scholarly journals Complete Sequence of the IncA/C1Plasmid pCf587 CarryingblaPER-2fromCitrobacter freundii

2018 ◽  
Vol 62 (5) ◽  
Author(s):  
Melina Ruggiero ◽  
Delphine Girlich ◽  
Laura Dabos ◽  
Pablo Power ◽  
Thierry Naas ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Multilocus Sequence Typing ◽  
Complete Sequence ◽  
Sequence Type ◽  
Class 1 Integron ◽  
Class 1 ◽  
Resistance Island

ABSTRACTTheblaPER-2-harboring plasmid pCf587 (191,541 bp) belongs to lineage IncA/C1and is closely related to pRA1. It contains a large resistance island including theblaPER-2gene between two copies of ISKox2-like elements, the toxin-antitoxin modulepemK-pemI, several other resistance genes inserted within a Tn2transposon, a Tn21-like structure, and a class 1 integron. pCf587 belongs to sequence type 13 (ST13), a new plasmid multilocus sequence typing (pMLST) ST.

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 Occurrence and Characterization of Salmonella Isolated from Large-Scale Breeder Farms in Shandong Province, China

2019 ◽  
Vol 2019 ◽  
pp. 1-8 ◽  
Author(s):  
Jie Yang ◽  
Siwei Gao ◽  
Yajie Chang ◽  
Mingliu Su ◽  
Yutong Xie ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Antimicrobial Susceptibility ◽  
Multilocus Sequence Typing ◽  
Large Scale ◽  
Shandong Province ◽  
Sequence Type ◽  
Class 1 ◽  
Resistance Rates

This study aimed to investigate the prevalence and antimicrobial resistance of Salmonella spp. isolated from large-scale breeder farms in Shandong Province, China. A total of 63 Salmonella isolates (63/409, 15.4%) were identified from 409 samples collected from five large-scale breeder farms in Shandong Province. These Salmonella isolates were assayed for serotype, antimicrobial susceptibility, prevalence of class 1 integrons, quinolone resistance genes, and β-lactamase genes and subtyped by multilocus sequence typing (MLST). Among these isolates, S. Enteritidis (100%) was the predominant serovar, and high antimicrobial resistance rates to nalidixic acid (100.0%), streptomycin (100.0%), ampicillin (98.4%), and erythromycin (93.7%) were observed. All of the isolates carried blaTEM. MLST results showed that only one sequence type (ST11) was identified. Our findings indicated that Salmonella was generally prevalent not only on broiler farms but also on breeder farms.

scholarly journals Identification and antibiotic resistance profiling of bacterial isolates from septicaemic soft-shelled turtles (Pelodiscus sinensis)

2017 ◽  
Vol 62 (No. 3) ◽  
pp. 169-177 ◽  
Author(s):  
TH Chung ◽  
SW Yi ◽  
BS Kim ◽  
WI Kim ◽  
GW Shin
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Present Report ◽  
Antibiotic Resistance Genes ◽  
Tetracycline Resistance ◽  
Edwardsiella Tarda ◽  
Pelodiscus Sinensis ◽  
Class 1 Integron ◽  
Class 1 ◽  
M 14

