, India
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Chambe E, Bortolotti P, Diesnis R, Laurans C, Héquette-Ruz R, Panaget S, Herbecq P, Vachée A, Meybeck A. Performance and Impact on Antibiotic Prescriptions of a Multiplex PCR in a Real-Life Cohort of Critically Ill Patients with Suspected Ventilated Pneumonia: A Retrospective Monocentric Observational Study. Antibiotics (Basel) 2023; 12:1646. [PMID: 38136680 PMCID: PMC10741159 DOI: 10.3390/antibiotics12121646] [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: 10/29/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Pulmonary multiplex polymerase chain reaction (m-PCR) allows rapid pathogen detection. We aimed to assess its impact on initial antibiotic prescriptions in ventilated patients with suspected pneumonia. Between November 2020 and March 2022,ventilated patients with suspected pneumonia hospitalized in our ICU who benefited from respiratory sampling simultaneously tested using conventional microbiological methods and m-PCR were included. The proportion of appropriate changes in the initial antibiotic therapy following m-PCR results was assessed. We analyzed 104 clinical samples. Of the 47 negative m-PCR results, 16 (34%) led to an appropriate antibiotic strategy: 8 cessationsand 8 lack of initiation. Of the 57 positive m-PCR results, 51 (89%) resulted in an appropriate antibiotic strategy: 33 initiations, 2 optimizations, and 9 de-escalations. In the multivariate analysis, a positive m-PCR was associated with an appropriate antibiotic change (OR: 96.60; IC95% [9.72; 960.20], p < 0.001). A higher SAPS II score was negatively associated with an appropriate antibiotic change (OR: 0.96; IC95% [0.931; 0.997], p = 0.034). In our cohort, a positive m-PCR allowed for early initiation or adjustment of antibiotic therapy in almost 90% of cases. A negative m-PCR spared antibiotic use in onethird of cases. The impact of m-PCR results was reduced in the most severe patients.
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Affiliation(s)
- Emma Chambe
- Department of Critical Care, Victor Provo Hospital, 59100 Roubaix, France; (E.C.); (P.B.); (P.H.)
| | - Perrine Bortolotti
- Department of Critical Care, Victor Provo Hospital, 59100 Roubaix, France; (E.C.); (P.B.); (P.H.)
- Infectious Risk Management Unit, Victor Provo Hospital, 59100 Roubaix, France; (C.L.); (R.H.-R.); (S.P.)
| | - Rémy Diesnis
- Department of Biostatistics, Victor Provo Hospital, 59100 Roubaix, France;
| | - Caroline Laurans
- Infectious Risk Management Unit, Victor Provo Hospital, 59100 Roubaix, France; (C.L.); (R.H.-R.); (S.P.)
| | - Rozenn Héquette-Ruz
- Infectious Risk Management Unit, Victor Provo Hospital, 59100 Roubaix, France; (C.L.); (R.H.-R.); (S.P.)
| | - Sophie Panaget
- Infectious Risk Management Unit, Victor Provo Hospital, 59100 Roubaix, France; (C.L.); (R.H.-R.); (S.P.)
| | - Patrick Herbecq
- Department of Critical Care, Victor Provo Hospital, 59100 Roubaix, France; (E.C.); (P.B.); (P.H.)
| | - Anne Vachée
- Department of Microbiology, Victor Provo Hospital, 59100 Roubaix, France;
| | - Agnès Meybeck
- Infectious Risk Management Unit, Victor Provo Hospital, 59100 Roubaix, France; (C.L.); (R.H.-R.); (S.P.)
- University Department of Infectious Diseases, Centre Hospitalier Dron Hospital, 59200 Tourcoing, France
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Esteban J, Salar-Vidal L, Schmitt BH, Waggoner A, Laurent F, Abad L, Bauer TW, Mazariegos I, Balada-Llasat JM, Horn J, Wolk DM, Jefferis A, Hermans M, Verhoofstad I, Butler-Wu SM, Umali-Wilcox M, Murphy C, Cabrera B, Craft D, von Bredow B, Leber A, Everhart K, Dien Bard J, Flores II, Daly J, Barr R, Holmberg K, Graue C, Kensinger B. Multicenter evaluation of the BIOFIRE Joint Infection Panel for the detection of bacteria, yeast, and AMR genes in synovial fluid samples. J Clin Microbiol 2023; 61:e0035723. [PMID: 37877730 PMCID: PMC10662359 DOI: 10.1128/jcm.00357-23] [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: 03/23/2023] [Accepted: 09/07/2023] [Indexed: 10/26/2023] Open
Abstract
The bioMérieux BIOFIRE Joint Infection (JI) Panel is a multiplex in vitro diagnostic test for the simultaneous and rapid (~1 h) detection of 39 potential pathogens and antimicrobial resistance (AMR) genes directly from synovial fluid (SF) samples. Thirty-one species or groups of microorganisms are included in the kit, as well as several AMR genes. This study, performed to evaluate the BIOFIRE JI Panel for regulatory clearance, provides data from a multicenter evaluation of 1,544 prospectively collected residual SF samples with performance compared to standard-of-care (SOC) culture for organisms or polymerase chain reaction (PCR) and sequencing for AMR genes. The BIOFIRE JI Panel demonstrated a sensitivity of 90.9% or greater for all but six organisms and a positive percent agreement (PPA) of 100% for all AMR genes. The BIOFIRE JI Panel demonstrated a specificity of 98.5% or greater for detection of all organisms and a negative percent agreement (NPA) of 95.7% or greater for all AMR genes. The BIOFIRE JI Panel provides an improvement over SOC culture, with a substantially shorter time to result for both organisms and AMR genes with excellent sensitivity/PPA and specificity/NPA, and is anticipated to provide timely and actionable diagnostic information for joint infections in a variety of clinical scenarios.
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Affiliation(s)
- Jaime Esteban
- IIS-Fundacion Jimenez Diaz, CIBERINFEC-CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Llanos Salar-Vidal
- IIS-Fundacion Jimenez Diaz, CIBERINFEC-CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Bryan H. Schmitt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Amy Waggoner
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | | | | | | | | | - Jared Horn
- The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | | | | | | | | | | | | | - Caitlin Murphy
- University of Nebraska Medical Center Omaha, Omaha, Nebraska, USA
| | - Barbara Cabrera
- University of Nebraska Medical Center Omaha, Omaha, Nebraska, USA
| | - David Craft
- The Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | | | - Amy Leber
- Nationwide Children’s Hospital, Columbus, Ohio, USA
| | | | | | | | - Judy Daly
- Primary Children’s Hospital, Salt Lake City, Utah, USA
| | - Rebecca Barr
- Primary Children’s Hospital, Salt Lake City, Utah, USA
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Stein A, Soukup D, Rath PM, Felderhoff-Müser U. Diagnostic Accuracy of Multiplex Polymerase Chain Reaction in Early Onset Neonatal Sepsis. Children (Basel) 2023; 10:1809. [PMID: 38002900 PMCID: PMC10670518 DOI: 10.3390/children10111809] [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] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023]
Abstract
Early onset neonatal sepsis is a significant contributor to neonatal morbidity and mortality. Although blood cultures remain the diagnostic gold standard, they detect pathogens in only a minority of suspected cases. This study compared the accuracy of blood cultures with a rapid multiplex PCR test. Newborns at risk of neonatal sepsis were prospectively screened as recommended per national guidelines. Evaluations included laboratory parameters (CrP, IL6, differential blood count), blood culture, and a molecular multiplex PCR test (ROCHE LightCycler SeptiFast®) identifying 20 common microbial agents. Blood samples were taken simultaneously from umbilical cord or venous sources on the first day of life. Of 229 infants included, 69% were born preterm. Blood culture and multiplex PCR sensitivity were 7.4% and 14.8%, respectively. Specificity, negative and positive predictive values between methods showed no significant variance, although multiplex PCR had more false positives due to contamination. The limited sensitivity of blood cultures for early onset neonatal sepsis is concerning. Despite quicker results, multiplex PCR does not enhance diagnostic accuracy or antibiotic therapy guidance, thus it cannot be recommended for this indication.
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Affiliation(s)
- Anja Stein
- Department of Pediatrics I, Neonatology and Experimental Perinatal Neurosciences, Center for Translational and Behavioral Neuroscience, CTNBS, University Hospital Essen, Faculty of Medicine, University Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany; (D.S.); (U.F.-M.)
| | - Daniel Soukup
- Department of Pediatrics I, Neonatology and Experimental Perinatal Neurosciences, Center for Translational and Behavioral Neuroscience, CTNBS, University Hospital Essen, Faculty of Medicine, University Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany; (D.S.); (U.F.-M.)
