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Wales SQ, Pandiscia A, Kulka M, Sanchez G, Randazzo W. Challenges for estimating human norovirus infectivity by viability RT-qPCR as compared to replication in human intestinal enteroids. Int J Food Microbiol 2024; 411:110507. [PMID: 38043474 DOI: 10.1016/j.ijfoodmicro.2023.110507] [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: 08/22/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Viability RT-qPCR, a molecular detection method combining viability marker pre-treatment with RT-qPCR, has been proposed to infer infectivity of viruses which is particularly relevant for non-culturable viruses or sophisticated cell culture systems. Being human noroviruses (HuNoV) most frequently associated with foodborne outbreaks, this study compared different viability techniques and infectivity in human intestinal enteroids (HIE) to ultimately determine whether the molecular approaches could serve as rapid assays to predict HuNoV inactivation in high-risk food. To this end, the performance of three viability RT-qPCR assays with different intercalating markers ((Viability PCR Crosslinker Kit (CL), propidium monoazide (PMAxx™), and platinum chloride (PtCl4)) in estimating survival of HuNoV exposed to thermal and high pressure (HPP) treatments was compared to replication tested in the HIE cell culture model. A nearly full-length genomic molecular assay coupled with PMAxx™ to infer HuNoV thermal inactivation was also assessed. The experimental design included HuNoV genogroup I.3 [P13], GII.4 Sydney [P16], GII.6 [P7], along with Tulane virus (TV) serving as surrogate. Finally, viability RT-qPCR was tested in HPP-treated strawberry puree, selected as a food matrix with high viral contamination risk. PMAxx™ and CL performed evenly, while PtCl4 affected HuNoV infectivity. Taking all experimental data together, viability RT-qPCR was demonstrated to be an improved method over direct RT-qPCR to estimate viral inactivation at extreme thermal (95 °C) and HPP (450 MPa) exposures, but not under milder conditions as amplification signals were detected. Despite its complexity and limitations, the HIE demonstrated a more robust model than viability RT-qPCR to assess HuNoV infectivity.
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Affiliation(s)
- Samantha Q Wales
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, United States
| | - Annamaria Pandiscia
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain; Department of Veterinary Medicine, University of Bari, Provincial Road to Casamassima Km 3, Bari, Valenzano 70010, Italy
| | - Michael Kulka
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, United States
| | - Gloria Sanchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain.
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Fappani C, Gori M, Bianchi S, Canuti M, Colzani D, Baggieri M, Gioacchini S, D'Ugo E, Tanzi E, Magurano F, Amendola A. Letter to the editor: Further identification of a measles variant displaying mutations impacting molecular diagnostics, Northern Italy, 2024. Euro Surveill 2024; 29:2400079. [PMID: 38362623 PMCID: PMC10986655 DOI: 10.2807/1560-7917.es.2023.29.7.2400079] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 02/17/2024] Open
Affiliation(s)
- Clara Fappani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università Degli Studi di Milano, Milan, Italy
- These authors contributed equally to this work and share first authorship
| | - Maria Gori
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università Degli Studi di Milano, Milan, Italy
- These authors contributed equally to this work and share first authorship
| | - Silvia Bianchi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università Degli Studi di Milano, Milan, Italy
| | - Marta Canuti
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Daniela Colzani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università Degli Studi di Milano, Milan, Italy
| | - Melissa Baggieri
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Silvia Gioacchini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Emilio D'Ugo
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Elisabetta Tanzi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università Degli Studi di Milano, Milan, Italy
| | - Fabio Magurano
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonella Amendola
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università Degli Studi di Milano, Milan, Italy
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Huang C, Solis D, Sahoo MK, Pinsky BA. Assessment of an automated Cytomegalovirus nucleic acid amplification test using clinical plasma, bronchoalveolar lavage, and tissue specimens. J Clin Virol 2023; 168:105582. [PMID: 37788527 DOI: 10.1016/j.jcv.2023.105582] [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: 07/01/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Cytomegalovirus (CMV) causes significant morbidity and mortality in immunocompromised patients, particularly transplant recipients. Quantitation of CMV DNA in peripheral blood is used to monitor prophylactic and pre-emptive approaches to prevent CMV disease, whereas CMV DNA testing of non-plasma specimens may aid in the diagnosis of end-organ disease. METHODS The analytical performance of the FDA-approved Aptima CMV Quant Assay was evaluated using reference CMV (SeraCare) diluted in defibrinated human plasma, as well as negative bronchoalveolar lavage fluid and tissue. Agreement was determined using 100 clinical acid-citrate-dextrose (ACD) plasma specimens, 77 bronchoalveolar lavage (BAL) fluids, and 101 tissues previously tested using artus CMV qPCR. RESULTS Aptima CMV lower limit of detection (LLOD) was 169 IU/mL for ACD plasma, 100 IU/mL for BAL, and 50 IU/mL for tissue. Positive percent agreement (PPA) was 100.0% (50/50; 95% CI: 92.9% - 100.0%) and negative percent agreement (NPA) was 94.0% (47/50; 95% CI: 83.5% - 98.8%) for ACD plasma. Bland-Altman analysis revealed a bias of 0.20 log10 IU/mL (Aptima - artus) with 95% limits of agreement of -0.53 to 0.93. For BAL fluids, PPA was 70.0% (14/20; 95% CI: 45.7% - 88.1%) and NPA was 82.4% (43/51; 95% CI: 69.1% - 91.6%). For tissues, PPA was 90.0% (45/50; 95% CI: 78.2% - 96.7%) and NPA was 94.0% (47/50; 95% CI: 83.5% - 98.8%). CONCLUSIONS The Aptima CMV Quant Assay demonstrates high analytical sensitivity and good overall agreement using clinical plasma and tissue specimens.
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Affiliation(s)
- ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Solis
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Das T, Joseph J, Simunovic MP, Grzybowski A, Chen KJ, Dave VP, Sharma S, Staropoli P, Flynn H. Consensus and controversies in the science of endophthalmitis management: Basic research and clinical perspectives. Prog Retin Eye Res 2023; 97:101218. [PMID: 37838286 DOI: 10.1016/j.preteyeres.2023.101218] [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: 07/25/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023]
Abstract
Infectious endophthalmitis is a severe intraocular infection caused by bacteria, or less commonly by fungi. It can occur after penetrating eye procedures, trauma, or the spread of infection from contiguous structures or via emboli from distant organs. Because of the time-critical nature of the treatment, endophthalmitis is treated with the clinical diagnosis and modified by the microbiological report of the intraocular contents. The current strategy for managing endophthalmitis relies on pre-clinical literature, case series, and one large multi-center randomized clinical trial on post-cataract surgery endophthalmitis. Culture-susceptibility of the microorganisms from undiluted vitreous guides the definitive treatment in non-responsive cases. Strategies to reduce the incidence of endophthalmitis after penetrating eye procedures have been developed concurrently with refined means of treatment. Despite these advances, outcomes remain poor for many patients. Although consensus articles have been published on managing endophthalmitis, treatment patterns vary, and controversies remain. These include (1) the use of newer methods for early and precise microbiological diagnosis; (2) the choice of intravitreal antibiotics; (3) the need for systemic therapy; (4) early and complete vitrectomy. Here, we review the current consensus and address controversies in diagnosing and managing endophthalmitis. This review is intended to familiarize physicians and ophthalmologists with different aspects of endophthalmitis management to make informed decisions.
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Affiliation(s)
- Taraprasad Das
- Anant Bajaj Retina Institute, Srimati Kanuri Santhamma Centre for Vitreoretinal Disease, L V, Prasad Eye Institute, Hyderabad, India.
| | - Joveeta Joseph
- Jhaveri Microbiology Center, L V Prasad Eye Institute, Hyderabad, India.
| | - Matthew P Simunovic
- Save Sight Institute, University of Sydney, NSW, 2006, Australia; Sydney Eye Hospital, 8 Macquarie St., Sydney, NSW, 2000, Australia.
| | - Andrzej Grzybowski
- Institute for Research in Ophthalmology, Foundation for Ophthalmology Development, Poznan, Poland.
| | - Kuan-Jen Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Vivek Pravin Dave
- Anant Bajaj Retina Institute, Srimati Kanuri Santhamma Centre for Vitreoretinal Disease, L V Prasad Eye Institute, Hyderabad, India.
| | - Savitri Sharma
- Jhaveri Microbiology Center, L V Prasad Eye Institute, Hyderabad, India.
| | - Patrick Staropoli
- Anant Bajaj Retina Institute, Srimati Kanuri Santhamma Centre for Vitreoretinal Disease, L V Prasad Eye Institute, Hyderabad, India.
| | - Harry Flynn
- Bascom Palmer Eye Institute, Miami, FL, USA.
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Panizzolo M, Gea M, Carraro E, Gilli G, Bonetta S, Pignata C. Occurrence of human pathogenic viruses in drinking water and in its sources: A review. J Environ Sci (China) 2023; 132:145-161. [PMID: 37336605 DOI: 10.1016/j.jes.2022.07.035] [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: 02/22/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 06/21/2023]
Abstract
Since many waterborne diseases are caused by human pathogenic viruses, virus monitoring of drinking water (DW) and DW sources is crucial for public health. Therefore, the aim of this review was to describe the occurrence of human pathogenic viruses in DW and DW sources; the occurrence of two viruses proposed as novel indicators of human faecal contamination (Pepper mild mottle virus and Tobacco mosaic virus) was also reported. This research was focused on articles that assessed viral occurrence using molecular methods in the surface water used for DW production (SW-D), groundwater used for DW production (GW-D), DW and bottled-DW (BW). A total of 1544 studies published in the last 10 years were analysed, and 79 were ultimately included. In considering the detection methods, filtration is the most common concentration technique, while quantitative polymerase chain reaction is the most common quantification technique. Regarding virus occurrence in SW-D, GW-D, and DW, high percentages of positive samples were reported for adenovirus, polyomavirus and Pepper mild mottle virus. Viral genomes were frequently detected in SW-D and rarely in GW-D, suggesting that GW-D may be a safe DW source. Viral genomes were also detected in DW, posing a possible threat to human health. The lowest percentages of positive samples were found in Europe, while the highest were found in Asia and South America. Only three articles assessed viral occurrence in BW. This review highlights the lack of method standardization and the need for legislation updates.
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Affiliation(s)
- Marco Panizzolo
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126, Torino, Italy
| | - Marta Gea
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126, Torino, Italy.
| | - Elisabetta Carraro
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126, Torino, Italy
| | - Giorgio Gilli
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126, Torino, Italy
| | - Silvia Bonetta
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123, Torino, Italy
| | - Cristina Pignata
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126, Torino, Italy
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Köffer J, Frontzek A, Eigner U. Development and validation of a bacterial gastrointestinal multiplex RT-PCR assay for use on a fully automated molecular system. J Microbiol Methods 2023; 210:106754. [PMID: 37263528 DOI: 10.1016/j.mimet.2023.106754] [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: 04/04/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/03/2023]
Abstract
PCR-based enteric multiplex panels represent a rapid and reliable alternative to conventional "classical" phenotypic stool diagnostics. The aim of this study was to establish a laboratory-developed non-commercial multiplex Real-Time-PCR panel for the detection of the most important bacterial stool pathogens, Salmonella spp., Shigella spp., Yersinia enterocolitica/ pseudotuberculosis and Campylobacter jejuni/coli. on the "open" cobas omni Utility Channel (UC) of the cobas 6800 system (Roche). The aim was to replace the laborious phenotypical stool diagnostics with a high throughput Real-Time PCR method. The respective primers and probes were designed to cover conserved genomic regions of the pathogens and validated using Ultramer oligonucleotides, positive stool material and reference strains. To further validate the multiplex PCR-assay, the following parameters were evaluated: analytical-sensitivity and -specificity, cross-reactivity, linearity and inter- and intra-assay variance as well as limit of detection (LOD). In addition a retrospective analysis of culture positive and negative samples from daily routine was performed using 745 native stool samples. The Gastro assay was linear over a 5-log-unit and within the expected dynamic range with amplification efficiencies ranging from 94.6% to 120%. In addition, all targets showed excellent coefficients of repeatability (≤ 1.11%), intermediate precision (≤ 1.02%) and total variance (≤ 1.39%). In terms of analytical sensitivity the assay demonstrated detection limits ranging from 7.83 copies per reaction to 14.4 copies per reaction. The assay showed excellent agreement with culture methods (>95%) and a 100% sensitivity and specificity after resolution of discrepant results. The multiplex-PCR assay provides a comprehensive, rapid and sensitive alternative to conventional methods for the detection of the major bacterial stool pathogens in diagnostic laboratories.
