scholarly journals Molecular detection of Brucella spp. from broth culture of clinical samples in Nigeria: Its role in vaccine quality control

2009 ◽  
Vol 8 (21) ◽  
pp. 5661-5665 ◽  
Author(s):  
F Antiabong J ◽  
Yakubu B ◽  
A Owolodun O ◽  
Bertu W ◽  
A Ocholi R
2020 ◽  
Author(s):  
Teshager Dubie Tegegne ◽  
Tsedale Amare Mengiste

Abstract Background: Among the top listed economically important transboundary livestock diseases of cattle, foot and mouth disease (FMD) is the leading bottleneck in livestock production and productivity in Ethiopia. On the basis of FMDV active outbreak cases, a cross sectional study was undertaken to collect samples from January, 2019 to March, 2020 intended for isolation, serotyping and molecular detection of FMDV in the study district. Purposive sampling method was applied to select the study area for the reason that the presence of current active FMD outbreak case report during the study period. Totally, 27 FMD suspected clinical samples were collected from clinically affected study population during field outbreak. Out of 27 samples, 18 of them were inoculated on cultured Baby hamster kidney (BHK-21) monolayer cells and all 27 samples were tested using conventional RT-PCR and sets of specific universal primers. Finally, the PCR products were visualized with UV illumination and imaged with gel documentation system. Results: The current study result revealed that out of 18 clinical samples subjected to virus isolation, 72.2%(n=13) of these cultures exhibited FMDV induced cytopathic effect (CPE) and the identified serotype was SAT-2 FMD virus. Out of 27 clinical samples tested by conventional RT-PCR, only 12 FMDV samples were found to be FMDV positive by universal primers. Out of 27 clinical samples detected by conventional reverse transcription polymerase chain reaction (RT-PCR), only 12 FMDV samples were found to be FMDV positive by universal primers.Conclusions: Our study finding indicated FMDV is prevalent in the study area and FMDV serotype SAT-2 was the causality for the outbreaks of the disease in the study area. Hence, region wise regular FMD outbreaks investigation, further phylogenetic analysis and vaccine matching field isolates should be carried out to know in depth data about FMDV serotypes and topotypes involving in afar region of Ethiopia for effective vaccine development and control of the disease.


2021 ◽  
Vol 8 (9) ◽  
pp. 396-407
Author(s):  
Sheriff Wakil ◽  
Mustafa Alhaji Isa ◽  
Adam Mustapa

Multidrug resistance among Escherichia coli causing urinary tract infections (UTIs) and diarrhea are major public health problem worldwide which cause difficulty in treating the infections caused by Escherichia coli due to the high resistances. The study is aimed to determine the phenotypic and molecular detection of multidrug resistant E. coli isolated from clinical samples of patients attending selected Hospitals in Damaturu, Yobe State-Nigeria. Methods: Two hundred (200) clinical samples were collected aseptically from patient diagnosed with (100 stool samples) and UTI’s (100 urine samples) using sterile universal container. The samples were processed using standard microbiological methods for identification of E. coli. Samples were cultured on MacConkey agar (stool) and Cystine lactose electrolyte deficient agar (urine). The resulting colonies of isolates were further subculture on Eosin methylene blue agar for confirmatory and followed by gram stain, biochemical identification at Microbiology laboratory unit of Yobe State Specialist and Yobe State Teaching Hospital respectively. The antimicrobial susceptibility patterns were determined using Kirby-Bauer disc diffusion techniques and the phenotypic expression of extended spectrum beta-lactamases (ESBLs) were determined using modified double disc synergy test (MDDST) and also the three (3) resistance genes (blaTEM, accC1 and qnrA) were detected using polymerase chain reaction. Results: One hundred and twenty-two (122) isolates were resistant to antibiotics. The highest level of resistance was against amoxicillin (90.2%) while the least resistance was against sparfloxacin (24.3%). Thirty-seven (37) E. coli isolates shows MDR; the highest MDR was (24.3%) while least MDR was (5.4%). The PCR amplification of resistant genes (blaTEM, accC1 and qnrA) were detected on E. coli that shows positive ESBL and the bands were separated using agarose gel electrophoresis. Conclusion: The findings of this study show augmentin, ciprofloxacin and sparfloxacin are the most effective antibiotics against E. coli isolated from patients attending the two hospitals in Damaturu; who are diagnose with UTI and diarrheic infection. The resistant genes include; blaTEM, accC1 and qnrA coding for beta-lactam, aminoglycoside and quinolones were present in E. coli isolated from patients attending selected Hospitals in Yobe State, Nigeria. Keywords: Multidrug resistant, Escherichia coli, extended spectrum beta lactamase, resistance-associated genes, urinary tract infections, diarrheic.


