Chromosomal Integration of Huge and Complex blaNDM-Carrying Genetic Elements in Enterobacteriaceae

Abstract

In this study, a detailed genetic dissection of the huge and complex blaNDM-carrying genetic elements and their related mobile genetic elements was performed in Enterobacteriaceae. An extensive comparison was applied to 12 chromosomal genetic elements, including six sequenced in this study and the other six from GenBank. These 12 genetic elements were divided into five groups: a novel IME Tn6588; two related IMEs Tn6523 (SGI1) and Tn6589; four related ICEs Tn6512 (R391), Tn6575 (ICEPvuChnBC22), Tn6576, and Tn6577; Tn7 and its derivatives Tn6726 and 40.7-kb Tn7-related element; and two related IMEs Tn6591 (GIsul2) and Tn6590. At least 51 resistance genes, involved in resistance to 18 different categories of antibiotics and heavy metals, were found in these 12 genetic elements. Notably, Tn6576 carried another ICE Tn6582. In particular, the six blaNDM-carrying genetic elements Tn6588, Tn6589, Tn6575, Tn6576, Tn6726, and 40.7-kb Tn7-related element contained large accessory multidrug resistance (MDR) regions, each of which had a very complex mosaic structure that comprised intact or residual mobile genetic elements including insertion sequences, unit or composite transposons, integrons, and putative resistance units. Core blaNDM genetic environments manifested as four different Tn125 derivatives and, notably, two or more copies of relevant Tn125 derivatives were found in each of Tn6576, Tn6588, Tn6589, and 40.7-kb Tn7-related element. The huge and complex blaNDM-carrying genetic elements were assembled from complex transposition and homolog recombination. Firstly identified were eight novel mobile elements, including three ICEs Tn6576, Tn6577, and Tn6582, two IMEs, Tn6588 and Tn6589, two composite transposons Tn6580a and Tn6580b, and one integron In1718.

A Genomic and Bioinformatics View of the Classification and Evolution of Morganella Species and Their Chromosomal Accessory Genetic Elements Harboring Antimicrobial Resistance Genes

“…Numbers in brackets indicate nucleotide positions within the chromosomes of strains 11759 and 21164, respectively. Accession number of IS CR2 - floR unit ( 53 ) used as reference is CP042857 .…”

“…Numbers in brackets indicate nucleotide positions within the chromosomes of strains ZJG944, 229813, ZJD581, 81703, and 12034, respectively. Accession numbers of IS 26 – mef (B)– sul3 –IS 440 unit ( 60 ), chrA – orf98 unit ( 53 ), IS Ec29 – mph (E)–IS26 unit ( 61 ), Tn 6581c , Tn 4352 ( 62 ), Tn 5393c ( 63 ), and IS CR2 – floR unit ( 53 ) are FJ196385 , CP042858 , AF550415 , CP042857 , CP042858 , AF262622 , and CP042857 , respectively.…”

Genetic Characterization of Four Groups of Chromosome-Borne Accessory Genetic Elements Carrying Drug Resistance Genes in Providencia

“…Herein, a detailed sequence comparison ( Figure 10 ) was applied to the three Tn 1696 derivatives Tn 6910 , T1696RE PROV002 , and T1696RE PROV013 (identified as the inner components of Tn 6874 , Tn 6861 , and Tn 6876 , respectively; see above), together with Tn 1696 , 35 Tn 6338 , 36 and Tn 6909 22 derived from GenBank. Tn 1696 was one of the Tn 3 -family prototype unit transposons, and it was originally found in plasmid R1003 from Pseudomonas aeruginosa and contained a core backbone structure: IRL (inverted repeat left)– tnpA – tnpR (resolvase)– res (resolution site)– mer –IRR (inverted repeat right).…”

“… 19 The conjugal transfer of an IME from a donor cell into a recipient cell relies on the T4SS gene sets of a helper conjugative element such as an IncA/C conjugative plasmid. 20 So far, three distinct families of IMEs, namely Tn 6523 (SGI1), 21 Tn 6588 , 22 and Tn 6591 22 have been reported in Providencia .…”

“…ICEs and IMEs can be transferred in an intercellular manner, while the Tn 7 -family unit transposons use a “cut-and-paste” transposition mechanism to transfer intracellularly, which is typically promoted by the core transposition determents TnsA (endonuclease), TnsB (transposase), TnsC (transposition regulator), and TnsD plus TnsE (target-site selection proteins). 23 Tn 7 -family transposons have widely been found as the vectors of diverse antimicrobial resistance genes in Morganellaceae including Providencia rettgeri , 22 Enterobacteriaceae, 24 Pseudomonadaceae, 25 Burkholderiaceae, 26 Acinetobacter , 27 Shewanella , 24 Hahella , 24 Pelobacter , 24 Idiomarina , 24 Acidithiobacillus , 24 Neisseria (eg N. brasiliensis with an accession number CP046027), Nitrosomonas (eg N. stercoris with an accession number AP019755), and Bacillus . 24 …”