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Affiliation(s)
| | - André Frontzek
- Roche Diagnostics (formerly, during study: Labor Stein, Mönchengladbach, Germany), Mannheim, Germany
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Hashemzadeh M, Dezfuli AA, Khosravi AD, Bandbal MM, Ghorbani A, Hamed M, Dezfuli SK. Molecular identification of non-tuberculous mycobacterial species isolated from extrapulmonary samples using real-time PCR and rpoB sequence analysis. AMB Express 2023; 13:43. [PMID: 37147556 PMCID: PMC10163175 DOI: 10.1186/s13568-023-01553-8] [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: 01/17/2023] [Accepted: 04/25/2023] [Indexed: 05/07/2023] Open
Abstract
Tuberculosis (TB) is one of the leading causes of mortality among infectious diseases and accounts for a serious health hazard wordwide. Apart from TB, the members of non-tuberculous mycobacteria (NTM), which includes around 170 species, may also cause different diseases in humans. Therefore this study aimed to investigate the distribution of NTM strains isolated from extrapulmonary (EP) samples by Real-Time PCR and PCR-sequencing methods in Southwest Iran. Three hundred and twenty-five suspected EP samples were collected from patients referred to the referral hospitals in Ahvaz, Iran. The isolates were initially screened by acid fast staining and identified by phenotypic culture and biochemical tests. The Real-Time PCR and rpoB- based PCR methods were performed followed by sequence analysis of rpoB gene. From 124 samples, 77 (62%) were positive for NTM by culture and rpoB sequence analysis. M. fortuitum was the most commonly isolated NTM in present study. In Real-Time PCR, only 69 (55.64%) isolates showed more homology with standard NTM isolates. In general, the growing trend of EPNTM infections in Iran needs specific programs and resources to get a better diagnosis. PCR sequencing is a reliable method, it can be used for definitive identification of positive cultures for identification of NTM species.
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Affiliation(s)
- Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Aram Asarehzadegan Dezfuli
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Maryam Moradi Bandbal
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Atousa Ghorbani
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahtab Hamed
- Immunobiology Center of Pasteur Medical Laboratory, Ahvaz, Iran
| | - Soolmaz Khandan Dezfuli
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Patrizio L, Elisabetta B, Annamaria P, Giancarlo B, Roberta P, Alessio M, Valentina T. Epidemiological and genetic evaluation of HEV in swine slaughtered in Sicily region (Italy). Int J Food Microbiol 2023; 388:110068. [PMID: 36623337 DOI: 10.1016/j.ijfoodmicro.2022.110068] [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: 08/24/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023]
Abstract
Hepatitis E virus (HEV) is the etiological agent of acute viral hepatitis, a disease transmitted by the oral-faecal route. In Europe, zoonotic transmission of HEV-3 genotype is associated with the consumption of raw or slightly cooked meat of pigs and wild boars that are considered the main reservoirs. This work aims to assess the occurrence of swines' HEV RNA liver samples and rectal swabs slaughtered in Sicily using biomolecular methods. HEV-RNA was detected in 17.5 % (21/120) liver samples analyzed and in 3.7 % (3/81) rectal swabs examined. All positive samples were predicted as genotype 3 and subtype 3c (75 %). These data suggest a potential HEV transmission to humans through close contact with pig breeders, veterinarians, slaughterhouse personnel, and pork meat product consumption. Moreover, there are few scientific data evaluating the HEV spread around pigs and humans in Sicily. Therefore, further studies are necessary to correlate humans with swine serotypes and to assess the HEV presence and persistence in food and the risk during the slaughtering process. These surveys allow to clarify the role of the swine species as a potential source of infection for other domestic or wild animals and humans and to establish possible control measures throughout the food chain.
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Affiliation(s)
- Lorusso Patrizio
- Department of Veterinary Medicine- University of Bari, Provincial Road to Casamassima Km 3, 70010 Valenzano, Bari, Italy
| | - Bonerba Elisabetta
- Department of Veterinary Medicine- University of Bari, Provincial Road to Casamassima Km 3, 70010 Valenzano, Bari, Italy
| | - Pandiscia Annamaria
- Department of Veterinary Medicine- University of Bari, Provincial Road to Casamassima Km 3, 70010 Valenzano, Bari, Italy.
| | - Bozzo Giancarlo
- Department of Veterinary Medicine- University of Bari, Provincial Road to Casamassima Km 3, 70010 Valenzano, Bari, Italy
| | - Piredda Roberta
- Department of Veterinary Medicine- University of Bari, Provincial Road to Casamassima Km 3, 70010 Valenzano, Bari, Italy
| | - Manfredi Alessio
- Department of Veterinary Medicine- University of Bari, Provincial Road to Casamassima Km 3, 70010 Valenzano, Bari, Italy
| | - Terio Valentina
- Department of Veterinary Medicine- University of Bari, Provincial Road to Casamassima Km 3, 70010 Valenzano, Bari, Italy
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Pang F, Long Q. Recent advances in diagnostic approaches for orf virus. Appl Microbiol Biotechnol 2023; 107:1515-23. [PMID: 36723701 DOI: 10.1007/s00253-023-12412-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/02/2023]
Abstract
Orf virus (ORFV), the prototype species of the Parapoxvirus genus, is an important zoonotic virus, causing great economic losses in livestock production. At present, there are no effective drugs for orf treatment. Therefore, it is crucial to develop accurate and rapid diagnostic approaches for ORFV. Over decades, various diagnostic methods have been established, including conventional methods such as virus isolation and electron microscopy; serological methods such as virus neutralization test (VNT), immunohistochemistry (IHC) assay, immunofluorescence assay (IFA), and enzyme-linked immunosorbent assay (ELISA); and molecular methods such as polymerase chain reaction (PCR), real-time PCR, loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and recombinase-aided amplification (RAA) assay. This review provides an overview of currently available diagnostic approaches for ORFV and discusses their advantages and limitations and future perspectives, which would be significantly helpful for ORFV early diagnosis and surveillance to prevent outbreak of orf. KEY POINTS: • Orf virus emerged and reemerged in past years • Rapid and efficient diagnostic approaches are needed and critical for ORFV detection • Novel and sensitive diagnostic methods are required for ORFV detection.
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Razak NA, Masood I, Baneen U, Ahmad Z, Shamsi H. Eliminate TB by 2025? A case report of MDR TB to reaffirm the need of follow UP! Indian J Tuberc 2023; 70:134-138. [PMID: 36740311 DOI: 10.1016/j.ijtb.2022.05.002] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/30/2022] [Accepted: 05/16/2022] [Indexed: 02/07/2023]
Affiliation(s)
- Nader Abdul Razak
- Department of Tuberculosis & Respiratory Diseases, Jawaharlal Nehru Medical College, Aligarh Muslim University, India.
| | - Imrana Masood
- Department of Tuberculosis & Respiratory Diseases, Jawaharlal Nehru Medical College, Aligarh Muslim University, India
| | - Ummul Baneen
- Department of Tuberculosis & Respiratory Diseases, Jawaharlal Nehru Medical College, Aligarh Muslim University, India
| | - Zuber Ahmad
- Department of Tuberculosis & Respiratory Diseases, Jawaharlal Nehru Medical College, Aligarh Muslim University, India
| | - Hassan Shamsi
- Department of Tuberculosis & Respiratory Diseases, Jawaharlal Nehru Medical College, Aligarh Muslim University, India
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Salari S, Taghdiri A, Bamorovat M, Sharifi I, Ghasemi Nejad Almani P. A novel rapid LAMP test for identification of cutaneous leishmaniasis: An evaluation and comparative analysis of three molecular methods. Microb Pathog 2022;:105612. [PMID: 35660477 DOI: 10.1016/j.micpath.2022.105612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022]
Abstract
Leishmaniasis is a neglected and widespread parasitic disease that can lead to serious health problems. The conventional method in diagnostic health clinics is direct smear preparation of the lesion and staining with standard Giemsa to visualize the amastigote stage and by culturing the organism in an NNN (Novy-MacNeal-Nicolle) to observe the promastigote form of the parasite. In the case of urban-type leishmaniasis, microscopic diagnosis is sometimes not possible due to the reduction of amastigotes in patients' wounds. Because most endemic areas are located in regions that do not have access to laboratories equipped with molecular tools, access to a rapid test to diagnose the disease is essential. In this study, for the first time for DNA extraction, the scalpel used for sampling was washed and extracted by boiling method. Also, the LAMP technique in this study was modified so that the test can be performed in 10 minutes and the results can be recognized by color. We used four microscopic methods, conventional PCR, real-time PCR, and LAMP, to diagnose urban-type leishmaniasis and compared the results of these methods with each other. The sensitivity and specificity of LAMP were higher than other techniques used. Therefore, it allows rapid diagnosis for timely treatment of the disease to control the primary reservoir host more quickly in ACL as humans are the principal source of infection. This test is performed at a high-speed and is cost-effective. For its convenience, this test is highly recommended to be used in endemic areas.
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Tang B, Xu K, Liu Y, Zhou Z, Karthi S, Yang H, Li C. A review of physiological resistance to insecticide stress in Nilaparvata lugens. 3 Biotech 2022; 12:84. [PMID: 35251886 PMCID: PMC8882538 DOI: 10.1007/s13205-022-03137-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/02/2022] [Indexed: 01/02/2023] Open
Abstract
Insecticides are widely used in agriculture as effective means to control pests. However, pests have not been completely mitigated with the increased use of insecticides. Instead, many side effects have arisen, especially the '3Rs' (resistance, resurgence, and residue). The brown planthopper, Nilaparvata lugens, is one of the most threatening rice pests. The main insecticides for controlling N. lugens belong to organochlorine, organophosphorus, carbamate, neonicotinoid and pyrethroid groups. However, metabolic enzymes, including cytochrome P450s, esterases, glutathione-S-transferases, and ATP-binding cassette transporters, effectively promote the detoxification of insecticides. Besides, mutations of neurological target sites, such as acetylcholinesterase, nicotinic acetylcholine, γ-aminobutyric acid receptor, and ryanodine receptor, result in insensitivity to insecticides. Here, we review the physiological metabolic resistance in N. lugens under insecticide stress to provide a theoretical basis for identifying and developing more effective and harmless insecticides.
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Affiliation(s)
- Bin Tang
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, 550005 People’s Republic of China ,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121 Zhejiang People’s Republic of China
| | - Kangkang Xu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, 550005 People’s Republic of China ,Institute of Entomology, Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Guizhou University, Guiyang, 550025 People’s Republic of China
| | - Yongkang Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121 Zhejiang People’s Republic of China
| | - Zhongshi Zhou
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, 550005 People’s Republic of China
| | - Sengodan Karthi
- Division of Biopesticides and Environmental Toxicology, Sri Paramakalyani Centre for Excellence in Environmental Sciences, Manonmaniam Sundaranar University, Alwarkurichi, Tirunelveli, Tamil Nadu 627 412 India
| | - Hong Yang
- Institute of Entomology, Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Guizhou University, Guiyang, 550025 People’s Republic of China
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, 550005 People’s Republic of China
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Eroglu F, Dokur M, Ulu Y. The Molecular Epidemiology of Cystic and Alveolar Echinococcosis in Southeast Turkey. Iran J Parasitol 2021; 16:327-335. [PMID: 34557249 PMCID: PMC8418644 DOI: 10.18502/ijpa.v16i2.6284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/25/2020] [Indexed: 11/24/2022]
Abstract
Background The migration of humans and climatic and environmental changes cause the emergence of infectious diseases. This study aimed to investigate the changes in the molecular epidemiology of the echinococcosis in the southeast region of Turkey after migrations. Methods Overall, 159 tissues samples were taken from suspected cases of echinococcosis at the Kilis State Hospital in the southeast region of Turkey. All of the tissues samples were analyzed using histopathology methods, PCR, Real-time PCR methods, DNA sequencing, and phylogenetic analyses in laboratories. Results The positivity values of the histopathology, the polymerase chain reaction, and the Real-time PCR methods were found to be 14.5% (23/159),15.7% (25/159), and 16.9% (27/159), respectively. 32.0 % (8/25) E. multilocularis of Echinococcus isolates and 68% (17/25) E. granulosus of Echinococcus isolates were identified using PCR methods. 58.8% (10/17) of the E. granulosus isolates were found to be Genotype 1% and 41.2% (7/17) E. granulosus isolates were found to be Genotype 3. Conclusion Molecular methods play an important role in the epidemiology, treatment, and diagnosis of diseases. Increasing immigration in a geographical area may create social, economic, and health problems in that area. For this reason, epidemiological studies of infectious diseases should be updated in areas with immigration.
