scholarly journals Two New SGI1-LK Variants Found in Proteus mirabilis and Evolution of the SGI1-HKL Group of Salmonella Genomic Islands

mSphere ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Claire de Curraize ◽  
Eliane Siebor ◽  
Véronique Varin ◽  
Catherine Neuwirth ◽  
Ruth M. Hall
Keyword(s):  
Homologous Recombination ◽  
Proteus Mirabilis ◽  
Salmonella Enterica ◽  
Genomic Islands ◽  
Class 1 Integron ◽  
Antibiotic Resistant ◽  
Content Type ◽  
Novel Variants ◽  
Class 1 ◽  
Complex Forms

ABSTRACT Integrative mobilizable elements belonging to the SGI1-H, -K, and -L Salmonella genomic island 1 (SGI1) variant groups are distinguished by the presence of an alteration in the backbone (IS1359 replaces 2.8 kb of the backbone extending from within traN [S005] to within S009). Members of this SGI1-HKL group have been found in Salmonella enterica serovars and in Proteus mirabilis. Two novel variants from this group, designated SGI1-LK1 and SGI1-LK2, were found in the draft genomes of antibiotic-resistant P. mirabilis isolates from two French hospitals. Both variants can be derived from SGI1-PmGUE, a configuration found previously in another P. mirabilis isolate from France. SGI1-LK1 could arise via an IS26-mediated inversion in the complex class 1 integron that duplicated the IS26 element and the target site in IS6100. SGI1-LK1 also has a larger 8.59-kb backbone deletion extending from traN to within S013 and removing traG and traH. However, SGI1-LK1 was mobilized by an IncC plasmid. SGI1-LK2 can be derived from a hypothetical progenitor, SGI1-LK0, that is related to SGI1-PmGUE but lacks the aphA1 gene and one copy of IS26. The integron of SGI1-LK2 could arise via deletion of DNA adjacent to an IS26 and a deletion occurring via homologous recombination between duplicated copies of part of the integron 3′-conserved segment. SGI1-K can also be derived from SGI1-LK0. This would involve an IS26-mediated deletion and an inversion via homologous recombination of a segment between inversely oriented IS26s. Similar events can explain the configuration of the integrons in other SGI1-LK variants. IMPORTANCE Members of the SGI1-HKL subgroup of SGI1-type integrative mobilizable elements have a characteristic alteration in their backbone. They are widely distributed among multiply antibiotic-resistant Salmonella enterica serovars and Proteus mirabilis isolates. The SGI1-K type, found in the globally disseminated multiply antibiotic-resistant Salmonella enterica serovar Kentucky clone ST198 (sequence type 198), and various configurations in the original SGI1-LK group, found in other multiresistant S. enterica serovars and Proteus mirabilis isolates, have complex and highly plastic resistance regions due to the presence of IS26. However, how these complex forms arose and the relationships between them had not been analyzed. Here, a hypothetical progenitor, SGI1-LK0, that can be formed from the simpler SGI1-H is proposed, and the pathways to the formation of new variants, SGI1-LK1 and SGI1-LK2, found in P. mirabilis and other reported configurations via homologous recombination and IS26-mediated events are proposed. This led to a better understanding of the evolution of the SGI1-HKL group.

Antibiotic resistance profile of Salmonella enterica isolated from exotic and indigenous leafy green vegetables in Accra, Ghana

2021 ◽  
Author(s):  
Jinru Chen ◽  
Joycelyn Quansah
Keyword(s):  
Antibiotic Resistance ◽  
Salmonella Enterica ◽  
Gene Cassette ◽  
Nucleotide Sequencing ◽  
Dilution Method ◽  
Class 1 Integron ◽  
Antibiotic Resistant ◽  
Resistance Profile ◽  
Antibiotic Resistance Profile ◽  
Class 1

