Sir, The allele-specific PCR developed by Turton et al. is now widely used as a simple screen to detect Acinetobacter baumannii isolates that belong to one of the two clonal groups that are prevalent globally [global clones 1 and 2 (GC1 and GC2); European clones (ECs) I and II] and a third group that is largely found in Europe (EC III). This test involves two multiplex PCRs that detect specific alleles in three genes, blaOXA-Ab, csuE and ompA, that are characteristic of the two global clonal types; EC III yields specific amplicons in both PCRs. Recently a number of additional variant patterns have been reported. However, the relevance of these patterns has not been established by more detailed analysis. In the course of screening a large number of A. baumannii from Australian hospitals, we discovered a small set of multiply antibiotic-resistant isolates recovered from the same hospital in 2008 that yield two amplicons that are characteristic of GC1 isolates (SG2 in Turton et al.) and one (csuE) that is characteristic of GC2 (SG1 in Turton et al.). This combination has been designated SG6 and was found in a single isolate (A388) from a Greek hospital. The sequence of the blaOXA-Ab gene was determined for a single representative isolate, D13, and the allele was the same as that found in most GC1 isolates. We therefore examined the possibility that the Australian SG6 isolates were in fact members of the GC1 complex but with the csuE allele replaced. D13 was found to belong to ST109 (10-12-4-11-4-9-5) in the multilocus sequence typing scheme (http://pubmlst.org/ abaumannii/) hosted at the University of Oxford, which is a core GC1 type. As other Australian GC1 isolates in the ST109 cluster yielded a standard GC1 pattern in the allele-specific PCRs, we concluded that D13 had acquired a chromosomal segment that includes the csuE gene from another A. baumannii strain. To examine the sequence of the csuE gene, the 701 bp PCR amplicon from the SG1 multiplex was sequenced. The 662 bp sequence obtained after primer sequences were removed (GenBank accession number HM590877) differed from that found in sequenced GC1 isolates at 23 of the 662 nucleotide positions, and from that found in GC2 isolates at 18 positions. Thus the csuE gene of D13 is different and presumably derived from a different strain. We also examined the original SG6 isolate, A388 from Greece, which was kindly supplied by Dr Kevin Towner (Nottingham University Hospitals, NHS Trust, Nottingham, UK). A388 has recently been shown to belong to ST248 (10-18-4-11-4-11-5), and this is consistent with its assignment to GC1. However, we were unable to obtain an amplicon from the csuE gene using the allele-specific primers. We concluded that A388 had also acquired a chromosomal segment that includes the csuE gene from another A. baumannii strain, but that the event was distinct from the one that led to D13. Using mapping methods described previously, isolate D13 was shown to include a derivative of the AbaR3 island situated in the usual location for these genomic islands, in the comM gene. The sequences of comM adjacent to the left and right sides of the AbaR were also identical to those found in GC1 genomes and GC1 isolates, as described previously. D13 harbours a new AbaR island, AbaR8, that contains only the gene cassettes aacC1-orfP-orfQ-aadA1 and the sul1 gene in a class 1 integron, and the aphA1b gene in Tn6020 (Figure 1). Relative to AbaR3, AbaR8 has lost 17 852 bp, including the blaTEM and catA1 genes and the tet(A) determinant. The deletion extends from adjacent to the insertion sequence (IS) IS26 on the left side of Tn6020 (Figure 1) to within the mer module derived from Tn1696. In contrast, A388 carries all the antibiotic resistance genes found in AbaR3, again highlighting the differences between these two isolates, both of which had been assigned to SG6 using the allele-specific PCR test. We conclude that caution should be exercised before assuming that members of a particular SG are the same. The sequence of part of AbaR8, the blaOXA-Ab gene (allelic variant 69) and parts of the recA and csuE genes have been deposited in GenBank under accession number HM590877.
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Feb 26, 2024
Alberto Correa + 10
Open Access
