California Department of Health – How many people have really been sickened by Raw Farms LLC’s Milk?

I am speaking at IAFP in Long Beach in the morning, perhaps I will get some answers?

In October, San Diego County and Orange County Department of Health issued public notifications about a Salmonella Typhimurium outbreak investigation linked to Raw Farm LLC brand unpasteurized milk and milk products. At the time of those public notifications, 16 persons with Salmonella Typhimurium infections had been identified among residents of those counties, nine in San Diego and seven Orange County. Fresno County did not issue a press release, but two Fresno County residents with Salmonella Typhimurium infections linked to the outbreak were identified in October and December, 2023. 

When the public notifications were issued, all nine cases identified by San Diego County in October, 2023, reported consuming Raw Farm LLC brand raw milk or raw milk products. According to the FoodNet Population survey, 1.9% of people in California reported consuming raw milk, and 8.4% reported eating raw cheese in the 7 days prior to being surveyed. Therefore, 9 of 9 persons with the same strain of Salmonella Typhimurium reporting raw milk or milk products is much higher than expected by chance (statistically significant using a binomial probability model, p <0.0001). Furthermore, all the cases mentioned the same brand of product. The evidence linking these illnesses to Raw Farm LLC brand raw milk or raw milk products was already overwhelmingly strong when the public notifications were issued.

CDPH’s reported that as of January 4, 2024, the number of people that became ill as part of this outbreak had grown to 151, including 18 persons who required hospitalization. Persons became ill from September through November, 2023. Seventy-two percent of the persons who became ill with the same strain of Salmonella Typhimurium reported consuming raw milk. Among the California cases that reported consuming raw milk and remember the brand, 93% reported Raw Farm LLC brand raw milk. At that point in the investigation, raw milk consumption among ill persons in the outbreak continued to be much higher than expected based on the background raw milk consumption of 1.9% in California (statistically significant using a binomial probability model, p <0.0001).

Samples of milk collected on October 19 and 25, 2023 at the farm as part of the investigation tested positive for Salmonella Typhimurium of the outbreak strain. A retail sample of Raw Farm LLC raw milk with a best by date of October 27 also tested positive. The information on the report is consistent with the raw milk sequences on NCBI, which were indistinguishable (0 SNPs) and highly related to the other clinical samples that were part of this outbreak. The raw cheese sample on NCBI was uploaded after the report was written.

The California interim outbreak report was written when the outbreak was on-going. According to the PowerPoint summary of the investigation, as of February, 2024, the number of people ill had grown to 165, including 20 hospitalizations in four states, California, New Mexico, Washington and 1 unidentified, nearly 40% of the ill children aged five or younger. The sequence data on NCBI shows that the most recent upload associated with this outbreak occurred in June, 2024; therefore, the outbreak may still be still on-going.

It is important to note that four cases in the outbreak had co-infections-they had Salmonella Typhimurium and at least one other pathogen: Campylobacter and/or Shiga toxin-producing E. coli (STEC). Co-infections and/or outbreaks caused by more than one pathogen are not uncommon when the illnesses are associated with raw milk consumption.

Whole Genome Sequencing (WGS) is the analysis of the DNA of the organism of interest, in this case, Salmonella Typhimurium. It determines the order or sequence of almost all the bases that make up the organism’s genome. There are several ways to analyze the genomic sequencing data. One of those methods analyzes single nucleotide polymorphisms (SNPs) or differences in single base pairs (the DNA building blocks). This incredibly detailed information about the organism, the genetic sequence of bacteria, helps epidemiologists identify which illnesses may come from the same source. All the sequences from bacteria that are isolated from human samples, and from food or environmental sources are uploaded to a public facing database at the NCBI, where the relatedness of sequences can be easily evaluated. When people become ill from a common source, the bacteria isolated from their specimens are closely related (zero to a small number of SNP differences). WGS is a very powerful tool when used in conjunction with epidemiological data for identifying and solving outbreaks.

An NCBI search revealed 162 uploaded sequences that were highly related (0 to 6 SNPs, average 0 SNPs) from October, 2023 to June, 2024. Of the 162 sequences, 157 were listed as clinical (i.e., from human specimens). Four of the uploaded sequences (PNUSAS404312, PNUSAS404313, PNUSAS404314, PNUSAS408523) were environmental samples labeled as raw milk, uploaded on November 28 and December 13, 2023, by the CDPH Food and Drug Laboratory Branch (FDLB). The remaining one (PNUSAS419013) was from raw cheese, uploaded by FDLB on February 7, 2024. The high degree of relatedness among the isolates on NCBI means they were all part of a common-source outbreak. The Salmonella Typhimurium isolated from raw milk and cheese, or their production environment, conclusively links those 157 Salmonella Typhimurium isolates from clinical samples to those products.  In sum, the sequencing data confirm that approximately 157 persons were part of a common-source outbreak, and raw milk and raw cheese from Raw Farm LLC were the source of those illnesses.

The overwhelmingly high number of ill persons reporting consuming raw milk from Raw Farm LLC in the week prior to their illness, coupled with the positive raw milk and cheese samples and the WGS data conclusively linked the illnesses to consumption of those products.

Anyone have some answers?

Republished with permission from Bill Marler and Marler Clark. Copyright (c) Marler Clark LLP, PS. All rights reserved.