scholarly journals AcGI1, a novel genomic island carrying antibiotic resistance integron In687 in multidrug resistant Achromobacter xylosoxidans in a teaching hospital in Thailand

2020 ◽  
Vol 367 (14) ◽  
Author(s):  
Pisut Pongchaikul ◽  
Pitak Santanirand ◽  
Svetlana Antonyuk ◽  
Craig Winstanley ◽  
Alistair C Darby
Keyword(s):  
Antibiotic Resistance ◽  
Genetic Basis ◽  
Genomic Island ◽  
Hospital Setting ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Achromobacter Xylosoxidans ◽  
Whole Genome ◽  
Identical Nucleotide ◽  
Identical Nucleotide Sequence

ABSTRACT This study investigated the genetic basis of multidrug resistance in two strains of Achromobacter xylosoxidans isolated from patients attending a hospital in Thailand in 2012. These isolates were highly resistant to cephalosporins, aminoglycosides, fluoroquinolones, co-trimoxazole and carbapenems. Whole genome sequencing revealed that the two isolates were not clonally related and identified a carbapenem resistance gene-habouring integron (In687), residing in a novel genomic island, AcGI1. This In687 shares 100% identical nucleotide sequence with ones found in Acinetobacter baumannii Aci 16, isolated from the same hospital in 2007. We report the first analysis of multidrug-resistant A. xylosoxidans isolated in Thailand, and the first example of this island in A. xylosoxidans. Our data support the idea that resistance has spread in Thailand via horizontal gene transfer between species and suggest the possibility of A. xylosoxidans may serve as a reservoir of antibiotic resistance, especially in hospital setting.

scholarly journals Colistin and Carbapenem-Resistant Acinetobacter baumannii Aci46 in Thailand: Genome Analysis and Antibiotic Resistance Profiling

Antibiotics ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1054
Author(s):  
Nalumon Thadtapong ◽  
Soraya Chaturongakul ◽  
Sunhapas Soodvilai ◽  
Padungsri Dubbs
Keyword(s):  
Antibiotic Resistance ◽  
Acinetobacter Baumannii ◽  
Antibiotic Resistance Genes ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Diffusion Method ◽  
Whole Genome ◽  
Disk Diffusion Method ◽  
Genome Data ◽  
Carbapenem Resistant

Resistance to the last-line antibiotics against invasive Gram-negative bacterial infection is a rising concern in public health. Multidrug resistant (MDR) Acinetobacter baumannii Aci46 can resist colistin and carbapenems with a minimum inhibitory concentration of 512 µg/mL as determined by microdilution method and shows no zone of inhibition by disk diffusion method. These phenotypic characteristics prompted us to further investigate the genotypic characteristics of Aci46. Next generation sequencing was applied in this study to obtain whole genome data. We determined that Aci46 belongs to Pasture ST2 and is phylogenetically clustered with international clone (IC) II as the predominant strain in Thailand. Interestingly, Aci46 is identical to Oxford ST1962 that previously has never been isolated in Thailand. Two plasmids were identified (pAci46a and pAci46b), neither of which harbors any antibiotic resistance genes but pAci46a carries a conjugational system (type 4 secretion system or T4SS). Comparative genomics with other polymyxin and carbapenem-resistant A. baumannii strains (AC30 and R14) identified shared features such as CzcCBA, encoding a cobalt/zinc/cadmium efflux RND transporter, as well as a drug transporter with a possible role in colistin and/or carbapenem resistance in A. baumannii. Single nucleotide polymorphism (SNP) analyses against MDR ACICU strain showed three novel mutations i.e., Glu229Asp, Pro200Leu, and Ala138Thr, in the polymyxin resistance component, PmrB. Overall, this study focused on Aci46 whole genome data analysis, its correlation with antibiotic resistance phenotypes, and the presence of potential virulence associated factors.

scholarly journals Nosocomial Outbreak of Carbapenemase-Producing Proteus mirabilis With Two Novel Salmonella Genomic Island 1 Variants Carrying Different blaNDM–1 Gene Copies in China

