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

Posted November 9, 2023

Posted November 9, 2023

Food Safety Alert/Investigation Notice

CDC, public health, and regulatory officials in several states, and _____________________________ are investigating a multistate outbreak of Salmonella Infantis infections with this persistent strain linked to ________________. Do not eat, sell, or serve ______________________.

REPJJP01

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

Illness caused by this strain was first reported to PulseNet in late 2015. As of March 31, 2023, information from 2,423 people infected with REPJJP01 was reported to PulseNet. Among 1,378 people interviewed, 31% were hospitalized. Among 1,175 people with information on the outcome of infection, fewer than 1% died. Among 1,312 ill people, 63% self-identified as Hispanic/Latino, 33% 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 (49%) of 1,383 people with information reported traveling to Mexico before their illness began. People with illness caused by REPJJP01 also have reported consuming contaminated beef products from the United States and Mexico and consuming contaminated 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 21 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.

What is a persistent strain?

CDC uses “persistent” to describe some strains of bacteria that have caused illness for years. The strains continue to cause illness, even though the number of illnesses they cause might vary over time. The strains are sometimes linked to more than one source, making them harder to control.

Learn about these strains and CDC’s efforts to control them

Fast Facts
Learn fast facts about this rep strain.
Bacteria Salmonella enterica
Serotype Newport
Persistent Strain REPJJP01
First Illness Detected November 2015
                       Illnesses Reported in PulseNet 2,423
Outbreaks Investigated 8
Identified outbreak sources*

*Confirmed sources were implicated by
epidemiologic plus traceback or laboratory data.
Suspected sources were implicated
by epidemiologic data only. More info

  • Travel to Mexico
  • Cheese purchased in Mexico (confirmed)
  • Beef products (confirmed and suspected)

Last Updated: March 31, 2023

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 of Illness Onset Outbreak Source Geographic Location of Outbreak Source Reported Illnesses Number of States with Illnesses More Information
Summary of selected multistate outbreaks
Outbreak A August 2016–July 2017 Unknown Mexico and the United States 53 17
Outbreak B June 2018–March 2019 Cheese obtained in Mexico (confirmed), beef obtained in the United States (suspected), and unknown Mexico and the United States 255 32 2019 MMWR article
Outbreak C September 2021–January 2022 Dried beef from Mexico and beef obtained in the United States (suspected) Mexico and the United States 72 6 2023 MMWR article
Outbreak D December 2021 Beef obtained in the United States (suspected) The United States 5 1
Outbreak E August 2022 Ill food handler (suspected) The United States 7 1
Outbreak F August 2022–October 2022 Ground beef obtained in the United States (confirmed) The United States 22 6 2023 MMWR article
Outbreak G January 2023–March 2023 Unknown Mexico 24 17
Outbreak H February 2023–April 2023 Unknown Mexico 23 17

* 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 (i.e., 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.

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=2,423 for whom information was reported as of March 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 21 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 53 REPJJP01 isolates from animals and food products has been reported to PulseNet (Table). Most isolates were obtained from animal intestinal content and beef products and were detected as part of routine surveillance performed by the United States Department of Agriculture Food Safety and Inspection Service (USDA-FSIS) or as part 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).

Year Number of Isolates Isolate Category Isolate Type Geographic Location of Sample Reason Collected
Isolates from food, animal, and environmental samples
2016 1 Food Beef Texas Routine sampling by USDA FSIS
2018 2 Food Beef Texas Routine sampling by USDA FSIS
2018 1 Food Queso Fresco and Oaxaca Cheese California Outbreak B
2019 2 Intestinal content Beef Texas Routine sampling by USDA NARMS
2019 8 Food Beef California (2 isolates), Texas (5 isolates), & Utah (1 isolate) Routine sampling by USDA FSIS
2019 1 Food Papaya California Routine sampling by FDA
2020 3 Intestinal content Beef Arizona, Nebraska, & Texas (1 isolate each) Routine sampling by USDA NARMS
2020 6 Food Beef Florida (1 isolate) & Texas (5 isolates) Routine sampling by USDA FSIS
2020 3 Pet Food Bully Stick (Beef) Colorado Routine sampling by FDA
2021 5 Intestinal content Beef Texas (3 isolates), Kansas (1 isolate), & Maryland (1 isolate) Routine sampling by USDA NARMS
2021 8 Food Beef Illinois (1 isolate), Kansas (1 isolate), Missouri (1 isolate), Tennessee (1 isolate), Texas (3 isolates), & Wisconsin (1 isolate) Routine sampling by USDA FSIS
2021 1 Intestinal content Sheep California Routine sampling by USDA NARMS
2022 2 Food Beef Michigan Outbreak F
2022 1 Intestinal content Beef Texas Routine sampling by USDA NARMS
2022 9 Food Beef Alabama (1 isolate), Florida (1 isolate), Georgia (1 isolate), Illinois (2 isolates), Kansas (1 isolate), Texas (2 isolates), & Washington (1 isolate) Routine sampling by USDA FSIS

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 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 = 2,407), 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.