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Affiliation(s)
- Fadime Eroglu
- Department of Parasitology, Faculty of Medicine, Aksaray University, Aksaray, Turkey.,FaBiyosit Microbiology-Biotechnology R&D Co., Adana, Turkey
| | - Mehmet Dokur
- Department of Emergency, Biruni University, Istanbul, Turkey
| | - Yüksel Ulu
- Department of Medical Pathology, Kilis State Hospital, Kilis, Turkey.,Department of Medical Pathology, Istanbul Basaksehir Cam and Sakura City Hospital, Istabul, Turkey
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14
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Ciesielski M, Blackwood D, Clerkin T, Gonzalez R, Thompson H, Larson A, Noble R. Assessing sensitivity and reproducibility of RT-ddPCR and RT-qPCR for the quantification of SARS-CoV-2 in wastewater. J Virol Methods 2021; 297:114230. [PMID: 34252511 DOI: 10.1016/j.jviromet.2021.114230] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/29/2022]
Abstract
Throughout the COVID-19 global pandemic there has been significant interest and investment in using Wastewater-Based Epidemiology (WBE) for surveillance of viral pathogen presence and infections at the community level. There has been a push for widescale implementation of standardized protocols to quantify viral loads in a range of wastewater systems. To address concerns regarding sensitivity, limits of quantification, and large-scale reproducibility, a comparison of two similar workflows using RT-qPCR and RT-ddPCR was conducted. Sixty raw wastewater influent samples were acquired from nine distinct wastewater treatment plants (WWTP’s) served by the Hampton Roads Sanitation District (HRSD, Virginia Beach, Virginia) over a 6-month period beginning March 9th, 2020. Common reagents, controls, master mixes and nucleic acid extracts were shared between two individual processing groups based out of HRSD and the UNC Chapel Hill Institute of Marine Sciences (IMS, Morehead City, North Carolina). Samples were analyzed in parallel using One-Step RT-qPCR and One-Step RT-ddPCR with Nucleocapsid Protein 2 (N2) specific primers and probe. Influent SARS-CoV-2 N2 concentrations steadily increased over time spanning a range from non-detectable to 2.13E + 05 copies/L. Systematic dilution of the extracts indicated that inhibitory components in the wastewater matrices did not significantly impede the detection of a positive N2 signal for either workflow. The RT-ddPCR workflow had a greater analytical sensitivity with a lower Limit of Detection (LOD) at 0.066 copies/μl of template compared to RT-qPCR with a calculated LOD of 12.0 copies/μL of template. Interlaboratory comparisons using non-parametric correlation analysis demonstrated that there was a strong, significant, positive correlation between split extracts when employing RT-ddPCR for analysis with a ρ value of 0.86.
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15
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Franklin AM, Brinkman NE, Jahne MA, Keely SP. Twenty-first century molecular methods for analyzing antimicrobial resistance in surface waters to support One Health assessments. J Microbiol Methods 2021; 184:106174. [PMID: 33774111 DOI: 10.1016/j.mimet.2021.106174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 02/03/2021] [Accepted: 02/17/2021] [Indexed: 12/26/2022]
Abstract
Antimicrobial resistance (AMR) in the environment is a growing global health concern, especially the dissemination of AMR into surface waters due to human and agricultural inputs. Within recent years, research has focused on trying to understand the impact of AMR in surface waters on human, agricultural and ecological health (One Health). While surface water quality assessments and surveillance of AMR have historically utilized culture-based methods, culturing bacteria has limitations due to difficulty in isolating environmental bacteria and the need for a priori information about the bacteria for selective isolation. The use of molecular techniques to analyze AMR at the genetic level has helped to overcome the difficulties with culture-based techniques since they do not require advance knowledge of the bacterial population and can analyze uncultivable environmental bacteria. The aim of this review is to provide an overview of common contemporary molecular methods available for analyzing AMR in surface waters, which include high throughput real-time polymerase chain reaction (HT-qPCR), metagenomics, and whole genome sequencing. This review will also feature how these methods may provide information on human and animal health risks. HT-qPCR works at the nanoliter scale, requires only a small amount of DNA, and can analyze numerous gene targets simultaneously, but may lack in analytical sensitivity and the ability to optimize individual assays compared to conventional qPCR. Metagenomics offers more detailed genomic information and taxonomic resolution than PCR by sequencing all the microbial genomes within a sample. Its open format allows for the discovery of new antibiotic resistance genes; however, the quantity of DNA necessary for this technique can be a limiting factor for surface water samples that typically have low numbers of bacteria per sample volume. Whole genome sequencing provides the complete genomic profile of a single environmental isolate and can identify all genetic elements that may confer AMR. However, a main disadvantage of this technique is that it only provides information about one bacterial isolate and is challenging to utilize for community analysis. While these contemporary techniques can quickly provide a vast array of information about AMR in surface waters, one technique does not fully characterize AMR nor its potential risks to human, animal, or ecological health. Rather, a combination of techniques (including both molecular- and culture-based) are necessary to fully understand AMR in surface waters from a One Health perspective.
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Affiliation(s)
- A M Franklin
- Office of Research and Development, Center for Environmental Measurement and Modeling, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA.
| | - N E Brinkman
- Office of Research and Development, Center for Environmental Solutions and Emergency Response, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA
| | - M A Jahne
- Office of Research and Development, Center for Environmental Solutions and Emergency Response, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA
| | - S P Keely
- Office of Research and Development, Center for Environmental Measurement and Modeling, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA
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16
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Dordio AM, Beck R, Nunes T, Pereira da Fonseca I, Gomes J. Molecular survey of vector-borne diseases in two groups of domestic dogs from Lisbon, Portugal. Parasit Vectors 2021; 14:163. [PMID: 33736681 PMCID: PMC7977316 DOI: 10.1186/s13071-021-04650-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Canine vector-borne diseases (CVBDs) are caused by a wide range of pathogens transmitted by arthropods. They have been an issue of growing importance in recent years; however, there is limited information about the vector-borne pathogens circulating in Portugal. The aim of the present study was to detect canine vector-borne bacteria and protozoa of veterinary and zoonotic importance using molecular methods. METHODS One hundred and forty-two dogs from Lisbon, southern Portugal, were tested: 48 dogs from a veterinary hospital clinically suspected of vector-borne diseases and 94 apparently healthy dogs from shelters. Anaplasma spp./Ehrlichia spp., Babesia/Theileria spp., Hepatozoon spp., and Mycoplasma spp. infections were detected by PCR from blood samples and examined under light microscopy. Other information including clinical status and diagnostic test results were collected for each animal. RESULTS Infections were detected by PCR in 48 (33.80%) dogs. Single infections were found in 35 dogs (24.64%), and co-infections were found in 13 (9.15%) dogs. Twenty-nine (20.42%) dogs were positive for Hepatozoon spp., 15 (10.56%) for Mycoplasma spp., 11 (7.75%) for Anaplasma spp./Ehrlichia spp., and six (4.21%) for Babesia spp. DNA sequencing was used to identify Babesia vogeli (2.81%), Babesia canis (1.40%), Hepatozoon canis (20.42%), Mycoplasma haematoparvum (2.11%), Mycoplasma haemocanis (8.45%), Anaplasma platys (7.04%), and Ehrlichia canis (0.70%). CONCLUSIONS This is the first molecular identification of B. canis and M. haematoparvum in dogs from southern Portugal. This study highlights the importance of molecular methods to identify CVBD pathogens in endemic areas and helps to guide the clinical approach of veterinarians in practice.
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Affiliation(s)
- Ana Mafalda Dordio
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Universidade de Lisboa, Lisbon, Portugal.
| | - Relja Beck
- Croatia Veterinary Institute, Zagreb, Croatia
| | - Telmo Nunes
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Pereira da Fonseca
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Universidade de Lisboa, Lisbon, Portugal
| | - Jacinto Gomes
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Universidade de Lisboa, Lisbon, Portugal.,Instituto Nacional de Investigação Agrária e Veterinária, Oeiras, Portugal
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Broadhurst MJ, Garamani N, Hahn Z, Jiang B, Weber J, Huang C, Sahoo MK, Kurzer J, Hogan CA, Pinsky BA. Evaluation of a measles virus multiplex, triple-target real-time RT-PCR in three specimen matrices at a U.S. academic medical center. J Clin Virol 2021; 136:104757. [PMID: 33639409 DOI: 10.1016/j.jcv.2021.104757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/24/2021] [Accepted: 02/03/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Measles virus (MeV) is an important cause of acute febrile illness and pediatric mortality globally, with recent U.S. outbreaks associated with under-vaccination. MeV is highly contagious and timely diagnosis is critical to limit spread. RNA detection is the most sensitive method for acute measles diagnosis; however, MeV nucleic acid amplification assays are not widely available. METHODS We performed a diagnostic accuracy study of a triple-target, real-time RT-PCR (rRT-PCR) assay for simultaneous detection of MeV N, H, and L genes. RESULTS The MeV triple-target rRT-PCR was tested against serial dilutions (7.0-2.0 log10 copies/mL) of five MeV isolates representing circulating genotypes, and detected 98.7% (74/75) of nasopharyngeal (NP) swab dilutions, 100% (75/75) of plasma dilutions, and 85.3% (64/75) of urine dilutions. MeV RNA detection in urine was markedly improved with the addition of a nucleic acid stabilizing agent. A 95% lower limit of detection (LLOD) of < 3.0 log10 copies/mL was established in each specimen matrix. No cross-reactivity with relevant viruses or interfering substances were identified in specificity studies. The MeV triple-target rRT-PCR detected all three gene targets in a clinical NP swab from an individual with confirmed measles infection. Furthermore, pooled testing from 798 influenza A/B/RSV-negative pediatric NP swabs identified two specimens positive for MeV RNA, confirmed by N gene sequencing to represent shedding of the vaccine-type measles virus. CONCLUSIONS The MeV triple-target rRT-PCR assay showed high analytic sensitivity across circulating MeV genotypes in three clinically-relevant matrices. Implementation of this assay in the clinical laboratory may facilitate timely diagnosis of acute measles infection and implementation of appropriate infection control interventions.
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Affiliation(s)
- M Jana Broadhurst
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Natasha Garamani
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Zoe Hahn
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Becky Jiang
- Clinical Virology Laboratory, Stanford Health Care, California, United States
| | - Jenna Weber
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Jason Kurzer
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States; Clinical Virology Laboratory, Stanford Health Care, California, United States
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States; Clinical Virology Laboratory, Stanford Health Care, California, United States; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States.
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18
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Aylagas E, Borja A, Pochon X, Zaiko A, Keeley N, Bruce K, Hong P, Ruiz GM, Stein ED, Theroux S, Geraldi N, Ortega A, Gajdzik L, Coker DJ, Katan Y, Hikmawan T, Saleem A, Alamer S, Jones BH, Duarte CM, Pearman J, Carvalho S. Translational Molecular Ecology in practice: Linking DNA-based methods to actionable marine environmental management. Sci Total Environ 2020; 744:140780. [PMID: 32693276 DOI: 10.1016/j.scitotenv.2020.140780] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Molecular-based approaches can provide timely biodiversity assessments, showing an immense potential to facilitate decision-making in marine environmental management. However, the uptake of molecular data into environmental policy remains minimal. Here, we showcase a selection of local to global scale studies applying molecular-based methodologies for environmental management at various stages of implementation. Drawing upon lessons learned from these case-studies, we provide a roadmap to facilitate applications of DNA-based methods to marine policies and to overcome the existing challenges. The main impediment identified is the need for standardized protocols to guarantee data comparison across spatial and temporal scales. Adoption of Translational Molecular Ecology - the sustained collaboration between molecular ecologists and stakeholders, will enhance consensus with regards to the objectives, methods, and outcomes of environmental management projects. Establishing a sustained dialogue among stakeholders is key to accelerating the adoption of molecular-based approaches for marine monitoring and assessment.