Fresh produce-borne enteric bacterial pathogens with resistance to antibiotics have posed serious challenges to food safety and public health worldwide.  This study examined the antibiotic resistance profile of Salmonella enterica (n=33), previously isolated from exotic and indigenous leafy green vegetable samples (n=328) collected from 50 vegetable farms in 12 farming areas and 37 vegetable sellers in 4 market centers in Accra, Ghana during the period of March 2016 to March 2017, and determined the distribution of integrons among antibiotic-resistant isolates.  The susceptibility of the Salmonella isolates to 12 antibiotics was assayed using the standard disc diffusion assay.  The minimum inhibitory concentrations (MICs) of the five most resisted antibiotics were determined using the twofold macro dilution method.  PCR assay was used to detect the presence of integrons in Salmonella cells, and PCR product with amplified integron gene cassette was purified and sequenced using the Sanger sequencing technology.  The Salmonella isolates used in the study resisted at least one tested antibiotic, and multi-drug resistant (MDR) isolates were 30.3% (10/33).  Most isolates (81.8%) were resistant to sulfisoxazole.  The MICs of tetracycline, cefoxitin, streptomycin, ampicillin, and sulfisoxazole were 16, 32, 64, 64, and > 1,024 µg/ml, respectively.  A total of five different patterns of MDR were observed among the Salmonella isolates, and the common MDR patterns were AAuFox (30.3%) and AAuFoxSSu (18.1%).  One out of the 33 (3.0%) Salmonella isolates tested positive for class 1 integron with a gene cassette of about 800 bp.  Nucleotide sequencing revealed the class 1 integron carried a single gene dfrA7 .  Future studies are needed to confirm whether the consumption of contaminated leafy green vegetables is a route of acquiring antibiotic-resistant Salmonella by consumers in Accra, Ghana.

scholarly journals SGI0, a relative of Salmonella genomic islands SGI1 and SGI2, lacking a class 1 integron, found in Proteus mirabilis

Plasmid ◽  
2020 ◽  
Vol 107 ◽  
pp. 102453 ◽  
Author(s):  
Claire de Curraize ◽  
Eliane Siebor ◽  
Catherine Neuwirth ◽  
Ruth M. Hall
Keyword(s):  
Proteus Mirabilis ◽  
Genomic Islands ◽  
Class 1 Integron ◽  
Class 1

scholarly journals SGI1-K, a Variant of the SGI1 Genomic Island Carrying a Mercury Resistance Region, in Salmonella enterica Serovar Kentucky

2006 ◽  
Vol 51 (1) ◽  
pp. 317-323 ◽  
Author(s):  
Renee S. Levings ◽  
Sally R. Partridge ◽  
Steven P. Djordjevic ◽  
Ruth M. Hall
Keyword(s):  
Salmonella Enterica ◽  
Genomic Island ◽  
Mercury Resistance ◽  
Variant Form ◽  
Short Segment ◽  
Class 1 Integron ◽  
Antibiotic Resistant ◽  
Right Hand ◽  
Class 1 ◽  
The Right

ABSTRACT A multiple-antibiotic-resistant Salmonella enterica serovar Kentucky strain was found to contain SGI1-K, a variant form of the Salmonella genomic island 1 (SGI1) with an In4-type class 1 integron that contains only one cassette array, aacCA5-aadA7, and an adjacent mercury resistance module. Part of the 3′-conserved segment (3′-CS) of the integron, together with the inverted short segment from the right-hand end of the integron transposition module normally found between the 3′-CS and IS6100 in In4 family integrons, has been removed by an IS6100-mediated deletion. IRt, the right-hand inverted repeat found at the outer end of the integron, abuts a mercury resistance region instead of the usual SGI1 backbone segment. The mer module is a hybrid of those found in Tn501 and Tn21. This mer region and a further uncharacterized segment of at least 10 kb appear to have been incorporated between IRt and the SGI1 backbone. These findings demonstrate that the multidrug resistance region in SGI1 can incorporate new DNA segments in the same way as multiple antibiotic resistance regions in plasmids.

scholarly journals Early Strains of Multidrug-Resistant Salmonella enterica Serovar Kentucky Sequence Type 198 from Southeast Asia Harbor Salmonella Genomic Island 1-J Variants with a Novel Insertion Sequence

