Comparative evaluation of automated KingFisher Flex Purification System 96 (ThermoFisher Scientific) and manual QIAamp Viral RNA Mini Kit (Qiagen) extraction methods for SARS-CoV-2

*[1]Zouré, A. A., 1Compaoré, T. R., 2Beré, J. A., 1Sagna, T., 1Soubeiga, S. T., 1Dabiré, C., 1Nikiema, A. R., 3Barro, N., and 1Ouedraogo, H. G.

1Department of Biomedical and Public Health, Institute of Health Sciences Research (IRSS/CNRST), 03 BP 7047 Ouagadougou 03, Burkina Faso

2Unité de Formation et de Recherche en Science et Technique (UFR/ST), Université Catholique de l’Afrique de l’Ouest Unité Universitaire à Bobo Dioulasso (UCAO/UUB)

3Laboratoire de Biologie Moléculaire, d’Epidémiologie et de Surveillance des Agents, Transmissibles par les

Aliments (LaBESTA), Centre de Recherche en Sciences Biologiques Alimentaires et Nutritionnelles (CRSBAN),

Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso

*Correspondence to: abdouazaque@gmail.com; +22625363215; ORCiD: //orcid.org/000000029423024X

 

Abstract:

 Background: The extraction step of the viral material of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) influences the quality of reverse transcriptase-polymerase chain reaction (RT-PCR) results in diagnosis of coronavirus disease 2019 (COVID-19). The purpose of this cross-sectional study was to evaluate the diagnostic performance of the automated extraction system “KingFisher Flex Purification System 96 (ThermoFisher)” compared to the manual method with the “QIAamp Viral RNA Mini Kit (Qiagen)”.

Methodology: From October to December 2020, comparative diagnostic evaluation of two methods of SARSCoV-2 RNA extraction methods was conducted on 159 fresh and 120 frozen nasopharyngeal and oropharyngeal specimens collected from travellers and suspected cases or contacts of COVID-19 patients in Burkina Faso. The FastPlexTM Triplex 1-Step COVID 19 Detection Kit (RT-PCR, RNA extraction free) (Precigenome LLC) was used to amplify on the same PCR plate, RNA extracts from manual QIAamp Viral RNA Mini Kit and automated KingFisher Flex Purification System 96 (ThermoFisher) using the QuantStudio5 thermal cycler (Applied Biosystems). Analysis of the diagnostic performance of the SARS-CoV-2 RT-PCR assay following RNA extraction by the two methods was done using an online OpenEpi software. Continue reading “Comparative evaluation of automated KingFisher Flex Purification System 96 (ThermoFisher Scientific) and manual QIAamp Viral RNA Mini Kit (Qiagen) extraction methods for SARS-CoV-2”

A review of the possible prognostic values of biochemical changes in patients with SARS-CoV-2 infections

*1Adegboro, B., 2Babazhitsu, M., and 3Mba, N. I.

Departments of 1Medical Microbiology and Immunology, and 3Chemical Pathology, Nile University of Nigeria, Abuja 2Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria

*Correspondence to: boazadegboro@gmail.com; boaz.adegboro@nileuniversity.edu.ng

Abstract:
Because of high mortality and long-term hospital stay among patients with SARS-CoV-2 infections, it is important to search for biochemical changes in different organs and systems that could be useful in diagnosis and prognosis of COVID-19. We conducted a literature search of online databases including PubMed, Web of Science, Scopus and Google scholar for relevant materials on biochemical changes in SARS-COV-2 infections published between December 2019 and March 2021. The review shows that SARS-COV-2 uses the angiotensin converting enzyme 2 (ACE2) for attachment and entry into host cells. These ACE2 are abundantly expressed by the epithelial cells of the respiratory tract and moderately expressed by the epithelial cells of the esophagus, stomach, duodenum, ileum, rectum, cholangiocytes, liver hepatocytes, pancreatic beta cells, and kidney tubular cells. This explains the systemic nature of SARS-COV-2 infection, and the high morbidity and mortality associated with COVID-19. Although, tests to assess biochemical changes are not specific enough for the diagnosis of SARS-CoV-2 infection, they may be useful for predicting outcome of COVID-19. This review highlights biochemical parameters that are significantly elevated or reduced in SARS-COV-2 infections, and which can be used as predictive factors of the severity and prognosis in COVID-19 patients. Continue reading “A review of the possible prognostic values of biochemical changes in patients with SARS-CoV-2 infections”

Underutilization of the Clinical Microbiology Laboratory by Physicians in Nigeria

1Iregbu, K. C., 2Osuagwu, C. S., 3Umeokonkwo, C. D., 4Fowotade, A. A., 5Ola-Bello, O. I., 1Nwajiobi-Princewill, P. I., 6Taiwo S. S., 7Olayinka A. T., and *2Oduyebo, O. O.