2022 ◽  
Vol 12 ◽  
Author(s):  
Lang Yang ◽  
Hong He ◽  
Qichao Chen ◽  
Kaiying Wang ◽  
Yanfeng Lin ◽  
...  
Keyword(s):  
Proteus Mirabilis ◽  
Copy Number ◽  
Genomic Island ◽  
Gene Copy Number ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Gene Copy ◽  
Nosocomial Outbreak ◽  
Gene Copy Number Variation ◽  
Gene Copies

NDM-1-producing multidrug-resistant Proteus mirabilis brings formidable clinical challenges. We report a nosocomial outbreak of carbapenem-resistant P. mirabilis in China. Six P. mirabilis strains collected in the same ward showed close phylogenetic relatedness, indicating clonal expansion. Illumina and MinION sequencing revealed that three isolates harbored a novel Salmonella genomic island 1 carrying a blaNDM–1 gene (SGI1-1NDM), while three other isolates showed elevated carbapenem resistance and carried a similar SGI1 but with two blaNDM–1 gene copies (SGI1-2NDM). Four new single nucleotide mutations were present in the genomes of the two-blaNDM–1-harboring isolates, indicating later emergence of the SGI1-2NDM structure. Passage experiments indicated that both SGI variants were stably persistent in this clone without blaNDM–1 copy number changes. This study characterizes two novel blaNDM–1-harboring SGI1 variants in P. mirabilis and provides a new insight into resistance gene copy number variation in bacteria.

Insights on antibiotic resistance of Staphylococcus aureus from its whole genome: genomic island SCC

2003 ◽  
Vol 6 (1) ◽  
pp. 41-52 ◽  
Author(s):  
Teruyo Ito ◽  
Keiko Okuma ◽  
Xiao Xue Ma ◽  
Harumi Yuzawa ◽  
Keiichi Hiramatsu
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Genomic Island ◽  
Whole Genome

scholarly journals Antibiotic Resistance Genes and Salmonella Genomic Island 1 in Salmonella enterica Serovar Typhimurium Isolated in Italy

2002 ◽  
Vol 46 (9) ◽  
pp. 2821-2828 ◽  
Author(s):  
Alessandra Carattoli ◽  
Emma Filetici ◽  
Laura Villa ◽  
Anna Maria Dionisi ◽  
Antonia Ricci ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Genomic Island ◽  
Antibiotic Resistance Genes ◽  
Tetracycline Resistance ◽  
Gene Cassette ◽  
Multidrug Resistant ◽  
Phage Types ◽  
Serovar Typhimurium

ABSTRACT Fifty-four epidemiologically unrelated multidrug-resistant Salmonella enterica serovar Typhimurium isolates, collected between 1992 and 2000 in Italy, were analyzed for the presence of integrons. Strains were also tested for Salmonella genomic island 1 (SGI1), carrying antibiotic resistance genes in DT104 strains. A complete SGI1 was found in the majority of the DT104 strains. Two DT104 strains, showing resistance to streptomycin-spectinomycin and sulfonamides, carried a partially deleted SGI1 lacking the flost , tetR, and tetA genes, conferring chloramphenicol-florfenicol and tetracycline resistance, and the integron harboring the pse-1 gene cassette, conferring ampicillin resistance. The presence of SGI1 was also observed in serovar Typhimurium strains belonging to other phage types, suggesting either the potential mobility of this genomic island or changes in the phage-related phenotype of DT104 strains.

scholarly journals 2291. Evaluation of Multidrug-Resistant Pseudomonas aeruginosa Isolates in Patients Receiving Ceftolozane/tazobactam

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S785-S785
Author(s):  
Emily C Bodo ◽  
Aisling Caffrey ◽  
Vrishali Lopes ◽  
Jaclyn A Cusumano ◽  
Laura A Puzniak ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Retrospective Study ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Veterans Affairs ◽  
Carbapenem Resistant ◽  
Clinical Culture ◽  
Resistance Rates ◽  
Lactamase Inhibitor