- Service de Réanimation Pédiatrique, Centre Hospitalier Universitaire de Bordeaux, Place Amélie Raba Léon, 33000 Bordeaux, France
| | - Peter-Michael Rath
- Institute for Medical Microbiology, University Hospital Essen, Hufelandstraße 55, 45147 Essen, Germany;
| | - Ursula Felderhoff-Müser
- Department of Pediatrics I, Neonatology and Experimental Perinatal Neurosciences, Center for Translational and Behavioral Neuroscience, CTNBS, University Hospital Essen, Faculty of Medicine, University Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany; (D.S.); (U.F.-M.)
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27
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Anton A, Plinet M, Peyret T, Cazaudarré T, Pesant S, Rouquet Y, Tricoteaux MA, Bernier M, Bayette J, Fournier R, Marguerettaz M, Rolland P, Bayol T, Abbaoui N, Berry A, Iriart X, Cassaing S, Chauvin P, Bernard E, Fabre R, François JM. Rapid and Accurate Diagnosis of Dermatophyte Infections Using the DendrisCHIP ® Technology. Diagnostics (Basel) 2023; 13:3430. [PMID: 37998565 PMCID: PMC10670032 DOI: 10.3390/diagnostics13223430] [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: 10/18/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Dermatophytosis is a superficial fungal infection with an ever-increasing number of patients. Culture-based mycology remains the most commonly used diagnosis, but it takes around four weeks to identify the causative agent. Therefore, routine clinical laboratories need rapid, high throughput, and accurate species-specific analytical methods for diagnosis and therapeutic management. Based on these requirements, we investigated the feasibility of DendrisCHIP® technology as an innovative molecular diagnostic method for the identification of a subset of 13 pathogens potentially responsible for dermatophytosis infections in clinical samples. This technology is based on DNA microarray, which potentially enables the detection and discrimination of several germs in a single sample. A major originality of DendrisCHIP® technology is the use of a decision algorithm for probability presence or absence of pathogens based on machine learning methods. In this study, the diagnosis of dermatophyte infection was carried out on more than 284 isolates by conventional microbial culture and DendrisCHIP®DP, which correspond to the DendrisCHIP® carrying oligoprobes of the targeted pathogens implicated in dermatophytosis. While convergence ranging from 75 to 86% depending on the sampling procedure was obtained with both methods, the DendrisCHIP®DP proved to identify more isolates with pathogens that escaped the culture method. These results were confirmed at 86% by a third method, which was either a specific RT-PCR or genome sequencing. In addition, diagnostic results with DendrisCHIP®DP can be obtained within a day. This faster and more accurate identification of fungal pathogens with DendrisCHIP®DP enables the clinician to quickly and successfully implement appropriate antifungal treatment to prevent the spread and elimination of dermatophyte infection. Taken together, these results demonstrate that this technology is a very promising method for routine diagnosis of dermatophytosis.
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Affiliation(s)
- Aurore Anton
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Mathilde Plinet
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Thomas Peyret
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Thomas Cazaudarré
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Stéphanie Pesant
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Yannick Rouquet
- Laboratoire Inovie-CBM, 31000 Toulouse, France; (Y.R.); (M.-A.T.); (M.B.)
| | | | - Matthieu Bernier
- Laboratoire Inovie-CBM, 31000 Toulouse, France; (Y.R.); (M.-A.T.); (M.B.)
| | - Jérémy Bayette
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Remi Fournier
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Mélanie Marguerettaz
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Pierre Rolland
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Thibaud Bayol
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Nadia Abbaoui
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Antoine Berry
- Service de Parasitologie-Mycologie, Centre Hospitalier Universitaire Purpan de Toulouse, Institut Fédératif de biologie (IFB), 31300 Toulouse, France; (A.B.); (X.I.); (S.C.); (P.C.)
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Hôpital Purpan, 31024 Toulouse, France
| | - Xavier Iriart
- Service de Parasitologie-Mycologie, Centre Hospitalier Universitaire Purpan de Toulouse, Institut Fédératif de biologie (IFB), 31300 Toulouse, France; (A.B.); (X.I.); (S.C.); (P.C.)
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Hôpital Purpan, 31024 Toulouse, France
| | - Sophie Cassaing
- Service de Parasitologie-Mycologie, Centre Hospitalier Universitaire Purpan de Toulouse, Institut Fédératif de biologie (IFB), 31300 Toulouse, France; (A.B.); (X.I.); (S.C.); (P.C.)
| | - Pamela Chauvin
- Service de Parasitologie-Mycologie, Centre Hospitalier Universitaire Purpan de Toulouse, Institut Fédératif de biologie (IFB), 31300 Toulouse, France; (A.B.); (X.I.); (S.C.); (P.C.)
| | - Elodie Bernard
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Richard Fabre
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Jean-Marie François
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, Institut National des Sciences (INSA), 135 Avenue de Rangueil, 31077 Toulouse, France
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Tan D, Han J, Sun Q, Cheng X, Liu J, Liu J, Li Q, Dai L. Application of Multiplex Fluorescence Polymerase Chain Reaction for Detecting Pathogenic Bacteria in Sputum Samples from Patients with Lower Respiratory Tract Infection. Infect Drug Resist 2023; 16:6999-7005. [PMID: 37933294 PMCID: PMC10625741 DOI: 10.2147/idr.s431425] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/22/2023] [Indexed: 11/08/2023] Open
Abstract
Objective In this study, we conducted a multi-center research on six common lower respiratory tract pathogens using novel multiplex fluorescence quantitative polymerase chain reaction (PCR), and investigated the additional diagnostic value of this method, to provide a molecular diagnostic basis for clinical practice. Methods From March 2019 to October 2021, a total of 2047 respiratory sputum samples were collected from Hunan Provincial People's Hospital (the First Affiliated Hospital of Hunan Normal University), Hunan Provincial Children's Hospital, Jiangxi Provincial Children's Hospital, and Wuhan Infectious Disease Hospital. The samples were analyzed using a novel multiplex fluorescence quantitative PCR method for Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Pseudomonas aeruginosa, Legionella pneumophila, and Staphylococcus aureus. The results were compared to the results of bacterial culture and sequencing, as well as the results of third-party kits. Results Compared to the bacterial culture method, 2047 samples were detected with a sensitivity of 100%, a specificity of 72.22%, and an overall compliance rate of 81.91%. Compared to the sequencing method, the positive agreement percentage was 99.88%, the negative agreement percentage was 97.72%, and the overall agreement rate was 98.84%. Compared to similar control reagents, the positive agreement percentage was 100%, negative agreement percentage was 79.79%, and overall compliance rate was 96.19%. Conclusion The multiplex fluorescence PCR method has the advantages of simultaneously detecting multiple pathogenic bacteria and reducing the duration of pathogen culture identification. Combined detection can increase the detection rate, which has favorable performance and application prospects.
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Affiliation(s)
- Deyong Tan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008People’s Republic of China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078People’s Republic of China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, 410078People’s Republic of China
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, 410008People’s Republic of China
| | - Jianfeng Han
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
| | - Qingzhi Sun
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
| | - Xing Cheng
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
| | - Juan Liu
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
| | - Jia Liu
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008People’s Republic of China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078People’s Republic of China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, 410078People’s Republic of China
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, 410008People’s Republic of China
| | - Lizhong Dai
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
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Han M, Han S. A novel multiplex RT-qPCR assay for simultaneous detection of bovine norovirus, torovirus, and kobuvirus in fecal samples from diarrheic calves. J Vet Diagn Invest 2023; 35:742-750. [PMID: 37571922 PMCID: PMC10621540 DOI: 10.1177/10406387231191723] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023] Open
Abstract
Calf diarrhea results in significant economic loss and is caused by a variety of pathogens, including enteric viruses. Many of these viruses, including bovine norovirus (BNoV), bovine torovirus (BToV), and bovine kobuvirus (BKoV), are recognized as the causative agents of diarrhea; however, they remain understudied as major pathogens. We developed a multiplex reverse-transcription quantitative real-time PCR (RT-qPCR) assay for rapid and simple detection of BNoV, BToV, and BKoV. Our method had high sensitivity and specificity, with detection limits of 1 × 102 copies/μL for BNoV, BToV, and BKoV, which is a lower detection limit than conventional RT-PCR for BNoV and BKoV and identical for BToV. We tested fecal samples from 167 diarrheic calves with our multiplex RT-qPCR method. Viral detection was superior to conventional RT-PCR methods in all samples. The diagnostic sensitivity of the multiplex RT-qPCR method (100%) is higher than that of the conventional RT-PCR methods (87%). Our assay can detect BNoV, BToV, and BKoV in calf feces rapidly and with high sensitivity and specificity.
