Lillian Musila

United States Army Medical Research Directorate - Africa

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Cecilia Kyany’a

Wellcome Sanger Institute

Erick Odoyo

United States Army Medical Research Directorate - Africa

Rosemary Sang

International Centre of Insect Physiology and Ecology

Collins Kigen

United States Army Medical Research Directorate - Africa

Daniel Matano

Kenya Medical Research Institute

Martin Georges

United States Army Medical Research Directorate - Africa

Justin Nyasinga

Aga Khan University Nairobi

Willie Sang

United States Army Medical Research Directorate - Africa

Valerie Oundo

United States Army Medical Research Directorate - Africa

Samoel Khamadi

Kenya Medical Research Institute

Cooperative Institutions

Institute for Health Metrics and Evaluation

376

University of Washington

373

University of Sydney

Kenya Medical Research Institute

University of Electronic Science and Technology of China

Veterans Health Administration

Institute for Musculoskeletal Health

United States Army Medical Research Directorate - Africa

Royal North Shore Hospital

Tehran University of Medical Sciences

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High levels of toxigenic Clostridioides difficile contamination of hospital environments: a hidden threat in hospital-acquired infections in Kenya

Access Microbiology (2020)

Erick Odoyo Cecilia Kyany’a Winnie Mutai Lillian Musila

The contribution of Clostridioides difficile (formerly Clostridium difficile ) to the burden of hospital-associated infections (HAIs) remains undetermined in many African countries.This study aimed to identify a sensitive and readily adaptable C. difficile detection assay and to evaluate the C. difficile HAI risk in Kenya.Sterile swabs in neutralizing buffer were used to sample equipment or surfaces that patients and clinical staff touched frequently. These swabs were either plated directly on chromogenic agar or cultured in an enrichment broth before plating. The swab suspensions, enrichment broth and plate cultures were screened by quantitative PCR (qPCR) to determine the most efficient detection method. The HAI risk was evaluated by testing the C. difficile -positive samples by qPCR for the A, B and binary toxins.C. difficile was detected on 4/57 (7.0 %) equipment and surfaces by direct culture. The additional enrichment step increased the detection rate 10-fold to 43/57 (75.4 %). In total, 51/57 (89.5 %) environmental samples were positive for C. difficile detected through either culture or qPCR. The genes encoding the primary toxins, tcdA and tcdB, were detected on six surfaces, while the genes encoding the binary toxins, cdtA and cdtB, were detected on 2/57 (3.5 %) and 3/57 (5.3 %) surfaces, respectively. Different C. difficile toxin gene profiles were detected: the tcdA+/tcdB- gene profile on 4/10 (40 %) high-touch surfaces, tcdA-/tcdB+ on 3/10 (30 %) surfaces, tcdA+/tcdB+/cdtA+/cdtB+ on 2/10 (20 %) surfaces and tcdA-/tcdB+/cdtB+ on one high-touch surface.The widespread contamination of hospital environments by toxigenic C. difficile gives a strong indication of the high risk of C. difficile infections (CDIs). The two-step culture process described can easily be adapted for monitoring hospital environment contamination by C. difficile .

Clostridioides

Chromogenic

GeneXpert MTB/RIF

Pore-forming toxin

Diarrhoeal disease

Clinical Microbiology

10.1099/acmi.0.000171

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Citations (4)

Genomic Epidemiology of Multidrug-Resistant Escherichia coli and Klebsiella pneumoniae in Kenya, Uganda, and Jordan

Emerging infectious diseases (2024)

Denis K. Byarugaba Tamer Saied Osman Omar Sayyouh Godfrey Wokorach Collins Kigen

Surveillance of antimicrobial resistance in Kenya, Uganda, and Jordan identified multidrug-resistant high-risk bacterial clones: Escherichia coli sequence types 131, 1193, 69, 167, 10, 648, 410, 405 and Klebsiella pneumoniae sequence types 14, 147, 307, 258. Clones emerging in those countries exhibited high resistance mechanism diversity, highlighting a serious threat for multidrug resistance.

Klebsiella infections

Molecular Epidemiology

10.3201/eid3014.240370

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Citations (1)

Determination of Enterococcus faecalis and Enterococcus faecium Antimicrobial Resistance and Virulence Factors and Their Association with Clinical and Demographic Factors in Kenya

Journal of Pathogens (2022)

