Identification of Global Clone 1 Lineage 3 (under progress)

Global Clone 1 Lineage 3 (GC1 L3) was first identified in 2021 based on the results of a genome-wide recombination-free single nucleotide polymorphism (SNP)-based phylogenitic analysis of selected GC1 isolates (Hamidian & Hall, 2021). In this study, GC1 L3 included only four A. baumannii isolates (5457, VB2486, VB29123, and VB24139) that were all collected in India. A few months later, comparitive analysis of the arrays of clustered regularly interspaced short palindromic repeats (CRISPR) of 187 isolates belonging to GC1 demonstrated a well-demarcated cluster of six CRISPR-based sequence types (CST), namely CST57, CST58, CST59, CST60, CST63, and CST66, that were linked to GC1 L3 (Karah et al., 2021). This cluster included a total of 8 isolates (5457, VB2486, SP2486, VB24139, Ab-Pak-Lah-14, Ab-Pak-Pesh-05, Ab-Pak-Pesh-37, and MRSN15049) obtained between 2013 and 2019 from Afghanistan, Pakistan, and India. 

The acquisition of unique CRISPR spacers (Ab-935 to Ab-940) was considered as a characteristic event in the evolution of the CSTs of GC1 L3 (Karah et al., 2021). Accordingly, the nucleotide sequence of Ab-935 and the two surrounding repeats (GTTCATGGCGGCATACGCCATTTAGAAATTGCTTAACCTTCACGCCATTTGGATAAACTGGTTCATGGCGGCATACGCCA-TTTAGAAA) could be used as a BLASTn search query to screen whole-genome nucleotide databases for isolates belonging to GC1 L3.

GC1 L3 is also characterized by the occurence of bla_OXA-371 as their intrinsic bla_OXA-51-like gene. bla_OXA-371 has a nucleotide identity of 824/825 to bla_OXA-69 (GenBank accession numbers NG_049662.1 and NG_049809.1), 

The GC1 L3 isolates are assigned into ST1^P (1, 1, 1, 1, 5, 1, 1), ST623^P (1, 1, 2, 1, 5, 1, 1), and ST1106^P (2, 1, 2, 1, 5, 1, 1).

As of January 2023, our in-silico screening enabled us to detect 30 isolates that might belong to GC1 L3 (Table 1). The genomic records of these isolates either had Ab-935 and the two surrounding repeats, were positive for bla_OXA-371 (100% nucleotide identity), and/or belonged to ST623^P (1, 1, 2, 1, 5, 1, 1) or ST1106^P (2, 1, 2, 1, 5, 1, 1). 

The isolates were collected between 2013 and 2021 from Nepal (n=17), Pakistan (n=7), India (n=6), Afghanistan (n=1), and Bangladesh (n=1). One isolate was collected in Sweden!

Phylogenetic delineation (under progress)

Phenotypic and genotypic features (under progress)

Most of the GC1 L3 isolates are resistant to ≥3 classes of antibiotics and can be described as either multidrug-resistant or extensively drug-resistant (Galac et al., 2020; Karah et al., 2020; Vijayakumar et al., 2022).

most of the isolates (maybe all the isolates) have ISAba1 upstream of their intrinsic ampC genes.

Some isolates have ISAba1-ampC-8 or ISAba1-ampC-3. The nucleotide identity of ampC-8 (1167 bp) is 100% identical to ampC-3 (1152 bp) apart from having a duplicated segment of 15 nucleotides ().

A. baumannii isolate VB2486 (also known as AB28) carried four antibiotic resistance genes on the chromosome (Vijayakumar et al., 2022), namely: strA, strB, blaNDM−1, and sul2. In addition, VB2486 had 6 plasmids, on which additional four resistance genes were detected (blaOXA-23, mphE, msrE, and aphA6).

Tn6171-v1, a 49124-bp long transposon, was detected in the chromosome of A. baumannii strain 5457 (GenBank: CP045541.1) downstream of glmS surrounded by a target site duplication of 5 bp (AAGGC).

In addition to the transposition genes, Tn6171 contains genes encoding proteins with iron acquisition, metabolism, efflux pumps and regulatory predicted functions ().  

which is a variant of a Tn7-family transposon that carries genes for synthesis and uptake of the fimsbactin siderophore system, with other L3 members (VB24319, VB29123 and VB2486) carry another variant called Tn6171-v2 [38]. SP2486, which clusters with VB24319, VB29123 and VB2486, also carries the same variant, Tn6171-v2. However, MRSN15049 (recovered in Afghanistan) does not carry Tn6171 or a variant of Tn6171, indicating that it has evolved differently and that the acquisition of fimsbactin encoding transposons is associated with L3 strains recovered in India.

References

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