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Affiliation(s)
- Mina Han
- Institute of Chungbuk Provincial Veterinary Service and Research, Cheongju, South Korea
| | - Seongtae Han
- Institute of Chungbuk Provincial Veterinary Service and Research, Cheongju, South Korea
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Hajimohammadi Z, Alimohammadi-Bidhendi S, Bagheri Amiri F, Karimipoor M, Davoudi-Dehaghani E, Entezam M. Development of a Quantitative Multiplex PCR to Detect Three Common Alpha Thalassemia Deletions. Hemoglobin 2023; 47:163-166. [PMID: 37766586 DOI: 10.1080/03630269.2023.2260744] [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: 01/18/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023]
Abstract
Alpha thalassemia is an autosomal recessive genetic disorder with a high prevalence in the Middle East. The severe form of alpha-thalassemia is incompatible with life and can cause significant obstetric complications in the mother. Therefore, it is important to determine the genotype in parents who have a chance of having a fetus with one of the severe forms of this disease. A total of 112 samples that were previously analyzed for common alpha thalassemia mutations in Iran were used in this study. A new multiplex PCR including quantitative polymerase chain reaction to amplify the homologous regions of the alpha-globin gene cluster and fluorescent gap PCR was designed to identify -α3.7, -α4.2, --MED deletions. The ROC curve was used to determine the optimum cutoff points. Statistical analysis showed that there is a significant difference between the peak height ratios for different genotypes. The peak corresponding to the 297 bp fragment resulting from the amplification of the allele with MED-I deletion was detected in all the samples with this deletion. Different cutoffs for a range of sensitivities and specificities were determined by the ROC curve. The suggested method can identify three common large deletions in the alpha-globin gene cluster. A study with a larger sample size can provide more accurate information about the sensitivity and specificity of this test.
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Affiliation(s)
- Zahra Hajimohammadi
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sara Alimohammadi-Bidhendi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fahimeh Bagheri Amiri
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Elham Davoudi-Dehaghani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mona Entezam
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Wang L, Sun S, You D, Chen F, Guo Y, Zeng X, Wang W, Yang S. Comparison of two multiplex PCR tests for common pathogen detection in hospitalized children with acute respiratory infection. J Infect Dev Ctries 2023; 17:1474-1479. [PMID: 37956382 DOI: 10.3855/jidc.17999] [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: 01/29/2023] [Accepted: 04/28/2023] [Indexed: 11/15/2023] Open
Abstract
INTRODUCTION Multiplex PCR methods have significantly improved the diagnosis of acute respiratory tract infections (ARTIs) in children. The ResP-CE System coupled with capillary electrophoresis is a highly specialized, automated, and expensive technology for detecting common pathogens in ARTIs. The XYRes-MCA System, a remarkably less expensive multiplex PCR instrument, employs hybridization for the detection of ARTI pathogens. Both methods detect 9 common microorganisms in ARTIs, i.e., RSV, FLUAV, FLUBV, ADV, PIV, HMPV, HBOV, HCOV, and MP. In this study, we aimed to compare the performance of these two methods in the detection of pathogens from sputum specimens collected from children with ARTIs. METHODOLOGY Sputum specimens were collected from 237 hospitalized children with ARTIs. Nucleic acid was extracted on an automated workstation. The ResP-CE and XYres-MCA systems were applied to detect pathogens from the samples, and the test result agreement between the two methods was evaluated using Kappa statistics. RESULTS The ResP-CE and XYres-MCA identified pathogens, single or in combination, in 151 (63.7%) and 171 (72.1%) of 237 samples, respectively. Approximately 85% of positive samples identified by either method contained a single pathogen. Moderate to almost perfect concordance between the two methods was found in detecting the following 7 pathogens: RSV, FLUAV, FLUBV, PIV, HMPV, HBOV, and MP. CONCLUSIONS These two methods are comparable in detecting common pathogens of ARTIs in children. As XYres-MCA analysis is more cost-effective, it could play an important role in diagnosing ARTIs in children in less economically developed regions.
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Affiliation(s)
- Le Wang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang 050031, China
| | - Suzhen Sun
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang 050031, China
| | - Dianping You
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang 050031, China
| | - Fang Chen
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang 050031, China
| | - Yinghui Guo
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang 050031, China
| | - Xianping Zeng
- Ningbo Health Gene Tech Co., Ltd., Ningbo 315040, China
| | - Weijian Wang
- Ningbo Health Gene Tech Co., Ltd., Ningbo 315040, China
| | - Shuo Yang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang 050031, China
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Kiousi DE, Karadedos DM, Sykoudi A, Repanas P, Kamarinou CS, Argyri AA, Galanis A. Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers. Microorganisms 2023; 11:2553. [PMID: 37894211 PMCID: PMC10609308 DOI: 10.3390/microorganisms11102553] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Probiotics are microorganisms that exert strain-specific health-promoting effects on the host. Τhey are employed in the production of functional dairy or non-dairy food products; still, their detection in these complex matrices is a challenging task. Several culture-dependent and culture-independent methods have been developed in this direction; however, they present low discrimination at the strain level. Here, we developed a multiplex PCR assay for the detection of two potential probiotic lactic acid bacteria (LAB) strains, Lactiplantibacillus plantarum L125 and Lp. pentosus L33, in monocultures and yogurt samples. Unique genomic regions were identified via comparative genomic analysis and were used to produce strain-specific primers. Then, primer sets were selected that produced distinct electrophoretic DNA banding patterns in multiplex PCR for each target strain. This method was further implemented for the detection of the two strains in yogurt samples, highlighting its biotechnological applicability. Moreover, it can be applied with appropriate modifications to detect any bacterial strain with available WGS.
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Affiliation(s)
- Despoina E. Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Dimitrios M. Karadedos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Anastasia Sykoudi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Panagiotis Repanas
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Christina S. Kamarinou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece;
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece;
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
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Ahmed N, Roy BC, Hasan MM, Zim MMR, Biswas H, Talukder MH. Molecular and phylogenetic characterization of zoonotic Trichostrongylus species from goats for the first time in Bangladesh. Trans R Soc Trop Med Hyg 2023; 117:705-713. [PMID: 37309997 DOI: 10.1093/trstmh/trad034] [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: 09/15/2022] [Revised: 03/30/2023] [Accepted: 05/18/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Trichostrongylus is one of the most important nematodes infecting animals and humans. The current study was designed to identify the Trichostrongylus species infecting goats by multiplex PCR and phylogenetic analysis. METHODS A total of 124 goats' viscera were collected from different abattoirs of Mymensingh division. Trichostrongylus species were isolated and characterized based on morphometry, multiplex PCR and phylogenetic analysis. RESULTS Among 124 viscera of goats, 39 were positive with two species, Trichostrongylus colubriformis and Trichostrongylus vitrinus, revealing an overall 31.45% prevalence. Morphological identification of Trichostrongylus species was confirmed by multiplex PCR amplification of the ITS2 gene and sequencing. Partial sequencing of the ITS2 gene of two species revealed seven single nucleotide polymorphisms (three transitions and four transversions) in this study. The neighbor-joining phylogenetic tree demonstrated that T. colubriformis and T. vitrinus isolates were clustered together with the reference sequences that belong to the clade A and B without any geographical boundaries. CONCLUSIONS This is the first report on molecular and phylogenetic analysis of Trichostrongylus species from ruminants in Bangladesh. These results provide the baseline data for understanding the zoonosis and epidemiology of this parasite in Bangladesh and global perspectives.
