scholarly journals SELfies and CELLfies: Whole Genome Sequencing and Annotation of Five Antibiotic Resistant Bacteria Isolated from the Surfaces of Smartphones, An Inquiry Based Laboratory Exercise in a Genomics Undergraduate Course at the Rochester Institute of Technology

2019 ◽  
Vol 7 ◽  
pp. 26-30 ◽  
Author(s):  
Anutthaman Parthasarathy ◽  
Narayan H. Wong ◽  
Amanda N. Weiss ◽  
Susan Tian ◽  
Sara E. Ali ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant ◽  
Laboratory Exercise ◽  
Rochester Institute Of Technology ◽  
Institute Of Technology

scholarly journals Isolation and Whole-Genome Sequencing of 12 Mushroom-Associated Bacterial Strains: an Inquiry-Based Laboratory Exercise in a Genomics Course at the Rochester Institute of Technology

2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Narayan H. Wong ◽  
Andrew J. Rosato ◽  
Yara M. Rose ◽  
Trevor S. Penix ◽  
Janice B. Fung ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Life Sciences ◽  
Whole Genome ◽  
Bacterial Strains ◽  
Genome Sequences ◽  
Mushroom Species ◽  
Laboratory Exercise ◽  
Rochester Institute Of Technology ◽  
Institute Of Technology

Here, we report the isolation, identification, and whole-genome sequences of 12 bacterial strains associated with four mushroom species. The study was done as an inquiry-based exercise in an undergraduate genomics course (BIOL 340) in the Thomas H. Gosnell School of Life Sciences at the Rochester Institute of Technology.

scholarly journals How Do We Find the Source of Foodborne Superbug Outbreaks?

2021 ◽  
Vol 9 ◽  
Author(s):  
Joy Scaria ◽  
Shruti Menon ◽  
Maristela Rovai
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Food Supply ◽  
Supply System ◽  
New Method ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Testing Methods ◽  
Antibiotic Resistant ◽  
The World

Lately, there have been more foodborne “superbug” outbreaks than ever before, which creates a problem because superbugs are antibiotic-resistant bacteria that are difficult to treat. To reduce such outbreaks, better ways of finding the source of the infection are needed. Superbugs, such as Salmonella are often transmitted through food. The world’s food supply system has become so complex that it is often difficult to find the source of an outbreak with older testing methods. A new method called whole genome sequencing (WGS) has now been developed to track superbug infections. Using WGS, it is now possible to identify the source of an outbreak in one country that may be transmitted through food imported from the opposite side of the world. Good outbreak tracing methods help scientists make better predictions about outbreaks. Finding the source of an outbreak early on can lead to better containment and lower costs.

scholarly journals Whole-Genome Sequencing and Annotation of Exiguobacterium sp. RIT 452, an Antibiotic-Producing Strain Isolated from a Pond Located on the Campus of the Rochester Institute of Technology

2018 ◽  
Vol 7 (17) ◽  
Author(s):  
Anutthaman Parthasarathy ◽  
Narayan H. Wong ◽  
Nicole T. Cavanaugh ◽  
KayLee K. Steiner ◽  
Peter C. Wengert ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antibiotic Production ◽  
Whole Genome ◽  
Content Type ◽  
Rochester Institute Of Technology ◽  
Institute Of Technology

Exiguobacterium sp. RIT 452 is of biotechnological importance given its potential for antibiotic production.

scholarly journals Enterobacter cloacae Complex Sequence Type 171 Isolates Expressing KPC-4 Carbapenemase Recovered from Canine Patients in Ohio

2018 ◽  
Vol 62 (12) ◽  
Author(s):  
Joshua B. Daniels ◽  
Liang Chen ◽  
Susan V. Grooters ◽  
Dixie F. Mollenkopf ◽  
Dimitria A. Mathys ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Companion Animals ◽  
Enterobacter Cloacae ◽  
Sequence Type ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Content Type ◽  
Complex Sequence ◽  
Enterobacter Cloacae Complex

ABSTRACT Companion animals are likely relevant in the transmission of antimicrobial-resistant bacteria. Enterobacter xiangfangensis sequence type 171 (ST171), a clone that has been implicated in clusters of infections in humans, was isolated from two dogs with clinical disease in Ohio. The canine isolates contained IncHI2 plasmids encoding blaKPC-4. Whole-genome sequencing was used to put the canine isolates in phylogenetic context with available human ST171 sequences, as well as to characterize their blaKPC-4 plasmids.

scholarly journals Application of combined genomic and transfer analyses to identify factors mediating regional spread of antibiotic resistant bacterial lineages

