Molecular characterization of fluoroquinolone resistance genes in isolates obtained from patients with diarrhea in Machakos District Hospital, Kenya

Background: Diarrhea caused by Enterobacteriaceae such as Shigella species and Escherichia coli (E. coli) is endemic throughout the world, and is one of the most important causes of global childhood mortality and morbidity. There is a range of antibiotics that can be used for treatment among them quinolones. However, there is emerging increase in microbial resistance to quinolones use, with E. coli and Shigellae among the species of bacteria commonly associated with quinolone resistance. Objective: To investigate the prevalence of quinolone resistance genes in Shigellae and E. coli from patients presenting with diarrhea in Machakos District Hospital. Methods: Bacteria isolates were identified to species level by biochemical methods and serology and thereafter tested for 12 different antibiotics including quinolones, cephalosporins and aminoglycosides. Those resistant to quinolones with a zone diameter of ≤20 mm were tested for the presence of quinolone resistance genes using PCR. The gyrA resistance genes were further analyzed by sequencing to determine mutations within the quinolone resistance regions. Results: There were different E. coli pathotypes and Shigellae spp.  They resisted more than four antibiotics: Ciprofloxacin (4%), (Chloramphenical (28%), Cotrimoxazole (78%), Co-amoxilav (70%) Erythromycin (98%) Cefotoxime (18%) and Tetracycline (56%). Mutations responsible for fluoroquinolone resistance in the gyrA, gyrB, parC, and parE genes of E. coli and Shigella spp were: gyrA (17/30, 36%) gyrB (7/30, 23.3%) topoisomerase (parC 3/30, 10%) parE (3/30, 10%). Discussion: There is an increase in fluoroquinolone resistance in Shigellae and E.coli which points to a major challenge in current treatment strategies. In addition, detection of high resistance found to commonly used antibiotics should serve as a warning call for close surveillance and understanding of the epidemiology of the resistance. Key words: Quinolone antibiotics, resistance, Shigella, Escherichia col

The prevalence of TEM and SHV genes among Extended-Spectrum Beta-Lactamase-producing Klebsiella pneumoniae and Escherichia coli

Background: Antimicrobial resistance to cephalosporin, penicillin and aztreonam is mediated by Extended-Spectrum Beta-Lactamases (ESBL) via hydrolysis of antibiotics. The most common bacteria associated with ESBL among the Enterobacteriaceae are Escherichia coli and Klebsiella pneumonia. Pathogenic Escherichia coli is associated with diarrhoea affecting mostly elderly, children under five years and the immunocompromised. There are a number of antibiotic regimens for treatment among them cephalosporins. There is reported increase in microbial resistance to cephalosporin use and the resistance is mediated by either TEM or SHV genes. Objective: To investigate the prevalence of ESBL-producing E. coli and Klebsiella pneumonia from patients presenting with diarrhea in Machakos District Hospital, Kenya. Methods: Bacterial isolates were identified to species level by biochemical methods and tested for sensitivity to twelve different antibiotics including cephalosporins, aminoglycosides and quinolones. Those resistant to cephalosporins with a zone diameter of ≤20 mm were tested phenotypically for Extended Spectrum Beta Lactamase (ESBL) phantom development and confirmed by MicroScan. Resistant strains to cephalosporin were further tested for presence and frequency of TEM and SHV genes. Results: Out of the 200 K. pneumonia and 100 E.coli tested, 18 (6%) were positive for ESBL production phenotypically. These 18 (100 %) isolates demonstrated phantom phenomena phenotypically. Eight (4%) and 2 (1%) of the 200 K. pneumonia isolates had TEM and SHV resistant genes, respectively. There were 5 (5%) TEM and 3 (3%) SHV detected from 100 E. coli isolates. The 18 phenotypically detected and E-test-positive strains (10 Klebsiella spp. and 8 E. coli) were retested with VITEK (GNS-532 card), and 17 of these strains (94.4%) were subsequently found to be ESBL positive. One strain (5.6%) tested ESBL negative by VITEK. The cefotaxime ESBL strip detected the presence of ESBL activity in these 18 phenotypically-positive strains. Discussion: The detection of ESBL-producing E. coli and Klebsiella isolates from Machakos District Hospital was 6%. The findings point out the need for continuous surveillance to determine prevalence of ESBL-producing Enterobacteria strains for better management of diarrheal illness. Key words: Extended spectrum Beta Lactamases; Cephalosporin resistance genes; Enterobacteriacea

TparvaDB: a database to support Theileria parva vaccine development

We describe the development of TparvaDB, a comprehensive resource to facilitate research towards development of an East Coast fever vaccine, by providing an integrated user-friendly database of all genome and related data currently available for Theileria parva. TparvaDB is based on the Generic Model Organism Database (GMOD) platform. It contains a complete reference genome sequence, Expressed Sequence Tags (ESTs), Massively Parallel Signature Sequencing (MPSS) expression tag data and related information from both public and private repositories. The Artemis annotation workbench provides online annotation functionality. TparvaDB represents a resource that will underpin and promote ongoing East Coast fever vaccine development and biological research

