Betancor, Laura

Camou, Teresa

Chabalgoity, José Alejandro

Cordeiro, Nicolás F

Iriarte, Andrés

Vignoli, Rafael

Yim, Lucía

English

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Journal of Global Antimicrobial Resistance 20 (2020) 84–86Letter to the EditorContents lists available at ScienceDirectJournal of Global Antimicrobial Resistancejournal home page : www.e l sev ier .com/ loca te / jgarPlasmidome of a multiresistant Salmonellaenterica serovar Typhimurium isolate fromUruguaySir,We recently sequenced the genome of multiresistant Salmonellaenterica serovar Typhimurium strain STM3224 isolated from ahuman immunodeficiency virus (HIV)-positive patient in Mon-tevideo, Uruguay [1]. Here we describe the plasmidome of strainSTM3224 and compare it with similar enterobacterial plasmids.Plasmids were annotated using Rapid Annotation usingSubsystem Technology (RASTtk) and were manually curated usingArtemis 17.0.1 (https://www.sanger.ac.uk/science/tools/artemis).Plasmid multilocus sequence typing (pMLST) was performed usingpMLST 2.0 software (https://cge.cbs.dtu.dk/services/pMLST/),incompatibility (Inc) groups were determined using PlasmidFinder2.0 (https://cge.cbs.dtu.dk/services/PlasmidFinder/) and non-cod-ing RNAs (ncRNAs) were sought using the Rfam database (https://rfam.xfam.org/). Antimicrobial resistance genes were sought usingthe Comprehensive Antibiotic Resistance Database (CARD)(https://card.mcmaster.ca/). Plasmid transfer was assessed byconjugation assay.Strain STM3224 carried two plasmids (pUY_STM62 andpUY_STM96). Their complete nucleotide sequences were deposit-ed in GenBank under accession nos. MN241904 and MN241905,respectively.Plasmid pUY_STM62 belonged to IncN plasmid group, plasmidsequence type 5 (pST5) and was 62 060 bp in size with an averageG + C content of 51.2%. It harboured 77 predicted coding sequences(CDS) and a single ncRNA sequence. The backbone of pUY_STM62included replication, maintenance and conjugative transfer genes.Conversely, the variable region included three antimicrobialresistance gene modules and various mobile genetic elementsinserted in ‘integration hotspots’ (Fig. 1A).The first module, located between repA and uvp1, consisted ofthe β-lactamase genes blaTEM-1 and blaCTX-M-14, flanked by insertionsequence IS26 on both sides in facing orientation. A truncated copyof tnpR was located upstream of blaTEM-1, suggesting that this β-lactamase was recruited from a Tn3 transposon. Downstream ofblaTEM-1, genes encoding a hypothetical protein and a putativemethyl-accepting chemotaxis protein were detected. In contrast,blaCTX-M-14 was flanked upstream by DISEcp1 (truncated byinsertion of IS10) and downstream by IS903. This antimicrobialresistance region is highly similar to Tn6652 in pUR-ECO7(MH674341.1), an IncI plasmid obtained from an Escherichia coliclinical isolate from Uruguay [2]. Although IncN plasmids havehttp://dx.doi.org/10.1016/j.jgar.2019.11.0192213-7165/© 2019 International Society for Antimicrobial Chemotherapy. Published bycreativecommons.org/licenses/by-nc-nd/4.0/).been associated with the dissemination of several blaCTX-Mvariants, the occurrence of blaCTX-M-14 in IncN plasmids is rareand the few existing reports correspond to uncharacterisedplasmids from Asia [3].The second resistance region, located downstream of uvp1,consisted of a complex class 1 integron carrying dfrA25, followedby sul1 as part of the 3ʹ-CS; the second variable region of thisintegron, downstream of ISCR1, featured genes for a peptidetransport periplasmic protein (sapA), a hypothetical protein, thequinolone resistance gene qnrB2, a putative transcriptional factor(pspF), and a secondary 3ʹ-CS (3ʹ-CS2), albeit with a truncated copyof qacED1 and flanked by IS15D. The same complex integron wasdescribed in the multidrug resistance region of SGI1-X, aSalmonella genomic island 1 present in Proteus mirabilis [4].Finally, the third resistance region consisting of the tetracyclineresistance genes tetR–tet(A) was inserted between nuc and traIwithin the fertility inhibition gene fipA, and has already beendescribed in plasmid pKPI-6 (AB616660) [5].Plasmid pUY_STM96 belonged to the IncI group, sequence type80 (pST80), clonal complex 31 (CC31) and was 96 476 bp in sizewith an average G + C content of 49.3%. The number of predictedCDS was 115, and three ncRNAs were detected.The replication region was organised like other IncI plasmids.The origin of replication (oriV), located at genomic position 92 651–96 422, showed four single nucleotide polymorphisms (SNPs) inrelation to IncI plasmids R64 (AP005147.1) and ColIb-P9(AB021078).Several stability-related genes were identified (e.g. parAB, ibfA,resD and the rfsF site, and stbAB) as well as a single toxin–antitoxinsystem (pndAC).The transfer region was similar to other IncI plasmids: (i) traABCregulatory genes; (ii) type IV pilus biogenesis gene (pil); (iii)conjugation tra/trb genes; and (iv) an oriT operon.The resistance region, inserted between the resD gene and therfsF site, was composed of the azithromycin resistance gene ermBand its regulator ermBL. It was flanked on both sides by copies ofIS26 in direct orientation (Fig. 1B). Again, the closest matchbetween this resistance region and public databases correspondedto plasmid pUR-EC07, although in the latter the copies