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Affiliation(s)
- Nurnabi Ahmed
- Department of Parasitology, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Babul Chandra Roy
- Department of Parasitology, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | | | | | - Hiranmoy Biswas
- Department of Parasitology, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
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Furuya H, Ogura K, Takemoto N, Watanabe S, Yamazaki A, Ogai K, Sugama J, Okamoto S. A multilocus sequence typing method of Staphylococcus aureus DNAs in a sample from human skin. Microbiol Immunol 2023; 67:438-446. [PMID: 37574717 DOI: 10.1111/1348-0421.13094] [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: 04/07/2023] [Revised: 07/03/2023] [Accepted: 07/21/2023] [Indexed: 08/15/2023]
Abstract
The skin and mucous membranes are the primary sites of Staphylococcus aureus colonization, particularly those of health care personnel and patients in long-term care centers. We found that S. aureus colonized with a higher abundance ratio on skins which had recovered from pressure injury (PI) than on normal skins in our earlier research on the skin microbiota of bedridden patients. Multilocus sequence typing (MLST) is a useful tool for typing S. aureus isolated from clinical specimens. However, the MLST approach cannot be used in microbiota DNA owing to the contamination from other bacteria species. In this study, we developed a multiplex-nested PCR method to determine S. aureus MLST in samples collected from human skins. The seven pairs of forward and reverse primers were designed in the upstream and downstream regions, which were conserved specifically in S. aureus. The first amplifications of the seven pairs were conducted in a multiplex assay. The samples were diluted and applied to conventional PCR for MLST. We confirmed that the method amplified the seven allele sequences of S. aureus specifically in the presence of untargeted DNAs from human and other skin commensal bacteria. Using this assay, we succeeded in typing sequence types (STs) of S. aureus in the DNA samples derived from the skins healed from PI. Peaks obtained by Sanger sequencing showed that each sample contained one ST, which were mainly categorized into clonal complex 1 (CC1) or CC5. We propose that this culture-free approach may be used in detecting S. aureus in clinical specimens without isolation.
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Affiliation(s)
- Hiroka Furuya
- Department of Clinical Laboratory Science, Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kohei Ogura
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, Japan
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Gokasho, Japan
| | - Norihiko Takemoto
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Shinjuku-ku, Japan
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Shimotsuke-shi, Tochigi, Japan
| | - Ayaka Yamazaki
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kazuhiro Ogai
- AI Hospital/Macro Signal Dynamics Research and Development Center, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Junko Sugama
- Research Center for Implementation Nursing Science Initiative, Fujita Health University, Toyoake, Aichi, Japan
| | - Shigefumi Okamoto
- Department of Clinical Laboratory Science, Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, Japan
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Taleb M, Bakour M, Brahim AT, Ghaber SM, Abdem SAE, Mohamed A, Lyoussi B. Molecular Characterization of Erythrocyte Glucose-6-Phosphate Dehydrogenase Deficiency in Different Ethnic Groups of Blood Donors in Mauritania. Front Biosci (Schol Ed) 2023; 15:11. [PMID: 37806950 DOI: 10.31083/j.fbs1503011] [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: 06/06/2023] [Revised: 07/18/2023] [Accepted: 08/17/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Glucose-6-phosphate-dehydrogenase (G6PD) deficiency is the most frequent enzymopathy worldwide; it is a genetic disorder that affects red blood cells and causes hemolysis. Here, we conducted a study on G6PD-deficient subjects in Mauritania to evaluate the molecular characteristics associated with a deficiency in this enzyme and the frequency of nucleotide polymorphisms in the glucose-6-phosphate dehydrogenase gene. METHOD AND MATERIALS A total of 943 blood samples were collected from blood donors (803 males and 140 females; 364 white Moors; 439 black Moors; 112 Pulaar; 18 Wolof; 10 Soninke). All blood samples were analyzed using a rapid screening test. G6PD status was analyzed quantitatively by the Randox G6PD test. Samples deficient in G6PD were extracted from the whole blood samples and subjected to DNA genotyping. The most frequent G6PD variants were determined by two molecular techniques: restriction fragment length polymorphism (RFLP) and multiplex PCR using the GENESPARK G6PD African kit. A total of six single nucleotide polymorphisms (SNPs) (G202A, A376G, A542T, G680T, C563T, and T968C) were identified. RESULTS The prevalence of G6PD deficiency in this population sample was 8.1%. The most common mutation was A376G/202A and was characterized by the G6PD A-phenotype, which is more common in the G6PD-deficient black Moors population. The wilaya in Nouakchott was the most affected among the 13 wilayas studied. CONCLUSIONS This study shows, for the first time, the presence of the G680T mutation.
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Affiliation(s)
- Mariem Taleb
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Department of Biology, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, 30000 Fez, Morocco
- Medical Analysis Laboratory (Maurilab), 2434 Nouakchott, Mauritania
| | - Meryem Bakour
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Department of Biology, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, 30000 Fez, Morocco
- The Higher Institute of Nursing Professions and Health Techniques, 30000 Fez, Morocco
| | - Aminetou Taleb Brahim
- Medical Analysis Laboratory (Maurilab), 2434 Nouakchott, Mauritania
- Faculty of Sciences and Techniques, Department of Biology, Nouakchott University, 2373 Nouakchott, Mauritania
| | - Sidi Mohamed Ghaber
- Medical Analysis Laboratory (Maurilab), 2434 Nouakchott, Mauritania
- Faculty of Medecine, Department of Basic Sciences, Nouakchott University, 2373 Nouakchott, Mauritania
| | - Seyid Abdellahi Ebnou Abdem
- Center of Urban Systems (CUS), Mohamed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Aminetou Mohamed
- Medical Analysis Laboratory (Maurilab), 2434 Nouakchott, Mauritania
- Faculty of Sciences and Techniques, Department of Biology, Nouakchott University, 2373 Nouakchott, Mauritania
| | - Badiaa Lyoussi
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Department of Biology, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, 30000 Fez, Morocco
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Yu Z, Xu Z, Chen J, Chen L, Liao N, Zhang R, Cheng D. Quantitative Risk Assessment of Five Foodborne Viruses in Shellfish Based on Multiplex qPCR. Foods 2023; 12:3462. [PMID: 37761170 PMCID: PMC10530164 DOI: 10.3390/foods12183462] [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] [Received: 08/29/2023] [Revised: 09/09/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Foodborne diseases are currently the most critical food safety issue in the world. There are not many hazard identification and exposure assessments for foodborne viruses (Norovirus GI, GII, Hepatitis A Virus, Rotavirus, Adenovirus) in shellfish. Multiplex qPCR for the simultaneous detection of five foodborne viruses was established and used to assess infection risk based on a 1-year pathogenesis study. The sensitivity, specificity and reproducibility of the multiplex qPCR method are consistent with that of conventional qPCR, which saves more time and effort. Overall, 37.86% of shellfish samples had one or more foodborne viruses. Risk assessment formulae and matrices were used to develop risk assessments for different age groups, different seasons and different shellfish. The annual probability of contracting a foodborne virus infection from shellfish is greater than 1.6 × 10-1 for all populations, and even for infants aged 0-4 years, it is greater than 1.5 × 10-2, which is much higher than the risk thresholds recommended by WHO (10-6) and the US EPA (10-4). High risk (level IV) is associated with springtime, and medium risk (level III) is associated with Mussel consumption. This study provides a basis for the risk of foodborne viral infections in people of different ages, in different seasons, and by consuming different shellfish.
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Affiliation(s)
- Zhendi Yu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China; (Z.Y.)
| | - Zhangkai Xu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China; (Z.Y.)
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310013, China
| | - Jiang Chen
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China; (Z.Y.)
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Lili Chen
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Ningbo Liao
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ronghua Zhang
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Dongqing Cheng
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China; (Z.Y.)
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Teksoy N, Ilktac M, Ongen B. Investigating the Significance of Non- jejuni/ coli Campylobacter Strains in Patients with Diarrhea. Healthcare (Basel) 2023; 11:2562. [PMID: 37761759 PMCID: PMC10530337 DOI: 10.3390/healthcare11182562] [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] [Received: 08/12/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Campylobacter is one of the most commonly reported foodborne bacteria worldwide. Although Campylobacter jejuni and Campylobacter coli have been reported to be responsible for the great majority of campylobacteriosis, the burden of infections by species other than C. jejuni and C. coli have been increasing as a result of a transition to diagnostic test methods that enable the isolation of emerging species. The aim of the present study was to recover C. jejuni, C. coli, and emerging species from the stool samples of 500 patients with gastroenteritis and 100 healthy subjects via the use of a filtration method and culture techniques using Butzler agar and mCCDA under a microaerobic or hydrogen-enriched atmosphere, identify the species by multiplex PCR methods and assess the significance of emerging species in enteric diseases. Thirty-one (6.2%) Campylobacter spp. were isolated from the stool samples of diarrheic patients but none from healthy individuals. Of 31 isolates, 21 (67.8%), nine (29%), and one (3.2%) were identified as C. jejuni, C. coli, and Campylobacter concisus by multiplex PCR, respectively. The filtration method was superior to the culture technique using mCCDA under a microaerobic atmosphere. C. concisus was evaluated as the etiology of gastroenteritis as a result of laboratory and clinical evaluations. The present study was the first to indicate that emerging Campylobacter species are rarely detected and C. concisus is linked to acute gastroenteritis in Turkey where additional studies are warranted to clarify the significance of emerging species in gastroenteritis.
