scholarly journals Determining antimicrobial susceptibility in Salmonella enterica serovar Typhimurium through whole genome sequencing: a comparison against multiple phenotypic susceptibility testing methods

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Nana Mensah ◽  
Yue Tang ◽  
Shaun Cawthraw ◽  
Manal AbuOun ◽  
Jackie Fenner ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Salmonella Enterica ◽  
Susceptibility Testing ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Whole Genome ◽  
Testing Methods ◽  
Serovar Typhimurium ◽  
Phenotypic Susceptibility

scholarly journals Laboratory-Acquired Infection with Salmonella enterica Serovar Typhimurium Exposed by Whole-Genome Sequencing

2015 ◽  
Vol 54 (1) ◽  
pp. 190-193 ◽  
Author(s):  
David C. Alexander ◽  
Stephen F. Fitzgerald ◽  
Rachel DePaulo ◽  
Rosanne Kitzul ◽  
Dawn Daku ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Professional Training ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Whole Genome ◽  
Source Attribution ◽  
Laboratory Design ◽  
Serovar Typhimurium

Despite advances in laboratory design, professional training, and workplace biosafety guidelines, laboratory-acquired infections continue to occur. Effective tools are required to investigate cases and prevent future illness. Here, we demonstrate the value of whole-genome sequencing as a tool for the identification and source attribution of laboratory-acquired salmonellosis.

scholarly journals Expanding U.S. Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole-Genome Sequencing through the CDC's Antibiotic Resistance Laboratory Network

2020 ◽  
Vol 58 (4) ◽  
Author(s):  
Ellen N. Kersh ◽  
Cau D. Pham ◽  
John R. Papp ◽  
Robert Myers ◽  
Richard Steece ◽  
...  
Keyword(s):  
Public Health ◽  
Antibiotic Resistance ◽  
Neisseria Gonorrhoeae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Whole Genome ◽  
Content Type ◽  
Laboratory Capacity

ABSTRACT U.S. gonorrhea rates are rising, and antibiotic-resistant Neisseria gonorrhoeae (AR-Ng) is an urgent public health threat. Since implementation of nucleic acid amplification tests for N. gonorrhoeae identification, the capacity for culturing N. gonorrhoeae in the United States has declined, along with the ability to perform culture-based antimicrobial susceptibility testing (AST). Yet AST is critical for detecting and monitoring AR-Ng. In 2016, the CDC established the Antibiotic Resistance Laboratory Network (AR Lab Network) to shore up the national capacity for detecting several resistance threats including N. gonorrhoeae. AR-Ng testing, a subactivity of the CDC’s AR Lab Network, is performed in a tiered network of approximately 35 local laboratories, four regional laboratories (state public health laboratories in Maryland, Tennessee, Texas, and Washington), and the CDC’s national reference laboratory. Local laboratories receive specimens from approximately 60 clinics associated with the Gonococcal Isolate Surveillance Project (GISP), enhanced GISP (eGISP), and the program Strengthening the U.S. Response to Resistant Gonorrhea (SURRG). They isolate and ship up to 20,000 isolates to regional laboratories for culture-based agar dilution AST with seven antibiotics and for whole-genome sequencing of up to 5,000 isolates. The CDC further examines concerning isolates and monitors genetic AR markers. During 2017 and 2018, the network tested 8,214 and 8,628 N. gonorrhoeae isolates, respectively, and the CDC received 531 and 646 concerning isolates and 605 and 3,159 sequences, respectively. In summary, the AR Lab Network supported the laboratory capacity for N. gonorrhoeae AST and associated genetic marker detection, expanding preexisting notification and analysis systems for resistance detection. Continued, robust AST and genomic capacity can help inform national public health monitoring and intervention.

scholarly journals Genome Sequences of 13 Isolates of Salmonella enterica Serovar Typhimurium var. Copenhagen Obtained from Wild Pigeons in Canada

2018 ◽  
Vol 6 (20) ◽  
Author(s):  
Bridget Xie ◽  
Andrée Ann Dupras ◽  
Marc-Olivier Duceppe ◽  
Nooshin Fattahi-Ghazi ◽  
Lawrence Goodridge ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Virulence Plasmid ◽  
Avian Host ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Phage Types ◽  
Serovar Typhimurium

ABSTRACT Pigeon-adapted strains of Salmonella enterica serovar Typhimurium var. Copenhagen phage types 2 and 99 obtained from the provinces of Alberta, British Columbia, and Ontario, Canada, were analyzed using whole-genome sequencing. All isolates contained the Salmonella virulence plasmid despite the low pathogenicity of this lineage in their avian host.

scholarly journals Arthrobacter woluwensis Bacteremia: A Clinical and Genomic Report

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 443
Author(s):  
Shu-Yuan Li ◽  
Chin-Chuan Kao ◽  
Yu-Cheng Hu ◽  
Chung-Hsu Lai ◽  
Yi-Ping Jiang ◽  
...  
Keyword(s):  
Case Report ◽  
Whole Genome Sequencing ◽  
Clinical Isolate ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Immunocompromised Host ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Commercial Kits

