Detection of multidrug-resistant organisms of concern including Stenotrophomonas maltophilia and Burkholderia cepacia at a referral hospital in Kenya.

Regular monitoring of bacterial susceptibility to antibiotics in clinical settings is key for ascertaining the current trends as well as re-establish empirical therapy. This study aimed to determine bacterial contaminants and their antimicrobial susceptibility patterns from medical equipment, inanimate surfaces and clinical samples obtained from Thika Level V Hospital (TLVH), Thika, in Central Kenya. Three hundred and five samples were collected between the period of March 2021 to November 2021 and comprised urine, pus swabs, catheter swabs, stool, and environmental samples. Bacterial identification and antimicrobial susceptibility were performed using VITEK 2 and disc diffusion respectively. We observed that Coagulase-negative Staphylococci (28 /160, 17.5%) were the most commonly isolated species from clinical samples followed by E. coli (22 /160 13.8%) and S. aureus (22/160, 13.8%). The bed rails were the mostly contaminated surface with S. aureus accounting for 14.2% (6/42). Among the clinical samples, pus swabs yielded the highest number of pathogens was pus (92/160). Trauma patients had the highest proportion of isolates (67/160, 41.8%). High level of antimicrobial resistance to key antimicrobials, particularly among Enterobacterales was observed. Extended Spectrum Beta Lactamase (ESBL) phenotype was noted in 65.9% (29/44) of enteric isolates. While further ESBL genetic confirmatory studies are needed, this study highlights the urgent need for actions that mitigate the spread of antibiotic-resistant bacteria.

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

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.

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

Background: 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. Results: 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). Conclusion: 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.

Speciation and antifungal susceptibility of Candida isolates from diabetic foot ulcer patients in a tertiary hospital in Kenya.

Introduction: diabetic foot ulcer is the leading cause of hospital admissions, lower limb amputation and death among diabetic patients. Little information is available on fungal isolation in diabetic foot ulcer patients, especially in sub-Saharan Africa. This study aimed to describe Candida species infecting diabetic foot ulcers in patients receiving clinical care at Kenyatta National Hospital and assess their antifungal susceptibility profile. Methods: this was a cross-sectional study carried out at Kenyatta National Hospital among adult diabetic foot ulcer patients over a three-month period. Species identification of Candida was performed using VITEK - 2 System and further confirmed by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. Antifungal susceptibility testing was determined using VITEK-2 System. Data were analysed using WHONET and SPSS. Results: among the 152 study patients recruited, 98% (n=149) had type 2 diabetes. Sixty one percent of the participants were male. The mean age of the study participants was 50.7 years (SD 12.9). A total of 36 Candida species were isolated, of which 75% (n=27) were Candida albicans. Candida lusitaniae (8%, n=3) and C. dubliniensis (5%, n=2) were the predominant non-albicans Candida species. The overall prevalence of diabetic foot ulcer candidiasis was 20% (n=31). C. albicans isolates (26%) were resistant to caspofungin, fluconazole, micafungin, and voriconazole but highly susceptible to amphotericin B and flucytosine (81-96%). Non-albicans Candida species isolated were susceptible (90-100%) to a majority of the antifungal agents tested. Conclusion: Candida albicans was the predominant species isolated and showed low resistance rates to the commonly administered antifungal agents. There is need to include fungal diagnosis in the investigation of diabetic foot ulcer infection.

Assessment of independent comorbidities and comorbidity measures in predicting healthcare facility-onset Clostridioides difficile infection in Kenya.

