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

Molecular Characterization of Human Enteroviruses Detected in Children Under Five Years Old in Kenya 2009 - 2015

   Introduction:  Human enterovirus (HEVs) infection is common, with an extensive array of clinical displays ranging from asymptomatic to life-threatening. Presentation include nonspecific febrile illness often accompanied by muscle pain, sore throat, abdominal discomfort, rash, headache, encephalitis, aseptic meningitis and acute flaccid paralysis [2]. Objectives: The study objective was to investigate the natural selection and genetic variability of HEVs and to identify HEV serotypes in circulation among children below 5 years old with diarrhea in an informal settlement(Kibera) in Kenya. Methodology: Specimens (n=628) from a prospective cohort study assessing the incidence and etiology of diarrhea from 2009-2015 were analyzed. Enteric Taqman array cards (TAC) were used for initial screening where two hundred and nine (78%) tested positive for HEVs. Of these specimens, 72 (42%) had a cycle threshold (Ct) ≤30 and were tested by conventional PCR targeting the 3’ regions of the viral protein 1 (VP1) gene. A total of 48 (67%) underwent sequencing; 11 (23%) of which yielded nucleotide sequences. Phylogenetic analyses clustered the Kenyan serotypes to HEVs groups C, B and A. Evaluation of the VP1 amino acid sequences revealed numerous amino acid substitutions in relation to reference strains, which were confirmed to be due to natural selection by negative or positive selection. Conclusion: The Heterogeneous nature of stool samples is known to influence disparities in viral nucleic acid yields. TAC detected 209 of which 171 (82%) were confirmed positive for HEVs by real-time reverse transcription polymerase chain reaction (RRT-PCR), targeting the 5’ NTR regions. Therefore, the results may not be a representative of all circulating HEVs in the study area. Since this was a retrospective study of previously collected samples, it is possible that some HEVs strains may have failed to amplify

Profile: The Kenya Multi-Site Serosurveillance (KEMIS) collaboration

The Kenya Multi Site Serosurveillance (KEMIS) collaboration set out to implement an integrated, nationally representative, population-based program of serological surveillance for past infection for a number of important infectious diseases in Kenya. The project started in December 2021 and built on a portfolio of SARS-CoV-2 research conducted in 2020 and 2021. In this profile paper, we describe the background of the KEMIS collaboration, its aim and objectives, the Health and Demographic Surveillance System sites that were involved in data collection, and the key activities undertaken. We also explain how we established governance and management of the KEMIS collaboration, and reflect on opportunities, challenges, lessons learned, and future directions.</ns4:p

Additional file 1: Figure S1. of The contribution of respiratory pathogens to fatal and non-fatal respiratory hospitalizations: a pilot study of Taqman Array Cards (TAC) in Kenya

Schematic diagram of the two versions of Taqman array cards (TAC) used in the study. Table S1. Viral and bacterial pathogens detected using Taqman array cards (TAC) among non-fatal and fatal cases and asymptomatic controls, by age group, western Kenya, 2009-11. Table S2. Distribution of respiratory pathogens among cases (non-fatal and fatal) and corresponding asymptomatic controls in rural western Kenya, 2009-11. (DOCX 614 kb

Seroprevalence of Infections with Dengue, Rift Valley Fever and Chikungunya Viruses in Kenya, 2007.

