Comparative analysis of clinical breakpoints, normalized resistance interpretation and epidemiological cut-offs in interpreting antimicrobial resistance of Escherichia coli isolates originating from poultry in different farm types in Tanzania.

Introduction: Existing breakpoint guidelines are not optimal for interpreting antimicrobial resistance (AMR) data from animal studies and low-income countries, and therefore their utility for analysing such data is limited. There is a need to integrate diverse data sets, such as those from low-income populations and animals, to improve data interpretation. Gap statement: There is very limited research on the relative merits of clinical breakpoints, epidemiological cut-offs (ECOFFs) and normalized resistance interpretation (NRI) breakpoints in interpreting microbiological data, particularly in animal studies and studies from low-income countries. Aim: The aim of this study was to compare antimicrobial resistance in Escherichia coli isolates using ECOFFs, CLSI and NRI breakpoints. Methodology: A total of 59 non-repetitive poultry isolates were selected for investigation based on lactose fermentation on MacConkey agar and subsequent identification and confirmation as E. coli using chromogenic agar and uidA PCR. Kirby Bauer disc diffusion was used for susceptibility testing. For each antimicrobial agent, inhibition zone diameters were measured, and ECOFFs, CLSI and NRI bespoke breakpoints were used for resistance interpretation. Results: According to the interpretation of all breakpoints except ECOFFs, tetracycline resistance was significantly higher (TET) (67.8 -69.5 %), than those for ciprofloxacin (CIPRO) (18.6 -32.2 %), imipenem (IMI) (3.4 -35 %) and ceftazidime (CEF) (1.7 -45.8 %). Prevalence estimates of AMR using CLSI and NRI bespoke breakpoints did not differ for CEF (1.7 % CB and 1.7 % COWT), IMI (3.4 % CB and 4.0 % COWT) and TET (67.8 % CB and 69.5 % COWT). However, with ECOFFs, AMR estimates for CEF, IMI and CIP were significantly higher (45.8, 35.6 and 64.4 %, respectively; P<0.05). Across all the three breakpoints, resistance to ciprofloxacin varied significantly (32.2 % CB, 64.4 % ECOFFs and 18.6 % COWT, P<0.05). Conclusion: AMR interpretation is influenced by the breakpoint used, necessitating further standardization, especially for microbiological breakpoints, in order to harmonize outputs. The AMR ECOFF estimates in the present study were significantly higher compared to CLSI and NRI.

Assessment of hepatitis B vaccination status and hepatitis B surface antibody titres among health care workers in selected public health hospitals in Kenya.

Healthcare workers (HCWs) have a significant occupational risk of hepatitis B virus (HBV) infection. Vaccination remains the most effective measure recommended to avert the risk. However, there's limited information on hepatitis B vaccine uptake rates and the seroprotection status of HCWs, especially in sub-Saharan Africa. This study aimed to assess hepatitis B vaccination status and also seroprotection status of HCWs in three selected public hospitals in Kenya. This was a cross-sectional study carried out among HCWs at Kenyatta National Hospital (KNH), Naivasha and Mbagathi County hospitals. Data on participants' demographics and hepatitis B vaccination status was collected using an interviewer-guided questionnaire. Blood samples were collected and tested for hepatitis B surface antigen (HBsAg), hepatitis B surface antibodies (anti-HBs), and hepatitis B core antibodies (anti-HBc) using Enzyme Linked Immuno Sorbent Assay technique. Data were analyzed using Statistical Package for the Social Sciences (SPSS) and Graph pad prism. Of the 145 eligible HCWs, 120 (82.8%) were vaccinated, with 77 (53.1%) having received the recommended three doses. Three quarters (108/145) of the vaccinated HCWs were seroprotected (titres ≥10 mIU/ml) against HBV infection, while 16.6% were non-responders (titres <10 mIU/ml). Vaccination with more than two doses and HBV exposure were significantly associated with anti-HBs titre levels (P<0.05). HCWs who received less than 2 doses of the vaccine were 70% less likely to have high anti-HBs titre levels (aOR, 0.3; 95% CI, 0.1-0.8; P = 0.013). Nearly all HCWs were vaccinated against hepatitis B virus. The majority of all HCWs were seroprotected against hepatitis B virus but a number of them had an insufficient immunity to the virus despite vaccination or prior exposure. There's need to sensitize HCWs and enforce mandatory full vaccination as per the recommended vaccination schedule.

Genomic transmission analysis of multidrug-resistant Gram-negative bacteria within a newborn unit of a Kenyan tertiary hospital: A four-month prospective colonization study.

Objective: Multidrug-resistant organisms (MDRO), especially carbapenem-resistant organisms (CRO), represent a threat for newborns. This study investigates the colonization prevalence of these pathogens in a newborn unit at a Kenyan tertiary hospital in an integrated approach combining routine microbiology, whole genome sequencing (WGS) and hospital surveillance data. Methods: The study was performed in the Kenyatta National Hospital (KNH) in 2019 over a four-month period and included 300 mother-baby pairs. A total of 1,097 swabs from newborns (weekly), mothers (once) and the hospital environment were taken. Routine clinical microbiology methods were applied for surveillance. Of the 288 detected MDRO, 160 isolates were analyzed for antimicrobial resistance genes and phylogenetic relatedness using whole genome sequencing (WGS) and bioinformatic analysis. Results: In maternal vaginal swabs, MDRO detection rate was 15% (n=45/300), including 2% CRO (n=7/300). At admission, MDRO detection rate for neonates was 16% (n=48/300), including 3% CRO (n=8/300) with a threefold increase for MDRO (44%, n=97/218) and a fivefold increase for CRO (14%, n=29/218) until discharge. Among CRO, K. pneumoniae harboring bla NDM-1 (n=20) or bla NDM-5 (n=16) were most frequent. WGS analysis revealed 20 phylogenetically related transmission clusters (including five CRO clusters). In environmental samples, the MDRO detection rate was 11% (n=18/164), including 2% CRO (n=3/164). Conclusion: Our study provides a snapshot of MDRO and CRO in a Kenyan NBU. Rather than a large outbreak scenario, data indicate several independent transmission events. The CRO rate among newborns attributed to the spread of NDM-type carbapenemases is worrisome.

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.

Draft genome sequences of three emerging beta-lactamase-producing Escherichia coli in the camel production system in Northern Kenya.

We report the draft genome sequences and annotation of three beta-lactamase-producing Escherichia coli ( E.coli) strains isolated from fecal samples of healthy camels in Laikipia county, Kenya. This data adds to the online genome resources to support the ongoing antimicrobial resistance surveillance in the livestock-wildlife interface.

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.