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Polymerase chain reaction detection of haemolysin D gene (hlyD) in uropathogenic Escherichia coli as a novel diagnostic test for urinary tract infection

[1]Abubakar, N. H., [2]Aliyu, M., *[3]Jibril, M., and 2Mohammed, Y.

1Kano State Secondary Schools Management Board, Kano, Nigeria                     

2Department of Medical Microbiology and Parasitology, Faculty of Clinical Sciences, College of Health Sciences Bayero University, Kano, Nigeria

3Department of Pharmacology and Therapeutics, Faculty of Pharmaceutical Sciences, College of Natural and Pharmaceutical Sciences, Bayero University, Kano, Nigeria

*Correspondence to: murtalamj@yahoo.com; +2348034453990; ORCID: 0000-0003-2554-5552

 

Abstract:

 Background:  Urinary tract infection (UTI) is a common and sometime serious infectious disease diagnosed using conventional urine culture as the ‘gold standard’ for identifying Escherichia coli, the most common causative agent. However, due to the slow turn-around-time and other challenges of urine culture, this study explores the use of a novel biomolecular polymerase chain reaction (PCR) approach to detect the presence of haemolysin D gene (hlyD) that encodes a unique virulence factor of uropathogenic E. coli (UPEC) for its rapid identification in UTI.

Methodology: Primers from UPEC CFT073 and non-pathogenic E. coli K-12 MG1655 strains provided by Nottingham Trent University, England, UK were used to investigate the presence of haemolysin D gene (hlyD) in UPEC. The hlyD primers were developed from hlyD with locus number C_RS01660 on UPEC CFT073 strain using the NCBI, virulence finder, and Island viewer, and used in a PCR assay to target the hlyD in UPEC. Three sets of PCR templates were designed (UPEC, E. coli, and “No template”), each with internal and external controls amplified in a multiplex PCR assay, and agarose gel electrophoresis was used to separate the amplicons, and determine the specificity of hlyD for UPEC. Continue reading “Polymerase chain reaction detection of haemolysin D gene (hlyD) in uropathogenic Escherichia coli as a novel diagnostic test for urinary tract infection”

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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”

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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

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Serum and sputum surfactants -A and -D in multidrug-resistant and drugsensitive tuberculosis patients

A.A. Onifade, V.F. Edem, O.G. Arinola

 

Abstract

Abnormal production and function of surfactants are associated with pulmonary diseases. Also, pulmonary infections alter surfactant metabolism. Due to lack of information on the levels of surfactants A (SP-A) and D (SP-D) in Nigerian tuberculosis (TB) patients, this study assessed these surfactants in both sputum and serum of drug sensitive- and multidrug resistant- TB patients using ELISA. The aim is to explore the diagnostic or therapeutic potential of SP-A and SP-D in TB patients. Also, to find out appropriate sample for the analyses of SP-A and SP-D in TB patients.

The mean serum levels of SP-A and SP-D were not significantly reduced in MDR-TB (n=30) and DS-TB patients (n=30) compared with non-TB apparently healthy controls (n=30) (p > 0.05). Mean sputum levels of SP-A and SP-D were significantly reduced in DS-TB patients compared with the levels in MDR-TB patients (p < 0.05). These findings suggest that the sputum SP-D and SP-A levels but not serum SP-D and SP-A levels are useful indicators of the disease activity in pulmonary TB patients.

Keywords: Tuberculosis, Surfactants, Diagnosis, Nigeria

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Serum and sputum surfactants -A and -D in multidrug-resistant and drugsensitive tuberculosis patients

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Laboratory diagnosis of malaria in children under five years in a rural community: microscopy versus malaria PF test

CP Enwuru, SI Umeh, UM Abasi, RC Egbuobi

 

Abstract

The morbidity and mortality associated with malaria in children below 5 years is really worrisome especially in the rural communities with little or no laboratory diagnostic facilities. This study was carried out to compare microscopy with Malaria Pf test for the diagnosis of malaria in a rural community in Ideato North Local Government Area of Imo State. Two hundred and fifty blood smears of children below 5 years were stained with Giemsa and examined microscopically for malaria parasites. Also the Malaria Pf rapid diagnostic test was used to test the same blood samples for malaria antigens. Thirty two per cent of the blood samples were positive for malaria parasite. Compared with microscopy, the sensitivity of the Malaria Pf test was 90.0%, the specificity was 98.2%. The positive predictive value was 96.0% and negative predictive value was 95.4%. The Malaria Pf test is reliable in the parasite based diagnosis of malaria in children under 5 years. We recommend the application of this test for parasitological confirmation of malaria in all places where it is not possible to provide facilities for good quality microscopy especially in the rural communities.

KEY WORDS: MALARIA, DIAGNOSIS, CHILDREN, MICROSCOPY, MALARIA PF

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Laboratory diagnosis of malaria in children under five years in a rural community microscopy versus malaria PF test

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COMPARATIVE STUDY ON SPECIFIC AND EARLY DETECTION OF PULMONARY MYCOBACTERIA COMPLEX USING SMEAR AND CULTURE METHOD AND SEROLOGICAL PATHOZYME EIA KITS

CA Enwuru, EO Idigbe, NV Ezeobi, CT Oparaugo, U Udensi Kalu, JI Onyewuche, J Ibiam

 

Abstract

The objective of this study was to compare the sensitivity and specificity of smear and culture methods with rapid serological EIA myco kits manufactured by Omega diagnostics, for the early detection of Mycobacterium tuberculosis (MTB) complex. Sera from various categories of smear and culture results were compared with the result of 38KDa, 16KDa and purified protein for IgA, IgM and IgG antibodies with sensitivity of 4%, 24% and 76%, respectively and with specificity of100% for IgG in Smear and Culture Positive (S+)C+)) category. The sensitivity of the test improved to a level of 80% for IgG + IgA without affecting the specificity. A combination of IgG + IgA and IgM further improved the sensitivity to 88% but reduced the specificity to 91%. Amongst the S–)C+) and S–)C–) 64% and 14.7% were positive for IgG respectively. The predictive value of the kit using S+)C+) subject was 96%. For all culture positivity (n=78), there was 2.6%, 33.3% and 71.8% sensitivity for IgA, IgM and IgG respectively. IgA +IgG and IgA + IgM + IgG combination gave 74.4% and 84.6% sensitivity respectively with the same level of specificity. Fifty-five percent of culture positive subjects were found to be MTB complex positive by routine biochemical tests, while 40% through PATHOZYME TB COMPLEX PLUS kit (high positive (H+)) values). When high positivity is combined with low positivity of the same kit (H+) + L+)), 65% of the isolates were found to be MTB complex. Our study showed 88% sensitivity and 91% specificity for combined IgA + IgM + IgG antibodies recorded for MTB (S+)C+) group) and 85% sensitivity and 91% specificity for all culture positives. Our study has demonstrated that the myco kits and TB complex plus kit produced by Omega Diagnostics are a good tool for specific, early and rapid identification of active tuberculosis for both diagnostic and epidemiological purposes.

Key Words: Tuberculosis, diagnosis, comparative, specificity, sensitivity, culture and serological technique.

Afr. J. Clin. Exper. Microbiol. 2004; 5(2): 182 – 188.