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Affiliation(s)
- Nermin Teksoy
- Medical Microbiology Department, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey; (N.T.); (B.O.)
| | - Mehmet Ilktac
- Faculty of Pharmacy, Eastern Mediterranean University, via Mersin 10 Turkey, Famagusta 99628, Cyprus
| | - Betigul Ongen
- Medical Microbiology Department, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey; (N.T.); (B.O.)
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Trovato L, Calvo M, Domina M, De Pasquale R, Scalia G, Oliveri S. Multiplex real-time PCR for skin fungal infections: The diagnostic reliability in a one-year non-interventional study. Med Mycol 2023; 61:myad092. [PMID: 37740445 DOI: 10.1093/mmy/myad092] [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: 05/16/2023] [Revised: 08/03/2023] [Accepted: 09/20/2023] [Indexed: 09/24/2023] Open
Abstract
The skin fungal infection diagnostic workflow currently includes microscopic and culture-based methods as the gold standard. Recent published data described the possible limitations of these conventional techniques documenting the possibility of reducing response time intervals. The present study reports an evaluation of the DermaGenius® (DG) multiplex kit (PathoNostics) for rapid C. albicans and dermatophytes identification directly from skin samples. The investigations involved 90 specimens that underwent DNA extraction and amplification simultaneously to microscopic and culture methods. According to current guidelines, we defined a dermatophytic skin infection as the simultaneous presence of clinical evidence of skin lesions and positive results for dermatophyte elements from microscopy and/or cultures. The collected data remarked on the advantages of the molecular assay, especially in terms of sensitivity and rapidity. A statistical evaluation analysed a comparison between conventional and innovative diagnostic methods. The sensitivity, specificity, positive predictive value, and negative predictive value of DG-PCR in the cutaneous dermatophytosis were, respectively, 94.7%, 78.8%, 88.5%, and 89.6%. Based on our experience, the molecular technique could represent a diagnostic confirmation in the case of previous antifungal treatment, little biological material available, or urgent clinical conditions.
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Affiliation(s)
- Laura Trovato
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- U.O.C. Laboratory Analysis Unit, A.O.U. "Policlinico-San Marco", Catania, Italy
| | - Maddalena Calvo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- U.O.C. Laboratory Analysis Unit, A.O.U. "Policlinico-San Marco", Catania, Italy
| | - Maria Domina
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Rocco De Pasquale
- Department of General Surgery and Surgical-Medical Specialites, Unit of Dermatology, University of Catania, Catania, Italy
| | - Guido Scalia
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- U.O.C. Laboratory Analysis Unit, A.O.U. "Policlinico-San Marco", Catania, Italy
| | - Salvatore Oliveri
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
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Yang M, Tao C. Diagnostic efficiency of the FilmArray blood culture identification (BCID) panel: a systematic review and meta-analysis. J Med Microbiol 2023; 72. [PMID: 37712641 DOI: 10.1099/jmm.0.001608] [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] [Indexed: 09/16/2023] Open
Abstract
Introduction. The FilmArray blood culture identification panel (BCID) panel is a multiplex PCR assay with high sensitivity and specificity to identify the most common pathogens in bloodstream infections (BSIs).Hypothesis. We hypothesize that the BCID panel has good diagnostic performance for BSIs and can be popularized in clinical application.Aim: To provide summarized evidence for the diagnostic accuracy of the BCID panel for the identification of positive blood cultures.Methodology. We searched the MEDLINE, EMBASE and Cochrane databases through March 2021 and assessed the efficacy of the diagnostic test of the BCID panel. We performed a meta-analysis and calculated the summary sensitivity and specificity of the BCID panel. Systematic review protocols were registered in the International Prospective Register of Systematic Reviews (PROSPERO) (registration number CRD42021239176).Results. A total of 16 full-text articles were eligible for analysis. The overall sensitivities of the BCID panel on Gram-positive bacteria, Gram-negative bacteria and fungi were 97 % (95 % CI, 0.96-0.98), 100 % (95 % CI, 0.98-01.00) and 99 % (95 % CI, 0.87-1.00), respectively. The pooled diagnostic specificities were 99 % (95 % CI, 0.97-1.00), 100 % (95 % CI, 1.00-1.00) and 100 % (95 % CI, 1.00-1.00) for Gram-positive bacteria, Gram-negative bacteria and fungi, respectively.Conclusions. The BCID panel has high rule-in value for the early detection of BSI patients. The BCID panel can still provide valuable information for ruling out bacteremia or fungemia in populations with low pretest probability.
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Affiliation(s)
- Mei Yang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Chuanmin Tao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
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Jayagandan S, Singh J, Mudliar SR, Shankar P, Maurya AK, Malhotra AG, Malik S, Purwar S, Singh S. Evaluation of Xpert MTB/RIF Assay on Stool Samples for the Diagnosis of Pulmonary Tuberculosis among the Pediatric Population. J Lab Physicians 2023; 15:329-335. [PMID: 37564227 PMCID: PMC10411201 DOI: 10.1055/s-0042-1757721] [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: 02/07/2023] Open
Abstract
Objective Microbiological confirmation of tuberculosis (TB) in pediatric cases is challenging due to its paucibacillary nature and difficulty in specimen collection. This study aimed to validate stool as an alternative sample for the diagnosis of pediatric pulmonary TB via Xpert MTB/RIF (Xpert) assay. Materials and Methods This cross-sectional study included 75 pediatric patients up to 10 years of age with signs and symptoms suggestive of TB. From each recruited patient, pulmonary and stool samples were collected in a sterile container. The collected samples were subjected to Ziehl-Neelsen staining, BACTEC MGIT 960 culture (MGIT), Xpert, and in-house multiplex polymerase chain reaction for TB diagnosis. Results About 13.33% (10/75) of the pulmonary samples and, of them, 50% (5/75) of the stool samples were positive by Xpert assay. The sensitivity and specificity of Xpert assay with stool and pulmonary samples were 50 (95% confidence interval [CI]: 18.71-81.29%) and 100% (95% CI: 94.48-100%), respectively. Conclusion The Xpert assay on stool samples showed limited sensitivity and good specificity in the diagnosis of pulmonary TB. Therefore, it can be proposed as an alternative screening sample to diagnose TB in pediatric cases for which getting a respiratory sample is extremely difficult. However, further studies with greater number of samples and multiple baseline variables are required to support our findings. Strategies to optimize stool Xpert assay should be performed to enhance the sensitivity of this method to detect Mycobacterium tuberculosis in children.
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Affiliation(s)
- Sangitha Jayagandan
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Jitendra Singh
- Department of Translational Medicine, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Shivkumar Rashmi Mudliar
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Prem Shankar
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Anand Kumar Maurya
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Anvita Gupta Malhotra
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Shikha Malik
- Department of Paediatrics, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Shashank Purwar
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Sarman Singh
- Former Director, All India Institute of Medical Sciences, Bhopal, India
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Berinson B, Spenke L, Krivec L, Tanida K, Both A, Keller J, Rolvien T, Christner M, Lütgehetmann M, Aepfelbacher M, Klatte TO, Rohde H. Performance and Hypothetical Impact on Joint Infection Management of the BioFire Joint Infection Panel: a Retrospective Analysis. J Clin Microbiol 2023; 61:e0059223. [PMID: 37439678 PMCID: PMC10446873 DOI: 10.1128/jcm.00592-23] [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: 05/08/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
Pathogen identification is key in septic arthritis. Culture-based techniques are challenging, especially when patients have been pretreated with antibiotics or when difficult-to-culture bacteria are encountered. The BioFire joint infection assay (BJA) is a multiplex PCR panel which detects 31 of the most prevalent bacterial and fungal pathogens causing septic arthritis. Here, 123 cryoconserved contemporary synovial fluid samples from 120 patients underwent BJA analysis. Results were compared to those of culture-based diagnostics (standard of care [SOC]). Clinical data were collected, and the possible impact of the molecular diagnostic application on patient management was evaluated. Fifteen of 123 synovial fluid cultures grew bacterial pathogens. All on-panel pathogens (9/15) were correctly identified by the BJA. The BJA identified four additional bacterial pathogens in four SOC-negative cases. BJA sensitivity and specificity were 100% (95% confidence interval [CI], 69.2% to 100%) and 100% (95% CI, 96.8% to 100%), respectively. Compared to the SOC, the BJA would have resulted in faster provision of species identification and molecular susceptibility data by 49 h and 99 h, respectively. Clinical data analysis indicates that in BJA-positive cases, faster species ID could have led to timelier optimization of antibiotic therapy. This retrospective study demonstrates high sensitivity and specificity of the BJA to detect on-panel organisms in bacterial arthritis. The usefulness of the BJA in prosthetic-joint infections is limited, as important pathogens (i.e., coagulase negative staphylococci and Cutibacterium acnes) are not covered. Evidence from patient data analysis suggests that the assay might prove valuable for optimizing patient management in acute arthritis related to fastidious organisms or for patients who received antibiotics prior to specimen collection.