Arthrobacter woluwensis is a Gram-positive, aerobic Actinobacteria that is widely distributed in the environment worldwide. Little is known about A. woluwensis infection and it is commonly mis-identified by culturing with commercial kits. To date, only six cases of bacteremia caused by A. woluwensis have been reported in the literature. Herein, we report a case of Arthrobacter woluwensis bacteremia in an immunocompromised host. In this case report, the results of antimicrobial susceptibility testing showed that this clinical isolate of A. woluwensis is sensitive to vancomycin, teicoplanin, but resistant to penicillin, cephalosporin and ciprofloxacin. Additionally, whole genome sequencing analysis identified common subunits of the urease system.

scholarly journals A study of the correlation between phenotypic antimicrobial susceptibility testing methods and the associated genotypes determined by whole genome sequencing for a collection of Escherichia coli of bovine origin

2021 ◽  
Author(s):  
Thomas J. Maunsell ◽  
Scott Nguyen ◽  
Farid El Garach ◽  
Christine Miossec ◽  
Emmanuel Cuinet ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Disk Diffusion ◽  
Whole Genome ◽  
Antimicrobial Compounds ◽  
Perfect Agreement ◽  
Positive Predicted Value

Antimicrobial resistance (AMR) has increased at an alarming pace in the recent years. Molecular-based methods such as whole genome sequencing (WGS) offer a potential alternative to the conventional labour-intensive methods traditionally used to characterise AMR phenotypes. The aim of this study was to investigate whether WGS could be used as a predictor of AMR in Escherichia coli isolates of bovine origin. Genomes of 143 E. coli cultured from cattle presenting with diarrhoea or mastitis were sequenced on an Illumina MiSeq platform. AMR genes were identified using the ResFinder and AMRFinder databases. Antimicrobial susceptibility testing by disk diffusion was performed on a panel of 10 antibiotics, covering 7 antimicrobial classes. Minimum inhibitory concentration (MIC) measurements were made using the Sensititre plate with 6 antibiotics, covering 5 antimicrobial classes. Correlation between genotype and phenotype was assessed statistically by means of a two-by-two table analysis and Cohen's kappa (κ) test. The overall κ correlation between WGS and disk diffusion was 0.81, indicating a near perfect agreement, and the average positive predicted value was 77.4 %. Correlation for individual antimicrobial compounds varied, with five yielding near perfect agreement (κ = 0.81-1.00; amoxicillin, florfenicol, gentamicin, tetracycline and trimethoprim-sulfamethoxazole), one showing substantial agreement (κ = 0.65; nalidixic acid), and four showing moderate agreement (κ = 0.41-0.60). The overall κ correlation between WGS and MIC was 0.55 indicating moderate agreement, and the average positive predicted value was 68.6 %. Three antibiotics yielded near perfect agreement (gentamicin, tetracycline and trimethoprim-sulfamethoxazole) and a further three showed fair agreement (κ = 0.21-0.40). WGS is a useful tool that can be used for the prediction of AMR phenotypes, and correlates well with disk diffusion results. MIC measurements may be necessary for antimicrobial compounds with a high proportion of intermediately resistant isolates recorded, such as cephalothin.

scholarly journals Comparative Genomic Analysis and Phenotypic Characterization of Bronchoscope-Associated Klebsiella Aerogenes

2020 ◽  
Author(s):  
Fang Huang ◽  
Shuang Li ◽  
Xiaohui Chi ◽  
Peipei Wen ◽  
Hao Fu ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Antimicrobial Susceptibility Testing ◽  
Klebsiella Aerogenes ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes

Abstract Background: Bronchoscopes has been linked to the outbreaks of nosocomial infections. We aim to investigate the phenotypic and genomic profiles of bronchoscope-associated Klebsiella aerogenes isolates, and their association with genome public available isolates from human and environment.Methods: We performed a prospective single-center study sampling echoendoscopes after clinical use and after normal decontamination procedures. Bacterial screening was conducted by culturing the sample on Mueller-Hinton agar plates. Antimicrobial susceptibility testing was performed using the broth microdilution method. Whole-genome sequencing of K. aerogenes isolates was performed using an Illumina HiSeq system and comparative genomics analysis were conducted.Results: Over the 5-month period, a total of 358 isolates and 13 isolates were recovered from samples after clinical procedures and samples after decontamination procedures, respectively. Antimicrobial susceptibility testing found 7 K. aerogenes isolates to exhibit low-level resistance to antimicrobial agents. Among 7 K. aerogenes isolates, we found 5 sequence types (STs). Whole genome sequencing and comparison analysis observed the genetic diversity in our bacterial collection, which clustered into three main clades. Furthermore, we identified a total of 43 antimicrobial resistance genes in the K. aerogenes core genomes. As expected, human isolates encoded more antimicrobial resistance genes than that environmental isolates. Conclusions: This study first described the phenotypic and genomics characteristics of bronchoscope-associated K. aerogenes. The present observations demonstrated that broadly investigation of specific pathogens using publicly available global genomes offered the opportunity to identify prevalent clones associated with various hosts, sources, and geographical locations.

Sign in / Sign up

Export Citation Format

Share Document