Acquisition and Spread of Antimicrobial Resistance: A tet(X) Case Study

Abstract

Understanding the mechanisms leading to the rise and dissemination of antimicrobial resistance (AMR) is crucially important for the preservation of power of antimicrobials and controlling infectious diseases. Measures to monitor and detect AMR, however, have been significantly delayed and introduced much later after the beginning of industrial production and consumption of antimicrobials. However, monitoring and detection of AMR is largely focused on bacterial pathogens, thus missing multiple key events which take place before the emergence and spread of AMR among the pathogens. In this regard, careful analysis of AMR development towards recently introduced antimicrobials may serve as a valuable example for the better understanding of mechanisms driving AMR evolution. Here, the example of evolution of tet(X), which confers resistance to the next-generation tetracyclines, is summarised and discussed. Initial mechanisms of resistance to these antimicrobials among pathogens were mostly via chromosomal mutations leading to the overexpression of efflux pumps. High-level resistance was achieved only after the acquisition of flavin-dependent monooxygenase-encoding genes from the environmental microbiota. These genes confer resistance to all tetracyclines, including the next-generation tetracyclines, and thus were termed tet(X). ISCR2 and IS26, as well as a variety of conjugative and mobilizable plasmids of different incompatibility groups, played an essential role in the acquisition of tet(X) genes from natural reservoirs and in further dissemination among bacterial commensals and pathogens. This process, which took place within the last decade, demonstrates how rapidly AMR evolution may progress, taking away some drugs of last resort from our arsenal.

Keywords: antimicrobial resistance; horizontal gene transfer; mobile genetic elements; natural reservoirs; next-generation tetracyclines; tetracyclines.

Figure 1

Phylogenetic reconstruction of flavin-dependent monooxygenase (FMO)/Tet X evolution produced with fast minimum evolution algorithm [46] using FMO and Tet X amino acid sequences predicted from gene sequences. The dataset of 76 non-redundant amino acid sequence was retrieved from GenBank using the Tet X2 sequence from Bacteroides fragilis (GenBank accession number WP_063856436) as a query (highlighted in yellow). Uncultured/environmental sample sequences were excluded from the analysis. Sequences were aligned using Constraint-based Multiple Alignment Tool (Cobalt) at the NCBI site (https://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi, accessed on 8 March 2021). Amino acid positions from 11 to 388 were used to construct the tree. FAD-dependent monooxygenase from Pedobacter sp. ASV28 (GenBank accession number WP_199119858.1) was used to root the tree. MULTISPECIES indicates that identical amino acid sequences were present in multiple species. The scale bar is in fixed amino acid substitutions per sequence position. Nodes and branches of the CFB group bacteria (Bacteroidetes phylum) are in blue, Gammaproteobacteria in yellow, Enterobacteria in green, and unspecified bacteria in grey.

Figure 2

Expansion of the branch with 31 organisms in Figure 1. All corresponding designations are the same as in Figure 1.

Figure 3

Schematic representation of tet(X) evolution.