Medical Laboratory Science- Scholarly Publications

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    Open Access
    'Understanding the use of real time reverse trascriptase polymerase chain reaction (Rrt-PCR) for COVID 19 Diagnosis2
    (Pan African Journal of Life Sciences, 2020-08-01) Olalekan, A; Iwalokun, B; Adekunle, O; Makun, H; Mirabeau, T; Akinloye, O
    Background: Adequ ate know ledge of r eal tim e Rever se Tr anscr iptase-Polymerase Chain Reaction (rRT-PCR) is critical for accurate implementation of the assay, interpretation of results and reporting. This mini-review describes the principles, procedures, and level of development of rRT-PCR assays for the control of the COVID-19 pandemic. Methods: A n ar r ative r eview w as car r ied out to descr ibe th e pr inciples of r RT-PCR, provide an update on the landscape of rRT-PCR protocols and elucidate the process control involved in preanalytical, analytical and post-analytical stages of COVID-19 testing . Review Findings: Th e r RT-PCR is currently considered to be the acceptable standard for confirming COVID-19 diagnosis based on SARS-CoV-2 RNA detection via conversion to cDNA and amplification of target genes in real time using sequence specific TaqMan® probes. Available evidence indicates that different rRT-PCR protocols varying in number and type of target genes within SARS-CoV-2 genome are currently available for validation and emergency use approval (EUA) in pandemic countries. A total of 1 – 3 target genes, comprising the ORF1a, ORF1b, RNA dependent RNA polymerase (RdRp), Nucleoplasid protein gene (N), Spike glycoprotein gene (S) and Envelope protein gene (E) are detected by these protocols. Conclusion: r RT-PCR remains the most sensitive method for confirming, monitoring and managing COVID-19 disease in the ongoing pandemic in all affected countries. The need for validation of every rRTPCR protocol prior to deployment for COVID-19 testing and research into the development of alternative testing protocols are strongly recommended
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    Open Access
    Case Report on Pleural Empyema Thoracis and Urinary Tract Infection Caused by Chromobacterium violaceum from Lagos, Nigeria
    (Hindawi Case Reports in Medicine, 2019-02-07) Olalekan, A; Itua, F; Mutiu, B; Egwuatu, T; Akinloye, O; Iwalokun, B
    Chromobacterium violaceum has been implicated as an important cause of invasive diseases such as septicaemia in neonates and immune-compromised adults with high risk of misdiagnosis, mistreatment, and poor outcomes. Here, we report three new cases of C. violaceum infections in three different hospitalised patients with empyema thoracis (one case) and urinary tract infections (two cases) in a tertiary Hospital in Lagos, Nigeria, and the diagnosis was confirmed with the MALDI-TOF MS instrument. )e patients were admitted and treated with parenteral antibiotics (ciprofloxacin, cefotaxime, and ceftriaxone) and discharged after clinical cure. Clinical and Laboratory findings from this study revealed C. violaceum as an emerging and an “underdiagnosed” pathogen causing human infections in Nigeria with ciprofloxacin identified as an effective empirical treatment. Follow-up of cases treated with microbiologically efficacious antibiotics indicates a good treatment outcome.