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Affiliation(s)
- Eva Aylagas
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Angel Borja
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia, Portualdea s/n, 20110 Pasaia, Spain
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Nigel Keeley
- Benthic Resources and Processors Group, Institute of Marine Research, Postboks 6606 Langnes, 9296 Tromsø, Norway
| | - Kat Bruce
- Nature Metrics Ltd, CABI site, Bakeham Lane, Egham TW20 9TY, United Kingdom
| | - Peiying Hong
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD 21037, USA; Aquatic Bioinvasion Research and Policy Institute, Environmental Science and Management, Portland State University, Portland, OR 97201, USA
| | - Eric D Stein
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, CA 92626-1437, USA
| | - Susanna Theroux
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, CA 92626-1437, USA
| | - Nathan Geraldi
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alejandra Ortega
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Laura Gajdzik
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Darren J Coker
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yasser Katan
- Environmental Protection Department, Saudi Aramco, Dhahran 3131, Saudi Arabia
| | - Tyas Hikmawan
- Environmental Protection Department, Saudi Aramco, Dhahran 3131, Saudi Arabia
| | - Ammar Saleem
- The General Authority of Meteorology and Environmental Protection, The Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Sultan Alamer
- The General Authority of Meteorology and Environmental Protection, The Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Burton H Jones
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - John Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Lafeuille E, Jauréguiberry S, Devriese F, Sadowski E, Fourniols E, Aubry A; CRIOAC Pitié-Salpêtrière. First evaluation of the automated-multiplex-PCR Unyvero ITI G2 cartridge for rapid diagnosis of osteo-articular infections. Infect Dis Now 2021; 51:179-86. [PMID: 33010353 DOI: 10.1016/j.medmal.2020.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/28/2020] [Accepted: 09/24/2020] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Conventional microbiological methods (CMM), including long-term culture, for the diagnosis of osteo-articular infections (OAI) fail in at least 5% of all cases. Only one IOA dedicated molecular method has been commercialized, and only the first version of this kit has been studied. The aim of this work was to evaluate the concordance between test results obtained with the second version of the Unyvero ITI G2 cartridge (Curetis) and CMM. The cartridge, combining one-step automated lysis/DNA extraction with multiplex PCR and amplicon detection by array hybridization, allows for the detection of 102 prevalent pathogens and their antibiotic resistance markers directly in clinical specimens (liquid [n=8] or solid [n=32]). MATERIAL AND METHODS Frozen samples from 40 patients who underwent orthopedic surgery at Pitié-Salpêtrière hospital were tested retrospectively with the cartridge: 5 were culture-negative, 25 revealed monomicrobial and 10 polymicrobial OAI. The 2 main surgical sites were hip (22.5%) and knee (17.5%). RESULTS Extraction, amplification and hybridization reactions were completed in 28 of the 40 cases, failed in all cartridge chambers in 6 cases, and in 1 or 2 chambers in an additional 6 cases. Overall sensitivity and specificity for microorganism identification were estimated at 67.6% and 98.2%, when complete and partial failures were excluded. CONCLUSIONS These results show that the performances of the second version of the Unyvero ITI G2 cartridge should be further enhanced before considering avoiding conventional microbiological methods.
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Abstract
Rapid advancements in the area of lung cancer therapy were determined by the discovery of molecular markers and the possibility of their therapeutic exploitation. Today's lung cancer diagnosis places high demands on pathologists. In the majority of cases, small tissue samples must suffice for diagnosis and testing of all relevant biomarkers. The minimum panel required for advanced non-small-cell lung carcinoma (NSCLC) with nonsquamous histology includes testing of EGFR, BRAF, ALK, ROS1, and PD-L1-expression. So far, only PD-L1-IHC (immunohistochemistry, IHC) is required for squamous cell carcinoma. If possible, newer biomarkers such as RET, MET, HER2, NTRK, and KRAS should be integrated in test panels. Fluorescence in situ hybridization (FISH) is a well-established molecular method for the detection of chromosomal aberrations, such as ALK-, ROS1-, and RET- translocations and amplifications, such as Her2/neu or MET. The relevance of MET-FISH for the detection of amplifications in the first-line setting is controversial, but of high importance in the recurrent setting. All equivocal or discrepant results should be validated using orthogonal methods. IHC is a suitable, thoroughly validated method for ALK and ROS1 aberration detection with the advantage of quick and cost-efficient test results and tissue conservation. All other translocations, or discrepancy between IHC and FISH, require a sequencing-based confirmation procedure. The low frequency of NTRK fusions, and high sensitivity of NTRK-IHC, suggest using IHC as a prescreening tool with subsequent sequencing-based analysis for IHC positive cases.
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Affiliation(s)
- Lena Hieggelke
- Institut für Pathologie, Uniklinik Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| | - Anne M Schultheis
- Institut für Pathologie, Uniklinik Köln, Kerpener Str. 62, 50937, Köln, Deutschland.
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Firuzi P, Asl Hashemi A, Samadi Kafil H, Gholizadeh P, Aslani H. Comparative study on the microbial quality in the swimming pools disinfected by the ozone-chlorine and chlorine processes in Tabriz, Iran. Environ Monit Assess 2020; 192:516. [PMID: 32666262 DOI: 10.1007/s10661-020-08470-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Applying a desirable disinfestation process is necessary to control the pathogenic microorganisms in the swimming pools and prevent both dermal and intestinal effects. Therefore, the present study was conducted to compare the bacterial community and diversity in the two swimming pools disinfected by the chlorine and ozone (O3)-chlorine processes. A total of 24 samples were taken from the two swimming pools in three distinct seasons to analyze the bacterial and physico-chemical indicators. Culture and molecular methods were used to evaluate the microbial quality. Two sets of sample taken from the pools with the maximum swimmer load in the summer were investigated by the next-generation sequencing (NGS) technique. In total, 410 and 406 bacterial species were identified in the chlorine- and ozone-chlorine-disinfected pools, respectively. Among the eight dominant bacterial species in each swimming pool, Pseudomonas alcaliphila, Pseudomonas stutzeri, and Pseudomonas acnes were common species between the two studied pools. Oleomonas sagaranensis (350 reads/18593), Staphylococcus caprae (302 reads /18593), and Anaerococcus octavius (110 reads/18593) were among the dominant bacteria in the chlorine-disinfected pool. Bacterial diversity was lower in the ozone-chlorine-disinfected pool than the other one, and the highest bacterial sequencing belonged to the genus Pseudomonas (85.79%). Results showed that water quality of in O3-chlorine-disinfected pool was more desirable than the chlorine-disinfected pool. Molecular methods along with conventional culture methods would be advantageous for microbial assessment in the swimming pools.
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Affiliation(s)
- Parisa Firuzi
- Department of Environmental Health Engineering, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Asl Hashemi
- Department of Environmental Health Engineering, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hassan Aslani
- Health and Environment Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Jalali SF, Oodi A, Azarkeivan A, Gudarzi S, Amirizadeh N. Kidd Blood Group Genotyping for Thalassemia Patient in Iran. Indian J Hematol Blood Transfus 2020; 36:550-5. [PMID: 32647431 DOI: 10.1007/s12288-020-01283-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 04/18/2020] [Indexed: 01/26/2023] Open
Abstract
We aimed to determine the JK genotype in thalassemia patients from Iran using different molecular methods to compare with phenotyping results. We also aimed to standardize for the first time, the Tetra-Primer ARMS PCR method for JK genotyping. The serology method cannot correctly determine the phenotype of blood group antigens in patients with multiple blood transfusions. Peripheral blood samples were taken from two hundred alloimmunized thalassemic patients in Tehran Adult Thalassemic Clinic. The samples were tested phenotypically by routine serological methods. After DNA Extraction, SSP-PCR was performed. DNA sequencing and PCR-RFLP were used to confirm the SSP-PCR results. Discrepancies were found between the phenotype and genotype in 32 out of 200 cases. In 16 cases phenotype was determined as Jk (a + b +) but genotype was JK*A/JK*A, in 14 cases phenotype was Jk (a + b +) while the genotype showed JK*B/JK*B, 1 case had been phenotyped as Jk (a + b -) but it was genotyped as JK*A/JK*B and 1 case had been phenotyped as Jk (a - b +) but it was genotyped as JK*A/JK*B. Serological results for a few samples could not be confirmed because of mix-field agglutination. The genotyping however verified the presence of Kidd alleles. Molecular methods are a valuable tool to predict blood group phenotypes in multi-transfused patients in order to select RBC units for a perfect matching improving blood transfusion and preventing alloimmunization. Also Tetra-Primer ARMS PCR is simple and cost effective methods that could be alternative by conventional Molecular methods.
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Sigmund IK, Renz N, Feihl S, Morgenstern C, Cabric S, Trampuz A. Value of multiplex PCR for detection of antimicrobial resistance in samples retrieved from patients with orthopaedic infections. BMC Microbiol 2020; 20:88. [PMID: 32290833 PMCID: PMC7155317 DOI: 10.1186/s12866-020-01741-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 03/03/2020] [Indexed: 11/18/2022] Open
Abstract
Background The performance of multiplex PCR (mPCR) for detection of antimicrobial resistance from clinical isolates is unknown. We assessed the ability of mPCR to analyse resistance genes directly from clinical samples. Patients with orthopedic infections were prospectively included. Phenotypical and genotypical resistance was evaluated in clinical samples (synovial and sonication fluid) where identical pathogens were identified by culture and mPCR. Result A total of 94 samples were analysed, including 60 sonication fluid and 34 synovial fluid samples. For coagulase-negative staphylococcus strains, mPCR detected resistance to oxacillin in 10 of 23 isolates (44%) and to rifampin in none of 6 isolates. For S. aureus isolates, detection rate of oxacillin and rifampin-resistance was 100% (2/2 and 1/1, respectively). Fluoroquinolone-resistance was confirmed by mPCR in all 3 isolates of Enterobacteriaceae, in enterococci resistance to aminoglycoside-high level was detected in 1 of 3 isolates (33%) and in streptococci resistance to macrolides/lincosamides in none of 2 isolates. The overall sensitivity for different pathogens and antimicrobials was 46% and specificity 95%, the median concordance was 80% (range, 57–100%). Full agreement was observed for oxacillin in S. aureus, vancomycin in enterococci, carbapenems/cephalosporins in Enterobacteriaceae and rifampin in Cutibacterium species. Conclusion The overall sensitivity for detection of antimicrobial resistance by mPCR directly from clinical samples was low. False-negative mPCR results occurred mainly in coagulase-negative staphylococci, especially for oxacillin and rifampin. However, the specificity of mPCR was high and a positive result reliably predicted antimicrobial resistance. Including universal primers in the PCR test assay may improve the detection rate but requires additional sequencing step. Trial registration www.clinicaltrials.gov No. NCT02530229, registered at 21 August 2015 (retrospectively registered).
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Affiliation(s)
- Irene Katharina Sigmund
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Center for Musculoskeletal Surgery (CMSC), Charitéplatz 1, 10117, Berlin, Germany.,Department of Orthopaedics and Trauma Surgery, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - Nora Renz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Center for Musculoskeletal Surgery (CMSC), Charitéplatz 1, 10117, Berlin, Germany
| | - Susanne Feihl
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Center for Musculoskeletal Surgery (CMSC), Charitéplatz 1, 10117, Berlin, Germany
| | - Christian Morgenstern
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Center for Musculoskeletal Surgery (CMSC), Charitéplatz 1, 10117, Berlin, Germany
| | - Sabrina Cabric
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Center for Musculoskeletal Surgery (CMSC), Charitéplatz 1, 10117, Berlin, Germany.,Department of Orthopaedics and Trauma Surgery, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - Andrej Trampuz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Center for Musculoskeletal Surgery (CMSC), Charitéplatz 1, 10117, Berlin, Germany. .,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Föhrer Strasse 15, 13353, Berlin, Germany.