1Department of Medical Microbiology, National Hospital, Abuja

2Department of Medical Microbiology and Parasitology, College of Medicine, University of Lagos

3Department of Community Medicine, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State

4Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan

5Department of Medical Microbiology, State Specialist Hospital, Akure

6Department of Medical Microbiology and Parasitology, College of Health Sciences, Ladoke Akintola University of Technology, Ogbomoso

7Department of Medical Microbiology, College of Health Sciences, Ahmadu Bello University, Zaria *Correspondence to: oyinoduyebo@yahoo.com; +2348023163319; ORCiD: 0000-0002-2894-4367

Abstract:
Background: Clinical laboratories are critical to correct diagnosis of medical conditions to ensure appropriate management. Point prevalence survey (PPS) of antimicrobial use and resistance performed in Nigeria in 2015 and 2017 showed high rates of antibiotic use, but poor laboratory utilization for definitive diagnosis of the infections for which the antimicrobials were prescribed. This study investigated the reasons for clinicians‟ poor utilization of the clinical laboratory for definitive diagnosis and treatment of infections. Methods: A cross sectional survey of clinicians attending the 2018 annual scientific conference and general meeting of the National Postgraduate Medical College of Nigeria (NPMCN) in Owerri, Southeastern Nigeria, was conducted using self-administered structured questionnaire to obtain information on the sub-optimal utilization of the clinical microbiology laboratory. Results: Of 283 respondents, 14.8% were general practitioners and 85.2% were specialists who have been in practice for a median period of 20 years (range 3 – 48 years). The specialists included surgeons (26%), family physicians (19.8%), internists (14.3%), pathologists (13.9%), paediatricians (8.8%), obstetricians and gynecologists (8.1%), community medicine physicians (6.2%), and dental surgeons (2.6%). Majority of the respondents (90.8%) work in public, 88.3% work in tertiary and 9.9% in secondary care hospitals. For diagnosis of infections, 16% and 49.8% reported using laboratory “always” and “very often” respectively. Among these, the most commonly utilized investigations were microscopy, culture and sensitivity (62.4%), DNA detection (18.3%), GeneXpert for tuberculosis (17.2%), and antigen detection (16.7%). Among clinicians that “hardly make use” of the laboratory, their reasons for non-use were; clinical diagnosis being sufficient (39.7%), delayed results (17.2%), having knowledge of „potent‟ antibiotics (15.5%), lack of access to microbiology laboratory (13.8%), absence of pathologists to assure quality of tests (12.1%), and no need of the laboratory to manage patients with infections (8.6%). Conclusion: These findings indicate that poor use of the microbiology laboratory seems mainly associated with perception and attitude of the physicians to the relevance of the laboratory, and perceived inadequacy of microbiology practice in some others. There is need to raise physicians‟ awareness on the relevance and what constitutes optimal use of the clinical microbiology laboratory for accurate diagnosis of infections and appropriate antimicrobial use.

Key words: utilization, microbiology laboratory, diagnosis, antimicrobials, infectious diseases

Received October 17, 2019; Revised October 24, 2019; Accepted October 25, 2019
Copyright 2020 AJCEM Open Access. This article is licensed and distributed under the terms of the Creative Commons Attrition 4.0 International License (//creativecommmons.org/licenses/by/4.0), which permits unrestricted use, distribution and reproduction in any medium, provided credit is given to the original author(s) and the source.
Underutilization of clinical microbiology laboratory in Nigeria Afr. J. Clin. Exper. Microbiol. 2020; 21 (1): 53-59

Sous-utilisation du laboratoire de microbiologie clinique par des médecins au Nigéria

