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Fig. 6 | Genome Biology

Fig. 6

From: Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center

Fig. 6

The conservation of integrons and mobile units across the species vs the dynamic broader genetic context. The guidance trees are based on the core gene alignment for Klebsiella pneumoniae (a) and Enterobacter cloacae (b). The conservation of the genetic environment of the main acquired resistance genes blaCTX-M-15, blaTEM1, blaOXA1, aac(6′)-Ib-cr, and aac(3)-IIa was tested by mapping against the predominantly observed cassettes surrounding these genes as mobile units. Whilst blaCTX-M-15 moves by itself in the Tn2021 structure, and blaTEM-1 moves with a tnpR gene, the blaOXA-1, aac(6′)-Ib-cr, and cat (chloramphenicol-resistance) genes are conserved in an integron element and the aac(3)-IIa and tmrB (tunicamycin resistance) genes are conserved together. This highlights that even though there is high variability in the plasmid content, there is a core set of resistance gene cassettes that is stable in both populations, and strains very often carry all of them combined. Long-read assemblies (Pacbio) resolved the plasmid content and location of the CTX-M-15 gene in several representatives of Enterobacter spp. and Klebsiella spp., as indicated by the arrows to the core gene guide trees. The respective boxes illustrate the plasmid content with the Inc-type and their respective sizes. The arrow diagrams illustrate the location of the CTX-M-15 gene, which is highly mobile, and can be seen to be integrated into the chromosomes in three out of our nine examples, each at different locations, as well as on plasmids belonging to the IncR, IncFIB(K)/IncFIIK, IncHI2/IncHI2A, and IncHIB types

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