Genomic analysis and phylogenetic position of the complex IncC plasmid found in the Spanish monophasic clone of Salmonella enterica serovar Typhimurium

Abstract

AbstractpUO-STmRV1 is an IncC plasmid discovered in the Spanish clone of the emergent monophasic variant of Salmonella enterica serovar Typhimurium, which has probably contributed to its epidemiological success. The sequence of the entire plasmid determined herein revealed a largely degenerated backbone with accessory DNA incorporated at four different locations. The acquired DNA constitutes more than two-thirds of the pUO-STmRV1 genome and originates from plasmids of different incompatibility groups, including IncF (such as R100 and pSLT, the virulence plasmid specific of S. Typhimurium), IncN and IncI, from the integrative element GIsul2, or from yet unknown sources. In addition to pSLT virulence genes, the plasmid carries genes conferring resistance to widely-used antibiotics and heavy metals, together with a wealth of genetic elements involved in DNA mobility. The latter comprise class 1 integrons, transposons, pseudo-transposons, and insertion sequences, strikingly with 14 copies of IS26, which could have played a crucial role in the assembly of the complex plasmid. Typing of pUO-STmRV1 revealed backbone features characteristically associated with type 1 and type 2 IncC plasmids and could therefore be regarded as a hybrid plasmid. However, a rooted phylogenetic tree based on core genes indicates that it rather belongs to an ancient lineage which diverged at an early stage from the branch leading to most extant IncC plasmids detected so far. pUO-STmRV1 may have evolved at a time when uncontrolled use of antibiotics and biocides favored the accumulation of multiple resistance genes within an IncC backbone. The resulting plasmid thus allowed the Spanish clone to withstand a wide variety of adverse conditions, while simultaneously promoting its own propagation through vertical transmission.

Colistin Resistance in Monophasic Isolates of Salmonella enterica ST34 Collected From Meat-Derived Products in Spain, With or Without CMY-2 Co-production

“…Interestingly, a copy of IS26 is present in the IncX4 plasmid, close to the mcr-1.1 gene. In contrast to ISApl1, IS26, once gained by a plasmid or the chromosome, is able to proliferate, actively contributing to the generation of complex resistance regions containing multiple copies of the element (Harmer and Hall, 2014;He et al, 2015;Vazquez et al, 2021). It would be worth to follow the activity of IS26 within IncX4 plasmids carrying mcr-1.1.…”

Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the blaCTX-M-65 Gene with or without fosA3 in pESI-like Plasmids

“…The selective pressure caused by the use of heavy metals, and also of nalidixic acid, tetracyclines, sulfonamides and nitrofurans in livestock production, could have contributed to the selection of pESI-positive isolates of S . Infantis, as it was probably the case for other successful clones of different non-typhoidal serovars of S. enterica [ 13 , 18 , 19 , 20 , 21 ].…”

“…Typhimurium LSP 146/02 and S . Typhimurium 4,5,12:i:- (monophasic) LSP 389/97 were included as negative or positive controls [ 21 , 22 , 23 ].…”

“…S. enterica serovar Typhimurium strain LT2 was included as negative control. S. enterica serovar Typhimurium strain LSP 146/02 and S. enterica serovar 4,5,12:i:- strain LSP 389/97 were included as positive controls of resistance to some of the antimicrobials tested [ 21 , 22 , 23 ]. b , CTX, cefotaxime; NAL, nalidixic acid; CIP, ciprofloxacin; NIT, nitrofurantoin; FOS: fosfomycin.…”

“…Infantis isolate, the conjugative megaplasmid would rapidly become established in the local population because of the selective advantages it confers to the host bacteria [ 16 ]. Such advantages are not only provided by the presence of antibiotics resistance genes, but also by genes coding for resistances to quaternary ammonium compounds and heavy metals, which are likewise widespread in other successful clones of non-typhoid serovars of S. enterica [ 13 , 18 , 19 , 20 , 21 ]. Moreover, pESI-like megaplasmids also provide genes involved in colonization, virulence and fitness, including those encoding two types of fimbriae (Fim and K88-like) and the siderophore yersiniabactin, as well as toxin–antitoxin systems (like CcdBA, PemKI) [ 7 , 16 ].…”