Putative mutations associated with tetracycline resistance detected in Treponema spp.: an analysis of 4,355 Spirochaetales genomes

Abstract

The resurgence of syphilis has necessitated novel prophylactic strategies, such as the use of doxycycline post-exposure prophylaxis. However, the potential for increased doxycycline use to select for tetracycline resistance represents significant challenges in managing this sexually transmitted infection. This study aims to identify chromosomal mutations associated with tetracycline resistance in Spirochaetales to inform molecular surveillance tools. Whole-genome sequences (WGSs) from the Spirochaetales order, including 4,355 genomes, were analysed for the presence of mutations in 16S rRNA and non-synonymous mutations in the rpsC and rpsJ genes. The study utilized WGS from GenBank® and sequence data from the PubMLST Treponema pallidum isolate collection. Genetic resistance to tetracycline was detected using a combination of blastn searches and gene-gene analysis. A transition mutation TGA to TGG at positions 965-967 in the 16S rRNA gene was detected in 5.6% of Treponema spp. and 4.0% of Spirochaeta spp. genomes. The rpsJ gene exhibited a V57G aa substitution across a significant subset of Treponema spp. (n=14) and Spirochaeta spp. (n=1). Notably, the V57K substitution was present in Spirochaeta spp. (n=17) and Treponema spp. (n=15). The rpsC gene had the H178Q mutation and was found to be present in the Spirochaetales bacterium (n=4). The identification of putative mutations associated with tetracycline resistance in Spirochaetales provides a foundation for the development of rapid molecular tests. This study underscores the complexity of antibiotic resistance mechanisms and the critical importance of surveillance of genetic resistance determinants in the era of antibiotic prophylaxis for sexually transmitted infection management.

Keywords: Treponema pallidum; doxycycline post-exposure prophylaxis (PEP); tetracycline resistance.

Fig. 1.. Flowchart describing genomes and sequences used in the analyses.

Fig. 2.. Bar graph showing the mutations detected in the 16S rRNA gene and substitutions in ribosomal proteins RpsJ (30S subunit protein S10) and RpsC (30S subunit protein S3). Light blue bars represent the total number of genomes analysed for each organism or group, while red squares indicate the number of genomes in which the corresponding mutation or substitution was detected. Mutation counts are annotated above each red square.