scholarly journals Megaplasmids on the Rise: Combining Sequencing Approaches to Fully Resolve a Carbapenemase-Encoding Plasmid in a Proposed NovelPseudomonasSpecies

2019 ◽  
Author(s):  
João Botelho ◽  
Cédric Lood ◽  
Sally R. Partridge ◽  
Vera van Noort ◽  
Rob Lavigne ◽  
...  
Keyword(s):  
Hospital Setting ◽  
Antibiotic Resistance Genes ◽  
Heavy Metal Resistance ◽  
Multidrug Resistant ◽  
Metal Resistance ◽  
Resistant Bacteria ◽  
Class 1 Integron ◽  
Routine Surveillance ◽  
Class 1 ◽  
Selective Forces

AbstractHorizontal transfer of plasmids plays a pivotal role in the dissemination of antibiotic resistance genes and emergence of multidrug-resistant bacteria. Sequencing of plasmids is thus paramount for the success of accurate epidemiological tracking strategies in the hospital setting and routine surveillance. Here, we combine Nanopore and Illumina sequencing to fully assemble a carbapenemase-encoding megaplasmid carried by a clinical isolate belonging to a putative novelPseudomonasspecies. FFUP_PS_41 has a multidrug resistance phenotype and was initially identified asPseudomonas putida, but an average nucleotide identity below the cut-off for species delineation suggests a new species related to theP. putidaphylogenetic group. FFUP_PS_41 harbors a 498,516-bp untypable megaplasmid (pJBCL41) with low similarity compared with publicly available plasmids. pJBCL41 contains a full set of genes for self-transmission and genes predicted to be responsible for plasmid replication, partitioning, maintenance and heavy metal resistance. pJBCL41 carries a class 1 integron with the |aacA7|blaVIM-2|aacA4| cassette array (In103) located within a defective Tn402-like transposon that forms part of a 50,273-bp mosaic region bound by 38-bp inverted repeats typical of the Tn3family and flanked by 5-bp direct repeats. This region is composed of different elements, including additional transposon fragments, five insertion sequences and a Tn3-Derived Inverted-Repeat Miniature Element. The hybrid Nanopore/Illumina approach resulted in contiguous assemblies and allowed us to fully resolve a carbapenemase-encoding megaplasmid fromPseudomonasspp. The identification of novel megaplasmids will shed a new light on the evolutionary effects of gene transfer and the selective forces driving AR.

scholarly journals First Occurrence of the OXA-198 Carbapenemase in Enterobacterales

2020 ◽  
Vol 64 (4) ◽  
Author(s):  
Rémy A. Bonnin ◽  
Agnès B. Jousset ◽  
Lauraine Gauthier ◽  
Cécile Emeraud ◽  
Delphine Girlich ◽  
...  
Keyword(s):  
Multidrug Resistant ◽  
Routine Screening ◽  
Conjugative Plasmid ◽  
Resistant Bacteria ◽  
Multidrug Resistant Bacteria ◽  
Class 1 Integron ◽  
Carbapenem Resistant ◽  
Carbapenemase Gene ◽  
Class 1 ◽  
First Occurrence

ABSTRACT A carbapenem-resistant Citrobacter sp. was recovered from routine screening of multidrug-resistant bacteria. This isolate coproduced OXA-48 and OXA-198. OXA-48 was carried by the prototypical IncL plasmid, whereas OXA-198 was carried by a peculiar IncHI-type plasmid. This carbapenemase gene was inserted within a class 1 integron located on a conjugative plasmid. This report describes the first occurrence of OXA-198 in Enterobacterales.