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Puebla LEJ, Núñez Fernández FA, Nodarse JF, Millán IA, Rodríguez IC, Santos LP, Saavedra YP, Moreno LR, Robertson LJ. Sporadic cyclosporiasis in symptomatic Cuban patients: Confirmation of positive results from conventional diagnostic methods by molecular assay. Diagn Microbiol Infect Dis 2020; 97:115048. [PMID: 32327205 DOI: 10.1016/j.diagmicrobio.2020.115048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/13/2020] [Accepted: 03/22/2020] [Indexed: 11/21/2022]
Abstract
In Cuba, there are few studies on cyclosporiasis. Here, we report results from 1247 stool samples from symptomatic patients that were examined by microscopy methods and positive cases confirmed by nested PCR targeting the 18S rRNA gene, followed by sequencing. Seven positive samples, all diagnosed during May-June, were confirmed by the molecular method, indicating an occurrence in this patient cohort of 0.56%.
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Sigamani S, Perumal M, Thivakaran GA, Thangavel B, Kandasamy K. DNA barcoding of macrofauna act as a tool for assessing marine ecosystem. Mar Pollut Bull 2020; 152:107891. [PMID: 27423443 DOI: 10.1016/j.marpolbul.2016.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 07/09/2016] [Accepted: 07/11/2016] [Indexed: 06/06/2023]
Abstract
Nowadays, marine ecosystem monitoring and assessment are increasingly depending on variety of molecular tools. With these background, DNA barcoding play a key role in species identification with increasing speed and accuracy, and although the suitability for developing genetic tools like genomic AMBI (gAMBI). Presently we have submitted 13 benthic polychaete species using mtCOI to GenBank. Of these, nine species were newly submitted, and hence they act as a benchmark and reference organism for identifying respective polychaete species worldwide in the near future. Based on that, our study results tend to be helpful for motivating among the researcher in order to implementing the genomic AMBI (gAMBI).
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Affiliation(s)
- Sivaraj Sigamani
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India.
| | - Murugesan Perumal
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India
| | | | - Balasubramanian Thangavel
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India
| | - Kathiresan Kandasamy
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India
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Comai G, Mistral De Pascali A, Busutti M, Morini S, Ortalli M, Conte D, Re MC, La Manna G, Varani S. Screening strategies for the diagnosis of asymptomatic Leishmania infection in dialysis patients as a model for kidney transplant candidates. J Nephrol 2021; 34:191-5. [PMID: 32002798 DOI: 10.1007/s40620-020-00705-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 01/14/2020] [Indexed: 11/02/2022]
Abstract
Despite being considered a tropical disease, visceral leishmaniasis (VL) caused by L. infantum is also endemic in the Mediterranean Europe and represents an increasing cause of morbidity and mortality in solid organ transplant (SOT) recipients. VL occurring in kidney transplant recipients is a severe event, often worsening the renal damage and leading to poor outcome. It is believed that most of VL cases in transplant recipients are caused by reactivation of a pre-existent, dormant leishmanial infection induced by the immunosuppressive drugs. Nevertheless, the prevalence of asymptomatic Leishmania infection in candidates to kidney transplant residing in or visiting endemic areas is unknown. As L. infantum is highly circulating in northeastern Italy, we aimed to examine the occurrence of this parasitic infection in 119 dialysis patients living in the mentioned area, 71 of whom were potential candidates to kidney transplant. By employing a combination of sensitive serological and molecular methods, we observed a prevalence of 15.9% asymptomatic Leishmania infection in the study cohort. This finding emphasizes the need of further evaluating potential screening strategies for Leishmania infection in solid organ transplant candidates residing in or visiting endemic areas.
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Abstract
Traditional antimicrobial susceptibility test methods for detection of S. aureus resistant to oxacillin (MRSA) such as disk diffusion, broth microdilution, and oxacillin screen plate require 18-24 h of incubation after having the organism growing in pure culture. Rapid and accurate identification of MRSA isolates is essential not only for patient care, but also for effective infection control programs to limit the spread of MRSA. In the last few years, several commercial rapid tests for detection of MRSA directly from nasal and wound swabs, as well as from positive blood cultures, have been developed for use in clinical laboratories. Chromogenic agar plates and real-time PCR and other molecular tests are gaining popularity as MRSA screening tests because they have the advantage of a lower turnaround time than that of traditional culture and susceptibility testing and they are capable of detecting MRSA directly from nasal and wound swabs, allowing rapid identification of colonized or infected patients. In addition, molecular methods able to detect and differentiate S. aureus and MRSA (SA/MRSA) directly from blood cultures are becoming a useful tool for rapid detection of bacteremia caused by MSSA and MRSA. This review focuses on the procedures for performing testing using rapid methods currently available for detection of MRSA directly from clinical specimens.
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Tilmanne A, Martiny D, Quach C, Wautier M, Vandenberg O, Lepage P, Hallin M. Enteropathogens in paediatric gastroenteritis: comparison of routine diagnostic and molecular methods. Clin Microbiol Infect 2019; 25:1519-24. [PMID: 31374260 DOI: 10.1016/j.cmi.2019.07.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Studies of acute gastroenteritis (AGE) are hampered by the lack of routine diagnostic methods with good sensitivity and specificity. Molecular methods are increasingly used for clinical purposes, but the clinical significance of a positive result remains a challenge. In this study we aimed to compare results of routine diagnostic methods and molecular methods in symptomatic children and asymptomatic controls. METHODS Patients presenting to the pediatric emergency departments of two university hospitals in Brussels with AGE were recruited prospectively from May 2015 to October 2016; asymptomatic controls were recruited from the same hospitals. Stool analyses were performed for all participants for common pathogenic bacteria (culture), virus (immunochromatography) and parasites (microscopy). Stools were also analysed with the Luminex Gastrointestinal Pathogen Panel, a multiplex-PCR for common enteropathogens. RESULTS Stools from 178 patients and 165 controls were analysed. An enteropathogen was detected in 62.4% (111/178) of cases when combining the two methods (56.2% (100/178) by Luminex, 42.7% (76/178) with routine methods) and 29.1% (48/165) of controls (24.2% (40/165) by Luminex and 10.3% (17/165) by routine methods). Some pathogens were detected more often with Luminex than with routine methods, such as Salmonella (16.3% (29/178) with Luminex and 3.9% (7/178) with routine method, p < 0.05), whereas others identified by culture methods, such as Campylobacter, Shigella, Yersinia, were missed by Luminex. CONCLUSIONS Molecular tools seem attractive methods, providing high positivity and a rapid turn-around time for the diagnosis of AGE. However, high rates of positivity in both cases and controls highlight the difficulty in interpreting results. Pathogens missed by Luminex but detected by culture methods raise more questions about the true clinical interest of the technique for our patients.
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Ko YJ, Kim J, Kim HN, Yoon SY, Lim CS, Lee CK. Diagnostic performance of the Xpert Carba-R assay for active surveillance of rectal carbapenemase-producing organisms in intensive care unit patients. Antimicrob Resist Infect Control 2019; 8:127. [PMID: 31384432 PMCID: PMC6664486 DOI: 10.1186/s13756-019-0579-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022] Open
Abstract
Background There are growing concerns regarding the spread of carbapenemase-producing organisms (CPOs) among patients in long-term care facilities (LTCFs) and hospitals in South Korea. We have established a screening protocol for the detection of CPOs in high-risk patients upon admission to intensive care units (ICUs). The diagnostic performance of the Xpert Carba-R assay was compared to that of rectal culture for CPO detection in high-risk patients upon ICU admission. Methods A total of 408 consecutive rectal swabs were obtained from December 2016 to December 2017. CPO screening was performed using the Xpert Carba-R assay (Cepheid, Sunnyvale, CA, USA). When a carbapenemase gene was detected, additional rectal swabs were incubated overnight and inoculated on chromID CARBA medium (bioMérieux, Marcy l’Etoile, France). Bacterial carbapenemase genes, including blaKPC, blaNDM, blaVIM, blaIMP-1, and blaOXA-48, were confirmed by conventional PCR. The diagnostic performance of the Carba-R assay was ascertained based on the culture results. Results The prevalence of CPO carriage was 7.4% according to the Carba-R assay and 3.7% according to rectal culture. The median Ct values of IMP-1 and KPC were significantly different (35.2 vs. 26.6, P = 0.0143). The overall sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the Carba-R assay were 100.0% (95% confidence interval [CI], 78.2–100.0), 96.7% (94.4–98.2), 53.6% (40.4–66.4) and 100.0% (99.0–100.0), respectively. Conclusions We demonstrated the prevalence of CPO carriage in high-risk patients upon ICU admission and evaluated the diagnostic performance of the Carba-R assay. The combined use of the Xpert Carba-R assay and culture produces rapid and reliable results for the active surveillance of rectal CPO in ICU patients.
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Affiliation(s)
- Young Jin Ko
- 1Department of Laboratory Medicine, Korea University College of Medicine, 126-1, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841 Republic of Korea.,2Present address: Department of Laboratory Medicine, Chosun University Hospital, Gwangju, Republic of Korea
| | - Jeeyong Kim
- 1Department of Laboratory Medicine, Korea University College of Medicine, 126-1, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841 Republic of Korea
| | - Ha-Nui Kim
- 1Department of Laboratory Medicine, Korea University College of Medicine, 126-1, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841 Republic of Korea
| | - Soo-Young Yoon
- 1Department of Laboratory Medicine, Korea University College of Medicine, 126-1, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841 Republic of Korea
| | - Chae Seung Lim
- 1Department of Laboratory Medicine, Korea University College of Medicine, 126-1, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841 Republic of Korea
| | - Chang Kyu Lee
- 1Department of Laboratory Medicine, Korea University College of Medicine, 126-1, Anam-dong 5-ga, Seongbuk-gu, Seoul, 02841 Republic of Korea
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Menegati SFP, Santos TD, Macedo MD, Castilho L. Discrepancies between red cell phenotyping and genotyping in daily immunohematology laboratory practice. Transfus Apher Sci 2019; 59:102585. [PMID: 31303508 DOI: 10.1016/j.transci.2019.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 05/06/2019] [Revised: 06/11/2019] [Accepted: 06/24/2019] [Indexed: 11/18/2022]
Abstract
False-positive and false-negative reactions exist for serological and molecular antigen typing methods. If the predicted phenotype is inconsistent with the patient`s known antibodies or serological phenotype, the discrepancy must be investigated. False-negative and false-positive results are clinically problematic in blood donors and patients. In this study, we investigated discrepant results between serology and molecular testing in patients and blood donors that occurred in daily molecular laboratory practice over a two year-period. SCD patients represented a large percentage of our cases of discrepancies but we also observed a high prevalence of discrepancies between phenotypes and genotypes in blood donors. The main reasons that led to discrepancies were recent transfusions and limitations of phenotyping. Discrepancies classified as false positive phenotype/true negative genotype and false negative phenotype/true positive genotype occurred mainly in patients with recent transfusions and individuals with RH variants while those classified as true negative phenotype/false positive genotype involved null phenotypes due to silent genes. Despite the limitations of molecular methods currently employed, we found more false-negative and false-positive phenotypes than genotypes demonstrating that genotyping is more efficient to define the blood types, especially in transfusion dependent patients.