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Affiliation(s)
- Benjamin Berinson
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Spenke
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lukas Krivec
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Konstantin Tanida
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Both
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes Keller
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Rolvien
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Christner
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Lütgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Orla Klatte
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Liu Y, Wei C, Wan H, Sarengaowa, Liang X, Jiang T, Dong Y, Zhao X, Zhong T. Preliminary Study on Rapid and Simultaneous Detection of Viable Escherichia coli O157:H7, Staphylococcus aureus, and Salmonella by PMA-mPCR in Food. Molecules 2023; 28:5835. [PMID: 37570805 DOI: 10.3390/molecules28155835] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Escherichia coli O157:H7, Staphylococcus aureus, and Salmonella are major foodborne pathogens that are widespread in nature and responsible for several outbreaks of food safety accidents. Thus, a rapid and practical technique (PMA-mPCR) was developed for the simultaneous detection of viable E. coli O157:H7, S. aureus, and Salmonella in pure culture and in a food matrix. To eliminate false positive results, propidium monoazide (PMA) was applied to selectively suppress the DNA amplification of dead cells. The results showed the optimum concentration of PMA is 5.0 µg/mL. The detection limit of this assay by mPCR was 103 CFU/mL in the culture broth, and by PMA-mPCR was 104 CFU/mL both in pure culture and a food matrix (milk and ground beef). In addition, the detection of mixed viable and dead cells was also explored in this study. The detection sensitivity ratio of viable and dead counts was less than 1:10. Therefore, the PMA-mPCR assay proposed here might provide an efficient detection tool for the simultaneous detection of viable E. coli O157:H7, S. aureus, and Salmonella and also have great potential for the detection and concentration assessment of VBNC cells.
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Affiliation(s)
- Yao Liu
- School of Pharmacy and Food Science, Zhuhai College of Science and Technology, Zhuhai 519041, China
| | - Caijiao Wei
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Hui Wan
- Nanchang Agricultural Technology Popularization Center, Nanchang 330299, China
| | - Sarengaowa
- School of Pharmacy and Food Science, Zhuhai College of Science and Technology, Zhuhai 519041, China
| | - Xiaoping Liang
- School of Pharmacy and Food Science, Zhuhai College of Science and Technology, Zhuhai 519041, China
| | - Tao Jiang
- School of Pharmacy and Food Science, Zhuhai College of Science and Technology, Zhuhai 519041, China
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao 999078, China
| | - Yuhe Dong
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao 999078, China
| | - Xihong Zhao
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Tian Zhong
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao 999078, China
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Awais M, Akter R, Boopathi V, Ahn JC, Lee JH, Mathiyalagan R, Kwak GY, Rauf M, Yang DC, Lee GS, Kim YJ, Jung SK. Discrimination of Dendropanax morbifera via HPLC fingerprinting and SNP analysis and its impact on obesity by modulating adipogenesis- and thermogenesis-related genes. Front Nutr 2023; 10:1168095. [PMID: 37621738 PMCID: PMC10446900 DOI: 10.3389/fnut.2023.1168095] [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: 02/17/2023] [Accepted: 06/28/2023] [Indexed: 08/26/2023] Open
Abstract
Dendropanax morbifera (DM), a medicinal plant, is rich in polyphenols and commonly used to treat cancer, inflammation, and thrombosis. However, to date, no study has been conducted on DM regarding the enormous drift of secondary metabolites of plants in different regions of the Republic of Korea and their effects on antiobesity, to explore compounds that play an important role in two major obesity-related pathways. Here, we present an in-depth study on DM samples collected from three regions of the Republic of Korea [Jeju Island (DMJ), Bogildo (DMB), and Jangheung (DMJG)]. We used high-performance liquid chromatography (HPLC) and multivariate component analyses to analyze polyphenol contents (neochlorogenic acid, chlorogenic acid, cryptochlorogenic acid, and rutin), followed by discrimination of the samples in DMJG using single nucleotide polymorphism and chemometric analysis. In silico and in vitro evaluation of major compounds found in the plant extract on two major anti-obesity pathways (adipogenesis and thermogenesis) was carried out. Furthermore, two extraction methods (Soxhlet and ultrasound-assisted extraction) were used to understand which method is better and why. Upon quantifying plant samples in three regions with the polyphenols, DMJG had the highest content of polyphenols. The internal transcribed region (ITS) revealed a specific gel-based band for the authentication of DMJG. PCA and PLS-DA revealed the polyphenol's discriminative power of the region DMJG. The anti-obesity effects of plant extracts from the three regions were related to their polyphenol contents, with DMJG showing the highest effect followed by DMJ and DMB. Ultrasound-assisted extraction yielded a high number of polyphenols compared to that of the Soxhlet method, which was supported by scanning electron microscopy. The present work encourages studies on plants rich in secondary metabolites to efficiently use them for dietary and therapeutic purposes.
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Affiliation(s)
- Muhammad Awais
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin si, Republic of Korea
| | - Reshmi Akter
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin si, Republic of Korea
| | - Vinothini Boopathi
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin si, Republic of Korea
| | - Jong Chan Ahn
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin si, Republic of Korea
| | - Jung Hyeok Lee
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin si, Republic of Korea
| | - Ramya Mathiyalagan
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin si, Republic of Korea
| | - Gi-Young Kwak
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin si, Republic of Korea
| | - Mamoona Rauf
- Department of Oriental Medicinal Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Republic of Korea
| | - Deok Chun Yang
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin si, Republic of Korea
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Geun Sik Lee
- Southwest Coast Hwangchil Cooperative, Chonnam National University, Gwangju si, Republic of Korea
- Jungwon University Industry Academic Cooperation Building, Goesan-gun, Republic of Korea
| | - Yeon-Ju Kim
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin si, Republic of Korea
| | - Seok-Kyu Jung
- Department of Horticulture, Kongju National University, Yesan, Republic of Korea
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Korber JT, Canale LC, Holland MM. Massively Parallel Sequencing of the Mitogenome from Human Hair Shafts in Forensic Investigations. Curr Protoc 2023; 3:e865. [PMID: 37579069 DOI: 10.1002/cpz1.865] [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] [Indexed: 08/16/2023]
Abstract
This article highlights methods used to perform DNA extraction, mitochondrial DNA quantification, multiplex PCR amplification, amplicon-based massively parallel sequencing, and data analysis of the mitochondrial genome (mitogenome) from human hair shafts. The focus is on applications to forensic casework, but this set of protocols can be used for any purpose involving small cuttings (as small as 1 to 5 mm) of human hair shafts up to 40 years from the time of collection. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Extraction of mitochondrial DNA from human hair shafts Basic Protocol 2: Quantification of mitochondrial DNA (copies/μl) Basic Protocol 3: Multiplex amplification of the mitogenome Basic Protocol 4: Library preparation and sequencing of mitogenome amplicons Basic Protocol 5: Data analysis of mitogenome haplotypes.
