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. 2020 Jul 18;75(10):2760–2768. doi: 10.1093/jac/dkaa266

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© The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 3. — AbGRI4 configuration in ST2/ST281 and other clonal lineages. (a) Pairwise alignments of AbGRI4 and genomic regions amongst: ABUH796 (AbGRI4 positive), ABUH773 (AbGRI4 negative) and the reference genomes A320 and ACICU (both AbGRI4 negative). The genomic regions shown were extracted from ABUH796: EP550_07130 to EP550_07335; ABUH773: EQH48_07125 to EQH48_07330; ACICU: DMO12_04152 to DMO12_04257; and A320: A320_02326 to A320_02291 and displayed using Easyfig.⁵² (b) Variants of AbGRI4 identified in ST2/ST281, the ST406 group and other isolates. All isolates shared a conserved region (15 kb) [not shown in (b)] upstream of the hydrolase gene spanning a DEAD/DEAH box helicase gene up to EP550_07130 in ABUH796 as indicated in panel (a) (see Figure S3 for extended alignment of the region). In ST25 (Group 1), an intact hydrolase gene was detected. For ST406 (Group 2), putative precursor or intermediate forms of AbGRI4 were identified. The isolates also carried a 20 kb genomic region downstream of AbGRI4 including an intact reductase gene. ST2 isolates (Group 3), including ABUH796 together with ABUH763 and ABUH793, were whole-genome sequenced and finished in this study and carried exemplar copies of AbGRI4 flanked by IS26 elements. The AbGRI4 in ABIsac_ColiR was flanked by a recombinase gene and an IS1326 element instead of IS26. The AbGRI4 in HUMC1 carried an aphA1b resistance gene, upstream of the AbGRI4, and an ISAba1 insertion in the 20 kb genomic region. In AR_0078, a completely different set of resistance genes was identified including aphA1b, msrE and mphE. AR_0078 carried a hydrolase gene fragment (AM457_11345), but the reductase gene was not detected in the corresponding region. The genomic regions bounded by the hydrolase and reductase genes were as follows: NIPH146, F979_RS13625 to F979_RS13685; HWBA8, B7L46_16170 to B7L46_16265; ABBL20, APC64_12840 to APC64_12940; PR379, B9Y25_04090 to B9Y25_04245; ABUH639, BTH23_04090 to BTH23_04235; ARLG1833, CAS91_11670 to CAS91_11825; ABUH796, EP550_07220 to EP550_07290; ABIsac_ColiR, BN50_RS06860 to BN50_RS06920; and HUMC1, AWC45_RS08085 to AWC45_RS08260. Alignments of the genomic regions were performed using Easyfig.⁵² The asterisk is representative of isolates ABUH763, ABUH793 and ABUH796. Isolates shown in blue were whole-genome sequenced and finished in this study; n.a., not available. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.