Comparison of full gyrA, gyrB, parC and parE gene sequences between all Ureaplasma parvum and Ureaplasma urealyticum serovars to separate true fluoroquinolone antibiotic resistance mutations from non-resistance polymorphism

• Published in: Journal of antimicrobial chemotherapy 2009-09, Vol.64 (3), p.529-538
• Main Authors: Beeton, Michael L., Chalker, Victoria J., Kotecha, Sailesh, Spiller, O. Brad
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Amino Acid Substitution - genetics; Anti-Bacterial Agents - pharmacology; Antibiotics; Antibiotics. Antiinfectious agents. Antiparasitic agents; Bacteria; Bacterial Proteins - genetics; Biological and medical sciences; ciprofloxacin; Cluster Analysis; DNA gyrase; DNA Gyrase - genetics; DNA Mutational Analysis; DNA Topoisomerase IV - genetics; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; Drug resistance; Drug Resistance, Bacterial; Fluoroquinolones - pharmacology; genetic polymorphisms; Genomics; Genotype; Humans; Infant, Newborn; Medical sciences; Molecular Sequence Data; Mutation, Missense; Pharmacology. Drug treatments; Phylogeny; Polymorphism; Sequence Alignment; topoisomerase IV; United States; Ureaplasma; Ureaplasma - drug effects; Ureaplasma - genetics; Ureaplasma Infections - microbiology; Ureaplasma parvum; Ureaplasma urealyticum; Ureaplasma urealyticum - drug effects; Ureaplasma urealyticum - genetics
• ISSN: 0305-7453; 1460-2091
• DOI: 10.1093/jac/dkp218

Objectives To determine the role of amino acid substitutions in Ureaplasma GyrA, GyrB, ParC and ParE proteins in mediating fluoroquinolone resistance. Methods Nucleic acid sequences from gyrA, gyrB, parC and parE genes from all 14 Ureaplasma serovars were aligned. Full genome sequences for serovars 1, 3–7, 9 and 11–14 were available from the National Center for Biotechnology Information database and we sequenced the full topoisomerase genes from ciprofloxacin-susceptible reference strains of serovars 2, 8 and 10. Phylogenetic trees were constructed to analyse nucleotide sequence similarity. Deduced amino acid sequences were compared with all 33 previously reported fluoroquinolone-resistant strains to clarify true fluoroquinolone-resistance-associated substitutions. Results Non-resistance-associated polymorphisms were identified in GyrA (39), GyrB (26), ParC (107) and ParE (34) proteins. Phylogenetic analysis demonstrated species clustering for all genes, except parE in which serovars 4, 12, 10 and 13 formed a separate cluster more similar to Ureaplasma parvum than the remaining Ureaplasma urealyticum serovars. Examination of all previously reported fluoroquinolone-resistant strains found that one-third of identified residue substitutions could be attributed to normal species polymorphism; therefore, the mechanism of resistance for these strains is still undetermined. In particular, Glu or Asp at position 112 in GyrA and Ala or Thr at 125/136 in ParC were substitutions identified when U. urealyticum strain sequences were previously aligned with the published serovar 3 genome sequence. Conclusion Combining analysis of the recently available Ureaplasma genomes with sequences from the additional serovars has enabled us to clarify which substitutions found by previous investigators could potentially be responsible for fluoroquinolone resistance.