Salmonella genomic island 1 and class 1 integron in Salmonella isolates from stray dogs

ABSTRACT Salmonella genomic island 1 was identified for the first time in Salmonella enterica serovar Virchow isolated from humans in Taiwan. The complex class 1 integron conferring multidrug resistance was shown to be inserted within open reading frame (ORF) S023 and contains for the first time a partial transpositional module. The 5-bp target duplication flanking the complex integron suggests that its insertion in ORF S023 was by transposition.

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01229-06 ◽

2006 ◽

Vol 51 (1) ◽

pp. 317-323 ◽

Cited By ~ 43

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.

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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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00732-12 ◽

2012 ◽

Vol 56 (10) ◽

pp. 5096-5102 ◽

Cited By ~ 17

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.

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Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae

Microorganisms ◽

10.3390/microorganisms8020161 ◽

2020 ◽

Vol 8 (2) ◽

pp. 161 ◽

Cited By ~ 3

Author(s):

Max Laurence Cummins ◽

Mohammad Hamidian ◽

Steven Philip Djordjevic

Keyword(s):

Escherichia Coli ◽

Genomic Island ◽

Multiple Drug Resistance ◽

Genomic Islands ◽

Multiple Drug ◽

Class 1 Integron ◽

The United Kingdom ◽

Class 1 ◽

Providencia Stuartii ◽

Conserved Gene

Salmonella genomic island 1 (SGI1) is an integrative mobilisable element that plays an important role in the capture and spread of multiple drug resistance. To date, SGI1 has been found in clinical isolates of Salmonella enterica serovars, Proteus mirabilis, Morganella morganii, Acinetobacter baumannii, Providencia stuartii, Enterobacter spp, and recently in Escherichia coli. SGI1 preferentially targets the 3´-end of trmE, a conserved gene found in the Enterobacteriaceae and among members of the Gammaproteobacteria. It is, therefore, hypothesised that SGI1 and SGI1-related elements (SGI1-REs) may have been acquired by diverse bacterial genera. Here, Bitsliced Genomic Signature Indexes (BIGSI) was used to screen the NCBI Sequence Read Archive (SRA) for putative SGI1-REs in Gammaproteobacteria. Novel SGI-REs were identified in diverse genera including Cronobacter spp, Klebsiella spp, and Vibrio spp and in two additional isolates of Escherichia coli. An extensively drug-resistant human clonal lineage of Klebsiella pneumoniae carrying an SGI1-RE in the United Kingdom and an SGI1-RE that lacks a class 1 integron were also identified. These findings provide insight into the origins of this diverse family of clinically important genomic islands and expand the knowledge of the potential host range of SGI1-REs within the Gammaproteobacteria.

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IS6100-mediated genetic rearrangement within the complex class 1 integron In104 of the Salmonella genomic island 1

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkq163 ◽

2010 ◽

Vol 65 (7) ◽

pp. 1543-1545 ◽

Cited By ~ 19

Author(s):

H. Targant ◽

B. Doublet ◽

F. M. Aarestrup ◽

A. Cloeckaert ◽

J.-Y. Madec

Keyword(s):

Genomic Island ◽

Complex Class ◽

Class 1 Integron ◽

Class 1 ◽

Genetic Rearrangement

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Whole-Genome Analysis ofSalmonella entericaSerovar Typhimurium T000240 Reveals the Acquisition of a Genomic Island Involved in Multidrug Resistance via IS1Derivatives on the Chromosome

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01215-10 ◽

2010 ◽

Vol 55 (2) ◽

pp. 623-630 ◽

Cited By ~ 32

Author(s):

Hidemasa Izumiya ◽

Tsuyoshi Sekizuka ◽

Hideo Nakaya ◽

Masumi Taguchi ◽

Akio Oguchi ◽

...

Keyword(s):

