International Clones of High Risk of Acinetobacter Baumannii—Definitions, History, Properties and Perspectives

Abstract

Acinetobacter baumannii is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of A. baumannii is driven by several lineages named ‘international clones of high risk’ (ICs), two of which were first revealed in the 1970s. Epidemiological surveillance is a crucial tool for controlling the spread of this pathogen, which currently increasingly involves whole genome sequencing. However, the assignment of a particular A. baumannii isolate to some IC based on its genomic sequence is not always straightforward and requires some computational skills from researchers, while the definitions found in the literature are sometimes controversial. In this review, we will focus on A. baumannii typing tools suitable for IC determination, provide data to easily determine IC assignment based on MLST sequence type (ST) and intrinsic blaOXA-51-like gene variants, discuss the history and current spread data of nine known ICs, IC1-IC9, and investigate the representation of ICs in public databases. MLST and cgMLST profiles, as well as OXA-51-like presence data are provided for all isolates available in GenBank. The possible emergence of a novel A. baumannii international clone, IC10, will be discussed.

Genomic Epidemiology Dataset for the Important Nosocomial Pathogenic Bacterium Acinetobacter baumannii

“…These results are typical since IC2 is known to be the most successful and widespread clone of A. baumannii, being responsible for the majority of outbreaks worldwide [25]. The dominating ST was, not surprisingly, ST2, which constituted most of IC2 and was revealed in 63.3% (11,108) of cases. ST1 (3.59%, IC1) and ST499 (3.4%, NOIC) were also in the top three.…”

“…Another commonly used database, PubMLST [10], contains epidemiologically related and typing information for more than 8700 isolates, but the number of available genomes is about 3300 (https://pubmlst.org/ organisms/acinetobacter-baumannii, accessed on 23 October 2023). At the same time, as we described earlier, the assignment of a particular isolate to some international clone is not always straightforward, even when whole-genome data are available [11], and, to the best of our knowledge, no public database currently presents such assignment for large isolate datasets.…”

“…We already used this dataset to study the representation of known international clones in Genbank [11]. Deriving all this information from the available genomes requires an advanced level of bioinformatics expertise and significant computational resources.…”

“…'IC' stands for 'international clone of high risk' and shows the assignment of a particular isolate to know international clones. The procedure for such an assignment is described in the Methods section and our previous publication [11]. If an isolate is not assigned to any IC, this column has the 'NOIC' designation.…”

“…Some general statistics based on the dataset are provided below. As was noted previously [11,24], a Genbank set of genomes cannot be considered representative of the whole A. baumannii population since it is strongly biased towards multidrug-resistant or other clinically relevant isolates. At the same time, the statistics on particular STs, ICs, AMR genes, etc., can provide useful information for reference set selection and comparison purposes.…”