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 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.

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 Emergence of rare carbapenemases (FRI, GES-5, IMI, SFC, and SFH-1) in Enterobacterales isolated from surface waters in Japan

2021 ◽  
Author(s):  
Ryota Gomi ◽  
Yasufumi Matsumura ◽  
Michio Tanaka ◽  
Masaru Ihara ◽  
Yoshinori Sugie ◽  
...  
Keyword(s):  
Surface Waters ◽  
Carbapenem Resistance ◽  
Genomic Islands ◽  
Aquatic Environments ◽  
Genetic Determinants ◽  
Environmental Waters ◽  
Class 1 Integron ◽  
Genetic Characteristics ◽  
Class 1 ◽  
Potential Reservoir

ABSTRACTObjectivesCarbapenemase-producing Enterobacterales (CPE) pose serious threats to public health. Compared with clinical CPE, the genetic characteristics of environmental CPE are not well understood. This study aimed to characterize the genetic determinants of carbapenem resistance in CPE isolated from environmental waters in Japan.MethodsEighty-five water samples were collected from rivers and a lake in Japan. CPE were identified using selective media, and genome sequencing was performed for the obtained isolates (n = 21).ResultsVarious rare/novel carbapenemases were identified: GES-5 in Raoultella planticola (n = 1), FRI-8 and FRI-11 in Enterobacter spp. (n = 8), IMI-22 and IMI-23 in Serratia ureilytica (n = 3), and SFC-1, SFC-2 and SFH-1 in Serratia fonticola (n = 9). Genomes of 11 isolates could be closed, allowing the elucidation of the genetic contexts of the carbapenemase genes. The blaGES-5 gene was located within a class 1 integron, In2071 (cassette array, blaGES-5-aacA3-aadA16), on a 33 kb IncP6 plasmid. The blaFRI-8 genes were carried on IncFII(Yp) plasmids ranging in size from 191 kb to 244 kb, and the blaFRI-11 genes were carried on 70 kb and 74 kb IncFII(pECLA)/IncR plasmids. The blaIMI-22 and blaIMI-23 genes were colocated on a 107 kb plasmid. The blaSFC and blaSFH-1 genes were found on putative genomic islands inserted at tRNA-Phe genes in chromosomes.ConclusionsThis study revealed the presence of rare/novel carbapenemases among CPE in aquatic environments, suggesting that the environment may act as a potential reservoir of these minor carbapenemases.

scholarly journals Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae

2020 ◽  
Vol 8 (2) ◽  
pp. 161 ◽  
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.

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 Genomic islands 1 and 2 play key roles in the evolution of extensively drug-resistant ST235 isolates of Pseudomonas aeruginosa

Open Biology ◽  
2016 ◽  
Vol 6 (3) ◽  
pp. 150175 ◽  
Author(s):  
Piklu Roy Chowdhury ◽  
Martin Scott ◽  
Paul Worden ◽  
Peter Huntington ◽  
Bernard Hudson ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
De Novo ◽  
Direct Repeat ◽  
Genomic Islands ◽  
Opportunistic Pathogens ◽  
Class 1 Integron ◽  
Integrative Conjugative Element ◽  
Class 1 ◽  
Specific Proteins ◽  
Almost All

Pseudomonas aeruginosa are noscomially acquired, opportunistic pathogens that pose a major threat to the health of burns patients and the immunocompromised. We sequenced the genomes of P. aeruginosa isolates RNS_PA1, RNS_PA46 and RNS_PAE05, which displayed resistance to almost all frontline antibiotics, including gentamicin, piperacillin, timentin, meropenem, ceftazidime and colistin. We provide evidence that the isolates are representatives of P. aeruginosa sequence type (ST) 235 and carry Tn 6162 and Tn 6163 in genomic islands 1 (GI1) and 2 (GI2), respectively. GI1 disrupts the endA gene at precisely the same chromosomal location as in P. aeruginosa strain VR-143/97, of unknown ST, creating an identical CA direct repeat. The class 1 integron associated with Tn 6163 in GI2 carries a bla GES-5 – aacA4 – gcuE15 – aphA15 cassette array conferring resistance to carbapenems and aminoglycosides. GI2 is flanked by a 12 nt direct repeat motif, abuts a tRNA-gly gene, and encodes proteins with putative roles in integration, conjugative transfer as well as integrative conjugative element-specific proteins. This suggests that GI2 may have evolved from a novel integrative conjugative element. Our data provide further support to the hypothesis that genomic islands play an important role in de novo evolution of multiple antibiotic resistance phenotypes in P. aeruginosa .

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.

scholarly journals PGI2 Is a Novel SGI1-Relative Multidrug-Resistant Genomic Island Characterized in Proteus mirabilis

2018 ◽  
Vol 62 (5) ◽  
Author(s):  
Chang-Wei Lei ◽  
Yan-Peng Chen ◽  
Ling-Han Kong ◽  
Jin-Xin Zeng ◽  
Yong-Xiang Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Proteus Mirabilis ◽  
Genomic Island ◽  
Multidrug Resistant ◽  
Complex Class ◽  
Helper Plasmid ◽  
Class 1 Integron ◽  
Content Type ◽  
Class 1

ABSTRACT A novel 61,578-bp genomic island named Proteus genomic island 2 (PGI2) was characterized in Proteus mirabilis of swine origin in China. The 23.85-kb backbone of PGI2 is related to those of Salmonella genomic island 1 and Acinetobacter genomic island 1. The multidrug resistance (MDR) region of PGI2 is a complex class 1 integron containing 14 different resistance genes. PGI2 was conjugally mobilized in trans to Escherichia coli in the presence of a conjugative IncC helper plasmid.

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