Fluoroquinolone resistance in the environment and the human gut – Analysis of bacterial DNA sequences to explore the underlying genetic mechanisms

Doctoral thesis, 2014

Fluoroquinolones (FQs) are synthetic, broad-spectrum antibiotics that target type II topoisomerases. High-level resistance is often caused by mutations in the target genes of FQs, especially in gyrA and parC. In contrast, plasmid-mediated resistance genes, such as qnr, often confer moderate levels of resistance. Several sites near Patancheru, India, have been previously shown to be severely contaminated with FQs. To study how environmental bacteria adapt to this extreme environment, we first used whole-genome sequencing (454) of a highly multi-drug resistant strain of Ochrobactrum intermedium. The strain was isolated from a wastewater treatment plant (WWTP) in Patancheru that treats industrial effluent from pharmaceutical production. The strain was considerably more resistant to tetracyclines, sulphonamides, and FQs than to other O. intermedium strains, and it had, accordingly, acquired a tetracycline efflux pump, a sulphonamide resistance gene, and mutations in the target genes for FQs. In the second study, sequencing (Illumina) was used to characterise horizontally transferrable resistance plasmids captured from bacterial communities sampled from a lake with a history of FQ pollution, near Patancheru. All transconjugants had acquired qnr genes and this is, to the best of our knowledge, the first time qnrVC1 has been described on a conjugative plasmid. Furthermore, the bacteria from the lake sediments were significantly more resistant to FQs and sulphonamides compared to bacteria from Indian and Swedish reference lakes. In the third study, the Escherichia communities inhabiting a stream in Patancheru receiving WWTP effluent with high levels of FQs were tested for resistance mutations in gyrA and parC using amplicon sequencing (454). A stream receiving municipal WWTP effluent in Skövde, Sweden, and a remote highland lake were included as references. To our surprise, all communities showed high abundances of FQ resistance mutations, suggesting that these mutations are not associated with a fitness cost in the studied environments. The same method was utilised in the fourth study, on faecal samples collected from Swedish students before and after travel to India. The abundance of the amino acid substitution S83L in GyrA increased significantly, and the number of observed genotypes decreased after travel. This finding shows that international travel contributes to the spread of bacteria carrying chromosomal resistance mutations. Taken together, the development and spread of antibiotic resistance from antibiotic-polluted environments is a concern for everyone.