Multidrug-Resistant Klebsiella pneumoniae Isolated from Farm Environments and Retail Products in Oklahoma

2005 ◽  
Vol 68 (10) ◽  
pp. 2022-2029 ◽  
Author(s):  
SHIN-HEE KIM ◽  
CHENG-I WEI ◽  
YWH-MIN TZOU ◽  
HAEJUNG AN
Keyword(s):  
Antibiotic Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Meat Products ◽  
Antibiotic Resistance Genes ◽  
Enteric Bacteria ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Gene Encoding ◽  
Class 1

Multidrug-resistant enteric bacteria were isolated from turkey, cattle, and chicken farms and retail meat products in Oklahoma. Among the isolated species, multidrug-resistant Klebsiella pneumoniae was prevalently isolated from most of the collected samples. Therefore, a total of 132 isolates of K. pneumoniae were characterized to understand their potential roles in the dissemination of antibiotic-resistance genes in the food chains. Multidrug-resistant K. pneumoniae was most frequently recovered from a turkey farm and ground turkey products among the tested samples. All isolates were resistant to ampicillin, tetracycline, streptomycin, gentamycin, and kanamycin. Class 1 integrons located in plasmids were identified as a common carrier of the aadA1 gene, encoding resistance to streptomycin and spectinomycin. Production of β-lactamase in the K. pneumoniae isolates played a major role in the resistance to β-lactam agents. Most isolates (96%) possessed blaSHV-1. Five strains were able to express both SHV-11 (pI 6.2) and TEM-1 (pI 5.2) β-lactamase. Transfer of these antibiotic-resistance genes to Escherichia coli was demonstrated by transconjugation. The bacterial genomic DNA restriction patterns by pulsed-field gel electrophoresis showed that the same clones of multidrug-resistant K. pneumoniae remained in feathers, feed, feces, and drinking water in turkey environments, indicating the possible dissemination of antibiotic-resistance genes in the ecosystem and cross-contamination of antibiotic-resistant bacteria during processing and distribution of products.

Prevalence of Class 1 Integron in Klebsiella Pneumoniae Isolates from Hospitals of Sanandaj, Iran

2020 ◽  
Author(s):  
Pegah Shakib
Keyword(s):  
Klebsiella Pneumoniae ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Diffusion Method ◽  
Main Role ◽  
Class 1 Integron ◽  
Antibiotic Susceptibility Pattern ◽  
Class 1 Integrons ◽  
Class 1 ◽  
Polymerase Chain

Background and Aims: Integrons as mobile genetic elements are located on the chromosome or on a plasmid in bacteria. Integrons play a main role in the dissemination of antibiotic resistance genes among different families of bacteria. The aim of this study was to identify the prevalence of class 1 integron in Klebsiella pneumoniae isolates from hospitals of Sanandaj, Kurdistan province, Iran. Materials and Methods: Seventy Klebsiella pneumoniae isolates were collected from Hospitals of Sanandaj. Antibiotic susceptibility pattern was performed by disc diffusion method. Class 1 integrons gene was screened by polymerase chain reaction assay. Data were analyzed by Fisher tests with STATA software program. Results: The highest and lowest rates of resistance were related to cefotaxime and imipenem, respectively. Thirteen (18.5%) out of 70 Klebsiella pneumoniae isolates caring class 1 integron gene. Out of 28 multidrug resistant isolates, 11 isolates were identified to be positive for the existence of class 1 integrons. Conclusions: class 1 integron positive isolates, compared to class 1 integron negative isolates, reveals resistance to more antibiotics.

scholarly journals Characterization of Multidrug Resistant ESBL-ProducingEscherichia coliIsolates from Hospitals in Malaysia

2009 ◽  
Vol 2009 ◽  
pp. 1-10 ◽  
Author(s):  
King-Ting Lim ◽  
Rohani Yasin ◽  
Chew-Chieng Yeo ◽  
Savithri Puthucheary ◽  
Kwai-Lin Thong
Keyword(s):  
Antibiotic Resistance ◽  
Random Amplified Polymorphic Dna ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Public Hospitals ◽  
Class 1 Integron ◽  
E Coli ◽  
Antibiotic Management ◽  
Class 1