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Idelevich EA, Seifert H, Sundqvist M, Scudeller L, Amit S, Balode A, Bilozor A, Drevinek P, Kocak Tufan Z, Koraqi A, Lamy B, Mareković I, Miciuleviciene J, Müller Premru M, Pascual A, Pournaras S, Saegeman V, Schønheyder HC, Schrenzel J, Strateva T, Tilley R, Wiersinga WJ, Zabicka D, Carmeli Y, Becker K. Microbiological diagnostics of bloodstream infections in Europe-an ESGBIES survey. Clin Microbiol Infect 2019; 25:1399-1407. [PMID: 30980927 DOI: 10.1016/j.cmi.2019.03.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 01/29/2019] [Revised: 03/21/2019] [Accepted: 03/24/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVES High-quality diagnosis of bloodstream infections (BSI) is important for successful patient management. As knowledge on current practices of microbiological BSI diagnostics is limited, this project aimed to assess its current state in European microbiological laboratories. METHODS We performed an online questionnaire-based cross-sectional survey comprising 34 questions on practices of microbiological BSI diagnostics. The ESCMID Study Group for Bloodstream Infections, Endocarditis and Sepsis (ESGBIES) was the primary platform to engage national coordinators who recruited laboratories within their countries. RESULTS Responses were received from 209 laboratories in 25 European countries. Although 32.5% (68/209) of laboratories only used the classical processing of positive blood cultures (BC), two-thirds applied rapid technologies. Of laboratories that provided data, 42.2% (78/185) were able to start incubating BC in automated BC incubators around-the-clock, and only 13% (25/192) had established a 24-h service to start immediate processing of positive BC. Only 4.7% (9/190) of laboratories validated and transmitted the results of identification and antimicrobial susceptibility testing (AST) of BC pathogens to clinicians 24 h/day. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry from briefly incubated sub-cultures on solid media was the most commonly used approach to rapid pathogen identification from positive BC, and direct disc diffusion was the most common rapid AST method from positive BC. CONCLUSIONS Laboratories have started to implement novel technologies for rapid identification and AST for positive BC. However, progress is severely compromised by limited operating hours such that current practice of BC diagnostics in Europe complies only partly with the requirements for optimal BSI management.
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Affiliation(s)
- E A Idelevich
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - H Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany; German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - M Sundqvist
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - L Scudeller
- Clinical Epidemiology Unit, Scientific Direction, Fondazione IRCCS, Policlinico San Matteo Pavia Fondazione IRCCS, Pavia, Italy
| | - S Amit
- Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Centre, Jerusalem, Israel
| | - A Balode
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - A Bilozor
- Microbiology Laboratory, Diagnostic Clinic, East-Tallinn Central Hospital, Tallinn, Estonia
| | - P Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Z Kocak Tufan
- Infectious Diseases and Clinical Microbiology Department, Medical School of Ankara Yildirim Beyazit University, Ankara, Turkey
| | - A Koraqi
- Clinical Microbiology Laboratory, University Hospital Centre 'Mother Theresa', Tirana, Albania
| | - B Lamy
- Laboratory of Clinical Microbiology, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, INSERM U1065 (C3M), Nice, France
| | - I Mareković
- Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | | | - M Müller Premru
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - A Pascual
- Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen Macarena, Departamento de Microbiología, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
| | - S Pournaras
- Laboratory of Clinical Microbiology, Attikon Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - V Saegeman
- Department of Infection Control and Epidemiology, University Hospitals Leuven, Leuven, Belgium
| | - H C Schønheyder
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - J Schrenzel
- Bacteriology Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - T Strateva
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - R Tilley
- Department of Microbiology, University Hospitals Plymouth NHS Trust, Plymouth, UK
| | - W J Wiersinga
- Department of Infectious Diseases and Centre for Experimental Molecular Medicine, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - D Zabicka
- National Medicines Institute, Warsaw, Poland
| | - Y Carmeli
- Division of Epidemiology, Tel Aviv Sourasky Medical Centre, Tel Aviv, Israel
| | - K Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
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McClay D. Unlocking mechanisms of development through advances in tools. Methods Cell Biol 2019; 151:37-41. [PMID: 30948019 DOI: 10.1016/bs.mcb.2019.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This perspective describes how our understanding of sea urchin development has been enabled by advances in technology. The early conceptual discoveries that put the sea urchin embryo on the research map had to wait until technologies were available to explain how those concepts worked. The explanatory phase continues as a number of mechanisms continue to be understood in ever greater detail, all made possible by further technical advances.
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You Z, Yang X, Yu J, Zhang J, Ran Y. Chromoblastomycosis Caused by Fonsecaea nubica: First Report in Northern China and Literature Review. Mycopathologia 2018; 184:97-105. [PMID: 30547378 DOI: 10.1007/s11046-018-0307-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 11/19/2018] [Indexed: 02/05/2023]
Abstract
Chromoblastomycosis is found worldwide with higher incidence in tropical and subtropical regions. Fonsecaea spp. is one of the major causative agents of this disease. First case of chromoblastomycosis due to Fonsecaea nubica in Northern China is reported in a 75-year-old Chinese male. We firstly summarized molecular identification methods of Fonsecaea spp. and all the strains of F. nubica reported in the literature. Sequencing of internal transcribed spacer alone and/or combined with actin (ACT1), partial cell division cycle (CDC42) and partial beta-tubulin (BT2) were most commonly used to identify species, while lactase (Lac), homogentisate (HmgA) and polyketide synthase (PKS1) were also used in some cases. Most strains were isolated from South America and Eastern China. Five clinical cases of chromoblastomycosis due to F. nubica from Asia and Europe were also reviewed. All the five patients were male, over 30 years old, and their lesions occurred after trauma.
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Affiliation(s)
- Zimeng You
- Department of Dermatovenereology, West China Hospital, Sichuan University, No. 37, Guo Xue Xiang, Wuhou District, Chengdu, 610041, Sichuan Province, China
| | - Xiaoxiao Yang
- Department of Dermatology, First Affiliated Hospital, Zhengzhou University, No. 1, Jianshe East Road, Zhengzhou, 450052, Henan Province, China
| | - Jianbin Yu
- Department of Dermatology, First Affiliated Hospital, Zhengzhou University, No. 1, Jianshe East Road, Zhengzhou, 450052, Henan Province, China
| | - Jiangan Zhang
- Department of Dermatology, First Affiliated Hospital, Zhengzhou University, No. 1, Jianshe East Road, Zhengzhou, 450052, Henan Province, China.
| | - Yuping Ran
- Department of Dermatovenereology, West China Hospital, Sichuan University, No. 37, Guo Xue Xiang, Wuhou District, Chengdu, 610041, Sichuan Province, China.
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Haasis C, Rupp J, Andres S, Schlüter B, Kernbach M, Hillemann D, Kranzer K. Validation of the FluoroType ® MTBDR assay using respiratory and lymph node samples. Tuberculosis (Edinb) 2018; 113:76-80. [PMID: 30514516 DOI: 10.1016/j.tube.2018.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/13/2018] [Accepted: 09/17/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND Tuberculosis (TB), especially drug-resistant TB, is a global public health problem. This study aimed to validate a new molecular diagnostic test, the FluoroType® MTBDR. METHOD Samples underwent routine diagnostic procedures (fluorescence microscopy, culture, species differentiation and phenotypic drug susceptibility testing). Left over samples stored at -20° underwent DNA extraction using the Fluorolyse® kit, followed by FluoroType® MTBDR and Genotype MTBDRplus testing. RESULTS A total of 350 respiratory and 59 lymph node samples were included in the study; 71 respiratory and 16 lymph node samples were culture positive for M. tuberculosis complex (MTBC). The sensitivity of the FluoroType® MTBDR to detect MTBC DNA was 91.4% (95%CI 82.3-96.8%), 68.4% (95%CI 43.4-87.4%) and 62.5%, (95%CI 35.4-84.8%) for respiratory, smear negative respiratory and lymph node samples respectively. The correlating sensitivities of the GenoType MTBDRplus were 85.9% (95%CI 75.6-93.0%), 52.6% (95%CI 28.9-75.6%) and 56.3% (29.9-80.2). Sensitivity of the FluoroType® MTBDR to detect RMP and INH resistance for respiratory samples was 96.5% (95%CI 82.2-99.9) and 70% (95%CI 45.7-88.1), respectively. The GenoType MTBDRplus revealed sensitivities of 97.1% (95% 85.1-99.9) 70.6% (95%CI 52.5-84.9) for detection of RMP and INH resistance. Indeterminate results were 13/64 (20.3%), 23/64 (35.9%) and 16/64 (25.0%) for rpoB, katG and inhA using the FluoroType® MTBDR. CONCLUSION The FluoroType® MTBDR has a high sensitivity to detect MTBC DNA. However, the high proportion of indeterminate results across all three genes needs to be addressed.
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Affiliation(s)
- Carsten Haasis
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Jan Rupp
- University Hospital Schleswig-Holstein, Department of Infectious Diseases and Microbiology, Lübeck, Germany
| | - Sönke Andres
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Birte Schlüter
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Margrit Kernbach
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Doris Hillemann
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Katharina Kranzer
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany; London School of Hygiene and Tropical Medicine, London, United Kingdom.
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Abstract
Helicobacter pylori (H. pylori) is an organism that is widespread in the human population and is sometimes responsible for some of the most common chronic clinical disorders of the upper gastrointestinal tract in humans, such as chronic-active gastritis, duodenal and gastric ulcer disease, low-grade B-cell mucosa associated lymphoid tissue lymphoma of the stomach, and gastric adenocarcinoma, which is the third leading cause of cancer death worldwide. The routes of infection have not yet been firmly established, and different routes of transmission have been suggested, although the most commonly accepted hypothesis is that infection takes place through the faecal-oral route and that contaminated water and foods might play an important role in transmission of the microorganism to humans. Furthermore, several authors have considered H. pylori to be a foodborne pathogen because of some of its microbiological and epidemiological characteristics. H. pylori has been detected in drinking water, seawater, vegetables and foods of animal origin. H. pylori survives in complex foodstuffs such as milk, vegetables and ready-to-eat foods. This review article presents an overview of the present knowledge on the microbiological aspects in terms of phenotypic characteristics and growth requirements of H. pylori, focusing on the potential role that foodstuffs and water may play in the transmission of the pathogen to humans and the methods successfully used for the detection of this microorganism in foodstuffs and water.
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Affiliation(s)
- Nicoletta C Quaglia
- Department of Emergency and Organ Transplantation, Section of Veterinary Clinic and Animal Production, University of Bari “Aldo Moro”, Valenzano 70010, Italy
| | - Angela Dambrosio
- Department of Emergency and Organ Transplantation, Section of Veterinary Clinic and Animal Production, University of Bari “Aldo Moro”, Valenzano 70010, Italy
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Koroglu M, Demiray T, Ozbek A, Guclu E, Karabay O, Altindis M, Durmaz R. Nail scissors and fingernails as reservoirs of hepatitis B virus DNA: Role of nail scissors in household transmission of hepatitis B virus. Am J Infect Control 2018; 46:793-797. [PMID: 29395503 DOI: 10.1016/j.ajic.2017.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/14/2017] [Accepted: 12/14/2017] [Indexed: 11/25/2022]
Abstract
BACKGROUND No study in the current literature has scientifically clarified the transmission of hepatitis B virus (HBV) via personal hygiene tools. We determined risk of household transmission of HBV via nail scissors. Moreover, we assessed whether nails from HBV-infected people contained HBV, and evaluated correlations of HBV DNA levels of serum, nail specimens, and nail scissors. METHODS Seventy patients testing positive for the surface antigen of the hepatitis B virus (63 positive for HBV DNA) treated for HBV infection and 27 healthy individuals were included. Real-time polymerase chain reaction method was used to detect HBV DNA levels in sera, nail, and nail scissors. RESULTS HBV DNA was detected on 27% of nail scissors and in 50% of nail specimens from 63 serum HBV DNA-positive patients. Serum HBV DNA level >105 IU/mL was associated with 71.8% probability of nail scissors being HBV DNA-positive (P < .05). Serum HBV DNA level >107 IU/mL was associated with 71.5% probability of fingernails being HBV DNA-positive (P > .05). Shared-use of nail scissors was correlated with surface antigen of the hepatitis B virus positivity and total hepatitis B core antibody/immunoglobulin G positivity. A high HBV DNA level was detected in nail scissors and low level HBV DNA in the nails of persons with high serum HBV DNA levels. CONCLUSIONS Nail scissors, shared-use of nail scissors, and duration of shared use play important roles in household transmission of HBV. Level of education within society in this regard should be increased via mass media.
