Characterization of microbial resistome in bacteria isolated from human, environmental and animal sources using DNA microarray technology and genome sequencing

Adbaru, Mulatu Gashaw (2024): Characterization of microbial resistome in bacteria isolated from human, environmental and animal sources using DNA microarray technology and genome sequencing. Dissertation, LMU München: Faculty of Medicine

Abstract

Background: Antimicrobial resistance (AMR) is a growing threat to public health globally. The impact is even worse in resource constrained countries. The occurrence of antimicrobial resistant bacteria in animals, the environment, and apparently healthy humans exacerbates the problem and serves as a reservoir for further dissemination. In the study area, Jimma, Ethiopia, there is no comprehensive data about the prevalence, diversity, and distribution of AMR in various sectors. Therefore, the current study aimed to address the existing scarce data related to AMR and to provide comprehensive information on the matter. Methods: A cross-sectional study design was employed to understand the prevalence, diversity, and distribution of AMR in bacteria isolated from clinical, animal, environmental, and apparently healthy human samples. All the bacterial isolates were re-identified with matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS). Antibiotic susceptibility testing (AST) was determined using the Kirby-Bauer disk diffusion method and Etest strips. The phenotype ESBL screening was done by double disc synergetic test (DDST) and Mast isks. Molecular characterization of Gram-negative bacteria (GNB) was performed by multiplex polymerase chain reaction (PCR) and deoxyribonucleic acid (DNA) microarray techniques. Result: A wide range of bacterial species were identified in samples obtained from patients, animals, the environment, and apparently healthy humans. E. coli (22.9%) was the most predominant isolate followed by Klebsiella species (21.1%), Enterobacter species (10.7%), and Acinetobacter species (12.5%). In GNB, a high rate of resistance against ampicillin (90%), cefuroxime (82%), amoxicillin-clavulanic acid (76%), piperacillin (75%), and cefotaxime (74%) was observed. Extended spectrum beta-lactamase (ESBL) producers were isolated in all sample categories. However, the prevalence and diversity were variable. The highest proportion was exhibited in clinical samples (76.6%) followed by environmental (49.2%) and animal samples (28.2%). The molecular analysis of GNB showed that blaCTX-M and blaNDM were the predominant acquired ESBLs and carbapenemase encoding genes, respectively. The co-existence of multiple resistance genes was observed in a lot of isolates. Conclusions: The findings revealed a high rate of resistant bacterial species in clinical, environmental, animal, and human samples from apparently healthy subjects. Various genes encoding for beta-lactam resistance were identified in all sample categories, predominantly was blaCTX-M and blaNDM.

• Item Type: Theses (Dissertation, LMU Munich)
• Keywords: Antimicrobial resistance, Antibiotic resistance, Beta-lactam resistance, Carbapenemase, Carbapenem-resistance, Extended spectrum β-lactamase, Jimma Medical Center, KPC, Methicillin resistant S. aureus, Multidrug resistance, NDM, OXA, Resistome
• Subjects: 600 Technology, Medicine; 600 Technology, Medicine > 610 Medical sciences and medicine
• Faculties: Faculty of Medicine
• Language: English
• Date of oral examination: 16. December 2024
• 1. Referee: Wieser, Andreas
• Signature of the printed copy: 0700/UMD 22229