2012 ◽  
Vol 56 (10) ◽  
pp. 5096-5102 ◽  
Author(s):  
Simon Le Hello ◽  
François-Xavier Weill ◽  
Véronique Guibert ◽  
Karine Praud ◽  
Axel Cloeckaert ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Salmonella Enterica ◽  
Insertion Sequence ◽  
Genomic Island ◽  
Far East ◽  
Gene Clusters ◽  
Sequence Type ◽  
Class 1 Integron ◽  
Content Type ◽  
Class 1

ABSTRACTSalmonellagenomic island 1 (SGI1) is a 43-kb integrative mobilizable element that harbors a great diversity of multidrug resistance gene clusters described in numerousSalmonella entericaserovars and also inProteus mirabilis. The majority of SGI1 variants contain an In104-derivative complex class 1 integron inserted between resolvase generesand open reading frame (ORF) S044 in SGI1. Recently, the international spread of ciprofloxacin-resistantS. entericaserovar Kentucky sequence type 198 (ST198) containing SGI1-K variants has been reported. A retrospective study was undertaken to characterize ST198S. Kentucky strains isolated before the spread of the epidemic ST198-SGI1-K population in Africa and the Middle East. Here, we characterized 12 ST198S. Kentucky strains isolated between 1969 and 1999, mainly from humans returning from Southeast Asia (n= 10 strains) or Israel (n= 1 strain) or from meat in Egypt (n= 1 strain). All these ST198S. Kentucky strains did not belong to the XbaI pulsotype X1 associated with the African epidemic clone but to pulsotype X2. SGI1-J subgroup variants containing different complex integrons with a partial transposition module and inserted within ORF S023 of SGI1 were detected in six strains. The SGI1-J4 variant containing a partially deleted class 1 integron and thus showing a narrow resistance phenotype to sulfonamides was identified in two epidemiologically unrelated strains from Indonesia. The four remaining strains harbored a novel SGI1-J variant, named SGI1-J6, which containedaadA2,floR2,tetR(G)-tetA(G), andsul1resistance genes within its complex integron. Moreover, in all theseS. Kentucky isolates, a novel insertion sequence related to the IS630family and named ISSen5was found inserted upstream of the SGI1 complex integron in ORF S023. Thus, two subpopulations ofS. Kentucky ST198 independently and exclusively acquired the SGI1 during the 1980s and 1990s. Unlike the ST198-X1 African epidemic subpopulation, the ST198-X2 subpopulation mainly from Asia harbors variants of the SGI1-J subgroup that are encountered mainly in the Far East, as previously described forS. entericaserovars Emek and Virchow.

scholarly journals Molecular Epidemiology and Genetic Characteristics of VariousblaPERGenes in Shanghai, China

2016 ◽  
Vol 60 (6) ◽  
pp. 3849-3853 ◽  
Author(s):  
Lianyan Xie ◽  
Jun Wu ◽  
Fangfang Zhang ◽  
Lizhong Han ◽  
Xiaokui Guo ◽  
...  
Keyword(s):  
Proteus Mirabilis ◽  
Inverted Repeat ◽  
Transmission Mechanism ◽  
The Other ◽  
Complex Class ◽  
Class 1 Integron ◽  
Genetic Characteristics ◽  
Gram Negative ◽  
Content Type ◽  
Class 1

We describe the genetic characteristics and possible transmission mechanism ofblaPERin 25 clinical Gram-negative bacilli in Shanghai.blaPER, includingblaPER-1,blaPER-3, andblaPER-4, was located chromosomally or in different plasmids. Tn1213harboringblaPER-1was first identified in twoProteus mirabilisisolates in China. The otherblaPERvariants were preceded by an ISCR1element inside the complex class 1 integron associated with IS26, Tn21, Tn1696, and a miniature inverted-repeat transposable element.

scholarly journals Novel Variants of AbaR Resistance Islands with a Common Backbone in Acinetobacter baumannii Isolates of European Clone II

