Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2023

Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Strains Recovered from Chilean Hospitals Reveals Lineages Specific to South America and Multiple Routes for Acquisition of Antibiotic Resistance Genes (#147)

Jonathan Koong 1 , Barbra P Brito 1 , Aniela Wozniak Wozniak 2 3 4 , Andres Opazo-Capurro 3 5 , Joyce To 1 , Patricia Garcia 2 3 4 , Mehrad Hamidian 1
  1. Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
  2. Laboratory of Microbiology, Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
  3. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
  4. Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
  5. Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Facultad de Ciencias Biológicas, Concepción, Chile

Acinetobacter baumannii is a bacterial pathogen predominantly seen in health care settings, with many strains being resistant to carbapenems. The emergence of carbapenem resistance in A. baumannii is mainly due to the acquisition of mobile genetic elements (MGEs), including transposons, leading to the horizontal movement carbapenem resistance genes. However, while considered a global threat, studies into the emergence of resistance in South America is limited.

The genetic context of resistance genes in 34 A. baumannii strains recovered from two hospitals in Chile between 2010 and 2013 was determined. All genomes were sequenced using the Illimunia MiSeq system and the short reads assembled using Shovill. The genomes were analysing using bioinformatic software including, MLST, Prokka and ABRicate. For each sequence type (ST) present in this study, one representative was further sequenced using an Oxford Nanopore GridION flow cell to generate long reads. Long and short reads were assembled using Unicycler and the sequences analysed to determine the genetic context of resistance genes. Phylogenetic trees were generated for each ST using Snippy and Gubbins.

In total six STs were identified in the collection, ST1, ST15, ST138, ST79, ST162 and ST109 (Institut Pasteur scheme). Carbapenem resistance could be accounted for by the presence of the ISAba1 insertion sequence upstream of the intrinsic oxaAb gene and Tn2008 transposons carrying oxa23, inserted into chromosomes and plasmids. Similar mechanisms could account for resistance to other antibiotics. TnaphA6 transposons carrying the aphA6 kanamycin resistance gene, were either embedded within the chromosome or plasmid. Novel resistance island AbR36 contained the sul1, tet(A) and catA1 genes, providing resistance for sulphonamides, tetracycline and chloramphenicol respectively in ST1 strains.

Understanding the genetic context of resistance genes within South America, is crucial. This collection does not include any ST2, a sequence type responsible for the spread of carbapenem resistance globally. Also, phylogenetic analysis showed that these strains are unique to South America, having evolved differently to their North American counterparts. The diversity present within the small sample size highlights the unique nature of South American strains and the need for more research to be done to understand how resistance is spreading.