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Terio V, Bottaro M, Di Pinto A, Fusco G, Barresi T, Tantillo G, Martella V. Occurrence of Aichi virus in retail shellfish in Italy. Food Microbiol 2018; 74:120-124. [PMID: 29706327 DOI: 10.1016/j.fm.2018.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/05/2018] [Accepted: 02/15/2018] [Indexed: 11/25/2022]
Abstract
AiV-1 is considered an emerging human enteric pathogens and foodborne transmission has been documented as an important source of exposure for humans, chiefly in relation to non-safe, risky food habits. We surveyed the presence of AiV-1 in retail shellfish, including oysters and mussles, identifying the virus in 3/170 (1.8%) of the analysed samples. The AiV-1 positive samples were of different geographic origin. Upon sequence analysis of a portion of the 3CD junction region, two AiV strains identified from harvesting areas in Northern Italy were characterised as genotype B and displayed 99-100% identity at the nucleotide level to other AiV-1 strains detected in sewages in Central Italy in 2012, suggesting that such strains are stably circulating in Italian ecosystems. Interestingly, a strain identified from mussles harvested in Southern Italy could not be characterised firmly, as inferred in the Bayesian analysis and by sequence comparison, indicating that different AiV strains are also circulating in Italy. Viral contamination in retail shellfish challenges the microbiological guidelines for food control and requires the development and optimization of additional diagnostic and prevention strategies.
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Affiliation(s)
- Valentina Terio
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy.
| | - Marilisa Bottaro
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Angela Di Pinto
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Division of Caserta, Via Jervolino n. 19, 81029, Caserta, Italy
| | - Teodosio Barresi
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Giuseppina Tantillo
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Vito Martella
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
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GHOLIZADEH S, NASERI KARIMI N, ZAKERI S, DINPARAST DJADID N. The Role of Molecular Techniques on Malaria Control and Elimination Programs in Iran: A Review Article. Iran J Parasitol 2018; 13:161-171. [PMID: 30069199 PMCID: PMC6068378] [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] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The aim of this review was to describe the application of molecular methods in epidemiological aspects of malaria vectors, parasites, and human hosts in Iran and their critical role in malaria control and elimination programs. METHODS Medline, EMBASE, Web of Science, Scopus, and Google Scholar databases were searched systematically for original published papers on PCR, the molecular identification of malaria vectors, the molecular epidemiology of malaria, insecticide resistance, and drug-resistant parasites, in Iran. In total, 51 studies on molecular entomology and 36 studies on molecular parasitology of malaria and three on human host were selected. RESULTS Molecular methods are essential for improving the detection of malaria infection and monitoring antimalarial drugs and insecticide resistance in malaria elimination settings such as Iran. CONCLUSION The application of molecular methods may be of particular interest for malaria control/elimination programs, for monitoring progress towards malaria elimination, and for optimal orientation of program activities.
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Affiliation(s)
- Saber GHOLIZADEH
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran, Medical Entomology Department, School of Public Health, Urmia University of Medical Sciences, Urmia, Iran
| | - Nazanin NASERI KARIMI
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran, Medical Entomology Department, School of Public Health, Urmia University of Medical Sciences, Urmia, Iran
| | - Sedigheh ZAKERI
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran,Correspondence
| | - Navid DINPARAST DJADID
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran,Correspondence
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Huang Y, Ruan X, Li L, Zeng M. Prevalence of Eimeria species in domestic chickens in Anhui province, China. J Parasit Dis 2017; 41:1014-1019. [PMID: 29114135 PMCID: PMC5660027 DOI: 10.1007/s12639-017-0927-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/12/2017] [Indexed: 10/19/2022] Open
Abstract
Prevalence studies can adequately assist in the design of prophylaxis strategies for disease control. Here, the prevalence of Eimeria species in chickens was investigated in Anhui province, China, from July to September 2016. A total of 171 samples were tested by microscopic examination and molecular methods. The prevalence of coccidiosis in Anhui province was found to be 87.75% (150/171). Eimeria tenella was the most prevalent species (80.67%, 121/150), and Eimeria necatrix, Eimeria mitis, Eimeria maxima, Eimeria brunetti and Eimeria acervulina were 68% (102/150), 55.33% (83/150), 54.67% (82/150), 44.67% (67/150) and 2.67% (4/150), respectively. Eimeria praecox was not detected at all. The most common combinations are E. tenella, E. maxima, E. necatrix, E. brunetti and E. mitis (26.67%, 40/150), followed by E. tenella, E. maxima and E. necatrix (19.33%, 29/150). Eimeria necatrix exhibited the highest participation in multiple infections. The results of the present study suggested that Eimeria infection is mixed, severe and widespread in chickens, Therefore, integrated strategies should be performed to prevent and control coccidial infection in chickens in Anhui province.
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Affiliation(s)
- Yueyue Huang
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Xiangchun Ruan
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Lin Li
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Minghua Zeng
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
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Pereira A, Parreira R, Cotão AJ, Nunes M, Vieira ML, Azevedo F, Campino L, Maia C. Tick-borne bacteria and protozoa detected in ticks collected from domestic animals and wildlife in central and southern Portugal. Ticks Tick Borne Dis 2017; 9:225-234. [PMID: 28958791 DOI: 10.1016/j.ttbdis.2017.09.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 02/07/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 12/18/2022]
Abstract
Ticks are vectors of many human and animal pathogens. The aim of this study was to screen bacteria and protozoa from ticks infesting domestic animals and wildlife collected in central and southern Portugal. A total of 593 ticks, comprising 465 (78.4%) adults, 122 (20.6%) nymphs, and six (1.0%) larvae, were collected from 283 hosts of 25 different species (4 domestic and 21 wild). Overall, the analysis of DNA extracts prepared from ticks collected from hosts of 11 different species in the districts of Castelo Branco, Portalegre, Lisboa, Setúbal, Beja and Faro, revealed the presence of genomic sequences from Anaplasma sp., A. ovis, Babesia sp., relapsing fever-like Borrelia sp., Ehrlichia spp., Rickettsia aeschlimannii, Ri. helvetica, Ri. massiliae, Ri. raoultii, Ri. slovaca, Candidatus Ri. barbariae, Theileria annulata and T. ovis, in specimens of Dermacentor marginatus, Hyalomma lusitanicum, Hy. marginatum, Rhipicephalus bursa and Rh. sanguineus sensu lato. The obtained results suggest the circulation of a wide variety of infectious agents, some of zoonotic concern, in hard ticks from Portugal. Further studies should be conducted to better characterize (both genetically and phenotypically) the putative novel microorganisms detected, both in what regards their potential pathogenity towards vertebrates, and to assist the implementation of effective control strategies for the management of ticks and human and animal tick-borne pathogens.
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Affiliation(s)
- André Pereira
- Faculty of Veterinary Medicine, Universidade Lusófona de Humanidades e Tecnologias, Lisboa, Portugal; Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisboa, Portugal; Medical Parasitology Unit, IHMT, UNL, Portugal
| | - Ricardo Parreira
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisboa, Portugal; Medical Microbiology Unit, IHMT, UNL, Portugal
| | | | - Mónica Nunes
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisboa, Portugal; Medical Microbiology Unit, IHMT, UNL, Portugal
| | - Maria Luísa Vieira
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisboa, Portugal; Medical Microbiology Unit, IHMT, UNL, Portugal
| | | | - Lenea Campino
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisboa, Portugal; Medical Parasitology Unit, IHMT, UNL, Portugal
| | - Carla Maia
- Faculty of Veterinary Medicine, Universidade Lusófona de Humanidades e Tecnologias, Lisboa, Portugal; Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisboa, Portugal; Medical Parasitology Unit, IHMT, UNL, Portugal.
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Wang H, Bédard E, Prévost M, Camper AK, Hill VR, Pruden A. Methodological approaches for monitoring opportunistic pathogens in premise plumbing: A review. Water Res 2017; 117:68-86. [PMID: 28390237 PMCID: PMC5693313 DOI: 10.1016/j.watres.2017.03.046] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [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: 01/06/2017] [Revised: 03/19/2017] [Accepted: 03/22/2017] [Indexed: 05/06/2023]
Abstract
Opportunistic premise (i.e., building) plumbing pathogens (OPPPs, e.g., Legionella pneumophila, Mycobacterium avium complex, Pseudomonas aeruginosa, Acanthamoeba, and Naegleria fowleri) are a significant and growing source of disease. Because OPPPs establish and grow as part of the native drinking water microbiota, they do not correspond to fecal indicators, presenting a major challenge to standard drinking water monitoring practices. Further, different OPPPs present distinct requirements for sampling, preservation, and analysis, creating an impediment to their parallel detection. The aim of this critical review is to evaluate the state of the science of monitoring OPPPs and identify a path forward for their parallel detection and quantification in a manner commensurate with the need for reliable data that is informative to risk assessment and mitigation. Water and biofilm sampling procedures, as well as factors influencing sample representativeness and detection sensitivity, are critically evaluated with respect to the five representative bacterial and amoebal OPPPs noted above. Available culturing and molecular approaches are discussed in terms of their advantages, limitations, and applicability. Knowledge gaps and research needs towards standardized approaches are identified.
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Affiliation(s)
- Hong Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Emilie Bédard
- Department of Civil Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Anne K Camper
- Center for Biofilm Engineering and Department of Civil Engineering, Montana State University, Bozeman, MT 59717, USA
| | - Vincent R Hill
- Waterborne Disease Prevention Branch, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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Abstract
This article reviews the current diagnostic approaches, both serologic and molecular, for the detection of fungi associated with pulmonary disease. Classic serologic techniques, including immunodiffusion and complement fixation, both of which remain a cornerstone for fungal diagnostic testing, are reviewed and their performance characteristics presented. More recent advances in this field, including novel lateral-flow assays for fungal antigen detection, are also described. Molecular techniques for fungal identification both from culture and directly from patient specimens, including nucleic acid probes, mass spectrometry-based methods, nucleic acid amplification testing, and traditional and broad-range sequencing, are discussed and their performance evaluated.
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Affiliation(s)
- Poornima Ramanan
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street, Rochester, MN 55905, USA
| | - Nancy L Wengenack
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street, Rochester, MN 55905, USA
| | - Elitza S Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street, Rochester, MN 55905, USA.
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Amato E, Filipello V, Gori M, Lomonaco S, Losio MN, Parisi A, Huedo P, Knabel SJ, Pontello M. Identification of a major Listeria monocytogenes outbreak clone linked to soft cheese in Northern Italy - 2009-2011. BMC Infect Dis 2017; 17:342. [PMID: 28499357 PMCID: PMC5429568 DOI: 10.1186/s12879-017-2441-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 05/04/2017] [Indexed: 11/24/2022] Open
Abstract
Background Molecular subtyping and enhanced surveillance in Lombardy region identified a cluster of possibly related listeriosis cases from 2006 to 2010. This cluster grouped 31 isolates that belonged to serotype 1/2a and Sequence Type 38 (ST38) as defined by Multilocus Sequence Typing (MLST). Methods Our study expanded the previous investigation to include cases from 2011 to 2014 and used Multi-Virulence-Locus Sequence Typing (MVLST) on all ST38 isolates to better understand their epidemiology and possibly identify a common source outbreak. Results Out of 306 L. monocytogenes clinical isolates collected, 43 (14.1%) belonged to ST38 with cases occurring in nine out of twelve Lombardy provinces. The ST38 isolates were split by MVLST into two Virulence Types (VTs): VT80 (n = 12) and VT104 (n = 31). VT104 cases were concentrated between 2009 and 2011 in two provinces, Bergamo and Milan. An epidemiologic investigation was performed and in one case, a matching VT104 isolate was retrieved from a soft cheese sample from a patient’s refrigerator. Conclusions Our findings revealed a major listeriosis outbreak in Northern Italy linked to soft cheese in 2009–2011, which went undetected by local health authorities. Our study shows that integrating subtyping methods with conventional epidemiology can help identify the source of L. monocytogenes outbreak clones. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2441-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ettore Amato
- Department of Health Sciences, University of Milan, Via di Rudinì, 8, 20142, Milan, Italy
| | - Virginia Filipello
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini, 2, 10095, Grugliasco, Italy.,Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via A. Bianchi 9, 25124, Brescia, Italy
| | - Maria Gori
- Department of Health Sciences, University of Milan, Via di Rudinì, 8, 20142, Milan, Italy
| | - Sara Lomonaco
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini, 2, 10095, Grugliasco, Italy
| | - Marina Nadia Losio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via A. Bianchi 9, 25124, Brescia, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121, Foggia, Italy
| | - Pol Huedo
- Department of Health Sciences, University of Milan, Via di Rudinì, 8, 20142, Milan, Italy
| | - Stephen John Knabel
- Department of Food Science, The Pennsylvania State University, 405 Rodney A. Erickson Food Science Building, 16802 University Park, State College, PA, USA
| | - Mirella Pontello
- Department of Health Sciences, University of Milan, Via di Rudinì, 8, 20142, Milan, Italy. .,Coordinated Research Center "EpiSoMI", University of Milan, Via Carlo Pascal, 36, 20133, Milan, Italy.