The present study sought to identify pathogens associated with septicaemia in the Chinese soft-shelled turtle (Pelodiscus sinensis) and to characterise antibiotic resistance in these pathogens. Twenty-three isolates recovered from the livers of diseased soft-shelled turtles were genetically identified as Aeromonas hydrophila (n = 8), A. veronii (n = 3), Citrobacter freundii (n = 4), Morganella morganii (n = 3), Edwardsiella tarda (n = 2), Wohlfahrtiimonas chitiniclastica (n = 1), Chryseobacterium sp. (n = 1), and Comamonas sp. (n = 1). Most isolates (n = 21) were resistant to ampicillin whereas a low percentage of isolates was susceptible to aminoglycosides (amikacin, gentamicin, and tobramycin). PCR assays and sequence analysis revealed the presence of the qnrS2 and bla<sub>TEM</sub> antibiotic resistance genes in all isolates. The bla<sub>DHA-1</sub>, bla<sub>CTX-M-14</sub> and bla<sub>CMY-2</sub> genes were harboured by 17.4% (n = 4), 13.5% (n = 3) and 8.7% (n = 2) of the strains, respectively. One or more tetracycline resistance genes were detected in 60.9% (n = 14) of the isolates. Four isolates (17.4%) harboured single or multiple class 1 integron cassettes. Collectively, a variety of bacterial pathogens were involved in the occurrence of septicaemia in Chinese soft-shelled turtles and most of the isolates had multi-antibiotic resistant phenotypes. To our knowledge, the present report is the first to identify W. chitiniclastica and Comamonas sp. as causes of septicaemia in soft-shelled turtles and the first to identify Aeromonas spp. with bla<sub>CTX-M-14</sub> and bla<sub>DHA-1</sub> resistance genes.

scholarly journals Emergence of Pseudomonas aeruginosa with class 1 integron carrying blaVIM-2 and blaVIM-4 in the University Clinical Hospital of Bialystok (northeastern Poland)

2017 ◽  
Vol 71 (1) ◽  
pp. 0-0 ◽  
Author(s):  
Anna Michalska-Falkowska ◽  
Paweł Tomasz Sacha ◽  
Henryk Grześ ◽  
Tomasz Hauschild ◽  
Piotr Wieczorek ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Bacterial Resistance ◽  
Genetic Relatedness ◽  
Housekeeping Genes ◽  
Sequence Type ◽  
Class 1 Integron ◽  
Clinical Hospital ◽  
Class 1 ◽  
Severe Infections ◽  
The University

The effectiveness of carbapenems, considered as last-resort antimicrobials in severe infections, becomes compromised by bacterial resistance. The production of metallo-β-lactamases (MBLs) is the most significant threat to carbapenems activity among Pseudomonas aeruginosa. The aim of this study was to assess the presence and type of MBLs genes in carbapenem-resistant P. aeruginosa clinical strains, to identify the location of MBLs genes and to determine genetic relatedness between MBL-producers using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).The first identified MBL-positive (with blaVIM genes) P. aeruginosa strains were isolated from patients hospitalized in the University Clinical Hospital of Bialystok in the period from September 2012 to December 2013. Variants of MBLs genes and variable integron regions were characterized by PCR and sequencing. PFGE was performed after digesting of bacterial genomes by XbaI enzyme. By MLST seven housekeeping genes were analyzed for the determination of sequence type (ST). Three strains carried the blaVIM-2 gene and one harbored the blaVIM-4 gene. The blaVIM genes resided within class 1 integrons. PCR mapping of integrons revealed the presence of four different cassette arrays. Genetic relatedness analysis by PFGE classified VIM-positive strains into four unrelated pulsotypes (A–D). MLST demonstrated the presence of four (ST 111, ST27, and ST17) different sequence type including one previously undescribed new type of ST 2342. Antimicrobial susceptibility testing showed that VIM-positive strains were resistant to carbapenems, cephalosporins, aminoglycosides, and quinolones, intermediate to aztreonam, and susceptible only to colistin. Integrons mapping, PFGE, and MLST results may point to different origin of these strains and independent introduction into hospitalized patients.

scholarly journals Salmonella enterica Serovar Typhi Strains Isolated in Korea Containing a Multidrug Resistance Class 1 Integron

2003 ◽  
Vol 47 (6) ◽  
pp. 2006-2008 ◽  
Author(s):  
Hyunjoo Pai ◽  
Jeong-hum Byeon ◽  
Sunmi Yu ◽  
Bok Kwon Lee ◽  
Shukho Kim
Keyword(s):  
Multidrug Resistance ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Multidrug Resistant ◽  
Conjugative Plasmid ◽  
The Novel ◽  
Class 1 Integron ◽  
Salmonella Enterica Serovar Typhi ◽  
Class 1 ◽  
Clonal Spread