INTRODUCTION: Clostridioides difficile is primarily associated with hospital-acquired diarrhoea. The disease burden is aggravated in patients with comorbidities due to increased likelihood of polypharmacy, extended hospital stays and compromised immunity. The study aimed to investigate comorbidity predictors of healthcare facility-onset C. difficile infection (HO-CDI) in hospitalized patients. METHODOLOGY: We performed a cross sectional study of 333 patients who developed diarrhoea during hospitalization. The patients were tested for CDI. Data on demographics, admission information, medication exposure and comorbidities were collected. The comorbidities were also categorised according to Charlson Comorbidity Index (CCI) and Elixhauser Comorbidity Index (ECI). Comorbidity predictors of HO-CDI were identified using multiple logistic regression analysis. RESULTS: Overall, 230/333 (69%) patients had comorbidities, with the highest proportion being in patients aged over 60 years. Among the patients diagnosed with HO-CDI, 63/71(88.7%) reported comorbidities. Pairwise comparison between HO-CDI patients and comparison group revealed significant differences in hypertension, anemia, tuberculosis, diabetes, chronic kidney disease and chronic obstructive pulmonary disease. In the multiple logistic regression model significant predictors were chronic obstructive pulmonary disease (odds ratio [OR], 9.51; 95% confidence interval [CI], 1.8-50.1), diabetes (OR, 3.56; 95% CI, 1.11-11.38), chronic kidney disease (OR, 3.88; 95% CI, 1.57-9.62), anemia (OR, 3.67; 95% CI, 1.61-8.34) and hypertension (OR, 2.47; 95% CI, 1.-6.07). Among the comorbidity scores, CCI score of 2 (OR 6.67; 95% CI, 2.07-21.48), and ECI scores of 1 (OR, 4.07; 95% CI, 1.72-9.65), 2 (OR 2.86; 95% CI, 1.03-7.89), and ≥ 3 (OR, 4.87; 95% CI, 1.40-16.92) were significantly associated with higher odds of developing HO-CDI. CONCLUSION: Chronic obstructive pulmonary disease, chronic kidney disease, anemia, diabetes, and hypertension were associated with an increased risk of developing HO-CDI. Besides, ECI proved to be a better predictor for HO-CDI. Therefore, it is imperative that hospitals should capitalize on targeted preventive approaches in patients with these underlying conditions to reduce the risk of developing HO-CDI and limit potential exposure to other patients.

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

INTRODUCTION: The contribution of Clostridioides difficile (formerly Clostridium difficile ) to the burden of hospital-associated infections (HAIs) remains undetermined in many African countries. AIM: This study aimed to identify a sensitive and readily adaptable C. difficile detection assay and to evaluate the C. difficile HAI risk in Kenya. METHODOLOGY: 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. RESULTS: 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. CONCLUSION: 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 .

High Prevalence of Multidrug-Resistant Clostridioides difficile Following Extensive Use of Antimicrobials in Hospitalized Patients in Kenya.

Introduction: Clostridioides difficile is a neglected pathogen in many African countries as it is generally not regarded as one of the major contributors toward the diarrheal disease burden in the continent. However, several studies have suggested that C. difficile infection (CDI) may be underreported in many African settings. The aim of this study was to determine the prevalence of CDI in hospitalized patients, evaluate antimicrobial exposure, and detect toxin and antimicrobial resistance profiles of the isolated C. difficile strains. Methods: In this cross-sectional study, 333 hospitalized patients with hospital-onset diarrhoea were selected. The stool samples were collected and cultured on cycloserine-cefoxitin egg yolk agar (CCEY). Isolates were presumptively identified by phenotypic characteristics and Gram stain and confirmed by singleplex real-time PCR (qPCR) assays detecting the species-specific tpi gene, toxin A (tcdA) gene, toxin B (tcdB) gene, and the binary toxin (cdtA/cdtB) genes. Confirmed C. difficile isolates were tested against a panel of eight antimicrobials (vancomycin, metronidazole, rifampicin, ciprofloxacin, tetracycline, clindamycin, erythromycin, and ceftriaxone) using E-test strips. Results: C. difficile was detected in 57 (25%) of diarrheal patients over the age of two, 56 (98.2%) of whom received antimicrobials before the diarrheal episode. Amongst the 71 confirmed isolates, 69 (97.1%) harbored at least one toxin gene. More than half of the toxigenic isolates harbored a truncated tcdA gene. All isolates were sensitive to vancomycin, while three isolates (2.1%) were resistant to metronidazole (MIC >32 mg/L). High levels of resistance were observed to rifampicin (65/71, 91.5%), erythromycin (63/71, 88.7%), ciprofloxacin (59/71, 83.1%), clindamycin (57/71, 80.3%), and ceftriaxone (36/71, 50.7.8%). Among the resistant isolates, 61 (85.9%) were multidrug-resistant. Conclusion: Multidrug-resistant C. difficile strains were a significant cause of healthcare facility-onset C. difficile infections in patients with prior antimicrobial exposure in this Kenyan hospital.

Antimicrobial susceptibility pattern of Acinetobacter isolates from patients in Kenyatta National Hospital, Nairobi, Kenya.