2012 ◽  
Vol 56 (4) ◽  
pp. 1969-1973 ◽  
Author(s):  
Vaida Šeputienė ◽  
Justas Povilonis ◽  
Edita Sužiedėlienė
Keyword(s):  
Antibiotic Resistance ◽  
Acinetobacter Baumannii ◽  
Stress Protein ◽  
Antibiotic Resistance Genes ◽  
Structural Similarity ◽  
Chromosomal Dna ◽  
Class 1 Integron ◽  
Content Type ◽  
Novel Variants ◽  
Class 1

ABSTRACTIn this study, the genetic organization of three novel genomic antibiotic resistance islands (AbaRs) inAcinetobacter baumanniiisolates belonging to group of European clone II (EC II)comMintegrated sequences of 18-, 21-, and 23-kb resistance islands were determined. These resistance islands carry the backbone of AbaR-type transposon structures, which are composed of the transposition module coding for potential transposition proteins and other genes coding for the intact universal stress protein (uspA), sulfate permease (sul), and proteins of unknown function. The antibiotic resistance genesstrA,strB,tetB, andtetRand insertion sequence CR2 element were found to be inserted into the AbaR transposons. GenBank homology searches indicated that they are closely related to the AbaR sequences found integrated incomMin strains of EC II (A. baumanniistrains 1656-2 and TCDC-AB0715) and AbaR4 integrated in another location ofA. baumanniiAB0057 (EC I). All of the AbaRs showed structural similarity to the previously described AbaR4 island and share a 12,008-bp backbone. AbaRs contain Tn1213, Tn2006, and the multiple fragments which could be derived from transposons Tn3, Tn10, Tn21, Tn1000, Tn5393, and Tn6020, the insertion sequences IS26, ISAba1, ISAba14, and ISCR2, and the class 1 integron. Moreover, chromosomal DNA was inserted into distinct regions of the AbaR backbone. Sequence analysis suggested that the AbaR-type transposons have evolved through insertions, deletions, and homologous recombination. AbaR islands, sharing the core structure similar to AbaR4, appeared to be distributed in isolates of EC I and EC II via integration into distinct genomic sites, i.e.,phoandcomM, respectively.

Identification of Proteus genomic island 2 variants in two clonal Proteus mirabilis isolates with coexistence of a novel genomic resistance island PmGRI1

2020 ◽  
Vol 75 (9) ◽  
pp. 2503-2507
Author(s):  
Chang-Wei Lei ◽  
Tian-Ge Yao ◽  
Jia Yan ◽  
Bo-Yang Li ◽  
Xue-Chun Wang ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Proteus Mirabilis ◽  
Genomic Island ◽  
Genomic Islands ◽  
Class 1 Integron ◽  
E Coli ◽  
Class 1 Integrons ◽  
Class 1 ◽  
Resistance Island ◽  
Integrative And Conjugative Element

Abstract Objectives To characterize the MDR genomic islands (GIs) in Proteus mirabilis isolates. Methods Two P. mirabilis strains (C55 and C74) of chicken origin were subjected to WGS (HiSeq and PacBio) and the MDR GIs were determined. Results P. mirabilis strains C55 and C74 are clonal strains and harbour different Proteus genomic island 2 (PGI2) variants (PGI2-C55 and PGI2-C74). The MDR region of PGI2-C55 is composed of two class 1 integrons, separated by a region containing seven copies of IS26 and eight resistance genes, including blaCTX-M-3 and fosA3. The region in PGI2-C74 is a complete In4-type class 1 integron, harbouring five gene cassettes (dfrA16, blaCARB-2, aadA2, cmlA1 and aadA1). In addition, C55 and C74 carry an SXT/R391 integrative and conjugative element (ICEPmiJpn1), harbouring blaCMY-2, and a novel 50.46 kb genomic resistance island named PmGRI1-C55. PmGRI1-C55 harbours a tyrosine-type recombinase/integrase that might be responsible for the integration of PmGRI1-C55 at the 3′ end of tRNA-Sec. It carries an MDR region derived from Tn2670 that harbours a Tn21 region and carries six resistance genes (catA1, blaTEM-1b, aphA1a, sul2, strA and strB). Blast analysis showed diverse PmGRI1 variants in P. mirabilis and Escherichia coli strains. Conclusions The finding of the two new PGI2 variants highlights that the homologous recombination between shared components of class 1 integrons and transposition by IS26 promote the diversity of MDR regions in PGI2. PmGRI1 is a new GI that carries various resistance genes identified in P. mirabilis and E. coli.

