Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States

ABSTRACT

This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety.

HIGHLIGHTS

Multistate Outbreak of Escherichia coli O157:H7 Infections Associated with Consumption of Fresh Spinach: United States, 2006

During September to October, 2006, state and local health departments and the Centers for Disease Control and Prevention investigated a large, multistate outbreak of Escherichia coli O157:H7 infections. Case patients were interviewed regarding specific foods consumed and other possible exposures. E. coli O157:H7 strains isolated from human and food specimens were subtyped using pulsed-field gel electrophoresis and multiple-locus variable-number tandem repeat analyses (MLVA). Two hundred twenty-five cases (191 confirmed and 34 probable) were identified in 27 states; 116 (56%) case patients were hospitalized, 39 (19%) developed hemolytic uremic syndrome, and 5 (2%) died. Among 176 case patients from whom E. coli O157:H7 with the outbreak genotype (MLVA outbreak strain) was isolated and who provided details regarding spinach exposure, 161 (91%) reported fresh spinach consumption during the 10 days before illness began. Among 116 patients who provided spinach brand information, 106 (91%) consumed bagged brand A. E. coli O157:H7 strains were isolated from 13 bags of brand A spinach collected from patients' homes; isolates from 12 bags had the same MLVA pattern. Comprehensive epidemiologic and laboratory investigations associated this large multistate outbreak of E. coli O157:H7 infections with consumption of fresh bagged spinach. MLVA, as a supplement to pulsed-field gel electrophoresis genotyping of case patient isolates, was important to discern outbreak-related cases. This outbreak resulted in enhanced federal and industry guidance to improve the safety of leafy green vegetables and launched an independent collaborative approach to produce safety research in 2007.

Multistate outbreak of Escherichia coli O157:H7 infections associated with a national fast-food chain, 2006: a study incorporating epidemiological and food source traceback results

A multistate outbreak of Escherichia coli O157:H7 infections occurred in the USA in November-December 2006 in patrons of restaurant chain A. We identified 77 cases with chain A exposure in four states - Delaware, New Jersey, New York, and Pennsylvania. Fifty-one (66%) patients were hospitalized, and seven (9%) developed haemolytic uraemic syndrome; none died. In a matched analysis controlling for age in 31 cases and 55 controls, illness was associated with consumption of shredded iceberg lettuce [matched odds ratio (mOR) 8·0, 95% confidence interval (CI) 1·1-348·1] and shredded cheddar cheese (mOR 6·2, CI 1·7-33·7). Lettuce, an uncooked ingredient, was more commonly consumed (97% of patients) than cheddar cheese (84%) and a single source supplied all affected restaurants. A single source of cheese could not explain the regional distribution of outbreak cases. The outbreak highlights challenges in conducting rapid multistate investigations and the importance of incorporating epidemiological study results with other investigative findings.

Investigation of Laboratory cross-contamination of Mycobacterium tuberculosis cultures

Many clinicians and laboratory personnel are unaware that a culture positive for Mycobacterium tuberculosis may represent contamination. Laboratory cross-contamination with the M. tuberculosis laboratory control strain (H37Ra) occurs infrequently and therefore demands heightened awareness and recognition. We report 3 occurrences of laboratory cross-contamination from the same laboratory. These occurrences illustrate the importance of interpreting laboratory results in conjunction with the patient's clinical presentation. Failure to recognize laboratory cross-contamination with M. tuberculosis leads to both erroneous administration of unnecessary medications and expenditure of resources required to conduct contact investigations.

Measuring the requirements for nursing care in the acute head trauma patient

A measuring tool to assess the requirements for nursing care, define patient care goals, and document progress was developed in a 57-bed head trauma sub-acute rehabilitation center. The process of tool development and reliability testing is described.