Practical applications of whole genome sequencing for reservoir epidemiology, molecular surveillance, and antimicrobial susceptibility testing of extended-spectrum ß-lactamase producing Escherichia coli

10.33540/779 ◽  
2021 ◽  
Author(s):  
◽  
Tess Daniëlle Verschuuren
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Antimicrobial Susceptibility Testing ◽  
Whole Genome ◽  
Molecular Surveillance ◽  
Practical Applications ◽  
Extended Spectrum

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.

scholarly journals Emergence and Genomic Characterization of a KPC-2-, NDM-1-, and IMP-4-Producing Klebsiella michiganensis Isolate

2022 ◽  
Vol 12 ◽  
Author(s):  
Yanyan Zhang ◽  
Danxia Gu ◽  
Xuemei Yang ◽  
Yuchen Wu ◽  
Congcong Liu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Colloidal Gold ◽  
Susceptibility Testing ◽  
Antimicrobial Susceptibility Testing ◽  
Pcr Analysis ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Sequencing Analysis

A rectal swab sample was collected from a patient with Guillain–Barré syndrome and enriched in lysogeny broth. Carbapenem-resistant bacteria were selected by China Blue agar plates containing 0.3 μg/ml meropenem. Carbapenemase-producing Klebsiella michiganensis was identified and characterized by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), immune colloidal gold technique, a conjugation experiment, PCR analysis, and antimicrobial susceptibility testing. The genome of K. michiganensis was determined by whole genome sequencing. Antimicrobial susceptibility testing showed that the K. michiganensis was resistant to imipenem, meropenem, ertapenem, cefmetazole, ceftazidime, cefotaxime, piperacillin/tazobactam, sulbactam/cefoperazone, ceftazidime/avibactam, cefepime, and aztreonam while susceptible to polymyxin B, ciprofloxacin, tigecycline, and amikacin. Immune colloidal gold technique suggested that this strain co-produced three different carbapenemases [Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-beta-lactamase (NDM), and Imipenem (IMP)]. Whole genome sequencing analysis indicated that this strain belonged to ST91, and blaKPC–2, blaNDM–1, and blaIMP–4 were carried on different conjugative plasmids. Besides, the co-existence and transferability of blaKPC–2, blaNDM–1, and blaIMP–4 in K. michiganensis facilitates the potential horizontal dissemination and nosocomial spread of resistance genes among multidrug-resistant organisms.

scholarly journals Whole genome sequencing identifies independent outbreaks of Shigellosis in 2010 and 2011 in La Pampa Province, Argentina

2016 ◽  
Author(s):  
Isabel Chinen ◽  
Marcelo Galas ◽  
Ezequiel Tuduri ◽  
Maria Rosa Viñas ◽  
Carolina Carbonari ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Diarrheal Disease ◽  
Genetic Material ◽  
Routine Data ◽  
Antimicrobial Susceptibility Testing ◽  
Whole Genome ◽  
Middle Income

AbstractShigella sonnei is an emergent cause of diarrheal disease in middle-income countries. The organism causes endemic disease and is also associated with sporadic outbreaks in susceptible populations. In 2010 and 2011 there were two suspected outbreaks of diarrheal disease caused by S. sonnei in La Pampa province in central Argentina. Aiming to confirm these as outbreaks and provide insight into the relationship of the strains causing these infections we combined antimicrobial susceptibility testing and pulsed field gel electrophoresis (PFGE) with whole genome sequencing (WGS). Antimicrobial susceptibility testing suggested the two events were unrelated; organisms isolated in 2010 exhibited resistance to trimethoprim sulphate whereas the 2011 S. sonnei were non-susceptible against ampicillin, trimethoprim sulphate and cefpodoxime. PFGE profiling confirmed the likelihood of two independent outbreaks, separating the isolates into two main XbaI restriction profiles. We additionally performed WGS on 17 isolates associated with these outbreaks. The resulting phylogeny confirmed the PFGE structure and separated the organisms into two comparatively distantly related clones. Antimicrobial resistant genes were common, and the presence of an OXA-1 was likely associated with resistance to cefpodoxime in the second outbreak. We additionally identified novel horizontally transferred genetic material that may impinge on the pathogenic phenotype of the infecting strains. Our study shows that even with a lack of supporting routine data WGS is an indispensible method for the tracking and surveillance of bacterial pathogens during outbreaks and is becoming a vital tool for the monitoring of antimicrobial resistant strains of S. sonnei.

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.

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.

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