ResFinder and Evolution code written by Biel Garcias Puigserver
Summary and Graphs code written by Jessica Kan
Collaborators: Jade Allum, Maliha Hakim, and Jack Clark
Supervisors: Prof Samuel Sheppard, Billy Monteith, Dr Evangelos Mourkas, and Dr Ben Pascoe
Property of the University of Bath
Bacterial antimicrobial resistance (AMR) is increasing global concern. AMR occurs due to random mutations and can be acquired through transmissible plasmids. Selective pressures, such as overuse in farming, increase the rate of AMR. This study analysed trends in AMR for 16 Gram-negative oxidase-positive bacteria species. 57,905 isolate genomes collected from 1912-2022 were investigated. Firstly, Genome Comparator was used to find which ResFinder AMR genes were present in each bacterial species. This was then combined with metadata from PubMLST and BIGSdb Pasteur. Next, the data were processed and analysed using R. Out of the 17 antimicrobial classes investigated, beta-lactams had the highest overall level of resistance. Also, Pseudomonas aeruginosa had the widest range of resistance across antimicrobial classes. The continent and country with the highest percentage of AMR was Asia (25.9%) and Uzbekistan (35.3%), respectively. Additionally, environmental sources (62.5%) had the highest percentage of AMR. Overall, AMR of Gram-negative oxidase-positive bacteria is increasing, and new antibiotics may be required to tackle this problem in future.
| Bacterial species | Number of isolates |
|---|---|
| Bordetella spp. | 2085 |
| Borrelia spp. | 104 |
| Brucella spp. | 108 |
| Burkholderia cepacia complex | 1407 |
| Burkholderia pseudomallei | 843 |
| Chlamydiales spp. | 703 |
| Dichelobacter nodosus | 173 |
| Glaesserella parasuis | 289 |
| Haemophilus influenzae | 2632 |
| Helicobacter pylori | 643 |
| Leptospira spp. | 737 |
| Neisseria spp. | 41336 |
| Pseudomonas aeruginosa | 2689 |
| Treponema pallidum | 602 |
| Vibrio cholerae | 1664 |
| Vibrio parahaemolyticus | 1892 |