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Abstract Background The aac(6′)-Im (aacA16) amikacin, netilmicin and tobramycin resistance gene cassette had been circulating globally undetected for many years in a sublineage of Acinetobacter baumannii global clone 2. Objectives To identify sources for the aac(6′)-Im fragment found in A. baumannii. Methods MinION long-read sequencing and Unicycler hybrid assemblies were used to determine the genetic context of the aac(6′)-Im gene. Quantitative reverse transcriptase PCR was used to measure expression. Results Among 60 000 non-Acinetobacter draft genomes in the MRSN collection, the aac(6′)-Im gene was detected in Pseudomonas putida and Enterobacter hormaechei isolates recovered from patients in Thailand between 2016 and 2019. Genomes of multiply resistant P. putida MRSN365855 and E. hormaechei MRSN791417 were completed. The class 1 integron containing the aac(6′)-Im cassette was in the chromosome in MRSN365855, and in an HI2 plasmid in MRSN791417. However, MRSN791417 was amikacin susceptible and the gene was not expressed due to loss of the Pc promoter of the integron. Further examples of aac(6′)-Im in plasmids from or the chromosome of various Gram-negative species were found in the GenBank nucleotide database. The aac(6′)-Im context in integrons in pMRSN791417-8 and a Klebsiella plasmid pAMR200031 shared similarities with the aac(6′)-Im region of AbGRI2-Im islands in A. baumannii. In other cases, the cassette array including the aac(6′)-Im cassette was different. Conclusions The aac(6′)-Im gene is widespread, being found so far in several different species and in several different gene cassette arrays. The lack of amikacin resistance in E. hormaechei highlights the importance of correlating resistance gene content and antibiotic resistance phenotype.
Harmer et al. (Tue,) studied this question.