The emergence ofEscherichia colithat produce extended spectrumβ-lactamases (ESBLs) and are multidrug resistant (MDR) poses antibiotic management problems. Forty-sevenE. coliisolates from various public hospitals in Malaysia were studied. All isolates were sensitive to imipenem whereas 36 were MDR (resistant to 2 or more classes of antibiotics). PCR detection using gene-specific primers showed that 87.5% of the ESBL-producingE. coliharbored theblaTEMgene. Other ESBL-encoding genes detected wereblaOXA,blaSHV, andblaCTX-M. Integron-encoded integrases were detected in 55.3% of isolates, with class 1 integron-encodedintI1integrase being the majority. Amplification and sequence analysis of the5′CS region of the integrons showed known antibiotic resistance-encoding gene cassettes of various sizes that were inserted within the respective integrons. Conjugation and transformation experiments indicated that some of the antibiotic resistance genes were likely plasmid-encoded and transmissible. All 47 isolates were subtyped by PFGE and PCR-based fingerprinting using random amplified polymorphic DNA (RAPD), repetitive extragenic palindromes (REPs), and enterobacterial repetitive intergenic consensus (ERIC). These isolates were very diverse and heterogeneous. PFGE, ERIC, and REP-PCR methods were more discriminative than RAPD in subtyping theE. coliisolates.

scholarly journals High Prevalence of Drug Resistance and Class 1 Integrons in Escherichia coli Isolated From River Yamuna, India: A Serious Public Health Risk

2021 ◽  
Vol 12 ◽  
Author(s):  
Nambram Somendro Singh ◽  
Neelja Singhal ◽  
Manish Kumar ◽  
Jugsharan Singh Virdi
Keyword(s):  
Escherichia Coli ◽  
Resistance Index ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Fecal Indicator ◽  
Class 1 Integron ◽  
E Coli ◽  
High Prevalence ◽  
Class 1 ◽  
River Yamuna

Globally, urban water bodies have emerged as an environmental reservoir of antimicrobial resistance (AMR) genes because resistant bacteria residing here might easily disseminate these traits to other waterborne pathogens. In the present study, we have investigated the AMR phenotypes, prevalent plasmid-mediated AMR genes, and integrons in commensal strains of Escherichia coli, the predominant fecal indicator bacteria isolated from a major urban river of northern India Yamuna. The genetic environment of blaCTX–M–15 was also investigated. Our results indicated that 57.5% of the E. coli strains were resistant to at least two antibiotic classes and 20% strains were multidrug resistant, i.e., resistant to three or more antibiotic classes. The multiple antibiotic resistance index of about one-third of the E. coli strains was quite high (>0.2), reflecting high contamination of river Yamuna with antibiotics. With regard to plasmid-mediated AMR genes, blaTEM–1 was present in 95% of the strains, followed by qnrS1 and armA (17% each), blaCTX–M–15 (15%), strA-strB (12%), and tetA (7%). Contrary to the earlier reports where blaCTX–M–15 was mostly associated with pathogenic phylogroup B2, our study revealed that the CTX-M-15 type extended-spectrum β-lactamases (ESBLs) were present in the commensal phylogroups A and B1, also. The genetic organization of blaCTX–M–15 was similar to that reported for E. coli, isolated from other parts of the world; and ISEcp1 was present upstream of blaCTX–M–15. The integrons of classes 2 and 3 were absent, but class 1 integron gene intI1 was present in 75% of the isolates, denoting its high prevalence in E. coli of river Yamuna. These evidences indicate that due to high prevalence of plasmid-mediated AMR genes and intI1, commensal E. coli can become vehicles for widespread dissemination of AMR in the environment. Thus, regular surveillance and management of urban rivers is necessary to curtail the spread of AMR and associated health risks.

Antimicrobial Resistance of Escherichia fergusonii Isolated from Broiler Chickens

2016 ◽  
Vol 79 (6) ◽  
pp. 929-938 ◽  
Author(s):  
KAREN SIMMONS ◽  
M. RASHEDUL ISLAM ◽  
HEIDI REMPEL ◽  
GLENN BLOCK ◽  
EDWARD TOPP ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Broiler Chickens ◽  
Antibiotic Resistance Genes ◽  
Enteric Bacteria ◽  
Resistant Bacteria ◽  
Genetic Determinants ◽  
Class 1 Integron ◽  
Class 1 ◽  
Disk Diffusion Assay ◽  
Commercial Broiler