Arthropod-borne viruses are a major constituent of emerging infectious diseases worldwide, but limited data are available on the prevalence, distribution, and risk factors for transmission in Kenya and East Africa. In this study, we used 1,091 HIV-negative blood specimens from the 2007 Kenya AIDS Indicator Survey (KAIS 2007) to test for the presence of IgG antibodies to dengue virus (DENV), chikungunya virus (CHIKV) and Rift Valley fever virus (RVFV).The KAIS 2007 was a national population-based survey conducted by the Government of Kenya to provide comprehensive information needed to address the HIV/AIDS epidemic. Antibody testing for arboviruses was performed on stored blood specimens from KAIS 2007 through a two-step sandwich IgG ELISA using either commercially available kits or CDC-developed assays. Out of the 1,091 samples tested, 210 (19.2%) were positive for IgG antibodies against at least one of the three arboviruses. DENV was the most common of the three viruses tested (12.5% positive), followed by RVFV and CHIKV (4.5% and 0.97%, respectively). For DENV and RVFV, the participant's province of residence was significantly associated (P≤.01) with seropositivity. Seroprevalence of DENV and RVFV increased with age, while there was no correlation between province of residence/age and seropositivity for CHIKV. Females had twelve times higher odds of exposure to CHIK as opposed to DENV and RVFV where both males and females had the same odds of exposure. Lack of education was significantly associated with a higher odds of previous infection with either DENV or RVFV (p <0.01). These data show that a number of people are at risk of arbovirus infections depending on their geographic location in Kenya and transmission of these pathogens is greater than previously appreciated. This poses a public health risk, especially for DENV

Use of Sentinel Surveillance Platforms for Monitoring SARS-CoV-2 Activity: Evidence From Analysis of Kenya Influenza Sentinel Surveillance Data

BackgroundLittle is known about the cocirculation of influenza and SARS-CoV-2 viruses during the COVID-19 pandemic and the use of respiratory disease sentinel surveillance platforms for monitoring SARS-CoV-2 activity in sub-Saharan Africa. ObjectiveWe aimed to describe influenza and SARS-CoV-2 cocirculation in Kenya and how the SARS-CoV-2 data from influenza sentinel surveillance correlated with that of universal national surveillance. MethodsFrom April 2020 to March 2022, we enrolled 7349 patients with severe acute respiratory illness or influenza-like illness at 8 sentinel influenza surveillance sites in Kenya and collected demographic, clinical, underlying medical condition, vaccination, and exposure information, as well as respiratory specimens, from them. Respiratory specimens were tested for influenza and SARS-CoV-2 by real-time reverse transcription polymerase chain reaction. The universal national-level SARS-CoV-2 data were also obtained from the Kenya Ministry of Health. The universal national-level SARS-CoV-2 data were collected from all health facilities nationally, border entry points, and contact tracing in Kenya. Epidemic curves and Pearson r were used to describe the correlation between SARS-CoV-2 positivity in data from the 8 influenza sentinel sites in Kenya and that of the universal national SARS-CoV-2 surveillance data. A logistic regression model was used to assess the association between influenza and SARS-CoV-2 coinfection with severe clinical illness. We defined severe clinical illness as any of oxygen saturation <90%, in-hospital death, admission to intensive care unit or high dependence unit, mechanical ventilation, or a report of any danger sign (ie, inability to drink or eat, severe vomiting, grunting, stridor, or unconsciousness in children younger than 5 years) among patients with severe acute respiratory illness. ResultsOf the 7349 patients from the influenza sentinel surveillance sites, 76.3% (n=5606) were younger than 5 years. We detected any influenza (A or B) in 8.7% (629/7224), SARS-CoV-2 in 10.7% (768/7199), and coinfection in 0.9% (63/7165) of samples tested. Although the number of samples tested for SARS-CoV-2 from the sentinel surveillance was only 0.2% (60 per week vs 36,000 per week) of the number tested in the universal national surveillance, SARS-CoV-2 positivity in the sentinel surveillance data significantly correlated with that of the universal national surveillance (Pearson r=0.58; P<.001). The adjusted odds ratios (aOR) of clinical severe illness among participants with coinfection were similar to those of patients with influenza only (aOR 0.91, 95% CI 0.47-1.79) and SARS-CoV-2 only (aOR 0.92, 95% CI 0.47-1.82). ConclusionsInfluenza substantially cocirculated with SARS-CoV-2 in Kenya. We found a significant correlation of SARS-CoV-2 positivity in the data from 8 influenza sentinel surveillance sites with that of the universal national SARS-CoV-2 surveillance data. Our findings indicate that the influenza sentinel surveillance system can be used as a sustainable platform for monitoring respiratory pathogens of pandemic potential or public health importance