Multidrug Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genome Analysis ◽

Genomic Island ◽

Whole Genome ◽

Class 1 Integron ◽

Serovar Typhimurium ◽

Class 1

ABSTRACTSalmonella entericaserovar Typhimurium is frequently associated with life-threatening systemic infections, and the recent global emergence of multidrug resistance inS. entericaisolates from agricultural and clinical settings has raised concerns. In this study, we determined the whole-genome sequence of fluoroquinolone-resistantS. entericaserovar Typhimurium T000240 strain (DT12) isolated from human gastroenteritis in 2000. Comparative genome analysis revealed that T000240 displays high sequence similarity to strain LT2, which was originally isolated in 1940, indicating that progeny of LT2 might be reemerging. T000240 possesses a unique 82-kb genomic island, designated as GI-DT12, which is composed of multidrug resistance determinants, including a Tn2670-like composite transposon (class 1 integron [intI1,blaoxa-30,aadA1,qacEΔ1, andsul1], mercury resistance proteins, and chloramphenicol acetyltransferase), a Tn10-like tetracycline resistance protein (tetA), the aerobactin iron-acquisition siderophore system (lutAandlucABC), and an iron transporter (sitABCD). Since GI-DT12 is flanked by IS1derivatives, IS1-mediated recombination likely played a role in the acquisition of this genomic island through horizontal gene transfer. The aminoglycoside-(3)-N-acetyltransferase (aac(3)) gene and a class 1 integron harboring thedfrA1gene cassette responsible for gentamicin and trimethoprim resistance, respectively, were identified on plasmid pSTMDT12_L and appeared to have been acquired through homologous recombination with IS26. This study represents the first characterization of the unique genomic island GI-DT12 that appears to be associated with possible IS1-mediated recombination inS. entericaserovar Typhimurium. It is expected that future whole-genome studies will aid in the characterization of the horizontal gene transfer events for the emergingS. entericaserovar Typhimurium strains.

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

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa215 ◽

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.

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Salmonella Genomic Island 1 Multidrug Resistance Gene Clusters in Salmonella enterica Serovar Agona Isolated in Belgium in 1992 to 2002

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.48.7.2510-2517.2004 ◽

2004 ◽

Vol 48 (7) ◽

pp. 2510-2517 ◽

Cited By ~ 48

Author(s):

Benoît Doublet ◽

Patrick Butaye ◽

Hein Imberechts ◽

David Boyd ◽

Michael R. Mulvey ◽

...

Keyword(s):

Multidrug Resistance ◽

Resistance Gene ◽

Salmonella Enterica ◽

Genomic Island ◽

Gene Clusters ◽

Complex Class ◽

Class 1 Integron ◽

Transposase Gene ◽

New Variant ◽

Class 1

ABSTRACT Salmonella genomic island 1 (SGI1) harbors a multidrug resistance (MDR) gene cluster which is a complex class 1 integron. Variant SGI1 MDR gene clusters conferring different MDR profiles have also been identified in several Salmonella enterica serovars and classified as SGI1-A to -F. A retrospective study was undertaken to characterize MDR regions from serovar Agona strains harboring SGI1 isolated from poultry in Belgium between 1992 and 2002. A total of 171 serovar Agona strains, displaying resistance to at least one antibiotic, were studied for the presence of SGI1. SGI1 was detected in 94 serovar Agona strains. The most prevalent variant was SGI1-A (85%), which harbors within the SGI1 complex class 1 integron a common region (CR1) containing orf513, a putative transposase gene, adjacent to the dfrA10 trimethoprim resistance gene. A new variant SGI1 named SGI1-G was identified in two strains. It consisted of the pse-1 gene cassette, as in SGI1-B, but with additional insertion of the orf513/dfrA10 region structure. Seven strains displaying the typical SGI1 MDR profile (Ap Cm Ff Sm Sp Su Tc) showed genetic variation at the 3′ end of SGI1. These strains harbored the insertion of the CR1 containing orf513 as in SGI1-A, -D, and -G. However, downstream the right end of CR1, they presented different 7.4- to 8.5-kb deletions of the SGI1 3′ end that extended to the chromosomal genes yieE and yieF. These results suggest a possible role of CR1 in deletion formation, as has been reported for some insertion sequences. Pulsed-field gel electrophoresis analysis showed that all the serovar Agona SGI1-carrying strains belonged to a single clone. Thus, SGI1 is largely encountered in serovar Agona strains isolated from poultry in Belgium, the most prevalent variant being SGI1-A. SGI1 MDR region undergoes recombinational events resulting in a diversity of MDR gene clusters.

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Variant Salmonella Genomic Island 1-L Antibiotic Resistance Gene Cluster in Salmonella enterica Serovar Newport

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00697-06 ◽

2006 ◽

Vol 50 (11) ◽

pp. 3944-3946 ◽

Cited By ~ 21

Author(s):

Axel Cloeckaert ◽

Karine Praud ◽

Benoît Doublet ◽

Marie Demartin ◽

François-Xavier Weill

Keyword(s):

Antibiotic Resistance ◽

Gene Cluster ◽

Resistance Gene ◽

Salmonella Enterica ◽

Genomic Island ◽

Antibiotic Resistance Gene ◽

Gene Cassette ◽

Class 1 Integron ◽

Resistance Gene Cluster ◽

Class 1

ABSTRACT We report a new Salmonella genomic island 1 variant antibiotic resistance gene cluster called SGI1-L in a Salmonella enterica serovar Newport isolate containing a dfrA15 gene cassette conferring resistance to trimethoprim. The isolate carried another class 1 integron containing the aacC5 and aadA7 gene cassettes conferring resistance to gentamicin and streptomycin/spectinomycin, respectively.

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