ABSTRACT Six strains of Salmonella enterica serovar Typhi which were resistant to ampicillin, chloramphenicol, trimethoprim-sulfamethoxazole, streptomycin, tetracycline, and gentamicin were isolated in Korea. This multidrug resistance was transferred by a conjugative plasmid of about 50 kb. The plasmid harbored a class 1 integron, which included six resistance genes, aacA4b, catB8, aadA1, dfrA1, aac(6′)-IIa, and the novel blaP2, in that order. All of the isolates showed the same-size plasmids and the same ribotyping patterns, which suggests a clonal spread of these multidrug-resistant isolates.

scholarly journals The Occurrence of Antibiotic Resistance Genes in an Urban River in Nepal

Water ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 450 ◽  
Author(s):  
Ocean Thakali ◽  
Sarmila Tandukar ◽  
John Brooks ◽  
Samendra Sherchan ◽  
Jeevan Sherchand ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Anthropogenic Activities ◽  
Quantitative Polymerase Chain Reaction ◽  
Antibiotic Resistance Genes ◽  
Urban River ◽  
Class 1 Integron ◽  
Upstream Site ◽  
Class 1 ◽  
The Impact

Urban rivers affected by anthropogenic activities can act as reservoirs of antibiotic resistance genes (ARGs). This study aimed to describe the occurrence of selected ARGs (blaTEM, ermF, mecA, and tetA) and a class 1 integron (intI1) in an urban river in Nepal. A total of 18 water samples were collected periodically from upstream, midstream, and downstream sites along the Bagmati River over a 1-year period. All ARGs except mecA and intI1 were consistently detected by a quantitative polymerase chain reaction in the midstream and downstream sites, with concentrations ranging from 3.1 to 7.8 log copies/mL. ARG abundance was significantly lower at the upstream site (p < 0.05), reflecting the impact of anthropogenic activities on increasing concentrations of ARGs at midstream and downstream sites. Our findings demonstrate the presence of clinically relevant ARGs in the urban river water of Nepal, suggesting a need for mitigating strategies to prevent the spread of antibiotic resistance in the environment.

scholarly journals Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated carbapenemase outbreak in an Australian hospital

2020 ◽  
Vol 75 (4) ◽  
pp. 873-882 ◽  
Author(s):  
A Kizny Gordon ◽  
H T T Phan ◽  
S I Lipworth ◽  
E Cheong ◽  
T Gottlieb ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Genetic Relatedness ◽  
Sequence Data ◽  
Environmental Isolates ◽  
Class 1 Integron ◽  
Oxford Nanopore ◽  
Class 1 ◽  
Long Read ◽  
Cleaning Methods ◽  
Burns Unit

Abstract Background Hospital outbreaks of carbapenemase-producing organisms, such as blaIMP-4-containing organisms, are an increasing threat to patient safety. Objectives To investigate the genomic dynamics of a 10 year (2006–15) outbreak of blaIMP-4-containing organisms in a burns unit in a hospital in Sydney, Australia. Methods All carbapenem-non-susceptible or MDR clinical isolates (2006–15) and a random selection of equivalent or ESBL-producing environmental isolates (2012–15) were sequenced [short-read (Illumina), long-read (Oxford Nanopore Technology)]. Sequence data were used to assess genetic relatedness of isolates (Mash; mapping and recombination-adjusted phylogenies), perform in silico typing (MLST, resistance genes and plasmid replicons) and reconstruct a subset of blaIMP plasmids for comparative plasmid genomics. Results A total of 46/58 clinical and 67/96 environmental isolates contained blaIMP-4. All blaIMP-4-positive organisms contained five or more other resistance genes. Enterobacter cloacae was the predominant organism, with 12 other species mainly found in either the environment or patients, some persisting despite several cleaning methods. On phylogenetic analysis there were three genetic clusters of E. cloacae containing both clinical and environmental isolates, and an additional four clusters restricted to either reservoir. blaIMP-4 was mostly found as part of a cassette array (blaIMP-4-qacG2-aacA4-catB3) in a class 1 integron within a previously described IncM2 plasmid (pEl1573), with almost complete conservation of this cassette across the species over the 10 years. Several other plasmids were also implicated, including an IncF plasmid backbone not previously widely described in association with blaIMP-4. Conclusions Genetic backgrounds disseminating blaIMP-4 can persist, diversify and evolve amongst both human and environmental reservoirs during a prolonged outbreak despite intensive prevention efforts.

