scholarly journals Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Suchawan Pornsukarom ◽  
Arnoud H M van Vliet ◽  
Siddhartha Thakur
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Phylogenetic Relatedness ◽  
Virulence Markers ◽  
Salmonella Serovars ◽  
Food Animals

scholarly journals Frequency of Antimicrobial Resistance Genes in Salmonella From Brazil by in silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades

2020 ◽  
Vol 11 ◽  
Author(s):  
Grazielle Lima Rodrigues ◽  
Pedro Panzenhagen ◽  
Rafaela Gomes Ferrari ◽  
Anamaria dos Santos ◽  
Vania Margaret Flosi Paschoalin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
In Silico ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Antimicrobial Resistance Genes

scholarly journals Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

2015 ◽  
Vol 82 (2) ◽  
pp. 459-466 ◽  
Author(s):  
S. Zhao ◽  
G. H. Tyson ◽  
Y. Chen ◽  
C. Li ◽  
S. Mukherjee ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Antimicrobial Agents ◽  
The United States ◽  
23S Rrna ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Content Type

ABSTRACTThe objectives of this study were to identify antimicrobial resistance genotypes forCampylobacterand to evaluate the correlation between resistance phenotypes and genotypes usingin vitroantimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114Campylobacterspecies isolates (82C. coliand 32C. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, includingtet(O),blaOXA-61,catA,lnu(C),aph(2″)-Ib,aph(2″)-Ic,aph(2′)-If,aph(2″)-Ig,aph(2″)-Ih,aac(6′)-Ie-aph(2″)-Ia,aac(6′)-Ie-aph(2″)-If,aac(6′)-Im,aadE,sat4,ant(6′),aad9,aph(3′)-Ic, andaph(3′)-IIIa, and mutations in two housekeeping genes (gyrAand 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs.

Phenotypic and Genotypic Characterization of Antimicrobial Resistance in Salmonella Strains Isolated from Chicken Carcasses and Parts Collected at Different Stages during Processing

2019 ◽  
Vol 82 (10) ◽  
pp. 1793-1801
Author(s):  
ALEJANDRA RAMIREZ-HERNANDEZ ◽  
MARIE BUGAREL ◽  
SANJAY KUMAR ◽  
HARSHAVARDHAN THIPPAREDDI ◽  
MINDY M. BRASHEARS ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Genome ◽  
Plate Count ◽  
Contamination Rate ◽  
Microbiological Analysis ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Poultry Processing

ABSTRACT Chicken carcass and parts rinsate samples and fecal samples were collected at different stages in a commercial poultry processing facility. Microbiological analysis was conducted to determine the levels of multiple indicator microorganisms and prevalence of Salmonella. Antibiotic susceptibility testing was conducted on Salmonella isolates to determine antimicrobial resistance profiles. Whole genome sequencing was performed for tracing isolates in the processing chain, serotyping, and determining genetic features associated with virulence and antimicrobial resistance in the bacterial genome. The overall contamination rate was 55% for Salmonella. Prevalence increased by 80% in chicken parts compared with the previous processing site (postchill carcasses), suggesting possible cross-contamination during the cutting and deboning processes. The levels of indicator organisms were reduced significantly from the prescalding to the parts processing sites, by 3.22 log CFU/mL for aerobic plate count, 3.92 log CFU/mL for E. coli, 3.70 log CFU/mL for coliforms, and 3.40 log CFU/mL for Enterobacteriaceae. The most frequent resistance in Salmonella was associated with tetracycline (49 of 50, 98%) and streptomycin (43 of 50, 86%). Some Salmonella isolates featured resistance to the cephems class of antibiotics (up to 15%). Whole genome sequencing analysis of Salmonella isolates identified nine different clonal populations distributed throughout the samples taken at different stages; serotype Kentucky was the most commonly isolated. This study provides insights into microbial profiling and antibiotic-resistant strains of chicken rinsate samples during poultry processing.

Whole-genome sequencing analysis of highly prevalent Salmonella serovars in wild boars from a national park in Sardinia

Food Control ◽  
2021 ◽  
pp. 108247
Author(s):  
F. Piras ◽  
V.Spanu ◽  
G. Siddi ◽  
P. Gymoese ◽  
C. Spanu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
National Park ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Wild Boars ◽  
Salmonella Serovars

Occurrence, antimicrobial resistance and whole-genome sequencing analysis of Salmonella isolates from chicken carcasses imported into Iraq from four different countries

2018 ◽  
Vol 284 ◽  
pp. 84-90 ◽  
Author(s):  
Ali Harb ◽  
Ihab Habib ◽  
Ezat Hussain Mezal ◽  
Hayder Shannoon Kareem ◽  
Tanya Laird ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Sequencing Analysis

1722-P: Colocalization of TOPMed Whole Genome Sequencing Analysis and Tissue-Specific eQTL Signals Detects Target Genes for Type 2 Diabetes Risk

Diabetes ◽  
2019 ◽  
Vol 68 (Supplement 1) ◽  
pp. 1722-P
Author(s):  
MINDY D. SZETO ◽  
HEATHER M. HIGHLAND ◽  
ALISA MANNING ◽  
Keyword(s):  
Type 2 Diabetes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Target Genes ◽  
Diabetes Risk ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Tissue Specific
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