Data Summary: Persistent Strain of Salmonella Infantis (REPJFX01)

At a glance

Last Updated: December 31, 2023

_{^*Confirmed sources were implicated by epidemiologic plus traceback or laboratory data. Suspected sources were implicated by epidemiologic data only. More information available in the latest summary of possible multistate enteric disease outbreaks.}

Key findings

REPJFX01 is a persistent, multidrug-resistant strain of Salmonella Infantis bacteria that has caused illnesses and outbreaks in the United States and globally.

Illness caused by this strain was first reported to PulseNet in 2012. Illnesses caused by this strain occur year-round but are most common in July and August.

This strain of Salmonella Infantis is relatively diverse genetically. Bacteria in the strain are within 82 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 the data show

Illnesses and outbreaks data

As of December 31, 2023, information from 3,442 patients with REPJFX01 infection was reported to PulseNet. The median age of patients was 54 years (interquartile range, 27–70 years), and 63% were female. The isolate source was stool in 65% and urine in 27% of cases. REPJFX01 has spread to people through contaminated chicken in the United States and through exposures during international travel.

Among a subset of 406 patients with records in the Foodborne Diseases Active Surveillance Network (FoodNet) during 2018–2022, 7% of patients traveled internationally in the 7 days before their illness began; most traveled to the Dominican Republic (32%), Peru (23%), Cambodia (9%), or Ecuador (9%). Among the same subset of patients, 29% were hospitalized, 5% were admitted to the intensive care unit, and 1% died. Among 124 patients who received antibiotics recommended as first-line or alternative treatment for salmonellosis, 73% had an isolate that was resistant to that antibiotic.

Outbreaks and other investigations

Although most enteric illnesses—including those caused by REPJFX01—are not part of an outbreak, investigation of outbreaks provides information that increases our understanding of bacteria, 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 clinical (e.g., stool) specimen.

CDC and local, state, and federal health and regulatory partners have investigated several clusters of Salmonella Infantis illness as possible outbreaks caused by the REPJFX01 strain.

Summary of selected multistate outbreaks and other investigations

Selected publications regarding REPJFX01 investigations

• A multidrug-resistant Salmonella Infantis clone is spreading and recombining in the United States (2021)
• Carriage and gene content variability of the pESI-like plasmid associated with Salmonella Infantis recently established in United States poultry production (2020)
• CTX-M-65 extended-spectrum β-lactamase-producing Salmonella enterica serotype Infantis, United States (2018)
• Outbreak epidemiologically linked with a composite product of beef, mechanically separated chicken and textured vegetable protein contaminated with multiple serotypes of Salmonella enterica including multidrug-resistant Infantis, California 2016 (2018)
• Comparative analysis of extended-spectrum-β-Lactamase CTX-M-65-producing Salmonella enterica serovar Infantis isolates from humans, food animals, and retail chickens in the United States (2017)

_{Selected publications on Salmonella Infantis are for reference; other publications regarding this strain are available.}

Timeline

People with Salmonella Infantis illnesses caused by the REPJFX01 strain, by month of isolate collection, 2012–2023

Map

Salmonella Infantis illnesses caused by the REPJFX01 strain, by state, 2012–2023^*

Laboratory Data

Whole genome sequencing analysis

Bacteria in this strain are within 82 allele differences of one another by cgMLST 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.

Isolates from food, animal, and environmental samples

Information from more than 7,000 REPJFX01 isolates from non-human sources has been reported to PulseNet, with the earliest in 2014. Most isolates are from chicken samples collected by the U.S. Department of Agriculture Food Safety and Inspection Service (FSIS), including 5,036 from FSIS sampling of food and food products and 506 from FSIS sampling of intestinal (cecal) content. Other non-human sources of bacteria sequences reported to PulseNet include turkey (222 isolates); pork (56); beef (35); water (20); and other food, animal, and environmental sources (40).

Although WGS data from U.S. Food and Drug Administration (FDA) samples have not always been submitted to PulseNet, more than 1,000 food and environmental isolates collected through FDA sampling programs are highly related to REPJFX01 isolates by WGS, including many samples from retail chicken products. More information about these isolates can be found through the National Center for Biotechnology Information or the NARMS Now: Integrated Data platform.

Number of REPJFX01 isolates from non-human sources submitted to PulseNet, by month of sample collection, 2012–2023^*

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).

Antimicrobial-resistant isolates

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), food animals (USDA), and retail meats (FDA) 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, ceftriaxone, ciprofloxacin, and trimethoprim-sulfamethoxazole. Most people with Salmonella illness recover without antibiotics. However, if antibiotics are needed, some illnesses resulting from REPJFX01 may be difficult to treat with commonly recommended antibiotics and may require a different antibiotic choice.

Percentage of human Salmonella REPJFX01 isolates that were antimicrobial resistant, by antimicrobial (n = 3,391), as of December 31, 2023 — NARMS

Collaborate with CDC

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

About the data

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 available in the latest summary of possible multistate enteric disease outbreaks.

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

Outbreak data were obtained from the National Outbreak Reporting System (NORS).

Selected publications

Selected publications on Salmonella Infantis are for reference; other publications regarding this strain are available.

Timeline

Includes N=3,442 human illnesses for which information was reported as of December 31, 2023.

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.

Map

Illness year is based on the date of isolate collection.

Most state public health laboratories do not routinely receive or sequence all Campylobacter isolates. Therefore, some cases of REPDBR01 may not have been detected.

Isolates from food, animal, and environmental samples

Includes N=7,271 non-human isolates for which information was reported as of December 31, 2023. Some collection dates have been estimated from other reported information.

This exploratory testing was performed on rehang samples (prior to evisceration and prior to application of all interventions).

Genomic information

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 allele vs. SNP thresholds occurs because NCBI's Pathogen Detection Pipeline uses an analysis pipeline different from the one used by 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-resistant isolates

Resistance was determined based on the results of antimicrobial susceptibility testing when available (n=204 isolates); otherwise, resistance was predicted based on whole genome sequencing (n=3,187).

Ciprofloxacin data includes isolates with an intermediate interpretation on antimicrobial susceptibility testing or a single quinolone resistance mechanism (a single mechanism is typically associated with intermediate interpretation in Salmonella).

Resistance determination is based only on predicted resistance from whole genome sequencing for hygromicin, tobramycin, trimethoprim, kanamycin, and fosfomycin.

Suggested citation

Centers for Disease Control and Prevention. (2024). Data Summary: Persistent Strain of Salmonella Infantis (REPJFX01) Linked to Chicken.