"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 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.
Fast Facts
Bacteria Salmonella enterica Serotype Infantis
Antimicrobial Resistance Profile Multidrug resistant (details below)
Persistent Strain REPJFX01
First Detection June 2012
Illnesses Reported in PulseNet 2,900
Outbreaks Investigated 7
Identified outbreak sources*
https://www.cdc.gov/ncezid/dfwed/outbreak-response/rep-strains/repjfx01.html
Persistent Strain of Salmonella Infantis (REPJFX01) Linked to Chicken
Posted July 21, 2023
REPJFX01
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. As of December 31, 2022, information from 2,900 patients with REPJFX01 infection was reported to PulseNet. The median age of patients was 54 years (interquartile range, 27–70 years), and 62% were female. The isolate source was stool in 65% and urine in 27% of cases. Illnesses caused by this strain occur year-round but are most common in July and August. In the past, REPJFX01 has spread to people through contaminated chicken in the United States and through exposures during international travel.
Among a subset of 251 patients with records in Foodborne Disease Active Surveillance Network (FoodNet) during 2018–2020, 10% of patients traveled internationally in the 7 days before their illness began; most traveled to the Dominican Republic (45%), Peru (25%), or Ecuador (10%). Among the same subset of patients, 29% were hospitalized, 7% were admitted to the intensive care unit, and fewer than 1% died. Among 85 patients who received antibiotics recommended as first-line or alternative treatment for salmonellosis, 78% had an isolate that was resistant to that antibiotic.
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.
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.
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 6,000 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): 4,176 are from FSIS sampling of food and food products and 345 are 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 (33).
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 (see below) or the NARMS Now: Integrated Data platform.
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 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 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 sick 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 sick 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.
Bacteria Salmonella enterica Serotype Infantis
Antimicrobial Resistance Profile Multidrug resistant (details below)
Persistent Strain REPJFX01
First Detection June 2012
Illnesses Reported in PulseNet 2,900
Outbreaks Investigated 7
Identified outbreak sources*
- Raw chicken products (confirmed): 1 outbreak
- Mechanically separated chicken (suspected): 1 outbreak
https://www.cdc.gov/ncezid/dfwed/outbreak-response/rep-strains/repjfx01.html
Persistent Strain of Salmonella Infantis (REPJFX01) Linked to Chicken
Posted July 21, 2023
REPJFX01
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. As of December 31, 2022, information from 2,900 patients with REPJFX01 infection was reported to PulseNet. The median age of patients was 54 years (interquartile range, 27–70 years), and 62% were female. The isolate source was stool in 65% and urine in 27% of cases. Illnesses caused by this strain occur year-round but are most common in July and August. In the past, REPJFX01 has spread to people through contaminated chicken in the United States and through exposures during international travel.
Among a subset of 251 patients with records in Foodborne Disease Active Surveillance Network (FoodNet) during 2018–2020, 10% of patients traveled internationally in the 7 days before their illness began; most traveled to the Dominican Republic (45%), Peru (25%), or Ecuador (10%). Among the same subset of patients, 29% were hospitalized, 7% were admitted to the intensive care unit, and fewer than 1% died. Among 85 patients who received antibiotics recommended as first-line or alternative treatment for salmonellosis, 78% had an isolate that was resistant to that antibiotic.
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.
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.
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 6,000 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): 4,176 are from FSIS sampling of food and food products and 345 are 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 (33).
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 (see below) or the NARMS Now: Integrated Data platform.
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 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 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 sick 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 sick 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.
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