2018 ◽  
Vol 10 (1) ◽  
Author(s):  
Rita Sembajwe ◽  
Tendai Shamu ◽  
Fortunate Machingura ◽  
Henry Chidawanyika

Objective: Understand the challenges that exist in the Zimbabwe health systems, that could be addressed through the integration of a Laboratory Information Management System (LIMS).Understand key aspects for consideration when selecting and adapting a LIMS in a resource limited setting.Showcase improvements in laboratory information management processes following adoption of a LIMS.Introduction: Zimbabwe's National Health Laboratory Services faces multiple challenges related to inadequate financial support and skilled human resources, insufficient infrastructure, and inefficient tracking of clinical samples collected by health facilities. The slow turnaround time and poor management of the sample testing process, as well as delivery of results remain critical challenges. Compounding these problems further is a manual system for tracking large volumes of samples. This laborious and time-consuming process is inefficient for management of high amounts of incoming medical samples, frequently resulting in incomplete and inaccurate data. Additionally, health facilities are unable to monitor clinical samples and results in transit, leading to misplaced samples and missing results. Furthermore, although the laboratory service runs on a tiered network system - with lower level laboratories referring surveillance samples to higher level laboratories, processing of samples is not fulfilled promptly. The solutions to these challenges are divergent - sometimes even pointing in different directions. To this end, the Zimbabwe Ministry of Health and Child Care (MoHCC) has identified and integrated a LIMS to improve tracking of samples from the time of collection through results delivery.Methods: Our methods included an environmental needs assessment, user requirement analysis, followed by a LIMS customization and integration. The overarching aim has been to integrate the electronic open source BIKA LIMS into Zimbabwe’s national health information systems (HIS), to improve laboratory information management.The user requirements gathering exercise, included focus group discussion meetings with potential LIMS users, and direct observations, to guide the establishment of LIMS specifications. The needs assessment focused on the system functionality. Specifically, it investigated those aspects that would improve the ability: to track clinical samples such as creating and activating an ‘alerting’ capability when results are not reported within the set turnaround time; for users to see lists and counts of clinical samples at various testing levels; to uniquely identify samples received in the laboratories. Guided by these requirements, an environmental scan of off-the-shelf and open source LIMS platforms was conducted to identify a few options for the Zimbabwe context. Primary factors for shortlisting included: an existing community of practice for support; interoperability; customizability and configurability; and local awareness of the platform. In a LIMS national user’s meeting, involving relevant levels of the health system (Laboratories, Central, Provincial and District hospitals), a review of LIMS platform options was performed to narrow down selections. It evaluated the extent to which the user requirements (Workflow, equipment interface, result management, inter-operable, quality control, and stock management) were being met. Based on the evaluation, a single system (LIMS) was selected, adopted and adapted for use at six representative laboratories, including Zimbabwe’s National Microbiology Reference Laboratory.On-Site classroom and desk-side training, for knowledge transfer to local LIMS users, characterised the implementation phase. Local champions were identified from laboratory technicians and equipped to offer first line support. Both on-site and remote support was provided to LIMS users. The monitoring phase is ongoing, using interview guides and LIMS user meetings to understand challenges and ways to improve the system.Results: A LIMS was successfully customized and integrated into Zimbabwe’s national health information system infrastracture in six regional laboratories, to improve overall laboratory information management, timeliness of reporting and quality control. Since its full implementation between 2013 and 2017, average turnaround time for results improved significantly from 10 to 21 days in 2013 to only 3 days in 2017. Data quality improved; the number of untested clinical samples reduced from an average of 6 in 100 in 2013, to average of less or equal to 1 in 100, in 2017 . Also, there have been observed improvements in Zimbabwe's laboratory information management workflow and results reporting. High user satisfaction and increased LIMS use have led to the demand for LIMS expansion to additional laboratories. The LIMS has also managed to reduce the time required to produce disease notification reports.Conclusions: LIMS are proving to be an effective method for tracking samples and laboratory results in low resource settings like Zimbabwe. LIMS has provided an efficient way for record, store, and track timely reporting of laboratory data, allowing for improved quality of data. Overall, LIMS has increased efficiency in laboratory workflow and introduced the ability to adequately track samples from time of collection.