ABSTRACT The objective of this study was to investigate the antibiotic resistance of Escherichia fergusonii isolated from commercial broiler chicken farms. A total of 245 isolates from cloacal and cecal samples of 28- to 36-day-old chickens were collected from 32 farms. Isolates were identified using PCR, and their susceptibility to 16 antibiotics was determined by disk diffusion assay. All isolates were susceptible to meropenem, amikacin, and ciprofloxacin. The most common resistances were against ampicillin (75.1%), streptomycin (62.9%), and tetracycline (57.1%). Of the 184 ampicillin-resistant isolates, 127 were investigated using a DNA microarray carrying 75 probes for antibiotic resistance genetic determinants. Of these 127 isolates, the β-lactamase blaCMY2, blaTEM, blaACT, blaSHV, and blaCTX-M-15 genes were detected in 120 (94.5%), 31 (24.4%), 8 (6.3%), 6 (4.7%), and 4 (3.2%) isolates, respectively. Other detected genes included those conferring resistance to aminoglycosides (aadA1, strA, strB), trimethoprims (dfrV, dfrA1), tetracyclines (tetA, tetB, tetC, tetE), and sulfonamides (sul1, sul2). Class 1 integron was found in 35 (27.6%) of the ampicillin-resistant isolates. However, our data showed that the tested E. fergusonii did not carry any carbapenemase blaOXA genes. Pulsed-field gel electrophoresis revealed that the selected ampicillin-resistant E. fergusonii isolates were genetically diverse. The present study indicates that the monitoring of antimicrobial-resistant bacteria should include enteric bacteria such as E. fergusonii, which could be a reservoir of antibiotic resistance genes. The detection of isolates harboring extended-spectrum β-lactamase genes, particularly blaCTX-M-15, in this work suggests that further investigations on the occurrence of such genes in broilers are warranted.

scholarly journals DNA Sequence and Comparative Genomics of pAPEC-O2-R, an Avian Pathogenic Escherichia coli Transmissible R Plasmid

2005 ◽  
Vol 49 (11) ◽  
pp. 4681-4688 ◽  
Author(s):  
Timothy J. Johnson ◽  
Kylie E. Siek ◽  
Sara J. Johnson ◽  
Lisa K. Nolan
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Agents ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Open Reading Frames ◽  
Beta Lactam ◽  
Class 1 Integron ◽  
E Coli ◽  
Serovar Typhimurium ◽  
Class 1

ABSTRACT In this study, a 101-kb IncF plasmid from an avian pathogenic Escherichia coli (APEC) strain (APEC O2) was sequenced and analyzed, providing the first completed APEC plasmid sequence. This plasmid, pAPEC-O2-R, has functional transfer and antimicrobial resistance-encoding regions. The resistance-encoding region encodes resistance to eight groups of antimicrobial agents, including silver and other heavy metals, quaternary ammonium compounds, tetracycline, sulfonamides, aminoglycosides, trimethoprim, and beta-lactam antimicrobial agents. This region of the plasmid is unique among previously described IncF plasmids in that it possesses a class 1 integron that harbors three gene cassettes and a heavy metal resistance operon. This region spans 33 kb and is flanked by the RepFII plasmid replicon and an assortment of plasmid maintenance genes. pAPEC-O2-R also contains a 32-kb transfer region that is nearly identical to that found in the E. coli F plasmid, rendering it transferable by conjugation to plasmid-less strains of bacteria, including an APEC strain, a fecal E. coli strain from an apparently healthy bird, a Salmonella enterica serovar Typhimurium strain, and a uropathogenic E. coli strain from humans. Differences in the G+C contents of individual open reading frames suggest that various regions of pAPEC-O2-R had dissimilar origins. The presence of pAPEC-O2-R-like plasmids that encode resistance to multiple antimicrobial agents and that are readily transmissible from APEC to other bacteria suggests the possibility that such plasmids may serve as a reservoir of resistance genes for other bacteria of animal and human health significance.