Abstract Background Multidrug-resistant (MDR) Pseudomonas aeruginosa is a challenging pathogen to treat. Ceftolozane/tazobactam (C/T) is a combination cephalosporin and β-lactamase inhibitor that has demonstrated activity against MDR P. aeruginosa, including carbapenem-resistant isolates. The objective of this study was to evaluate multidrug resistance in P. aeruginosa isolates obtained from patients treated with C/T across the Veterans Affairs (VA) Healthcare System nationally. Methods Hospitalized patients who received at least 1 dose of CT between January 2015 and April 2018 and had a positive P. aeruginosa culture were included in this retrospective study. Culture source and antimicrobial susceptibility reports were assessed for each P. aeruginosa isolate. Isolates were categorized as multidrug-resistant based on the Centers for Disease Control (CDC) definition. Resistance rates were categorized by source of culture. Results We identified 174 positive P. aeruginosa cultures among 154 patients who received at least one dose of C/T during the study period. The most common sources of isolates were lung (40% of patients), urine (21%), skin and soft tissue (15%), blood (14%), and bone/joint (14%). Most patients (98.1%) had isolates that were MDR, with high rates of carbapenem (84.4%), extended-spectrum cephalosporin (82.5%), and fluoroquinolone (79.9%) resistance. In this cohort, 50.6% of patients received at least one antibiotic prior to initiating C/T to which their clinical culture was not susceptible. Conclusion Antibiotic resistance was high in this cohort of patients with P. aeruginosa, and as a result, use of non-susceptible antibiotics occurred in 50.6% of patients before C/T was started. The high carbapenem resistance rates are of great clinical concern, but highlight an area of utilization for C/T given its activity against carbapenem-resistant P. aeruginosa. Disclosures All authors: No reported disclosures.

scholarly journals Carriage of Carbapenem-Resistant Enterobacterales in Adult Patients Admitted to a University Hospital in Italy

Antibiotics ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 61
Author(s):  
Pamela Barbadoro ◽  
Daniela Bencardino ◽  
Elisa Carloni ◽  
Enrica Omiccioli ◽  
Elisa Ponzio ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Resistance Rate ◽  
Coli Strain ◽  
Adult Patients ◽  
University Hospital ◽  
E Coli ◽  
Genetic Features ◽  
Phenotypic Tests

The emerging spread of carbapenemase-producing Enterobacterales (CPE) strains, in particular, Klebsiella pneumoniae and Escherichia coli, has become a significant threat to hospitalized patients. Carbapenemase genes are frequently located on plasmids than can be exchanged among clonal strains, increasing the antibiotic resistance rate. The aim of this study was to determine the prevalence of CPE in patients upon their admission and to analyze selected associated factors. An investigation of the antibiotic resistance and genetic features of circulating CPE was carried out. Phenotypic tests and molecular typing were performed on 48 carbapenemase-producing strains of K. pneumoniae and E. coli collected from rectal swabs of adult patients. Carbapenem-resistance was confirmed by PCR detection of resistance genes. All strains were analyzed by PCR-based replicon typing (PBRT) and multilocus sequence typing (MLST) was performed on a representative isolate of each PBRT profile. More than 50% of the strains were found to be multidrug-resistant, and the blaKPC gene was detected in all the isolates with the exception of an E. coli strain. A multireplicon status was observed, and the most prevalent profile was FIIK, FIB KQ (33%). MLST analysis revealed the prevalence of sequence type 512 (ST512). This study highlights the importance of screening patients upon their admission to limit the spread of CRE in hospitals.

scholarly journals Whole Genome Sequence-Based Prediction of Resistance Determinants in High-Level Multidrug-Resistant Campylobacter jejuni Isolates in Lithuania

2020 ◽  
Vol 9 (1) ◽  
pp. 66
Author(s):  
Jurgita Aksomaitiene ◽  
Aleksandr Novoslavskij ◽  
Egle Kudirkiene ◽  
Ausra Gabinaitiene ◽  
Mindaugas Malakauskas
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Mobile Genetic Elements ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Genome Sequences ◽  
Resistance Determinants ◽  
High Level