Martin Georges Erick Odoyo Daniel Matano Fredrick Tiria Cecilia Kyany’a

Enterococci are clinically significant because of their increasing antibiotic resistance and their ability to cause severe infections due to an arsenal of virulence genes. Few studies in the developing world have examined virulence factors that may significantly impact patient outcomes. This study describes the antimicrobial resistance profiles and prevalence of five key Enterococcal virulence genes gelE, asa, cylA, esp, and hyl in forty-four clinical Enterococcus faecalis and E. faecium isolates in Kenya and their association with patients' demographic and clinical characteristics.All E. faecium isolates were obtained from hospital-acquired skin and soft tissue infections. While E. faecalis was associated with community-acquired urinary tract infections. All isolates were resistant to erythromycin, whereas 11/44 (27.5%), 25/44 (56.8%), 28/44 (63.6%), 37/44 (84.1%), 40/44 (90.0%), and 43/44 (97.5%) were susceptible to tetracycline, levofloxacin, gentamicin, ampicillin, nitrofurantoin, and teicoplanin, respectively. All isolates were susceptible to tigecycline, vancomycin, and linezolid. There was little difference in the antibiotic resistance profiles between E. faecalis and E. faecium. The prevalence of the virulence genes among the 44 isolates were 27 (61.4%) for gelE, 26 (59.1%) for asa1, 16 (36.3%) for esp, 11 (25.0%) for cylA, and 1 (2.3%) for hyl. 72.9% of E. faecalis isolates had multiple virulence genes compared to 57% of E. faecium isolates with no virulence genes. The hyl gene was only detected in E. faecium, while cylA and asa1 were only detected in E. faecalis. A significant correlation was observed between the presence of asa1 and esp virulence genes and tetracycline resistance (P=0.0305 and 0.0363, respectively). A significant correlation was also observed between the presence of virulence genes gelE and asa1 and nitrofurantoin resistance (P=0.0175 and 0.0225, respectively) and ampicillin resistance (P=0.0005 and 0.0008, respectively).The study highlights the high levels of erythromycin resistance in E. faecalis and E. faecium, the demographic factors influencing the species distribution among patients, and the accumulation of multiple virulence genes in E. faecalis. The significant association of gelE, asa1, and esp virulence genes with drug resistance could explain the pathogenic success of E. faecalis and provides a guide for future studies.

Teicoplanin

Enterococcus faecalis

Linezolid

Enterococcus faecium

Nitrofurantoin

Tigecycline

10.1155/2022/3129439

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Citations (20)

Phenotypic and Genotypic Characteristics of Uropathogenic Escherichia coli Isolates from Kenya

Microbial Drug Resistance (2021)

Catherine Muriuki Lilian Ogonda Cecilia Kyany’a Daniel Matano Clement Masakhwe

Introduction: Uropathogenic Escherichia coli (UPECs) are a significant cause of urinary tract infections (UTIs). In Kenya, UTIs are typically treated with β-lactam antibiotics without antibiotic susceptibility testing, which could accelerate antibiotic resistance among UPEC strains. Aim: This study determined the occurrence of UPEC producing extended-spectrum β-lactamases (ESBLs), the genes conferring resistance to β-lactams, and the phylogenetic groups associated with ESBLs in Kenyan UPECs. Methodology: Ninety-five UPEC isolates from six Kenyan hospitals were tested for ESBL and plasmid-mediated AmpC β-lactamase (pAmpC) production by combined disk diffusion and disk approximation tests, respectively. Real-time and conventional polymerase chain reactions (PCRs) were used to detect three ESBL and six pAmpC genes, respectively, and phylogenetic groups were assigned by a quadruplex PCR method. Results: Twenty-four percent UPEC isolates were ESBL producers with blaCTX-M (95.6%), blaTEM (95.6%), and blaSHV (21.7%) genes detected. Sixteen isolates had blaCTX-M/TEM, whereas five had blaTEM/CTX-M/SHV. A total of 5/23 ESBLs were cefoxitin resistant, but no AmpC genes were detected. The UPECs belonged predominantly to phylogenetic groups B2 (31/95; 32.6%) and D (30/95; 31.6%), while groups B2 and A had the most ESBL producers. Conclusions: β-Lactam antibiotics have reduced utility for treating UTIs as a quarter of UPECs were ESBL producing. Single or multiple ESBL genes were present in UPECs, belonging primarily to phylogenetic groups B2 and A.

Sulfamethoxazole

Beta-lactamase

10.1089/mdr.2020.0432

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Citations (20)

Staphylococcus aureus from three geographical regions of Kenya reveals distinct spa diversity

