scholarly journals Genomic characterization of an extensively-drug resistance Salmonella enterica serotype Indiana strain harboring blaNDM-1 gene isolated from a chicken carcass in China

2017 ◽  
Vol 204 ◽  
pp. 48-54 ◽  
Author(s):  
Wei Wang ◽  
Zixin Peng ◽  
Zulqarnain Baloch ◽  
Yujie Hu ◽  
Jin Xu ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Salmonella Enterica ◽  
Chicken Carcass ◽  
Genomic Characterization ◽  
Extensively Drug Resistance

scholarly journals Genomic Characterization of Extended-Spectrum Cephalosporin-Resistant Salmonella enterica in the Colombian Poultry Chain

2018 ◽  
Vol 9 ◽  
Author(s):  
Luis Ricardo Castellanos ◽  
Linda van der Graaf-van Bloois ◽  
Pilar Donado-Godoy ◽  
Maribel León ◽  
Viviana Clavijo ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Extended Spectrum ◽  
Genomic Characterization

scholarly journals A Gene Panel NGS-Based Strategy for Genomic Characterization of Acute Myeloid Leukemias (AMLs)

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4952-4952
Author(s):  
Simona Bernardi ◽  
Federica Cattina ◽  
Andrea Di Palma ◽  
Erika Borlenghi ◽  
Francesca Schieppati ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Conflicts Of Interest ◽  
Leukemic Cell ◽  
Gene Panel ◽  
Prognostic Impact ◽  
Sequencing Analysis ◽  
Myeloid Leukemias ◽  
Genomic Characterization ◽  
Acute Myeloid

Abstract AMLs are clonal disorders characterized by high genomic heterogeneity and several chromosomal and molecular alterations affecting patients' outcome. In about 40% of AML patients who do not show any citogenetic alteration, sequencing analysis identified different gene mutations which play a pivotal role in leukemogenesis and have a negative prognostic impact: FLT3, ASXL1, TET2, IDH1, IDH2, RUNX1, CBL, CEBPα, DNMT3A and TP53. Conventional Sanger sequencing may detect clones representing more than 20% of the total tumor population, whereas Next Generation Sequencing (NGS) can identify mutations in less than 1% of leukemic cell burden. The detection of these variants is relevant because they can play an important role in driving drug resistance and disease relapse and for biologic risk assessment. To that purpose, we designed a 23-genes panel including: FLT3, DNMT3A, RUNX1, ASXL1, IDH1, IDH2, BCOR, NRAS, KRAS, TET2, TP53, U2AF1, ZRSR2, SF3B1, SRSF2, CBL, CEBPα, EZH2, NPM1, TERT, TERC, ETV6, GATA2. By using a 454 GS Junior by Roche Diagnostics with an amplicon-based sequencing approach and performing three sequencing runs per sample in order to reach a sensitivity of at least 1%, we settled an investigative strategy in order to assess the genomic profile of AMLs at diagnosis and possibly at the time of relapse or resistance. By this approach, we were able to confirm all the variants (i.e. FLT3, NPM1) previously documented with conventional tests; to reveal the presence of variants under the Sanger threshold of 20% in the genes resulted as wild type with routinely analysis; to evaluate the AML clonal heterogeneity, by assessing the coexistence of several mutated clones which have been described to be related to drug resistance, poor prognosis or to prior myelodysplastic syndrome. This gene panel NGS-based strategy may be proposed as a highly accurate and sensitive approach for genomic characterization of acute myeloid leukemias and as an useful tool for planning a target and personalized AML therapy. Disclosures No relevant conflicts of interest to declare.

scholarly journals In-Depth Genomic Characterization of a Meropenem-nonsusceptible Pseudomonas otitidis Strain Contaminating Chicken Carcass

2020 ◽  
Vol 48 ◽  
Author(s):  
Tatiana Regina Vieira ◽  
Gustavo Enck Sambrano ◽  
Núbia Michelle Vieira da Silva ◽  
Priscylla Carvalho Vasconcelos ◽  
Esther Ferraza Cavinatto de Oliveira ◽  
...  
Keyword(s):  
Public Health ◽  
Antimicrobial Resistance ◽  
Resistant Bacteria ◽  
Beta Lactamase ◽  
Food Animal ◽  
Chicken Carcass ◽  
Pseudomonas Species ◽  
Genes Encoding ◽  
Genomic Characterization

