Persistent Strain of Salmonella Newport (REPJJP01) Linked to Travel to Mexico, Beef, and Soft Cheese

Posted April 16, 2024

REPJJP01

REPJJP01 is a persistent, multidrug-resistant strain of Salmonella Newport bacteria that has caused illnesses and outbreaks in the United States and in other countries.

Illness caused by this strain was first reported to PulseNet in late 2015. As of December 31, 2023, information from 2,845 people infected with REPJJP01 was reported to PulseNet. Among 1,782 people interviewed, 31% were hospitalized. Among 1,587 people with information on the outcome of infection, fewer than 1% died. Among 1,678 ill people, 61% self-identified as Hispanic/Latino, 35% self-identified as non-Hispanic/Latino White, and 4% self-identified as being non-Hispanic/Latino and another race. The median age of ill people was 38 years (interquartile range, 22–55 years) and 55% were female. Illnesses caused by this strain happen throughout the year but are less common in winter.

Almost half (48%) of 1,778 people with international travel information reported traveling to Mexico and fewer than 1% reported traveling to Guatemala before their illness began. People with illness caused by REPJJP01 also have reported consuming beef products from the United States and Mexico and consuming cheese (including queso fresco and Oaxaca cheese) obtained in Mexico.

This strain of Salmonella Newport is relatively diverse genetically. Bacteria in this strain are within 23 allele differences of one another by core genome multilocus sequence typing (cgMLST). This is more genetically diverse than typical multistate foodborne outbreaks in which bacteria generally fall within 10 allele differences of one another.

Outbreaks and Outbreak-Related Illnesses

Although most enteric illnesses — including those caused by REPJJP01 — are not part of an outbreak, investigation of outbreaks provides information that increases our understanding of germs, sources, settings, and factors that contribute to illness. Moreover, lab-confirmed cases comprise only a small portion of the true number of illnesses that occur because most people do not seek medical care and even fewer submit a stool or other specimen for testing.

Starting in 2016, CDC and local, state, and federal health and regulatory partners have investigated several outbreaks of Salmonella Newport illnesses caused by the REPJJP01 strain.

Summary of Selected Multistate Outbreaks and Other Investigations

* Outbreak dates are based on reported or estimated illness onset dates.

^† Confirmed sources were implicated by epidemiologic plus traceback or laboratory data. Suspected sources were implicated by epidemiologic data only. More information

^‡The geographic location of a confirmed outbreak source may not always be known. This can happen when the product (e.g., ground meat) sold from or mixed with other products from multiple suppliers is confirmed as the source, but evidence cannot implicate a specific supplier. This can also happen when evidence confirms an outbreak source but traceback cannot pinpoint the exact geographic location of source. Here, geographic location of outbreak source represents where patients were likely infected.

^¶ The number of illnesses and states listed per outbreak in this table may differ from other reports (e.g., publications). This is because this table only includes illnesses with WGS data that meet the allele range for this REP strain (see Genomic Information section).

Timeline

This timeline, called an epidemiologic curve, shows when people got ill.

People with Salmonella Newport illnesses caused by the REPJJP01 strain, by month illness began, 2015–2023*^,†

* N=2,845 for whom information was reported as of December 31, 2023. Some illness onset dates have been estimated from other reported information.

^† PulseNet transitioned to using whole genome sequencing (WGS) as the standard subtyping method for Salmonella in July 2019. Before then, not all Salmonella isolates reported to PulseNet had WGS data available. Isolates are identified as part of this strain based on WGS. As a result, the number of people with lab-confirmed illness caused by this strain before 2019 may be underrepresented.

Download data [XLS – 23 KB]

Map

This map shows where people who were ill lived.

Laboratory Data

WGS analysis

Bacteria in this strain are within 23 allele differences of one another by cgMLST. This is more genetically diverse than typical multistate foodborne outbreaks in which bacteria generally fall within 10 allele differences of one another.

Isolates from food, animal, and environmental samples

Information from 74 REPJJP01 isolates from animals and food products has been reported to PulseNet (Table). Most isolates were obtained from beef products and cecal samples (hereafter, animal intestinal content) and were detected as part of routine surveillance performed by the United States Department of Agriculture Food Safety and Inspection Service (USDA-FSIS), United States Department of Agricultural Marketing Service (USDA-AMS), or of the sampling performed by the National Antimicrobial Resistance Monitoring System (NARMS). One isolate from a papaya and three isolates from pet treats were detected as part of routine surveillance performed by the United States Food and Drug Administration (FDA).

Genomic information

The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information. To view the full SNP cluster, click on the link to a representative isolate below, then within NCBI’s platform click the link underneath the “SNP Cluster” column.

SNP Cluster*: Isolates Browser – Pathogen Detection – NCBI (nih.gov)

*The SNP (Single Nucleotide Polymorphism) tree provided by NCBI’s Pathogen Detection Pipeline in the link above may include isolates that are not considered part of this strain. The difference in thresholds and allele/SNP differences occur because NCBI’s Pathogen Detection Pipeline uses an analysis pipeline different from CDC PulseNet. The link is provided to give context to the overall genetic relatedness of the strain reported on this page, as well as to provide links to raw sequence files. Moreover, the SNP trees on NCBI’s Pathogen Detection Pipeline are updated more frequently than this web page.

Antimicrobial resistance information

The National Antimicrobial Resistance Monitoring System (NARMS) is a national public health surveillance system that tracks antimicrobial resistance for certain intestinal bacteria from ill people (CDC), retail meats (FDA), and food animals (USDA) in the United States. The NARMS program helps protect public health by providing information about emerging antimicrobial resistance, the ways in which resistance is spread, and how resistant infections differ from susceptible infections.

Bacteria from most ill people’s samples showed resistance to multiple antimicrobials, including several that are recommended for first-line or alternative treatment: ampicillin, azithromycin, ciprofloxacin, and trimethoprim-sulfamethoxazole. Most people with Salmonella illness recover without antibiotics. However, if antibiotics are needed, some REPJJP01 illnesses may be difficult to treat with commonly recommended antibiotics and may require a different antibiotic choice. Learn more about the management of infections with this strain.

Figure: Percentage of Salmonella REPJJP01 isolates from ill people that were antimicrobial resistant, by antimicrobial (n = 2,826), as of March 31, 2023 — National Antimicrobial Resistance Monitoring System

Collaboration

Interested in collaborating on a project related to this strain? Contact CDC at REPStrains@cdc.gov.