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Affiliation(s)
- Jade T Korber
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania
| | - Lauren C Canale
- Department of Justice, Jan Bashinski DNA Laboratory, Richmond, California
| | - Mitchell M Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania
- Mitotyping Technologies, State College, Pennsylvania
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Jabrodini A, Sohrabizdeh M, Aboutalebian S, Hashemi SB, Zomorodian K, Alirezaie A, Rasti Jahromi M, Shamsdin SN, Motamedi M. Molecular strategy for the direct detection and identification of the most common fungal community in cerumen specimens by multiplex PCR. J Med Microbiol 2023; 72. [PMID: 37624031 DOI: 10.1099/jmm.0.001746] [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] [Indexed: 08/26/2023] Open
Abstract
Introduction. Otomycosis is a superficial fungal infection that is responsible for approximately 9-27 % of otitis externa. However, fungal communities in otomycosis are varied, but Aspergillus spp. and Candida spp. are the most common causes of this infection.Hypothesis Statement. The multiplex PCR assay is postulated to be able to directly detect more than one fungal genus in cerumen specimens.Aim. This study aimed to develop and evaluate the role of the multiplex PCR assay in detecting the most common genus of fungi that cause otomycosis directly from the cerumen specimens.Methodology. To detect Candida and Aspergillus/Penicillium genera, three pairs of primers, including pan-fungal, pan-Candida, and pan-Aspergillus/Penicillium, were used in a multiplex PCR. In order to evaluate the performance and reproducibility of the multiplex PCR. the cerumen of 140 patients suspected of otomycosis were investigated.Results. Pan-Candida and pan-Aspergillus/Penicillium primers were designed to amplify the ITS1-5.8S-ITS2 region and the β-tubulin gene, respectively. In the multiplex PCR assay, 64 (47.40 %) and 118 (87.40 %) specimens were positive with pan-Candida and pan-Aspergillus/Penicillium primers, respectively. Double amplicon bands of Candida and Aspergillus were obtained in 51 (37.77 %) specimens. In the culture method, yeast (n=18, 13.33 %) and mould (n=117, 86.66 %) were isolated from 135 cerumen specimens. The sensitivity, specificity, and positive and negative predictive values of the multiplex PCR assays using culture method results as the gold standard were determined to be 94, 33, 97, and 22 %, respectively.Conclusion. In our study, multiplex PCR assays enabled simultaneous detection of two common genera of the causative agent of otomycosis in a cerumen specimen. Regarding the high sensitivity of the first step of the multiplex PCR assay, this assay may be used for the direct detection of Candida and Aspergillus genera in other clinical specimens.
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Affiliation(s)
- Ahmad Jabrodini
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Sohrabizdeh
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Aboutalebian
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Basir Hashemi
- Otolaryngology Research Center, Department of Otolaryngology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamiar Zomorodian
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arefeh Alirezaie
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mona Rasti Jahromi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyedeh Neda Shamsdin
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Marjan Motamedi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Sufiawati I, Harmiyati R, Nur’aeny N, Indrati AR, Lesmana R, Wisaksana R, Amalia R. Detection of Human Herpesviruses in Sera and Saliva of Asymptomatic HIV-Infected Individuals Using Multiplex RT-PCR DNA Microarray. Pathogens 2023; 12:993. [PMID: 37623953 PMCID: PMC10457847 DOI: 10.3390/pathogens12080993] [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] [Received: 06/02/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
Human herpesviruses (HHVs) are frequently linked to an increased risk of acquiring human immunodeficiency virus (HIV), and vice versa. This study aimed to detect human herpesvirus (HHV) members in the sera and saliva of asymptomatic HIV-infected individuals. Paired saliva and serum samples were obtained from 30 asymptomatic HIV-infected individuals. HHVs were detected with a multiplex reverse transcription-polymerase chain reaction (RT-PCR) DNA microarray Clart®Entherpex kit. A total of 30 subjects were enrolled: 23 (76.67%) men and 7 (23.33%) women. The present study showed that at least one or more HHV members were detected in the saliva and sera of all (100%) of the subjects. In the saliva, we detected herpes simplex virus 1 (HSV-1) 6.67%, herpes simplex virus 2 (HSV-2) 6.67%, Epstein-Barr virus (EBV) 86.67%, cytomegalovirus (CMV) 63.33%, HHV-6 (40%), and HHV-7 (83.33%). In the sera, HSV-2 (20%), EBV (30%), CMV (40%), HHV-6 (0%), and HHV-7 (76.67%) were found, but not HSV-1. VZV and HHV-8 were not detected in either the saliva or sera. EBV and HHV6 were significantly more prevalent in the saliva than they were in the sera of asymptomatic HIV-infected individuals (p < 0.05). However, no significant differences were found in the prevalence of HSV-1, EBV, CMV, HHV-6, and HHV-7 in the saliva and sera of asymptomatic HIV-infected individuals (p > 0.05). In conclusion, the multiplex RT-PCR DNA microarray can serve as a valuable diagnostic tool that can be used as a screening tool or a first-line test for HHVs infections.
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Affiliation(s)
- Irna Sufiawati
- Department of Oral Medicine, Faculty of Dentistry, University of Padjadjaran, Bandung 40132, Indonesia;
| | - Rahmi Harmiyati
- Oral Medicine Residency Program, Faculty of Dentistry, University of Padjadjaran, Bandung 40132, Indonesia;
| | - Nanan Nur’aeny
- Department of Oral Medicine, Faculty of Dentistry, University of Padjadjaran, Bandung 40132, Indonesia;
| | - Agnes Rengga Indrati
- Department of Clinical Pathology, Faculty of Medicine, University of Padjadjaran, Bandung 45363, Indonesia;
| | - Ronny Lesmana
- Department of Biomedical Sciences, Faculty of Medicine, University of Padjadjaran, Bandung 45363, Indonesia;
| | - Rudi Wisaksana
- Department of Internal Medicine, Faculty of Medicine, University of Padjadjaran, Dr. Hasan Sadikin Central General Hospital, Bandung 45363, Indonesia;
| | - Riezki Amalia
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, University of Padjadjaran, Bandung 45363, Indonesia;
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de Araújo dos Santos SF, de Souza UJB, Oliveira MT, Jaime J, Spilki FR, Franco AC, Roehe PM, Campos FS. Recovery of complete genomes of canine parvovirus from clinical samples. bioRxiv 2023:2023.07.12.548703. [PMID: 37502963 PMCID: PMC10369981 DOI: 10.1101/2023.07.12.548703] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Canine parvovirus (CPV) is a highly pathogenic virus that affects dogs, especially puppies. CPV is believed to have evolved from feline panleukopenia virus (FPV), eventually giving rise to three antigenic types, CPV-2a, 2b, and 2c. CPV-2 is recognized for its resilience in contaminated environments, ease of transmission among dogs, and pathogenicity for puppies. Despite the relevance of the virus, complete genome sequences of CPV available at GenBank, to date, are scarce. In the current study, we have developed a methodology to allow the recovery of complete CPV-2 genomes directly from clinical samples. For this, seven fecal samples from Gurupi, Tocantins, North Brazil, were collected from puppies with clinical signals of viral enteritis, and submitted to viral DNA isolation and amplification. Two multiplex PCR strategies were designed including primers targeting fragments of 400 base pairs (bp) and 1,000 bp along the complete genome. Sequencing was performed with the Nanopore® technology and results obtained with the two approaches were compared. Genome assembly revealed that the 400 bp amplicons generated larger numbers of reads, allowing a more reliable coverage of the whole genome than those attained with primers targeting the larger (1000 bp) amplicons. Nevertheless, both enrichment methodologies were efficient in amplification and sequencing. Viral genome sequences were of high quality and allowed more precise typing and subtyping of viral genomes compared to the commonly employed strategy relying solely on the analysis of the VP2 region, which is limited in scope. The CPV-2 genomes recovered in this study belong to the CPV2a and CPV-2c subtypes, closely related to isolates from the neighboring Amazonian region. In conclusion, the technique reported here may contribute to increase the number of full CPV genomes available, which is essential for understanding the genetic mechanisms underlying the evolution and spread of CPV-2.