A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania

<div><p>Introduction</p><p>In low-resource settings, empiric case management of febrile illness is routine as a result of limited access to laboratory diagnostics. The use of comprehensive fever syndromic surveillance, with enhanced clinical microbiology, advanced diagnostics and more robust epidemiologic investigation, could enable healthcare providers to offer a differential diagnosis of fever syndrome and more appropriate care and treatment.</p><p>Methods</p><p>We conducted a year-long exploratory study of fever syndrome among patients ≥ 1 year if age, presenting to clinical settings with an axillary temperature of ≥37.5°C and symptomatic onset of ≤5 days. Blood and naso-pharyngeal/oral-pharyngeal (NP/OP) specimens were collected and analyzed, respectively, using AFI and respiratory TaqMan Array Cards (TAC) for multi-pathogen detection of 57 potential causative agents. Furthermore, we examined numerous epidemiologic correlates of febrile illness, and conducted demographic, clinical, and behavioral domain-specific multivariate regression to statistically establish associations with agent detection.</p><p>Results</p><p>From 15 September 2014–13 September 2015, 1007 febrile patients were enrolled, and 997 contributed an epidemiologic survey, including: 14% (n = 139) 1<5yrs, 19% (n = 186) 5-14yrs, and 67% (n = 672) ≥15yrs. AFI TAC and respiratory TAC were performed on 842 whole blood specimens and 385 NP/OP specimens, respectively. Of the 57 agents surveyed, <i>Plasmodium</i> was the most common agent detected. AFI TAC detected nucleic acid for one or more of seven microbial agents in 49% of AFI blood samples, including: <i>Plasmodium</i> (47%), <i>Leptospira</i> (3%), <i>Bartonella</i> (1%), <i>Salmonella enterica</i> (1%), <i>Coxiella burnetii</i> (1%), <i>Rickettsia</i> (1%), and West Nile virus (1%). Respiratory TAC detected nucleic acid for 24 different microbial agents, including 12 viruses and 12 bacteria. The most common agents detected among our surveyed population were: <i>Haemophilus influenzae</i> (67%), <i>Streptococcus pneumoniae</i> (55%), <i>Moraxella catarrhalis</i> (39%), <i>Staphylococcus aureus</i> (37%), <i>Pseudomonas aeruginosa</i> (36%), Human Rhinovirus (25%), influenza A (24%), <i>Klebsiella pneumoniae</i> (14%), Enterovirus (15%) and group A <i>Streptococcus</i> (12%). Our epidemiologic investigation demonstrated both age and symptomatic presentation to be associated with a number of detected agents, including, but not limited to, influenza A and <i>Plasmodium</i>. Linear regression of fully-adjusted mean cycle threshold (C_t) values for <i>Plasmodium</i> also identified statistically significant lower mean C_t values for older children (20.8), patients presenting with severe fever (21.1) and headache (21.5), as well as patients admitted for in-patient care and treatment (22.4).</p><p>Conclusions</p><p>This study is the first to employ two syndromic TaqMan Array Cards for the simultaneous survey of 57 different organisms to better characterize the type and prevalence of detected agents among febrile patients. Additionally, we provide an analysis of the association between adjusted mean C_t values for <i>Plasmodium</i> and key clinical and demographic variables, which may further inform clinical decision-making based upon intensity of infection, as observed across endemic settings of sub-Saharan Africa.</p></div

Clinical presentation of febrile patients aged 18–35 years seeking outpatient care in Mtwapa or Kilifi (February 2014- January 2015) with and without dengue virus infection (N = 489).

<p>Clinical presentation of febrile patients aged 18–35 years seeking outpatient care in Mtwapa or Kilifi (February 2014- January 2015) with and without dengue virus infection (N = 489).</p

Demographic and clinical characteristics of study participants (N = 489).

<p>Demographic and clinical characteristics of study participants (N = 489).</p