2021 ◽  
Author(s):  
Alisen Ayitewala ◽  
Isaac Ssewanyana ◽  
Charles Kiyaga

Abstract BackgroundHIV genotyping has had a significant impact on care and treatment of HIV/AIDS. At clinical level, the test guides physicians on the choice of treatment regimens. At surveillance level, it informs policy on consolidated treatment guidelines and microbial resistance control strategies. Until recently, the conventional test has utilized Sanger sequencing (SS) method. Unlike Next Generation Sequencing (NGS), SS is limited by low data throughput and the inability of detecting low abundant drug resistant variants. NGS has the capacity to improve sensitivity and quantitatively identify low-abundance variants; in addition, it has the potential to improve efficiency as well as lowering costs when samples are batched. Despite the NGS benefits, its utilization in clinical drug resistance profiling is faced with mixed reactions. These are largely based on lack of a consensus regarding the quality control strategy. Nonetheless, transitional views suggest validating the method against the gold-standard SS. Therefore, we present a validation report of an NGS-based in-house HIV genotyping method against SS method in Uganda. ResultsSince there were no established proficiency test panels for NGS-based HIV genotyping, fifteen (15) clinical plasma samples for routine care were utilized. The use of clinical samples allowed for accuracy and precision studies. The workflow involved four (4) main steps; viral RNA extraction, targeted amplicon generation, amplicon sequencing and data analysis. Accuracy of 98% with an average percentage error of 3% was reported for the NGS based assay against the SS platform demonstrating similar performance. The coefficient of variation (CV) findings for both the inter-run and inter-personnel precision showed no variability (CV ≤0%) at the relative abundance of ≥20%. For both inter-run and inter-personnel, variation that affected the precision was observed at 1% frequency. Overall, for all the frequencies, CV registered a small range of (0-2%).Conclusion The NGS-based in-house HIV genotyping method fulfilled the minimum requirements that support its utilization for drug resistance profiling in a clinical setting of a low-income country. For more inclusive quality control studies, well characterized wet panels need to be established.


2019 ◽  
Author(s):  
James Thornton ◽  
George S. Watts ◽  
Ken Youens-Clark ◽  
Lee D. Cranmer ◽  
Bonnie L. Hurwitz

ABSTRACTInfections are a serious health concern worldwide, particularly in vulnerable populations such as the immunocompromised, elderly, and young. Advances in metagenomic sequencing availability, speed, and decreased cost offer the opportunity to supplement or replace culture-based identification of pathogens with DNA sequence-based diagnostics. Adopting metagenomic analysis for clinical use requires that all aspects of the pipeline are optimized and tested, including data analysis. We tested the accuracy, sensitivity, and resource requirements of Centrifuge within the context of clinically relevant bacteria. Binary mixtures of bacteria showed Centrifuge reliably identified organisms down to 0.1% relative abundance. A staggered mock bacterial community showed Centrifuge outperformed CLARK while requiring less computing resources. Shotgun metagenomes obtained from whole blood in three febrile neutropenia patients showed Centrifuge could identify both bacteria and viruses as part of a culture-free workflow. Finally, Centrifuge results changed minimally by eliminating time-consuming read quality control and host screening steps.AUTHOR SUMMARYImmunocompromised patients, such as those with febrile neutropenia (FN), are susceptible to infections, yet cultures fail to identify causative organisms ~80% of the time. High-throughput metagenomic sequencing offers a promising approach for identifying pathogens in clinical samples. Mining through metagenomes can be difficult given the volume of reads, overwhelming human contamination, and lack of well-defined bioinformatics methods. The goal of our study was to assess Centrifuge, a leading tool for the identification and quantitation of microbes, and provide a streamlined bioinformatics workflow real-word data from FN patient blood samples. To ensure the accuracy of the workflow we carefully examined each step using known bacterial mixtures that varied by genetic distance and abundance. We show that Centrifuge reliably identifies microbes present at just 1% relative abundance and requires substantially less computer time and resource than CLARK. Moreover, we found that Centrifuge results changed minimally by quality control and host-screening allowing for further reduction in compute time. Next, we leveraged Centrifuge to identify viruses and bacteria in blood draws for three FN patients, and confirmed suspected pathogens using genome coverage plots. We developed a web-based tool in iMicrobe and detailed protocols to promote re-use.


2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Teshager Dubie ◽  
Tsedale Amare

Background. On the basis of FMDV outbreak cases, a cross-sectional study was undertaken to collect samples from January 2019 to March 2020 intended for isolation, serotyping, and molecular detection of FMDV in the study district. The purposive sampling method was applied to select the study area for the reason of the presence of FMD outbreak case report during the study period. Totally, 27 FMD clinical samples were collected from affected study population during field outbreak. Out of 27 samples, 18 of them were inoculated on cultured Baby hamster kidney (BHK-21) monolayer cells, and all 27 samples were tested using conventional RT-PCR and sets of specific universal primers. Finally, the PCR products were visualized with UV illumination and imaged with gel documentation system. Results. The current study results revealed that out of 18 clinical samples subjected to virus isolation, 72.2% (n = 13) of these cultures exhibited FMDV-induced cytopathic effect (CPE) and the identified serotype was SAT-2 FMD virus. Out of 27 clinical samples tested by conventional RT-PCR, only 12 FMDV samples were found to be FMDV positive by universal primers. Out of 27 samples detected by conventional RT-PCR, only 12 FMDV samples were found to be FMDV positive by universal primers. Conclusions. Our study finding indicated that FMDV is prevalent in the study area and FMDV serotype SAT-2 was the causality for the outbreaks of the disease in the study area. Hence, region-wise FMD outbreak investigation, further phylogenetic analysis, and vaccine matching field isolates should be carried out for effective vaccine development to control the disease.


Author(s):  
Vladimir Ivovic ◽  
Marija Vujanic ◽  
Tijana Zivkovic ◽  
Ivana Klun ◽  
Olgica Djurkovic-Djakovic

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