INTRODUCTION: Infection due to multidrug-resistant microorganisms is a growing threat in healthcare settings. Acinetobacter species specifically A. baumannii is increasingly becoming resistant to most antimicrobial agents recommended for treatment. This study aimed to determine the antimicrobial susceptibility pattern of Acinetobacter species isolated from patients in Kenyatta National Hospital. METHODS: We conducted a retrospective study based on VITEK 2 (BioMérieux) electronic records capturing identification and antimicrobial susceptibility of Acinetobacter isolates from patient samples analyzed between 2013 and 2015 at Kenyatta National Hospital microbiology laboratory. Generated data were analyzed using WHONET and SPSS. RESULTS: A total of 590 Acinetobacter isolates were analyzed. 85% of the isolates tested were multi-drug resistant (MDR). Among the 590 isolates, 273 (46%) were from tracheal aspirates and 285 (48%) from the critical care unit. A. baumannii was the most frequently isolated species with high susceptibility to amikacin (77%) and poor susceptibility to ciprofloxacin (69-76%), tobramycin (37%) and meropenem (27%). Both A. lwoffii and A. haemolyticus had high susceptibility to amikacin (80-100%) and meropenem (75-100%). CONCLUSION: A. baumannii is resistant to commonly administered antibiotics. There is need for continuous antimicrobial resistance surveillance especially in health care facilities and strengthening of antibiotic stewardship programmes which will contribute to enhancement of infection control policies.

Plasmid profiling and incompatibility grouping of multidrug resistant Salmonella enterica serovar Typhi isolates in Nairobi, Kenya.

OBJECTIVES: Plasmids harbour antibiotic resistance genes which contribute to the emergence of multidrug resistant pathogens. We detected the presence of plasmids in multidrug resistant Salmonella enterica serovar Typhi (S. Typhi) isolates from our previous study and consequently determined their incompatibility groups and possibility of conjugation transmission. Plasmids were extracted from 98 multidrug resistant S. Typhi isolates based on alkaline lysis technique. Plasmid incompatibility grouping was established by PCR replicon typing using 18 pairs of primers to amplify FIA, FIB, FIC, HI1, HI2, I1-Iγ, L/M, N, P, W, T, A/C, K, B/O, X, Y, F and FIIA replicons. Antibiotic resistance phenotypes were conjugally transferred from S. Typhi isolates with plasmids to Escherichia coli K12F strain devoid of plasmids. RESULTS: Approximately 79.6% of the MDR S. Typhi isolates were related to the existence of plasmids. We detected 93.6% of plasmids belonging to incompatibility (Inc) group HI1. The other incompatibility groups identified included IncFIC (16.7%), IncP (1.3%), and IncI1 (1.3%) which appeared together with Inc HI1. MDR S. Typhi isolated carried a homologous plasmid of incompatibility group HI1 most of which transferred the resistance phenotypes of ampicillin, tetracycline and chloramphenicol to the transconjugants.

Multi-drug resistant Salmonella enterica serovar Typhi isolates with reduced susceptibility to ciprofloxacin in Kenya.

BACKGROUND: Typhoid fever remains a public health concern in developing countries especially among the poor who live in informal settlements devoid of proper sanitation and clean water supply. In addition antimicrobial resistance poses a major challenge in management of the disease. This study assessed the antimicrobial susceptibility patterns of Salmonella enterica serotype Typhi (S. Typhi) isolated from typhoid fever cases (2004-2007). METHODS: A cross sectional study was conducted on 144 archived S. Typhi isolates (2004-2007) tested against 11 antimicrobial agents by quality controlled disk diffusion technique. Isolates resistant to ampicillin, chloramphenicol, and cotrimoxazole were considered Multidrug resistant (MDR). Thirty MDR isolates were selected randomly and further tested using minimum inhibitory concentration (MIC) E-test. RESULTS: Sixteen percent (23/144) of the isolates were susceptible to all the antibiotics tested while 68% were resistant to three or more of the 11 antibiotics tested. The isolates showed a high susceptibility to ceftriaxone (94%) and gentamicin (97%). A high percentage of resistance was observed for the conventional first-line antibiotics; ampicillin (72%), chloramphenicol (72%), and cotrimoxazole (70%). Sixty-nine percent of the isolates (100/144) showed reduced susceptibility to ciprofloxacin. All the 30 (100%) isolates selected for MIC test were susceptible to amoxicillin-clavulanic acid. All except one of the 30 isolates were susceptible to ceftriaxone while majority 21 (70%) recorded an intermediate susceptibility to ciprofloxacin with MIC of 0.12-0.5 µg/mL. CONCLUSION: A large proportion of S. Typhi isolates were MDR and also showed reduced susceptibility to ciprofloxacin. Fluoroquinolone resistance is emerging and this may pose a challenge in treatment of typhoid in future. There is need for routine surveillance to monitor this phenotype in clinical settings.