of IS26flanking ermB–ermBL are in diverging orientation (i.e. facingoutwards). The presence of ermB in Salmonella is rather infrequentand the only matching results in nucleotide databases correspondto IncA/C plasmids pSE12-01738-2 (CP027679.1) and pRH-1238(KR091911.1), obtained from S. enterica serovar Corvallis of animalorigin. However, in such plasmids ermB was flanked by IS91 andIS15D.The similarity between Tn6652 and Tn6651 in pUR-EC07, the β-lactam resistance region of pUY_STM62, and the macrolide Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://Fig. 1. Genetic context of the antimicrobial resistance regions of the plasmidome of Salmonella enterica serovar Typhimurium STM3224 and comparison with similarplasmids. (A) Resistance regions found in plasmid pUY_STM62 and comparison with other sequence type 5 (pST5) IncN plasmids available in public databases. (B) Geneticcontext of ermB in pUY_STM96 and comparison with similar pST80 IncI plasmids. Resistance regions are represented by solid arrows indicating the direction of transcription;resistance genes are shown in red; mobile genetic elements are depicted in tones of yellow, and miscellaneous coding sequences (CDS) are in orange; textured arrowsrepresent pseudogenes; integron-related promoters (Pc and PInt; cassette and integrase promoter, respectively) are indicated by small red arrows. Plasmid comparison:green, replication/stability and conjugal transfer; blue, recombination hotspots; red, resistance region; orange, miscellaneous. Regions of homology (BLASTn  99% identity)are shown as striped blocks; inverted DNA regions are depicted as chequered blocks.Letter to the Editor / Journal of Global Antimicrobial Resistance 20 (2020) 84–86 85resistance region of pUY_STM96, respectively, could be accountedfor by: (i) transfer of Tn6652 as a translocatable unit viacointegrative transposition between pUR-EC07 and an IncNplasmid at a pre-existing copy of IS26; and eventually (ii) anintramolecular transposition event in trans, generating an inver-sion of Tn6651. Alternatively, the presence of such transposons inpUY_STM62 and pUY_STM96 could be derived from other sources,although the lack of similar conserved genetic structures in publicdatabases suggests otherwise.To the best of our knowledge, this is the first report of aSalmonella Typhimurium clinical isolate displaying transferableresistance to oxyimino-cephalosporins, fluroquinolones and azi-thromycin encoded by blaCTX-M-14, qnrB2 and ermB, respectively.FundingNone.Competing interestsNone declared.Ethical approvalNot required.References[1] Cordeiro NF, D’Alessandro B, Iriarte A, Pickard D, Yim L, Chabalgoity JA, et al.Draft genome sequences of two multidrug-resistant Salmonella enterica serovarTyphimurium clinical isolates from Uruguay. Microbiol Resour Announc2018;7:, doi:http://dx.doi.org/10.1128/MRA.00917-18 pii: e00917-18.[2] Di Pilato V, Papa-Ezdra R, Chiarelli A, García-Fulgueiras V, Pallecchi L, Vignoli R.Characterization of the first blaCTX-M-14/ermB-carrying IncI1 plasmid from LatinAmerica. Plasmid 2019;102:1–5, doi:http://dx.doi.org/10.1016/j.plas-mid.2019.02.001.[3] Liao XP, Xia J, Yang L, Li L, Sun J, Liu YH, et al. Characterization of CTX-M-14-producing Escherichia coli from food-producing animals. Front Microbiol2015;6:1136, doi:http://dx.doi.org/10.3389/fmicb.2015.01136.[4] Lei CW, Zhang AY, Liu BH, Wang HN, Guan ZB, Xu CW, et al. Molecularcharacteristics of Salmonella genomic island 1 in Proteus mirabilis isolates frompoultry farms in China. Antimicrob Agents Chemother 2014;58:7570–2, doi:http://dx.doi.org/10.1128/AAC.03992-14.[5] Kayama S, Shigemoto N, Kuwahara R, Oshima K, Hirakawa H, Hisatsune J, et al.Complete nucleotide sequence of the IncN plasmid encoding IMP-6 and CTX-M-2 from emerging carbapenem-resistant Enterobacteriaceae in Japan. Anti-microb Agents Chemother 2015;59:1356–9, doi:http://dx.doi.org/10.1128/AAC.04759-14.Nicolás F. CordeiroDepartamento de Bacteriología y Virología, Instituto de Higiene,Facultad de Medicina, Universidad de la República, Alfredo Navarro3051, CP: 11600, Montevideo, UruguayAndrés IriarteaLucía YimaLaura Betancora,bJosé Alejandro ChabalgoityaaDepartamento de Desarrollo Biotecnológico, Instituto de Higiene,Facultad de Medicina, Universidad de la República, Alfredo Navarro3051, CP: 11600, Montevideo, UruguaybDepartamento de Bacteriología y Virología, Instituto de Higiene,Facultad de Medicina, Universidad de la República, Alfredo Navarro3051, CP: 11600, Montevideo, Uruguay86 Letter to the Editor / Journal of Global Antimicrobial Resistance 20 (2020) 84–86Teresa CamouDepartamento de Laboratorios, Ministerio de Salud Pública, AlfredoNavarro 3051, CP:11600, Montevideo, UruguayRafael Vignoli*Departamento de Bacteriología y Virología, Instituto de Higiene,Facultad de Medicina, Universidad de la República, Alfredo Navarro3051, CP: 11600, Montevideo, Uruguay* Corresponding author.E-mail address: rvignoli@higiene.edu.uy (R. Vignoli).Received 2 October 2019Available online 5 December 2019

Plasmidome of a multiresistant Salmonella enterica serovar Typhimurium isolate from Uruguay

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Plasmidome of a multiresistant Salmonella enterica serovar Typhimurium isolate from Uruguay

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