A large conjugative Acinetobacter baumannii plasmid carrying the sul2 sulphonamide and strAB streptomycin resistance genes

Abstract

whole genome sequence data was used to determine the plasmid content of strain A297 32 (RUH875), the reference strain for the globally disseminated multiply resistant A. baumannii 33 clone, global clone 1(GC1). A297 contains three plasmids. Two known plasmids were 34 present; one, pA297-1 (pRAY*), carries the aadB gentamicin, kanamycin and tobramycin 35 resistance gene and another is an 8.7 kb cryptic plasmid often found in GC1 isolates. The 36 third plasmid, pA297-3, is 200 kb and carries the sul2 sulphonamide resistance gene and 37 strAB streptomycin resistance gene within Tn6172 and a mer mercuric ion resistance module 38 elsewhere. pA297-3 transfered sulphonamide, streptomycin and mercuric ion resistance at 39 high frequency to a susceptible A. baumannii recipient, and contains several genes potentially 40 involved in conjugative transfer. However, a relaxase gene was not found. It also includes 41 several genes encoding proteins involved in DNA metabolism such as partitioning. However, 42 a gene encoding a replication initiation protein could not be found. pA297-3 includes two 43 copies of a Miniature Inverted-Repeat Transposable Element (MITE), named MITE-297, 44 bracketing a 77.5 kb fragment, which contains several IS and the mer module. 45Several plasmids related to but smaller than pA297-3 were found in the GenBank 46 nucleotide database. They were found in different A. baumannii clones and are wide spread. 47They all contain either Tn6172 or a variant in the same position in the backbone as Tn6172 in 48 pA297-3. Some related plasmids have lost the segment between the MITE-297 copies and 49 retain only one MITE-297. Others have segments of various lengths between two MITE-297 50 copies, and these can be derived from the region in pA297-3 via a deletion adjacent to IS 51 related to IS26 such as IS1007 or IS1007-like. pA297-3 and its relatives represent a third type 52 of conjugative Acinetobacter plasmid that contributes to the dissemination of antibiotic 53 resistance in this species. 54

Crucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1

“…Otherwise, our experimental studies revealed that AbaR GI is maintained over time in A144 as well as in A155 without antimicrobial pressure for at least one month. We can assume that there is a balance between conservation and plasticity of particular regions of the accessory genome, as previously described for the core genome regions of A. baumannii (Touchon et al, 2014;Hamidian et al, 2016). The other remaining "sedentary" modules, the cas genes from the type IF-b CRISPR-Cas system, RGP1, and RGP4, did not show signs of microevolution.…”

Genomic and Phenotypic Analyses of Acinetobacter baumannii Isolates From Three Tertiary Care Hospitals in Thailand

“…Antibiotic resistance genes were detected with the curated version of the ARG-ANNOT database available at the SRST2 site (Gupta et al, 2014;Inouye et al, 2014), rpoB SNP mutations were assessed comparing the sequences against described resistance mutations (Giannouli et al, 2012;Pérez-Varela et al, 2017), and virulence factors with VFDB (Chen et al, 2016), using the read-based search program ARIBA (Hunt et al, 2017). Plasmid replicons were detected with a custom database composed of 30 genes involved in plasmid replication, stabilization and mobilization from Acinetobacter plasmids (Bertini et al, 2010;Salto et al, 2018); some additional plasmids (Gao et al, 2011;Hamidian et al, 2012Hamidian et al, , 2016Zhang et al, 2013;Jones et al, 2014;Blackwell and Hall, 2017;Hamidian et al, 2017) were also included (full database Supplementary Dataset S1); and analyses were undertaken using ARIBA software v2.12.1 (Hunt et al, 2017). To account for potential variation in surface proteins or other virulence factors, a custom-made collection of A. baumannii virulence factors ( Supplementary Table S6) was searched against our isolates using phmmer (Eddy, 2011;Eijkelkamp et al, 2011Eijkelkamp et al, , 2014Harding et al, 2013;Scott et al, 2014;Weber et al, 2015;Lee et al, 2017).…”

Small, Enigmatic Plasmids of the Nosocomial Pathogen, Acinetobacter baumannii: Good, Bad, Who Knows?

“…One of the key features of the A. baumannii genome is an open pan genome with a wide variety of mobile genetic elements, particularly integrons and transposons in genomic islands, some of which are known as resistance islands due to the presence of multiple antibiotic resistance genes ( Fournier et al, 2006 ; Bonnin et al, 2012 ; Ramírez et al, 2013 ). Resistance genes are also plasmid-borne and in A. baumannii , plasmids range from as small as 2 kb to more than 100 kb in size ( Gallagher et al, 2015 ; Hamidian et al, 2016a , b ). The large plasmids of A. baumannii are often the focus of analyses due mainly to the presence of multiple antibiotic resistance genes and the self-transmissible nature of these plasmids ( Hamidian et al, 2014a , b , 2016a ; Hamidian and Hall, 2014 ) although small plasmids have been highlighted especially those that harbor antibiotic resistance genes ( D’Andrea et al, 2009 ; Merino et al, 2010 ; Grosso et al, 2012 ; Hamidian et al, 2012 , 2016b ).…”

“…Resistance genes are also plasmid-borne and in A. baumannii , plasmids range from as small as 2 kb to more than 100 kb in size ( Gallagher et al, 2015 ; Hamidian et al, 2016a , b ). The large plasmids of A. baumannii are often the focus of analyses due mainly to the presence of multiple antibiotic resistance genes and the self-transmissible nature of these plasmids ( Hamidian et al, 2014a , b , 2016a ; Hamidian and Hall, 2014 ) although small plasmids have been highlighted especially those that harbor antibiotic resistance genes ( D’Andrea et al, 2009 ; Merino et al, 2010 ; Grosso et al, 2012 ; Hamidian et al, 2012 , 2016b ). Despite the importance of plasmids in the potential transmission of resistance and virulence genes in A. baumannii , there has been surprisingly very little experimental work done on the basic biology of these plasmids.…”