scholarly journals Two Novel Salmonella Genomic Island 1 Variants in Proteus mirabilis Isolates from Swine Farms in China

2015 ◽  
Vol 59 (7) ◽  
pp. 4336-4338 ◽  
Author(s):  
Chang-Wei Lei ◽  
An-Yun Zhang ◽  
Bi-Hui Liu ◽  
Hong-Ning Wang ◽  
Li-Qin Yang ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Proteus Mirabilis ◽  
Salmonella Enterica ◽  
Genomic Island ◽  
Sequence Type ◽  
The Other ◽  
Content Type ◽  
Swine Farms ◽  
Novel Variants ◽  
Novel Variant

ABSTRACTFour differentSalmonellagenomic island 1 (SGI1) variants, including two novel variants, were characterized in oneSalmonella entericaserovar Rissen sequence type ST1917 isolate and threeProteus mirabilisisolates from swine farms in China. One novel variant was derived from SGI1-B with the backbone gene S021 disrupted by a 12.72-kb IS26composite transposon containing thedfrA17-aadA5cassettes and macrolide inactivation gene clustermphA-mrx-mphR. The other one was an integron-free SGI1 and contained a 183-bp truncated S025 next to IS6100and S044.

scholarly journals Diverse Mobilized Class 1 Integrons Are Common in the Chromosomes of Pathogenic Pseudomonas aeruginosa Clinical Isolates

2012 ◽  
Vol 56 (4) ◽  
pp. 2169-2172 ◽  
Author(s):  
Elena Martinez ◽  
Carolina Marquez ◽  
Ana Ingold ◽  
John Merlino ◽  
Steven P. Djordjevic ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Genomic Islands ◽  
Clonal Line ◽  
Class 1 Integron ◽  
Content Type ◽  
Class 1 Integrons ◽  
Class 1 ◽  
Genomic Locations

ABSTRACTEleven clinical class 1 integron-containingPseudomonas aeruginosaisolates from Australia and Uruguay were investigated for the genomic locations of these elements. Several novel class 1 integrons/transposons were found in at least four distinct locations in the chromosome, including genomic islands. These elements seem to be undergoing successful dispersal by lateral gene transfer since integrons were identified across several lineages and more than one clonal line.

scholarly journals Tn6450, a Novel Multidrug Resistance Transposon Characterized in a Proteus mirabilis Isolate from Chicken in China

2018 ◽  
Vol 62 (4) ◽  
pp. e02192-17 ◽  
Author(s):  
Yan-Peng Chen ◽  
Chang-Wei Lei ◽  
Ling-Han Kong ◽  
Jin-Xin Zeng ◽  
Xiu-Zhong Zhang ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Proteus Mirabilis ◽  
Mobile Elements ◽  
Fluoroquinolone Resistance ◽  
Class 1 Integron ◽  
Content Type ◽  
Antimicrobial Resistance Genes ◽  
Class 1

ABSTRACT A novel 65.8-kb multidrug resistance transposon, designated Tn6450, was characterized in a Proteus mirabilis isolate from chicken in China. Tn6450 contains 18 different antimicrobial resistance genes, including cephalosporinase gene blaDHA-1 and fluoroquinolone resistance genes qnrA1 and aac(6′)-Ib-cr. It carries a class 1/2 hybrid integron composed of intI2 and a 3′ conserved segment of the class 1 integron. Tn6450 is derived from Tn7 via acquisition of new mobile elements and resistance genes.

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