Antimicrobial Resistance and Presence of Class 1 Integrons Among Different Serotypes of Salmonella spp. Recovered From Children with Diarrhea in Tehran, Iran

2020 ◽  
Vol 20 (2) ◽  
pp. 160-166
Author(s):  
Seyedeh Hanieh Eshaghi Zadeh ◽  
Hossein Fahimi ◽  
Fatemeh Fardsanei ◽  
Mohammad Mehdi Soltan Dallal
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Multidrug Resistant ◽  
Salmonella Spp ◽  
Class 1 Integron ◽  
Class 1 Integrons ◽  
Food Borne ◽  
Class 1 ◽  
Resistance Patterns ◽  
C 30

Background: Salmonellosis is a major food-borne disease worldwide. The increasing prevalence of antimicrobial resistance among food-borne pathogens such as Salmonella spp. is concerning. Objective: The main objective of this study is to identify class 1 integron genes and to determine antibiotic resistance patterns among Salmonella isolates from children with diarrhea. Methods: A total of 30 Salmonella isolates were recovered from children with diarrhea. The isolates were characterized for antimicrobial susceptibility and screened for the presence of class 1 integron genes (i.e. intI1, sulI1, and qacEΔ1). Results: The most prevalent serotype was Enteritidis 36.7%, followed by Paratyphi C (30%), and Typhimurium (16.7%). The highest rates of antibiotic resistance were obtained for nalidixic acid (53.3%), followed by streptomycin (40%), and tetracycline (36.7%). Regarding class 1 integrons, 36.7%, 26.7%, and 33.3% of the isolates carried intI1, SulI, and qacEΔ1, respectively, most of which (81.8%) were multidrug-resistant (MDR). Statistical analysis revealed that the presence of class 1 integron was significantly associated with resistance to streptomycin and tetracycline (p = 0.042). However, there was no association between class 1 integron and other antibiotics used in this study (p > 0.05). Conclusion: The high frequency of integron class 1 gene in MDR Salmonella strains indicates that these mobile genetic elements are versatile among different Salmonella serotypes, and associated with reduced susceptibility to many antimicrobials.

scholarly journals Analysis of 56,348 Genomes Identifies the Relationship between Antibiotic and Metal Resistance and the Spread of Multidrug-Resistant Non-Typhoidal Salmonella

2021 ◽  
Vol 9 (7) ◽  
pp. 1468
Author(s):  
Gavin J. Fenske ◽  
Joy Scaria
Keyword(s):  
Antibiotic Resistance ◽  
Foodborne Pathogen ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Metal Resistance ◽  
Group 3 ◽  
Group 2 ◽  
Occurrence Matrix ◽  
Genome Assemblies ◽  
Group 1

Salmonella enterica is common foodborne pathogen that generates both enteric and systemic infections in hosts. Antibiotic resistance is common is certain serovars of the pathogen and of great concern to public health. Recent reports have documented the co-occurrence of metal resistance with antibiotic resistance in one serovar of S. enterica. Therefore, we sought to identify possible co-occurrence in a large genomic dataset. Genome assemblies of 56,348 strains of S. enterica comprising 20 major serovars were downloaded from NCBI. The downloaded assemblies were quality controlled and in silico serotyped to ensure consistency and avoid improper annotation from public databases. Metal and antibiotic resistance genes were identified in the genomes as well as plasmid replicons. Co-occurrent genes were identified by constructing a co-occurrence matrix and grouping said matrix using k-means clustering. Three groups of co-occurrent genes were identified using k-means clustering. Group 1 was comprised of the pco and sil operons that confer resistance to copper and silver, respectively. Group 1 was distributed across four serovars. Group 2 contained the majority of the genes and little to no co-occurrence was observed. Metal and antibiotic co-occurrence was identified in group 3 that contained genes conferring resistance to: arsenic, mercury, beta-lactams, sulfonamides, and tetracyclines. Group 3 genes were also associated with an IncQ1 class plasmid replicon. Metal and antibiotic co-occurrence from group 3 genes is mostly isolated to one clade of S. enterica I 4,[5],12:i:-.

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