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Miscellaneous bacterial isolates from outbreak laboratory

ABSTRACT: Miscellaneous bacterial isolates from outbreak laboratory

PROVIDER: PRJEB55131 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10025613_1.fastq.gz	Fastqsanger.gz
	ERR10025613_2.fastq.gz	Fastqsanger.gz
	ERR10025616_1.fastq.gz	Fastqsanger.gz
	ERR10025616_2.fastq.gz	Fastqsanger.gz

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Escherichia coli O157:H7 Isolates Related to the 2006 Spinach-associated Outbreak Exhibit Distinct Transcriptional Profiles

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Escherichia coli O157:H7 Isolates Related to the 2006 Spinach-associated Outbreak Exhibit Distinct Transcriptional Profiles

Project description:We compared the transcriptional profiles of 12 E. coli O157:H7 isolates grown to stationary phase in LB broth. These isolates possess the same two enzyme PFGE profile and are related temporally or geographically to the above outbreak. These E. coli O157:H7 isolates included three clinical isolates, five isolates from separate bags of spinach, and single isolates from pasture soil, river water, cow feces, and a feral pig. Twelve condition experiment, 12 E. coli O157:H7 isolates. Two biological replicates for isolates RM6067, RM6069, RM6101, RM6102, RM6103, RM6149, RM6655, RM6658, RM9992, RM9997, RM9998 and RM10002 independently grown to stationary phase in LB at 37°C and harvested. One replicate per array. A type 2 gene expression experimental design was used, with fluorescently labeled genomic DNA as a reference channel in each experiment as described by Lucchini, S., et al. 2005. Infect Immun 73:88-102.

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2010-09-01 | GSE9418 | GEO

Comparative genomic profiling and gene expression of Escherichia coli O103:H25 Oslo 2006 outbreak strain

Project description:A food-borne outbreak of haemorrhagic colitis (HC) and HUS caused by E. coli O103:H25 occurred in Norway, 2006. The outbreak included 17 registered cases, of which 10 developed HUS. The aim of this study was to characterize two E. coli O103:H25 isolates from this outbreak. Only one of the isolates carry the stx2 gene (by PCR). Since they have the same typing profile by typing method MLVA, we expect the isolates to have identical gene content except from an Stx2-encoding phage. Therefore, we further investigate whether the Stx2-encoding phage has any impact on the gene expression. Keywords: mixed, gene expression, comparative genomic hybridization Triplicate samples of mRNA from a test strain O157:H7 EDL933 and two outbreak strains - one Stx positive and one stx negative were co-hybridized with genomic DNA from the same strain. Triplicate samples of the Stx positive strain grown at acidic conditions was also co-hybridized with genomic DNA from the Stx positive strain. Genomic DNA for each strain is technical replicates only.

2010-09-01 | E-GEOD-9418 | biostudies-arrayexpress

Single laboratory evaluation of the (Q20+) nanopore sequencing kit for bacterial outbreak investigations

Project description:Single laboratory evaluation of the (Q20+) nanopore sequencing kit for bacterial outbreak investigations Raw sequence reads

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Comparison of gene expression profiles for heat-shocked and non-heat shocked stationary phase samples from heat tolerant isolates R1-0006 and R1-0007 and reference strain SL476

Project description:Salmonella Heidelberg is currently the 9th common serovar and has more than twice the average incidence of blood infections in Salmonella. A recent Salmonella Heidelberg outbreak in chicken infected 634 people during 2013-2014, with a hospitalization rate of 38% and an invasive illness rate of 15%. While the company’s history suggested longstanding sanitation issues, the strains’ characteristics which may have contributed to the outbreak are unknown. We hypothesized that the outbreak strains of S. Heidelberg might possess enhanced stress tolerance or virulence capabilities. Consequently, we obtained nine food isolates collected during the outbreak investigation and several reference isolates and tested their tolerance to processing stresses, their ability to form biofilms, and their invasiveness in vitro. We further performed RNA-sequencing on three isolates with varying heat tolerance to determine the mechanism behind our isolates’ enhanced heat tolerance. Ultimately, we determined that (i) many Salmonella Heidelberg isolates associated with a foodborne outbreak have enhanced heat resistance (ii) Salmonella Heidelberg outbreak isolates have enhanced biofilm-forming ability under stressful conditions, compared to the reference strain (iii) exposure to heat stress may also increase Salmonella Heidelberg isolates’ antibiotic resistance and virulence capabilities and (iv) Salmonella Heidelberg outbreak-associated isolates are primed to better survive stress and cause illness. This data helps explain the severity and scope of the outbreak these isolates are associated with and can be used to inform regulatory decisions on Salmonella in poultry and to develop assays to screen isolates for stress tolerance and likelihood of causing severe illness.

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Project description:F. hepatica is a parasite causing losses of great importance in animal production. It is also considered a zoonosis of growing importance. During the infection the parasite releases a number of antigens (called Excretory Secretory Products - ESP) facilitating the parasites survival. A number of ESP components have immunomodulatory properties. To determine if ES from various F. hepatica isolates have different immunomodulatory abilities LPS activated “BOMA” cells were stimulated with ES of laboratory Weybridge (FhWey-ES) and wild (FhWild-ES) Fasciola hepatica isolates.

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