Antimicrobial resistance gene lack in tick-borne pathogenic bacteria

Abstract

Tick-borne infections, including those of bacterial origin, are significant public health issues. Antimicrobial resistance (AMR), which is one of the most pressing health challenges of our time, is driven by specific genetic determinants, primarily by the antimicrobial resistance genes (ARGs) of bacteria. In our work, we investigated the occurrence of ARGs in the genomes of tick-borne bacterial species that can cause human infections. For this purpose, we processed short/long reads of 1550 bacterial isolates of the genera Anaplasma (n = 20), Bartonella (n = 131), Borrelia (n = 311), Coxiella (n = 73), Ehrlichia (n = 13), Francisella (n = 959) and Rickettsia (n = 43) generated by second/third generation sequencing that have been freely accessible at the NCBI SRA repository. From Francisella tularensis, 98.9% of the samples contained the FTU-1 beta-lactamase gene. However, it is part of the F. tularensis representative genome as well. Furthermore, 16.3% of them contained additional ARGs. Only 2.2% of isolates from other genera (Bartonella: 2, Coxiella: 8, Ehrlichia: 1, Rickettsia: 2) contained any ARG. We found that the odds of ARG occurrence in Coxiella samples were significantly higher in isolates related to farm animals than from other sources. Our results describe a surprising lack of ARGs in these bacteria and suggest that Coxiella species in farm animal settings could play a role in the spread of AMR.

Figure 1

World map indicating the countries with at least one sample included in the analysis (red area). The countries with samples are the following: Australia, Austria, Belgium, Brazil, Canada, China, Denmark, Finland, France, Gambia, Germany, Ghana, Greece, Italy, Japan, Kazakhstan, Liechtenstein, Mexico, Namibia, Netherlands, Norway, Peru, Russia, Slovakia, Slovenia, South Korea, Spain, Sweden, Switzerland, Turkey, UK, USA, Zimbabwe. There were 142 samples without a designation on their country of origin.

Figure 2

Fourfold displays showing the difference between ARG positivity and farm animal origin, in the case of Coxiella burnetii (right-hand side) and the rest of the samples (without Francisella genus, left-hand side). The plot is visualising the contingency tables for these categories. Numbers in quadrants correspond to the number of observed cases in that category. Quarter circles are proportional to the ratio of the counts associated with the diagonal frequencies after standardisation. A significant imbalance is apparent in the case of Coxiella based on the 95% confidence bands around the quadrants, as the Fisher’s exact tests showed (p < 0.001) also (see the Results section for details).