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Background  Chlamydiae are intracellular bacteria that cause various severe diseases in humans and animals. The common treatment for chlamydia infections are antibiotics. However, when antibiotics are misused (overuse or self-medication), this may lead to resistance of a number of chlamydia species, causing a real public health problem worldwide.    Materials and methods  In the present work, a comprehensive literature search was conducted in the following databases: PubMed, Google Scholar, Cochrane Library, Science direct and Web of Science. The primary purpose is to analyse a set of data describing the genes and mutations involved in Chlamydiae resistance to antibiotic mechanisms. In addition, we proceeded to a filtration process among 704 retrieved articles, then finished by focusing on 24 studies to extract data that met our requirements.    Results  The present study revealed that  Chlamydia trachomatis  may develop resistance to macrolides via mutations in the  23S rRNA ,  rplD ,  rplV  genes, to rifamycins via mutations in the  rpoB  gene, to fluoroquinolones via mutations in the  gyrA ,  parC  and  ygeD  genes, to tetracyclines via mutations in the  rpoB  gene, to fosfomycin via mutations in the  murA  gene, to MDQA via mutations in the secY gene. Whereas,  Chlamydia pneumoniae  may develop resistance to rifamycins via mutations in the  rpoB  gene, to fluoroquinolones via mutations in the  gyrA  gene. Furthermore, the extracted data revealed that  Chlamydia psittaci  may develop resistance to aminoglycosides via mutations in the  16S rRNA  and  rpoB  genes, to macrolides via mutations in the  23S rRNA  gene. Moreover,  Chlamydia suis  can become resistance to tetracyclines via mutations in the  tet(C)  gene .  In addition,  Chlamydia caviae  may develop resistance to macrolides via variations in the  23S rRNA  gene. The associated mechanisms of resistance are generally: the inhibition of bacteria’s protein synthesis, the inhibition of bacterial enzymes’ action and the inhibition of bacterial transcription process.    Conclusion  This literature review revealed the existence of diverse mutations associated with resistance to antibiotics using molecular tools and targeting chlamydia species’ genes. Furthermore, these mutations were shown to be associated with different mechanisms that led to resistance. In that regards, more mutations and information can be shown by a deep investigation using the whole genome sequencing. Certainly, this can help improving to handle chlamydia infections and healthcare improvement by decreasing diseases complications and medical costs.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12941-021-00465-4.

An overview of genes and mutations associated with Chlamydiae species’ resistance to antibiotics