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bioRxiv · 10.1101/2024.05.09.593323

Characterisation of the carbapenem-resistant Acinetobacter baumannii clinical reference isolate BAL062 (CC2:KL58:OCL1): resistance properties and capsular polysaccharide structure

Shashkov, A.·Arbatsky, N.·Senchenkova, S. N.·Dmitrenok, A.·Shneider, M. M.·Knirel, Y.·Hall, R. M.·Kenyon, J. J.
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Abstract

The carbapenem resistant Acinetobacter baumannii isolate BAL062 is a clinical reference isolate used in several recent experimental studies. It is from a ventilator associated pneumonia (VAP) patient in an intensive care unit at the Hospital for Tropical Diseases (HTD), Ho Chi Minh City, Vietnam in 2009. Here, BAL062 was found to belong to the B sub-lineage of global clone 2 (GC2) isolates in the previously reported outbreak (2008 and 2012) of carbapenem-resistant VAP A. baumannii at the HTD. While related sub-lineage B outbreak isolates were extensively antibiotic resistant and carry GC2-associated genomic resistance islands, AbGRI1, AbGRI2 and AbGRI3, BAL062 has lost AbGRI3 and three aminoglycoside resistance genes, armA, aacA4 and aphA1, leading to amikacin and kanamycin susceptibility. The location of Tn2008VAR found in the chromosome of this sub-lineage was also corrected. Like many of the outbreak isolates, BAL062 carries the KL58 gene cluster at the capsular polysaccharide (CPS) synthesis locus and an annotation key is provided. As information about K type is important for development of novel CPS-targeting therapies, the BAL062 K58-type CPS structure was established using NMR spectroscopy. It is most closely related to K2 and K93, sharing similar configurations and linkages between K units and contains the rare higher monosaccharide, 5,7-diacetamido-3,5,7,9-tetradeoxy-O_SCPLOWDC_SCPLOW-glycero-O_SCPLOWLC_SCPLOW-manno-non-2-ulosonic acid (5,7-di-N-acetyl-8-epipseudaminic acid; 8ePse5Ac7Ac), the 8-epimer of Pse5Ac7Ac (5,7-di-N-acetylpseudaminic acid). Inspection of publicly available A. baumannii genomes revealed a wide distribution of the KL58 locus in geographically diverse isolates belonging to several sequence types that were recovered over two decades from clinical, animal, and environmental sources. IMPORTANCEMany published experimental studies aimed at developing a clearer understanding of the pathogenicity of carbapenem resistant Acinetobacter baumannii strains currently causing treatment failure due to extensive antibiotic resistance are undertaken using historic, laboratory adapted isolates. However, it is ideal if not imperative that recent clinical isolates are used in such studies. The clinical reference isolate characterized here belongs to the dominant A. baumannii GC2 clone causing extensively resistant infections, and has been used in various recent studies. Correlation of resistance profiles and resistance gene data is key to identifying genes available for gene knockout and complementation analyses, and we have mapped the antibiotic resistance genes to find candidates. Novel therapies, such as bacteriophage or monoclonal antibody therapies, currently under investigation as alternatives or adjuncts to antibiotic treatment to combat difficult-to-treat CRAb infections often exhibit specificity for specific structural epitopes of the capsular polysaccharide (CPS), the outer-most polysaccharide layer. Here, we have solved the structure of the CPS type found in BAL062 and other extensively resistant isolates. As consistent gene naming and annotation are important for locus identification and interpretation of experimental studies, we also have correlated automatic annotations to the standard gene names.

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Shashkov, A., Arbatsky, N., Senchenkova, S. N., Dmitrenok, A., Shneider, M. M., Knirel, Y., Hall, R. M., Kenyon, J. J.. 2024-05-09. Characterisation of the carbapenem-resistant Acinetobacter baumannii clinical reference isolate BAL062 (CC2:KL58:OCL1): resistance properties and capsular polysaccharide structure. https://doi.org/10.1101/2024.05.09.593323

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