Cecilia Kyany’a Justin Nyasinga Valerie Oundo Daniel Matano Simon Waciira

Background : Staphylococcus aureus is an important cause of infections in Kenya. Spa typing is commonly used to classify S. aureus isolates and particular spa types have been associated with increased virulence and resistance globally. Data on spa diversity in Kenyan isolates are mostly from single – site studies therefore this study sought to determine the spa diversity, distribution and evolutionary relationships of isolates from three geographical regions of Kenya. Methods : Specimens from subjects with bacterial infections were collected from hospitals in Kericho, Nairobi and Kisumu counties and cultured. S. aureus isolates were identified using standard procedures. DNA was extracted and published primers used for PCR amplification of the variable X region of the spa gene. Amplicons were sequencing and spa types determined using Ridom StaphType. Evolutionary relationships were inferred by phylogenetic analysis using CLC bio software. Findings : Fifty four S. aureus isolates were identified. Of these, 64.81% (35/54) were assigned a spa type, while 14.81% (8/54) had novel spa types. Overall, 16 known spa types were identified. t355 was the most dominant and was found in both Kericho and Nairobi. t064 was the leading spa type in Kisumu. Kericho had the greatest spa type diversity with 10 different types. Each region had unique combinations of spa types with minimal spa type overlap between regions. Phylogeny showed close relatedness among isolates within a given region with common ancestry from the globally distributed t355 type. Conclusions : The study showed a significant spa type diversity among S. aureus isolates in Kenya with distinct geographical profiles suggestive of independent evolution of isolates in each region from a common strain type. The detection of known and novel spa types contributes to our understanding of the local diversity of S. aureus isolates and allows for identification and targeted monitoring of strains associated with drug resistance and virulence.

Kenya

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Validation of two methods for the detection, identification and quantification of arboviruses in resource-limited settings

International Journal of Infectious Diseases (2012)

Lillian Musila A. Nyunja Albina Makio E. Koskei Samoel Khamadi

Background: Recent Rift Valley Fever and Dengue outbreaks and the detection of arboviruses in vectors point to the real threat of arboviral disease in Kenya. Current methods for identifying and isolating these viruses include tissue culture, EIAs or conventional PCR. These methods are limited by difficulty in identifying novel or multiple infections, time to diagnosis, assay reliability and reproducibility and the availability and cost of stocking reagents for these rare and episodic diseases. In this study we evaluated whether the Evagreen© dye for real-time PCR and automated cell monitoring systems could address these challenges. Methods: Chikungunya virus was inoculated into Vero cells and monitored for cytopathic effects (CPE) daily using standard microscopy or in real-time using the xCELLigence® system which detects changes in electrode impedence caused by adherent cells. Reverse-transcribed viral RNA was detected by conventional PCR or by quantitative real-time PCR with Evagreen® dye. A virus neutralization test for Chikungunya using sero-positive human serum was performed using standard plaque assays and the xCELLigence® system. The financial and time investments, quality and reliability of results were determined for each method. Results: Viral cultures monitored by microscopy required ∼ 40 minutes of staff time daily with CPE detected at day 3 and confirmed by a second 3-day passage. On xCELLigence®, CPE was detected by 40hrs with a signature proliferation profile that could be distinguished from cellular anomalies and other virus profiles and required ∼5 minutes of staff time daily to monitor. The alternate methods for virus neutralization and antigen detection gave more consistent and reliable results compared to the conventional assays and reduced personnel times by ∼50%, assay times by ∼ 2X, and minimized reagent use significantly by capturing real-time data electronically. Conclusion: The xCELLigence® system and real-time PCR using Evagreen® dye adopted for the detection and quantification of viruses and diagnosis of arboviral infections delivered significant gains in timeliness of reporting, quality and quantity of data outputs. In spite of high initial costs, the long-term savings on reagents and human resource are ideal for resource-limited laboratories to achieve sustainable and quality arbovirus diagnostic and research outputs.

Vero cell

Rift Valley Fever

10.1016/j.ijid.2012.05.540

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Citations (0)

Phage banks as potential tools to rapidly and cost-effectively manage antimicrobial resistance in the developing world

Current Opinion in Virology (2022)

Tobi E. Nagel Lillian Musila Milkah Muthoni Mikeljon P. Nikolich Jesca Nakavuma

Pandemic

10.1016/j.coviro.2022.101208

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Citations (42)

The AFHSC-Division of GEIS Operations Predictive Surveillance Program: a multidisciplinary approach for the early detection and response to disease outbreaks

BMC Public Health (2011)

Clara J. Witt Allen L. Richards Penny Masuoka Desmond H. Foley Anna L. Buczak

The Armed Forces Health Surveillance Center, Division of Global Emerging Infections Surveillance and Response System Operations (AFHSC-GEIS) initiated a coordinated, multidisciplinary program to link data sets and information derived from eco-climatic remote sensing activities, ecologic niche modeling, arthropod vector, animal disease-host/reservoir, and human disease surveillance for febrile illnesses, into a predictive surveillance program that generates advisories and alerts on emerging infectious disease outbreaks. The program's ultimate goal is pro-active public health practice through pre-event preparedness, prevention and control, and response decision-making and prioritization. This multidisciplinary program is rooted in over 10 years experience in predictive surveillance for Rift Valley fever outbreaks in Eastern Africa. The AFHSC-GEIS Rift Valley fever project is based on the identification and use of disease-emergence critical detection points as reliable signals for increased outbreak risk. The AFHSC-GEIS predictive surveillance program has formalized the Rift Valley fever project into a structured template for extending predictive surveillance capability to other Department of Defense (DoD)-priority vector- and water-borne, and zoonotic diseases and geographic areas. These include leishmaniasis, malaria, and Crimea-Congo and other viral hemorrhagic fevers in Central Asia and Africa, dengue fever in Asia and the Americas, Japanese encephalitis (JE) and chikungunya fever in Asia, and rickettsial and other tick-borne infections in the U.S., Africa and Asia.