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de Souza M, Matsuzawa T, Sakai K, Muraosa Y, Lyra L, Busso-Lopes AF, Levin ASS, Schreiber AZ, Mikami Y, Gonoi T, Kamei K, Moretti ML, Trabasso P. Comparison of DNA Microarray, Loop-Mediated Isothermal Amplification (LAMP) and Real-Time PCR with DNA Sequencing for Identification of Fusarium spp. Obtained from Patients with Hematologic Malignancies. Mycopathologia 2017; 182:625-32. [PMID: 28324245 DOI: 10.1007/s11046-017-0129-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 02/24/2017] [Indexed: 01/17/2023]
Abstract
The performance of three molecular biology techniques, i.e., DNA microarray, loop-mediated isothermal amplification (LAMP), and real-time PCR were compared with DNA sequencing for properly identification of 20 isolates of Fusarium spp. obtained from blood stream as etiologic agent of invasive infections in patients with hematologic malignancies. DNA microarray, LAMP and real-time PCR identified 16 (80%) out of 20 samples as Fusarium solani species complex (FSSC) and four (20%) as Fusarium spp. The agreement among the techniques was 100%. LAMP exhibited 100% specificity, while DNA microarray, LAMP and real-time PCR showed 100% sensitivity. The three techniques had 100% agreement with DNA sequencing. Sixteen isolates were identified as FSSC by sequencing, being five Fusarium keratoplasticum, nine Fusarium petroliphilum and two Fusarium solani. On the other hand, sequencing identified four isolates as Fusarium non-solani species complex (FNSSC), being three isolates as Fusarium napiforme and one isolate as Fusarium oxysporum. Finally, LAMP proved to be faster and more accessible than DNA microarray and real-time PCR, since it does not require a thermocycler. Therefore, LAMP signalizes as emerging and promising methodology to be used in routine identification of Fusarium spp. among cases of invasive fungal infections.
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Terio V, Bottaro M, Pavoni E, Losio MN, Serraino A, Giacometti F, Martella V, Mottola A, Di Pinto A, Tantillo G. Occurrence of hepatitis A and E and norovirus GI and GII in ready-to-eat vegetables in Italy. Int J Food Microbiol 2017; 249:61-65. [PMID: 28319799 DOI: 10.1016/j.ijfoodmicro.2017.03.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 01/25/2016] [Revised: 01/19/2017] [Accepted: 03/11/2017] [Indexed: 02/08/2023]
Abstract
Fresh vegetables and their ready-to-eat (RTE) salads have become increasingly recognized as potential vehicles for foodborne diseases. The EU Reg. 1441/2007 establishes microbiological criteria for bacterial pathogens for products placed on the market during their shelf-life (i.e. Salmonella spp., Listeria monocytogenes) for pre-cut fruits and vegetables (RTE) whilst it does not address the problem of contamination by enteric viruses. In this study we investigated the contamination by hepatitis A virus (HAV), hepatitis E virus (HEV) and norovirus (NoV) in 911 ready-to-eat vegetable samples taken from products at retail in Apulia and in Lombardia. The vegetable samples were tested using validated real-time PCR (RT-qPCR) assays, ISO standardized virological methods and ISO culturing methods for bacteriological analysis. The total prevalence of HAV and HEV was 1.9% (18/911) and 0.6% (6/911), respectively. None of the samples analysed in this study was positive for NoV, Salmonella spp. or Listeria monocytogenes. The detection of HAV and HEV in RTE salads highlights a risk to consumers and the need to improve production hygiene. Appropriate implementation of hygiene procedures is required at all the steps of the RTE vegetable production chain and this should include monitoring of emerging viral pathogens.
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Affiliation(s)
- V Terio
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy.
| | - M Bottaro
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - E Pavoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi no. 9, 25124 Brescia, Italy
| | - M N Losio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi no. 9, 25124 Brescia, Italy
| | - A Serraino
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy
| | - F Giacometti
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy
| | - V Martella
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - A Mottola
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - A Di Pinto
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - G Tantillo
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy
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Miao J, Chen L, Wang J, Wang W, Chen D, Li L, Li B, Deng Y, Xu Z. Current methodologies on genotyping for nosocomial pathogen methicillin-resistant Staphylococcus aureus (MRSA). Microb Pathog 2017; 107:17-28. [PMID: 28284852 DOI: 10.1016/j.micpath.2017.03.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 11/23/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a common pathogen in hospitals and the community. As the rapid spread and wide distribution of antimicrobial resistance (such as MRSA), treatment for infectious diseases caused by microorganisms has become a vital threat. Thus, early identification and genotyping are essential for further therapeutic treatment and the control of rapid expansion of MRSA. In combination with applications and data feedbacks, this review focused on the currently available molecular-based assays on their utility and performance for rapid typing of MRSA, especially on effective molecular-based methods. Besides, a common mobile element SCCmec and prevalence of HA-MRSA, LA-MRSA and CA-MRSA were introduced in this review in order to provide a more complete profile of MRSA.
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Abstract
Detection of carbapenemases in clinical microbiology labs is a challenging issue. Comparison of the results of susceptibility testing with the breakpoint values of carbapenems is the first step in the screening of carbapenemase producers. To date, screening of carbapenemase-producing (CP) bacteria has been mostly performed by a selective medium. Although these media are practical for the detection of most CP isolates, the inoculated plates have to be incubated overnight. Subsequently, we need the confirmation of the carbapenemase producers present in the culture medium by additional testing [e.g. inhibition studies with liquid or solid media, modified Hodge test (MHT), or gradient strips], which can take up to another 48 hours. Despite the lack of discrimination between the three different classes of carbapenemases (KPC, MBL and OXA) and difficulties in the interpretation of the results, the MHT is usually deemed as the phenotypic reference method for the confirmation of carbapenemase production. Molecular techniques, such as real-time polymerase chain reaction (PCR) assays, in contrast to phenotypic methods that are very time consuming, are faster and allow for the quick identification of carbapenemase genes. These techniques can detect and characterize carbapenemases, including NDM- and KPC-mediated resistance, which is critical for epidemiological investigations. The aim of this review is to gather a summary of the available methods for carbapenemase detection and describe the strengths and weaknesses of each method.
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Affiliation(s)
- Abed Zahedi Bialvaei
- a Drug Applied Research Center, Faculty of Medical Sciences , Tabriz University of Medical Sciences , Iran
| | - Hossein Samadi Kafil
- a Drug Applied Research Center, Faculty of Medical Sciences , Tabriz University of Medical Sciences , Iran
| | | | - Mohammad Yousef Memar
- c Infectious Disease and Tropical Medicine Research Center , Tabriz University of Medical Sciences , Iran
| | - Mehdi Yousefi
- d Immunology Research Center , Tabriz University of Medical Sciences , Iran
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Abstract
The use of small animal models for the study of infectious disease is critical for understanding disease progression and for developing prophylactic and therapeutic treatment options. For many diseases, Syrian golden hamsters have emerged as an ideal animal model due to their low cost, small size, ease of handling, and ability to accurately reflect disease progression in humans. Despite the increasing use and popularity of hamsters, there remains a lack of available reagents for studying hamster immune responses. Without suitable reagents for assessing immune responses, researchers are left to examine clinical signs and disease pathology. This becomes an issue for the development of vaccine and treatment options where characterizing the type of immune response generated is critical for understanding protection from disease. Despite the relative lack of reagents for use in hamsters, significant advances have been made recently with several hamster specific immunologic methods being developed. Here we discuss the progress of this development, with focus on classical methods used as well as more recent molecular methods. We outline what methods are currently available for use in hamsters and what is readily used as well as what limitations still exist and future perspectives of reagent and assay development for hamsters. This will provide valuable information to researchers who are deciding whether to use hamsters as an animal model.
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Yoo K, Lee TK, Choi EJ, Yang J, Shukla SK, Hwang SI, Park J. Molecular approaches for the detection and monitoring of microbial communities in bioaerosols: A review. J Environ Sci (China) 2017; 51:234-247. [PMID: 28115135 DOI: 10.1016/j.jes.2016.07.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [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: 04/27/2016] [Revised: 07/04/2016] [Accepted: 07/08/2016] [Indexed: 05/21/2023]
Abstract
Bioaerosols significantly affect atmospheric processes while they undergo long-range vertical and horizontal transport and influence atmospheric chemistry and physics and climate change. Accumulating evidence suggests that exposure to bioaerosols may cause adverse health effects, including severe disease. Studies of bioaerosols have primarily focused on their chemical composition and largely neglected their biological composition and the negative effects of biological composition on ecosystems and human health. Here, current molecular methods for the identification, quantification, and distribution of bioaerosol agents are reviewed. Modern developments in environmental microbiology technology would be favorable in elucidation of microbial temporal and spatial distribution in the atmosphere at high resolution. In addition, these provide additional supports for growing evidence that microbial diversity or composition in the bioaerosol is an indispensable environmental aspect linking with public health.
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Affiliation(s)
- Keunje Yoo
- Department of Civil and Environmental Engineering, Yonsei University, Seoul 03722, South Korea; Division of Natural Resources Conservation, Korea Environment Institute, Sejong-si 30147, South Korea
| | - Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University, Wonju 26493, South Korea
| | - Eun Joo Choi
- Department of Systems Biology, Yonsei University, Seoul 03722, South Korea
| | - Jihoon Yang
- Division of Natural Resources Conservation, Korea Environment Institute, Sejong-si 30147, South Korea
| | - Sudheer Kumar Shukla
- Department of Built and Natural Environment, Caledonian College of Engineering, Sultanate of Oman
| | - Sang-Il Hwang
- Division of Natural Resources Conservation, Korea Environment Institute, Sejong-si 30147, South Korea
| | - Joonhong Park
- Department of Civil and Environmental Engineering, Yonsei University, Seoul 03722, South Korea.
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Eggerbauer E, Troupin C, Passior K, Pfaff F, Höper D, Neubauer-Juric A, Haberl S, Bouchier C, Mettenleiter TC, Bourhy H, Müller T, Dacheux L, Freuling CM. The Recently Discovered Bokeloh Bat Lyssavirus: Insights Into Its Genetic Heterogeneity and Spatial Distribution in Europe and the Population Genetics of Its Primary Host. Adv Virus Res 2017; 99:199-232. [PMID: 29029727 DOI: 10.1016/bs.aivir.2017.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In 2010, a novel lyssavirus named Bokeloh bat lyssavirus (BBLV) was isolated from a Natterer's bat (Myotis nattereri) in Germany. Two further viruses were isolated in the same country and in France in recent years, all from the same bat species and all found in moribund or dead bats. Here we report the description and the full-length genome sequence of five additional BBLV isolates from Germany (n=4) and France (n=1). Interestingly, all of them were isolated from the Natterer's bat, except one from Germany, which was found in a common Pipistrelle bat (Pipistrellus pipistrellus), a widespread and abundant bat species in Europe. The latter represents the first case of transmission of BBLV to another bat species. Phylogenetic analysis clearly demonstrated the presence of two different lineages among this lyssavirus species: lineages A and B. The spatial distribution of these two lineages remains puzzling, as both of them comprised isolates from France and Germany; although clustering of isolates was observed on a regional scale, especially in Germany. Phylogenetic analysis based on the mitochondrial cytochrome b (CYTB) gene from positive Natterer's bat did not suggest a circulation of the respective BBLV sublineages in specific Natterer's bat subspecies, as all of them were shown to belong to the M. nattereri sensu stricto clade/subspecies and were closely related (German and French positive bats). At the bat host level, we demonstrated that the distribution of BBLV at the late stage of the disease seems large and massive, as viral RNA was detected in many different organs.
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