Specifications include, but are not limited to: Whole Genome Sequencing of Carbapenem Resistant Organism (CRO) CRO organism: Enterobacteriales Samples must have genome coverage at or above ninety percent (90%) Sequence data and de-identified patient chart data will be uploaded to the Louisiana Department of Health, Office of Public Health (LDH/OPH) secure database. The successful vendor will be granted access to this database for submissions. Sequence data will be uploaded to Genbank. Prospective and retrospective CRO sample chart review and submission of chart data to the LDH/OPH Lab must include the following: • De-identification number (must allow for tracking of multiple samples from the same patient) • Sample source • Collection date • Location (hospital or clinic – for epidemiology) • Antibiotic usage – must collect all antibiotics administered eight (8) weeks before and up to four (4) weeks after original culture. • Patient outcome – must record death up to four (4) weeks after date of original culture. • Genbank ID Price shall include: Collection of isolates; identification and susceptibility testing of isolate; processing, subculture, cell pellet preparation, freeze sample, shipping. Sequencing of isolates (bacterial genomes >5Mb; includes Deoxyribonucleic Acid ((DNA) extraction). Bacterial whole genome sequence data analysis including pathogen classification, antimicrobial resistance genes, and genetic clusters. Data management and collection (chart review) and data entry. 1,544 EA; Whole Genome Sequencing of Carbapenem Resistant Organism (CRO) CRO organism: Acinetobacter Baumannii Samples must have genome coverage at or above ninety percent (90%). Sequence data and de-identified patient chart data will be uploaded to the Louisiana Department of Health, Office of Public Health (LDH/OPH) secure database. The successful vendor will be granted access to this database for submissions. Sequence data will be uploaded to Genbank. Prospective and retrospective CRO sample chart review and submission of chart data to the LDH/OPH Lab must include the following: • De-identification number (must allow for tracking of multiple samples from the same patient) • Sample source • Collection date • Location (hospital or clinic – for epidemiology) • Antibiotic usage – must collect all antibiotics administered eight (8) weeks before and up to four (4) weeks after original culture. • Patient outcome – must record death up to four (4) weeks after date of original culture. • Genbank ID Price shall include: Collection of isolates; identification and susceptibility testing of isolate; processing, subculture, cell pellet preparation, freeze sample, shipping. Sequencing of isolates (bacterial genomes >5Mb; includes Deoxyribonucleic Acid ((DNA) extraction). Bacterial whole genome sequence data analysis including pathogen classification, antimicrobial resistance genes, and genetic clusters. Data management and collection (chart review) and data entry. 1,544 EA; Whole Genome Sequencing of Carbapenem Resistant Organism (CRO) CRO organism: Pseudomonas aeruginosa Samples must have genome coverage at or above ninety (90%) Sequence data and de-identified patient chart data will be uploaded to the Louisiana Department of Health, Office of Public Health (LDH/OPH) secure database. The successful vendor will be granted access to this database for submissions. Sequence data will be uploaded to Genbank. Prospective and retrospective CRO sample chart review and submission of chart data to the LDH/OPH Lab must include the following: • De-identification number (must allow for tracking of multiple samples from the same patient) • Sample source • Collection date • Location (hospital or clinic – for epidemiology) • Antibiotic usage – must collect all antibiotics administered eight (8) weeks before and up to four (4) weeks after original culture. • Patient outcome – must record death up to four (4) weeks after date of original culture. • Genbank ID Price shall include: Collection of isolates; identification and susceptibility testing of isolate; processing, subculture, cell pellet preparation, freeze sample, shipping. Sequencing of isolates (bacterial genomes >5Mb; includes Deoxyribonucleic Acid ((DNA) extraction). Bacterial whole genome sequence data analysis including pathogen classification, antimicrobial resistance genes, and genetic clusters. Data management and collection (chart review) and data entry. 1,544 EA; Genomic Epidemiology Report: Report shall include observable changes in resistance genes and genetic relatedness of CRO isolates sequenced in lines 1-3. 12 MON