scholarly journals Molecular Characterization ofblaNDM-1in a Sequence Type 235 Pseudomonas aeruginosa Isolate from France

2013 ◽  
Vol 57 (7) ◽  
pp. 3408-3411 ◽  
Author(s):  
Frédéric Janvier ◽  
Katy Jeannot ◽  
Sophie Tessé ◽  
Marjorie Robert-Nicoud ◽  
Hervé Delacour ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Insertion Sequence ◽  
Variable Region ◽  
Sequence Type ◽  
Common Region ◽  
Class 1 Integron ◽  
Genetic Studies ◽  
Content Type ◽  
Class 1 ◽  
Previous Hospitalization

ABSTRACTAn NDM-1 carbapenemase-producingPseudomonas aeruginosaisolate was recovered from a patient hospitalized in France after a previous hospitalization in Serbia. Genetic studies revealed that theblaNDM-1gene was surrounded by insertion sequence ISAba125and a truncated bleomycin resistance gene. ThisblaNDM-1region was a part of the variable region of a new complex class 1 integron bearing IS common region 1 (ISCR1). The presence of ISPa7upstream of this integron suggests insertion in a chromosomally located Tn402-like structure.

scholarly journals Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology

2020 ◽  
Vol 11 ◽  
Author(s):  
Masaki Shintani ◽  
Eman Nour ◽  
Tarek Elsayed ◽  
Khald Blau ◽  
Inessa Wall ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Anthropogenic Pollution ◽  
Gene Clusters ◽  
Mobile Elements ◽  
Sequence Comparisons ◽  
Class 1 Integron ◽  
Class 1 ◽  
Abundance And Diversity

IncP-1 plasmids, first isolated from clinical specimens (R751, RP4), are recognized as important vectors spreading antibiotic resistance genes. The abundance of IncP-1 plasmids in the environment, previously reported, suggested a correlation with anthropogenic pollution. Unexpectedly, qPCR-based detection of IncP-1 plasmids revealed also an increased relative abundance of IncP-1 plasmids in total community DNA from the rhizosphere of lettuce and tomato plants grown in non-polluted soil along with plant age. Here we report the successful isolation of IncP-1 plasmids by exploiting their ability to mobilize plasmid pSM1890. IncP-1 plasmids were captured from the rhizosphere but not from bulk soil, and a high diversity was revealed by sequencing 14 different plasmids that were assigned to IncP-1β, δ, and ε subgroups. Although backbone genes were highly conserved and mobile elements or remnants as Tn501, IS1071, Tn402, or class 1 integron were carried by 13 of the sequenced IncP-1 plasmids, no antibiotic resistance genes were found. Instead, seven plasmids had a mer operon with Tn501-like transposon and five plasmids contained putative metabolic gene clusters linked to these mobile elements. In-depth sequence comparisons with previously known plasmids indicate that the IncP-1 plasmids captured from the rhizosphere are archetypes of those found in clinical isolates. Our findings that IncP-1 plasmids do not always carry accessory genes in unpolluted rhizospheres are important to understand the ecology and role of the IncP-1 plasmids in the natural environment.

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