Background: The indiscriminate use of antibiotics in food-animal production has a major impact on public health, particularly in terms of contributing to the emergence and dissemination of antimicrobial resistant bacteria in the food-animal production chain. Although Pseudomonas species are recognized as important spoilage organisms in foodstuff, they are also known as opportunistic pathogens associated with hospital-acquired infections. Furthermore, Pseudomonas can play a role as potential reservoirs of antimicrobial resistance genes, which may be horizontally transferred to other bacteria. Considering that cephalosporins (3rd and higher generations) and carbapenems are critically important beta-lactam antimicrobials in human medicine, this study reports the occurrence and genomic characterization of a meropenem-nonsusceptible Pseudomonas otitidis strain recovered from a chicken carcass in Brazil.Materials, Methods & Results: During the years 2018-2019, 72 frozen chicken carcasses were purchased on the retail market from different regions in Brazil. Aliquots from individual carcass rinses were screened for Extended Spectrum Beta-lactamase (ESBL)-producing bacteria in MacConkey agar supplemented with 1mg.L-1 cefotaxime. Phenotypically resistant isolates were further tested for resistance to other antimicrobials and confirmed as ESBL-producers by means of disk-diffusion method using Müller-Hinton agar. Only one meropenen-nonsusceptible isolate was detected and submitted to whole genome sequencing (WGS) in Illumina Miseq. The strain was identified as Pseudomonas otitidis by local alignment of the 16S rRNA sequence using BLASTn and confirmed by Average Nucleotide Identity (ANI) analysis using JspeciesWS database. Genes encoding for antimicrobial resistance were detected by means of Resfinder and Comprehensive Antibiotic Resistance Database (CARD) databases. The phenotypic non-susceptibility to meropenen was attributed to the gene blaPOM-1. A total of 192 different genes encoding for quorum sensing system, antiphagocytosis, iron uptake, efflux pump, endotoxin and toxin, adherence, and secretion systems were detected by means of Virulence Factor Database (VFDB). Pseudomonas otitidis-pan genome was built using Roary-rapid large-scale prokaryote pan genome analysis using the present strain (K_25) and other two P. otitidis genomes (PAM-1, DSM 17224) publicly available at the NCBI. The core genome analysis of the two human strains resulted in similar percentages.Discussion: Carbapenems are critically important drugs for human health and bacterial strains resistant to these antimicrobials pose a public health problem. The blaPOM-1 gene harbored by the Pseudomonas otitidis K_25 strain encodes a metallo-beta-lactamase (MBL) conferring resistance to carbapenems. Pseudomonas otitidis was the first confirmed pathogenic Pseudomonas species expressing MBL constitutively in the absence of inducible beta-lactamase genes. Furthermore, the several virulence genes associated with the capacity of the P. otitidis K_25 to colonize, evade the immune system and cause lesions in the human host confirm this strain as a potential opportunistic pathogen contaminating foodstuff. These reinforce the need to address antimicrobial resistance in a One Health perspective, in which resistant bacteria and resistance determinants circulate among environment, animals and humans.

scholarly journals Genomic Characterization of Multidrug-Resistant Escherichia coli BH100 Sub-strains

2021 ◽  
Vol 11 ◽  
Author(s):  
Rodrigo Carvalho ◽  
Flavia Aburjaile ◽  
Marcus Canario ◽  
Andréa M. A. Nascimento ◽  
Edmar Chartone-Souza ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Drug Resistance ◽  
Resistance Genes ◽  
Multidrug Resistant ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
E Coli ◽  
Brazilian Woman ◽  
Genomic Characterization

The rapid emergence of multidrug-resistant (MDR) bacteria is a global health problem. Mobile genetic elements like conjugative plasmids, transposons, and integrons are the major players in spreading resistance genes in uropathogenic Escherichia coli (UPEC) pathotype. The E. coli BH100 strain was isolated from the urinary tract of a Brazilian woman in 1974. This strain presents two plasmids carrying MDR cassettes, pBH100, and pAp, with conjugative and mobilization properties, respectively. However, its transposable elements have not been characterized. In this study, we attempted to unravel the factors involved in the mobilization of virulence and drug-resistance genes by assessing genomic rearrangements in four BH100 sub-strains (BH100 MG2014, BH100 MG2017, BH100L MG2017, and BH100N MG2017). Therefore, the complete genomes of the BH100 sub-strains were achieved through Next Generation Sequencing and submitted to comparative genomic analyses. Our data shows recombination events between the two plasmids in the sub-strain BH100 MG2017 and between pBH100 and the chromosome in BH100L MG2017. In both cases, IS3 and IS21 elements were detected upstream of Tn21 family transposons associated with MDR genes at the recombined region. These results integrated with Genomic island analysis suggest pBH100 might be involved in the spreading of drug resistance through the formation of resistance islands. Regarding pathogenicity, our results reveal that BH100 strain is closely related to UPEC strains and contains many IS3 and IS21-transposase-enriched genomic islands associated with virulence. This study concludes that those IS elements are vital for the evolution and adaptation of BH100 strain.

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