Spread of antibiotic resistance via mobile genetic elements associates with transfer of genes providing resistance against multiple antibiotics. Use of various comparative genomics analysis techniques enables to find intrinsic and acquired genes associated with phenotypic antimicrobial resistance (AMR) in Campylobacter jejuni genome sequences with exceptionally high-level multidrug resistance. In this study, we used whole genome sequences of seven C. jejuni to identify isolate-specific genomic features associated with resistance and virulence determinants and their role in multidrug resistance (MDR). All isolates were phenotypically highly resistant to tetracycline, ciprofloxacin, and ceftriaxone (MIC range from 64 to ≥256 µg/mL). Besides, two C. jejuni isolates were resistant to gentamicin, and one was resistant to erythromycin. The extensive drug-resistance profiles were confirmed for the two C. jejuni isolates assigned to ST-4447 (CC179). The most occurring genetic antimicrobial-resistance determinants were tetO, beta-lactamase, and multidrug efflux pumps. In this study, mobile genetic elements (MGEs) were detected in genomic islands carrying genes that confer resistance to MDR, underline their importance for disseminating antibiotic resistance in C. jejuni. The genomic approach showed a diverse distribution of virulence markers, including both plasmids and phage sequences that serve as horizontal gene transfer tools. The study findings describe in silico prediction of AMR and virulence genetics determinants combined with phenotypic AMR detection in multidrug-resistant C. jejuni isolates from Lithuania.

scholarly journals Tracking of antibiotic resistance transfer and rapid plasmid evolution in a hospital setting by Nanopore sequencing

2019 ◽  
Author(s):  
Silke Peter ◽  
Mattia Bosio ◽  
Caspar Gross ◽  
Daniela Bezdan ◽  
Javier Gutierrez ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Rapid Evolution ◽  
Hospital Setting ◽  
Gene Cassette ◽  
Multidrug Resistant ◽  
Nanopore Sequencing ◽  
Multidrug Resistance Gene ◽  
Plasmid Evolution ◽  
Resistance Gene Cassette

AbstractBackgroundInfection of patients with multidrug-resistant (MDR) bacteria often leave very limited or no treatment options. The transfer of antimicrobial resistance genes (ARG) carrying plasmids between bacterial species by horizontal gene transfer represents an important mode of expansion of ARGs. Here, we evaluated the application of Nanopore sequencing technology in a hospital setting for monitoring the transfer and rapid evolution of antibiotic resistance plasmids within and across multiple species.ResultsIn 2009 we experienced an outbreak with an extensively multidrug resistant P. aeruginosa harboring the carbapenemase enzyme blaIMP-8, and in 2012 the first Citrobacter freundii and Citrobacter werkmanii harboring the same enzyme were detected. Using Nanopore and Illumina sequencing we conducted a comparative analysis of all blaIMP-8 bacteria isolated in our hospital over a 6-year period (n = 54). We developed the computational platforms pathoLogic and plasmIDent for Nanopore-based characterization of clinical isolates and monitoring of ARG transfer, comprising de-novo assembly of genomes and plasmids, polishing, QC, plasmid circularization, ARG annotation, comparative genome analysis of multiple isolates and visualization of results. Using plasmIDent we identified a 40 kb plasmid carrying blaIMP-8 in P. aeruginosa and C. freundii, verifying that plasmid transfer had occurred. Within C. freundii the plasmid underwent further evolution and plasmid fusion, resulting in a 164 kb mega-plasmid, which was transferred to C. werkmanii. Moreover, multiple rearrangements of the multidrug resistance gene cassette were detected in P. aeruginosa, including deletions and translocations of complete ARGs.ConclusionPlasmid transfer, plasmid fusion and rearrangement of the multidrug resistance gene cassette mediated the rapid evolution of opportunistic pathogens in our hospital. We demonstrated the feasibility of tracking plasmid evolution dynamics and ARG transfer in clinical settings in a timely manner. The approach will allow for successful countermeasures to contain not only clonal, but also plasmid mediated outbreaks.

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