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Affiliation(s)
| | - Ueric José Borges de Souza
- Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, Brazil
| | - Martha Trindade Oliveira
- Virology Laboratory, Department of Microbiology, Immunology, and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
| | - Jairo Jaime
- Universidad Nacional de Colombia, Sede Bogotá. Facultad de Medicina Veterinaria y de Zootecnia, Departamento de Salud Animal. Centro de Investigación en Infectología e Inmunología Veterinaria (CI3V). Carrera 30 # 45-03, Bogotá D.C. CP 11132. Colombia
| | | | - Ana Cláudia Franco
- Virology Laboratory, Department of Microbiology, Immunology, and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
| | - Paulo Michel Roehe
- Virology Laboratory, Department of Microbiology, Immunology, and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
| | - Fabrício Souza Campos
- Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, Brazil
- Virology Laboratory, Department of Microbiology, Immunology, and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
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Song L, Tan R, Xiong D, Jiao X, Pan Z. Accurate identification and discrimination of Salmonella enterica serovar Gallinarum biovars Gallinarum and Pullorum by a multiplex PCR based on the new genes of torT and I137_14430. Front Vet Sci 2023; 10:1220118. [PMID: 37476820 PMCID: PMC10354433 DOI: 10.3389/fvets.2023.1220118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
Most cases of chicken salmonellosis are caused by Salmonella enterica serovar Gallinarum biovars Gallinarum and Pullorum, which lead to a significant morbidity and fatality rate. Although the conventional Kaufmann-White scheme is the reliable method for the serotyping of Salmonella, it does not distinguish between closely related biotypes like S. Pullorum and S. Gallinarum. Herein, we conducted a single one-step multiplex PCR assay that can identify and distinguish between S. Pullorum and S. Gallinarum in an accurate manner. This PCR method was based on three genes, including torT for S. Pullorum identification, I137_14430 for S. Gallinarum identification, and stn as the genus-level reference gene for Salmonella. By comparing S. Pullorum to S. Gallinarum and other serovars of Salmonella, in silico study revealed that only the former has a deletion of 126 bp-region in the carboxyl terminus of torT. The I137_14430 gene does not exist in S. Gallinarum. However, it is present in all other Salmonella serotypes. The multiplex PCR approach utilizes unique sets of primers that are intended to specifically target these three different genes. The established PCR method was capable of distinguishing between the biovars Pullorum and Gallinarum from the 29 distinct Salmonella serotypes as well as the 50 distinct pathogens that are not Salmonella, showing excellent specificity and exclusivity. The minimal amount of bacterial cells required for PCR detection was 100 CFU, while the lowest level of genomic DNA required was 27.5 pg/μL for both S. Pullorum and S. Gallinarum. After being implemented on the clinical Salmonella isolates collected from a poultry farm, the PCR test was capable of distinguishing the two biovars Pullorum and Gallinarum from the other Salmonella strains. The findings of the PCR assay were in line with those of the traditional serotyping and biochemical identification methods. This new multiplex PCR could be used as a novel tool to reinforce the clinical diagnosis and differentiation of S. Pullorum and S. Gallinarum, particularly in high-throughput screening situations, providing the opportunity for early screening of infections and, as a result, more effective management of the illness among flocks.
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Affiliation(s)
- Li Song
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, China
| | - Ruimeng Tan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, China
| | - Dan Xiong
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, China
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, China
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Bogdan I, Reddyreddy AR, Nelluri A, Maganti RK, Bratosin F, Fericean RM, Dumitru C, Barata PI, Tapalaga G, Marincu I. Fungal Infections Identified with Multiplex PCR in Severe COVID-19 Patients during Six Pandemic Waves. Medicina (Kaunas) 2023; 59:1253. [PMID: 37512065 PMCID: PMC10385930 DOI: 10.3390/medicina59071253] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/10/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023]
Abstract
Background and Objectives: With an increasing number of severe COVID-19 cases presenting with secondary fungal infections, this study aimed to determine the prevalence of fungal co-infections in severe COVID-19 patients across the six waves, identify the most common fungal pathogens associated with severe COVID-19, and explore any potential links between patient characteristics, therapeutic strategies, and the prevalence and type of fungal infection. Materials and Methods: A retrospective analysis was conducted on severe COVID-19 patients admitted to the Infectious Diseases and Pulmonology Hospital, "Victor Babes", Romania, between March 2020 and August 2022. Samples were collected from respiratory specimens, blood, and urine, after which a standard nucleic acid extraction protocol was employed. Patients were divided into groups with and without fungal infections, identified using multiplex PCR. The groups were compared based on demographic data, comorbidities, pandemic wave number, and clinical outcomes. Results: Out of 288 patients, 96 (33.3%) had fungal infections, with Candida spp. being the most common. Patients with fungal infections had higher rates of obesity (35.4% vs. 21.4%, p = 0.010) and a higher Charlson comorbidity index (CCI > 2) (37.5% vs 25.0%, p = 0.027). Ventilator use was significantly higher in the fungal infection group (45.8% vs. 18.8%; p < 0.001), as was ICU admission (39.6% vs. 26.6%; p = 0.024) and mortality (32.3% vs 12.0%; p < 0.001). The distribution of different fungal species varied across the pandemic waves, with no statistical significance (p = 0.209). The mortality risk notably increased with the degree of drug resistance (OR for three or more drug resistances = 6.71, p < 0.001). The second, fourth, and fifth pandemic waves were significantly associated with higher mortality risk (OR = 3.72, 3.61, and 4.08, respectively, all p < 0.001). Aspergillus spp. and Mucor spp. infections were significantly associated with increased mortality risk (OR = 4.61 and 6.08, respectively, both p < 0.001). Conclusions: Our study indicates a significant presence of fungal co-infections among severe COVID-19 patients that is associated with increased morbidity and mortality, particularly in patients with drug-resistant infections. These findings underline the necessity for comprehensive diagnostic approaches and tailored treatment strategies in managing COVID-19 patients, especially during specific pandemic waves and in patients with particular fungal infections. Further research is required to understand the implications of these co-infections and their management.
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Affiliation(s)
- Iulia Bogdan
- Department XIII, Discipline of Infectious Diseases, "Victor Babes" University of Medicine and Pharmacy, 300041 Timisoara, Romania
- Doctoral School, "Victor Babes" University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | | | - Aditya Nelluri
- School of General Medicine, Sri Siddhartha Medical College, Tumakuru 572107, India
| | - Ram Kiran Maganti
- School of General Medicine, Sri Devaraj Urs Academy of Higher Education and Research, Kolar 563101, India
| | - Felix Bratosin
- Department XIII, Discipline of Infectious Diseases, "Victor Babes" University of Medicine and Pharmacy, 300041 Timisoara, Romania
- Doctoral School, "Victor Babes" University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Roxana Manuela Fericean
- Doctoral School, "Victor Babes" University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Catalin Dumitru
- Department of Obstetrics and Gynecology, "Victor Babes" University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Paula Irina Barata
- Department of Physiology, Faculty of Medicine, "Vasile Goldis" Western University of Arad, 310025 Arad, Romania
- Center for Research and Innovation in Precision Medicine of Respiratory Diseases, "Victor Babes" University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Gianina Tapalaga
- Department of Odontotherapy and Endodontics, Faculty of Dental Medicine, "Victor Babes" University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Iosif Marincu
- Department XIII, Discipline of Infectious Diseases, "Victor Babes" University of Medicine and Pharmacy, 300041 Timisoara, Romania
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Richarme C, Pavese P, Rubens-Duval B, Seurat O, Le Marechal M, Boisset S. Diagnostic performances and therapeutic impact of the Unyvero Implant and Tissue Infection multiplex PCR in periprosthetic joint infections. Future Microbiol 2023; 18:723-734. [PMID: 37526180 DOI: 10.2217/fmb-2022-0245] [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] [Indexed: 08/02/2023] Open
Abstract
Aim: We evaluated the diagnostic performances of Unyvero Implant and Tissue Infection multiplex PCR (mPCR) (Curetis) and the clinical impact of this PCR on therapeutic decisions. Materials & methods: A mPCR was performed on 33 joint fluids in addition to standard culture. A group of experts analyzed a posteriori the impact of the mPCR in the patient management. Results: The rate of concordance with culture was 74% (20/27). The sensitivity of the PCR was 59% and the specificity 90%. Clinicians would have started an appropriate treatment sooner for six patients (from 2 to 22 days earlier). Conclusion: The PCR would improve the management of 22% of the patients. For other patients, mPCR results have to be completed with the culture.
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Affiliation(s)
- Claire Richarme
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
| | - Patricia Pavese
- Service de maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
| | - Brice Rubens-Duval
- Service de chirurgie orthopédique et de traumatologie du sport, Hôpital Sud, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
| | - Olivier Seurat
- Service de chirurgie orthopédique et traumatologique, Hôpital Nord, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
| | - Marion Le Marechal
- Service de maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
| | - Sandrine Boisset
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, 38044, France
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