1Iregbu, K. C., 2Osuagwu, C. S., 3Umeokonkwo, C. D., 4Fowotade, A. A., 5Ola-Bello, F. O., 1Nwajiobi-Princewill, P. I., 6Taiwo S. S., 7Olayinka A. T., et *2Oduyebo, O. O.
1Département de microbiologie médicale, hôpital national, Abuja 2Département de microbiologie médicale et de parasitologie, faculté de médecine, université de Lagos 3Département de médecine communautaire, Alex Ekwueme Hôpital universitaire fédéral, Abakaliki, Etat d’Ebonyi 4Département de médecine microbiologique et de parasitologie, Université universitaire Ibadan 5Département de microbiologie médicale, Hôpital d’État spécialisé, Akure 6Département de microbiologie médicale et de parasitologie, Collège des sciences de la santé, Université de technologie Ladoke Akintola, Ogbomoso 7Département de Microbiologie médicale et du Collège des sciences de la santé, Université Ahmadu Bello, Zaria *Correspondance à: oyinoduyebo@yahoo.com; +2348023163319; ORCiD: 0000-0002-2894-4367

Abstrait:
Contexte: Les laboratoires cliniques sont essentiels pour corriger le diagnostic des conditions médicales et assurer une prise en charge appropriée. Une enquête de prévalence ponctuelle (PPS) sur l’utilisation et la résistance aux antimicrobiens réalisée au Nigéria en 2015 et 2017 a montré des taux élevés d’utilisation d’antibiotiques, mais une faible utilisation en laboratoire pour le diagnostic définitif des infections pour lesquelles les antimicrobiens ont été prescrits. Cette étude a examiné les raisons de la faible utilisation du laboratoire par les cliniciens pour le diagnostic définitif et le traitement des infections. Méthodes: Une enquête transversale sur les cliniciens participant à la conférence scientifique annuelle et à l’assemblée générale de 2018 du Collège national des médecins diplômés du Nigéria (NPMCN) à Owerri, dans le sud-est du Nigéria, a été réalisée à l’aide d’un questionnaire structuré auto-administré visant à obtenir des informations sur le sous-optimal. utilisation du laboratoire de microbiologie clinique. Résultats: Sur 283 répondants, 14,8% étaient des omnipraticiens et 85,2% des spécialistes exerçant depuis 20 ans en moyenne (de 3 à 48 ans). Les spécialistes comprenaient des chirurgiens (26%), des médecins de famille (19,8%), des internistes (14,3%), des pathologistes (13,9%), des pédiatres (8,8%), des obstétriciens et des gynécologues (8,1%), des médecins de santé communautaires (6,2%), et chirurgiens dentistes (2,6%). La majorité des répondants (90,8%) travaillent en public, 88,3% dans le tertiaire et 9,9% dans les hôpitaux de soins secondaires. Pour le diagnostic des infections, 16% et 49,8% ont déclaré utiliser le laboratoire «toujours» et «très souvent» respectivement. Parmi ceux-ci, les examens les plus couramment utilisés étaient la microscopie, la culture et la sensibilité (62,4%), la détection de l’ADN (18,3%), GeneXpert pour la tuberculose (17,2%) et la détection de l’antigène (16,7%). Parmi les cliniciens qui «utilisent à peine» le laboratoire, les raisons de leur non-utilisation étaient: diagnostic clinique suffisant (39,7%), résultats tardifs (17,2%), connaissance d’antibiotiques «puissants» (15,5%), manque d’accès au laboratoire de microbiologie (13,8%), absence de pathologistes pour garantir la qualité des tests (12,1% ), et aucun laboratoire n‟a besoin de prendre en charge des patients infectés (8,6%). Conclusion: Ces résultats indiquent que la mauvaise utilisation du laboratoire de microbiologie semble principalement associée à la perception et à l’attitude des médecins à l’égard de la pertinence du laboratoire, et à l’insuffisance perçue de la pratique de la microbiologie chez certains autres. Il est nécessaire de sensibiliser les médecins à la pertinence et à l’utilisation optimale du laboratoire de microbiologie clinique pour un diagnostic précis des infections et une utilisation appropriée des antimicrobiens.

Mots-clés: utilisation, laboratoire de microbiologie, diagnostic, antimicrobiens, maladies infectieuses

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Underutilization of the Clinical Microbiology Laboratory by Physicians in Nigeria