2020 ◽  
Author(s):  
Joyce Wang ◽  
Betsy Foxman ◽  
Ali Pirani ◽  
Zena Lapp ◽  
Lona Mody ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Analysis ◽  
Patient Characteristics ◽  
Patient Transfer ◽  
Whole Genome ◽  
Nursing Facilities ◽  
Antibiotic Resistant ◽  
Patient Level ◽  
Healthcare Associated

ABSTRACTBackgroundPatients entering nursing facilities (NFs) are frequently colonized with antibiotic resistant organisms (AROs). To understand the determinants of ARO colonization on NF admission we applied whole-genome sequencing to track the spread of four ARO species across regional NFs and evaluated patient-level characteristics and transfer acute-care hospitals (ACHs) as risk factors for colonization.Methods584 patients from six NFs were surveyed for methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis/faecium (VREfc/VREfm) and ciprofloxacin-resistant Escherichia coli (CipREc) colonization. Genomic analysis was performed to quantify ARO spread between NFs and compared to patient-transfer networks. The association between admission colonization and patient-level variables and recent ACH exposures was examined using multivariable regression models.ResultsThe majority of ARO isolates across study sites belonged to major healthcare-associated lineages: MRSA (ST5;N=89/117); VREfc (ST6;N=68/75); CipREc (ST131; N=58/64), and VREfm (clade A; N=129/129). While the genomic similarity of strains between NF pairs was associated with overlap in their feeder ACHs (Spearman’s rho=0.44-0.75, p<0.05 for MRSA, VREfc and CipREc), limited phylogenetic clustering by either ACH or NF supported regional endemicity. Significant predictors for ARO colonization on NF admission included lower functional status (adjusted odds ratio [aOR]>1 for all four AROs) and recent exposure to glycopeptides (aOR>2 for VREfm, VREfc and MRSA) or 3rd/4th-generation cephalosporins (aOR>2 for MRSA and VREfm). Transfer from specific ACHs was an independent risk factor for only one ARO/ACH pair (VREfm/ACH19, aOR=2.48[1.06-5.83]).ConclusionIn this region, healthcare-associated ARO lineages are endemic among connected NFs and ACHs, making patient characteristics more informative of NF admission colonization risk than exposure to specific ACHs.SummaryUsing a combination of whole-genome sequencing, patient transfer and clinical data, we discerned the dissemination of four high-priority antibiotic-resistant organisms (ARO) in the regional healthcare network, and epidemiolocal drivers underlying the high ARO importation rate into regional nursing facilities.

scholarly journals Whole-genome sequencing reveals transmission of gonococcal antibiotic resistance among men who have sex with men: an observational study

2017 ◽  
Vol 94 (2) ◽  
pp. 151-157 ◽  
Author(s):  
Jason C Kwong ◽  
Eric P F Chow ◽  
Kerrie Stevens ◽  
Timothy P Stinear ◽  
Torsten Seemann ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Disease Transmission ◽  
Sexual Partners ◽  
Whole Genome ◽  
Global Public Health ◽  
Antibiotic Resistant ◽  
Treatment And Prevention ◽  
A Genome ◽  
Sex With Men

ObjectivesDrug-resistant Neisseria gonorrhoeae are now a global public health threat. Direct transmission of antibiotic-resistant gonococci between individuals has been proposed as a driver for the increased transmission of resistance, but direct evidence of such transmission is limited. Whole-genome sequencing (WGS) has superior resolution to investigate outbreaks and disease transmission compared with traditional molecular typing methods such as multilocus sequence typing (MLST) and N. gonorrhoeae multiantigen sequence (NG-MAST). We therefore aimed to systematically investigate the transmission of N. gonorrhoeae between men in sexual partnerships using WGS to compare isolates and their resistance to antibiotics at a genome level.Methods458 couples from a large prospective cohort of men who have sex with men (MSM) tested for gonorrhoea together between 2005 and 2014 were included, and WGS was conducted on all isolates from couples where both men were culture-positive for N. gonorrhoeae. Resistance-determining sequences were identified from genome assemblies, and comparison of isolates between and within individuals was performed by pairwise single nucleotide polymorphism and pangenome comparisons, and in silico predictions of NG-MAST and MLST.ResultsFor 33 of 34 (97%; 95% CI 85% to 100%) couples where both partners were positive for gonorrhoea, the resistance-determining genes and mutations were identical in isolates from each partner (94 isolates in total). Resistance determinants in isolates from 23 of 23 (100%; 95% CI 86% to 100%) men with multisite infections were also identical within an individual. These partner and within-host isolates were indistinguishable by NG-MAST, MLST and whole genomic comparisons.ConclusionsThese data support the transmission of antibiotic-resistant strains between sexual partners as a key driver of resistance rates in gonorrhoea among MSM. This improved understanding of the transmission dynamics of N. gonorrhoeae between sexual partners will inform treatment and prevention guidelines.

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