Spatial-temporal distribution and sequence diversity of Group A human respiratory syncytial viruses in Kenya preceding the emergence of ON1 genotype

Background Human respiratory syncytial virus (HRSV) is a major cause of severe viral acute respiratory illness and contributes significantly to severe pneumonia cases in Africa. Little is known about its spatial–temporal distribution as defined by its genetic diversity. Methods A retrospective study conducted utilizing archived nasopharyngeal specimens from patients attending outpatient clinics in hospitals located in five demographically and climatically distinct regions of Kenya; Coast, Western, Highlands, Eastern and Nairobi. The viral total RNA was extracted and tested using multiplex real time RT-PCR (reverse transcriptase polymerase chain reaction). A segment of the G-gene was amplified using one-step RT-PCR and sequenced by Sanger di-deoxy method. Bayesian analysis of phylogeny was utilized and subsequently median joining methods for haplotype network reconstruction. Results Three genotypes of HRSVA were detected; GA5 (14.0%), GA2 (33.1%), and NA1 (52.9%). HRSVA prevalence varied by location from 33% to 13.2% in the Highlands and the Eastern regions respectively. The mean nucleotide diversity (Pi[π]) varied by genotype: highest of 0.018 for GA5 and lowest of 0.005 for NA1. A total of 58 haplotypes were identified (GA5 10; GA2 20; NA1 28). These haplotypes were introduced into the population locally by single haplotypes and additional subsidiary seeds amongst the GA2 and the NA1 haplotypes. Conclusions HRSVA was found across all the regions throughout the study period and comprised three genotypes; GA5, GA2, and NA1 genotypes. The genotypes were disproportionately distributed across the regions with GA5 gradually increasing toward the Western zones and decreasing toward the Eastern zones of the country

falciparum dihydrofolate reductase and

Trends in drug resistance codons in Plasmodiu

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The relationship between C- reactive protein and oral squamous cell carcinoma in a Kenyan Centre: A case control study

Background: Oral squamous cell carcinoma (OSCC) is the sixth most common cancer in the world with several aetiological factors including inflammation having been associated with the disease. Inflammatory markers including interleukin 6(IL-6) and C-reactive protein (CRP), have been shown to be elevated in OSCC and wide geographical variations have been reported. Information about the association between CRP and OSCC in Kenya is scanty in the published literature and therefore this study aimed to determine the relationship between the disease and CRP in a Kenyan population. Objectives: To determine the relationship between C-reactive protein and Oral Squamous cell carcinoma in a Kenyan centre. Study design: This was a case control study Study participants: Cases were patients who presented to the Kenyatta National Hospital with OSCC while age and gender matched controls were patients in the same hospital who did not have the disease. Results: Of the 157 cases 61.8% and 38.2% were males and females respectively, with mean age of 58 Years (SD 13.2 years). The mean CRP levels were 10.55mg/l and 20.92mg/l for cases and controls respectively and this difference was significant (critical ratio 3.91, p<0.01). After setting up different cut-off points of 3mg/l, 5mg/l and 10mg/l patients with OSCC had a significant likelihood of having CRP levels of greater than 5mg/l (OR=19.98, 95% CI 6.65-60.05) Conclusion: This study reveals that patients with OSCC are more likely to have systemic inflammation resulting in production of C-reactive proteins. Assessment of CRP would be valuable in the management of this disease

Sociodemographic, clinical and pathological features of oral squamous cell carcinoma in a Kenyan Centre

Background: Oral squamous cell carcinoma is the sixth most common cancer in the world and despite advances in medical care the survival trends for OSCC have not significantly improved over the years . Information about the sociodemographic, clinical and pathological presentation of OSCC in Kenya is scanty in the published literature. In order to further understand the disease this study aimed to determine the sociodemographic and clinicopathological features of OSCC in a Kenyan hospital population.Objectives: To determine the sociodemographic and Clinicopathological features of Oral Squamous cell Carcinoma (OSCC) at a Kenyan Centre.Study design: This was a descriptive prospective study.Study participants: Patients who presented with oral squamous cell carcinoma at the Kenyatta National Hospital, Nairobi.Results: Out of the 157 cases 61.8% and 38.2% were males and females respectively. Mean age of 58 Years. Majority were of cases were farmers while most the controls were in the informal sector. Pain was the most common symptom among the cases with 68.15% complaining of moderate to severe pain. Palpable submandibular and cervical lymph nodes were more common among those with lymphadenopathy. The well differentiated histological type was prevalent. Tongue was the most common site among all cases although OSCC had a predilection buccal mucosa among females.Conclusion: This study reveals that OSCC is predominantly a disease of the older male, pain a major symptom and tongue the most common site. Well differentiated carcinoma was predominant. We recommend further studies to determine the prognostic value of these features in this population