Rift Valley Fever

Disease Surveillance

International Health Regulations

Viral hemorrhagic fever

Public health surveillance

Preparedness

Emerging infectious disease

10.1186/1471-2458-11-s2-s10

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Citations (91)

The Detection of Spotted Fever Group Rickettsia DNA in Tick Samples From Pastoral Communities in Kenya

Journal of Medical Entomology (2017)

Hellen Koka Rosemary Sang Helen L. Kutima Lillian Musila

In this study, ticks from pastoral communities in Kenya were tested for Rickettsia spp. infections in geographical regions where the presence of tick-borne arboviruses had previously been reported. Rickettsial and arbovirus infections have similar clinical features which makes differential diagnosis challenging when both diseases occur. The tick samples were tested for Rickettsia spp. by conventional PCR using three primer sets targeting the gltA, ompA, and ompB genes followed by amplicon sequencing. Of the tick pools screened, 25% (95/380) were positive for Rickettsia spp. DNA using the gltA primer set. Of the tick-positive pools, 60% were ticks collected from camels. Rickettsia aeschlimannii and R. africae were the main Rickettsia spp. detected in the tick pools sequenced. The findings of this study indicate that multiple Rickettsia species are circulating in ticks from pastoral communities in Kenya and could contribute to the etiology of febrile illness in these areas. Diagnosis and treatment of rickettsial infections should be a public health priority in these regions.

Tick-borne disease

10.1093/jme/tjw238

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Citations (30)

Environmental contamination across multiple hospital departments with multidrug-resistant bacteria pose an elevated risk of healthcare-associated infections in Kenyan hospitals

Antimicrobial Resistance and Infection Control (2023)

Erick Odoyo Daniel Matano Fredrick Tiria Martin Georges Cecilia Kyany’a

Abstract Background Healthcare-associated infections (HAIs) are often caused by multidrug-resistant (MDR) bacteria contaminating hospital environments which can cause outbreaks as well as sporadic transmission. Methods This study systematically sampled and utilized standard bacteriological culture methods to determine the numbers and types of MDR Enterococcus faecalis / faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii , Pseudomonas aeruginosa, Enterobacter species, and Escherichia coli (ESKAPEE) from high-touch environments of five Kenyan hospitals; level 6 and 5 hospitals (A, B, and C), and level 4 hospitals (D and E), in 2018. Six hundred and seventeen high-touch surfaces across six hospital departments; surgical, general, maternity, newborn, outpatient and pediatric were sampled. Results 78/617 (12.6%) of the sampled high-touch surfaces were contaminated with MDR ESKAPEE; A. baumannii , 23/617 (3.7%), K. pneumoniae , 22/617 (3.6%), Enterobacter species, 19/617 (3.1%), methicillin resistant S. aureus (MRSA), 5/617 (0.8%), E. coli , 5/617 (0.8%), P. aeruginosa , 2/617 (0.3%), and E. faecalis and faecium , 2/617 (0.3%). Items found in patient areas, such as beddings, newborn incubators, baby cots, and sinks were the most frequently contaminated. Level 6 and 5 hospitals, B, 21/122 (17.2%), A, 21/122 (17.2%), and C, 18/136 (13.2%), were more frequently contaminated with MDR ESKAPEE than level 4 hospitals; D, 6/101 (5.9%), and E, 8/131 (6.1%). All the sampled hospital departments were contaminated with MDR ESKAPEE, with high levels observed in newborn, surgical and maternity. All the A. baumannii , Enterobacter species, and K. pneumoniae isolates were non-susceptible to piperacillin, ceftriaxone and cefepime. 22/23 (95.6%) of the A. baumannii isolates were non-susceptible to meropenem. In addition, 5 K. pneumoniae isolates were resistant to all the antibiotics tested except for colistin. Conclusion The presence of MDR ESKAPEE across all the hospitals demonstrated gaps in infection prevention practices (IPCs) that should be addressed. Non-susceptibility to last-line antibiotics such as meropenem threatens the ability to treat infections.

Medical microbiology

Kenya

10.1186/s13756-023-01227-x

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Citations (13)