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    Open Access
    Characterization of Methicillin Resistant Staphylococcus haemolyticus Isolated from Neonatal, Postnatal and Labour Wards in Lagos, Nigeria
    (Pan African Journal of Life Sciences, 2019-03-21) Egwuatu, T; Olalekan, A; Orkeh, G; Egwuatu, T; Ogunsola, F
    Introduction: Staphylococcus haemolyticus is an important etiological agent of hospital infections but its epidemiological significance has not been studied in our institution. We therefore determine the prevalence, colonization rates and source of hospital-acquired Methicillin resistant Staphylococcus haemolyticus (MRSH) in La-gos, Nigeria. Methods: Axilla and umbilicus swab samples were collected from neonates (346), hand, nasal and axilla from health care workers (125), HVS from mothers (26) at the Lagos University Teaching Hospital (LUTH) and also samples from the environment (28). Using standard bacteriological methods, the samples were screened for S. haemolyticus. Possible person–to-person transmission was investigated by means of pulsed field gel electrophoresis. Results: Out of 525 samples collected, 112 (21.3%) were S. haemolyticus of which 17 (15.2%) were (MRSH). Neonates’ samples had 8 (15.0%) MRSH and 6 (30%) were Medical Doctors had their samples positive for MRSH. Also, 3 (11.1%) nurses’ samples were MRSH. None of the S. haemolyticus obtained from the mothers and the environment was MRSH. Pulsed field Gel Electrophoresis (PFGE) identified three main PFGE types (Type 1, 2 and 3) in the hospital. Type 1 and type 3 from babies in Neonatal unit. Type 2 and type 3 in babies from post-natal ward. Four doctors in the labour and neonatal wards had type 1 which was also recovered from a nurse on the labour ward. Conclusion: It appeared that the source of MRSH was from the hand and anterior nares of Healthcare workers in labour ward and Neonatal unit. This further highlights the need for proper infection control practice in the institution, especially single use of gloves for patients’ management.
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    Open Access
    Persistent Staphylococcus aureus nasal colonization in ambulatory HIV infected patients in Nigeria: Risk factors and molecular features
    (Journal of Microbiology, Immunology and Infection, 2016-12-01) Olalekan, A; Taiwo, S; Smith, S; Kolawole, D; Schaumburg, F
    This longitudinal study on Staphylococcus aureus colonization in Nigerian human immunodeficiency virus patients (n Z 187) found a trend towards a higher proportion of persistent S. aureus carriage in patients with advanced human immunodeficiency virus infection, low CD4þ cell counts, and a predominance of isolates belonging to ST8/spa-CC064 in persistent carriers.
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    Open Access
    High proportion of carbapenemase producing Escherichia coli and Klebsiella pneumoniae among extended spectrum β-lactamase producers in Nigerian
    (Journal of Global antimicrobial Resistance, 2019-09) Olalekan, A; Onwugamba, F; Iwalokun, B; Mellmann, A; Becker, K; Schaumburg, F
    Objectives: Carbapenem-resistant Enterobacterales are a global problem, however little is known about the burden and origin of carbapenem resistance in Africa. The objectives of this study were to determine the proportion of carbapenem-resistant isolates among extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E), to identify the underlying mechanisms of resistance and to assess the population structure of carbapenem-resistant isolates from Nigeria. Methods: ESBL-E isolates (n = 175) from infections were collected at four hospitals in Lagos, Nigeria, from July 2016 to January 2018 and were screened for carbapenem resistance using a VITEK12 automated system. All carbapenem-resistant ESBL-E (CRE) were screened for blaKPC, blaCTX-M, blaCMY-2, blaNDM, blaVIM, blaIMP, blaOXA-181 and blaOXA-48 genes. Genotyping of randomly selected isolates was performed by whole-genome sequencing. Results: The isolates included Escherichia coli (n = 113; 64.6%) and Klebsiella pneumoniae (n = 62; 35.4%). Of the 175 ESBL-E isolates, 48 (27.4%) were resistant to carbapenems (15 E. coli and 33 K. pneumoniae). CRE isolates carried blaNDM (n = 30; 62.5%), blaNDM + blaOXA-181 (n = 10; 20.8%), blaOXA-181 (n = 2; 4.2%) and blaNDM + blaOXA-48 (n = 1; 2.1%); no carbapenemase gene was detected in 5 isolates (10.4%). The isolates showed low diversity and were mainly associated with multilocus sequence typing (MLST) sequence types ST410 for E. coli and ST395 and ST147 for K. pneumoniae. Conclusion: Carbapenem resistance is frequent among ESBL-E in Nigeria and is mainly associated with blaNDM. Genotyping suggested that the observed clones possibly originated from Southeast Asia.