Data Summary: Emerging Strain of Salmonella Typhi (REPJPP01)

At a glance

Key findings

REPJPP01 is an emerging strain of Salmonella Typhi, the bacteria that cause typhoid fever. This strain was first identified in Pakistan in 2016, and illness caused by this strain was first reported in the United States in 2018. CDC monitors this strain due to its unusual resistance pattern – it was the first strain of Salmonella Typhi in Pakistan to show resistance to ceftriaxone, an antibiotic commonly recommended for treatment of typhoid fever. Most REPJPP01 isolates also are resistant to ampicillin, chloramphenicol, ciprofloxacin, and trimethoprim-sulfamethoxazole. Isolates resistant to all 5 of these antibiotics are commonly called extensively drug-resistant, or XDR. Antibiotics are recommended for all patients with typhoid fever, and typhoid fever caused by XDR Salmonella Typhi can be difficult to treat.

Illnesses caused by this strain occur year round, but are most common in summer and winter.

In the past, the REPJPP01 strain has spread to people in the United States during travel to Pakistan and neighboring countries.

This strain is relatively diverse genetically. Bacteria in REPJPP01 are within 13 allele differences of one another by whole genome sequencing, which is more diverse than typical typhoid fever outbreaks in which bacteria generally fall within 5 allele differences of one another. Increased diversity can occur over time as strains pass among human hosts in diverse settings with different selective pressures.

What the data show

Epidemiology

As of December 31, 2023, information from 150 U.S. patients with laboratory-confirmed REPJPP01 infection was reported to PulseNet, a national laboratory network that tests for and tracks enteric pathogens in humans. However, lab-confirmed cases comprise only a portion of the true number of illnesses that occur. Some people with typhoid fever do not seek medical care and even fewer submit a clinical specimen for testing.

The median age of patients was 11 years (interquartile range, 5–23 years), and 51% were male. The isolate source was blood in 87% and stool in 13% of cases. Among patients with available information, 92% traveled internationally in the 30 days before illness began. Ninety-one percent of patients were hospitalized for their illness for a median of 8 days (interquartile range, 6–11 days), and no patients died. No patients reported receiving vaccination for typhoid fever in the five years before their illness began.

Summary of international travel in the 30 days before illness began: REPJPP01

Timeline

People with typhoid fever caused by the REPJPP01 strain, by month of isolate collection, 2018–2023

Map

Typhoid fever caused by the REPJPP01 strain, by state, 2018–2023

Selected publications

• Extensively drug-resistant typhoid fever in the United States
• Extensively drug-resistant Salmonella Typhi infections among U.S. residents without international travel
• Update on extensively drug-resistant Salmonella serotype Typhi infections among travelers to or from Pakistan and report of ceftriaxone-resistant Salmonella serotype Typhi infections among travelers to Iraq—United States, 2018–2019
• Emergence of extensively drug-resistant Salmonella Typhi infections among travelers to or from Pakistan—United States, 2016–2018
• Emergence of an extensively drug-resistant Salmonella enterica serovar Typhi clone harboring a promiscuous plasmid encoding resistance to fluoroquinolones and third-generation cephalosporins
• Outbreak investigation of ceftriaxone-resistant Salmonella enterica serotype Typhi and its risk factors among the general population in Hyderabad, Pakistan: a matched case-control study

Laboratory data

Bacteria in REPJPP01 are within 13 allele differences of one another by core genome multilocus sequence typing (cgMLST), which is more diverse than typical typhoid fever outbreaks where bacteria generally fall within 5 allele differences of one another.

Due to the clonal nature of Salmonella Typhi, 31 additional isolates that are related to REPJPP01 isolates are within the same 13-allele range, but these isolates lack ceftriaxone resistance. Most patients with ceftriaxone-susceptible infections also traveled to Pakistan in the 30 days before their illness began.

Summary of international travel in the 30 days before illness began: ceftriaxone-susceptible isolates related to REPJPP01

The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information.

SNP cluster associated with isolate: PNUSAS044905

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 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 (90%) ill people's samples showed resistance to the antibiotics ampicillin, ceftriaxone, chloramphenicol, ciprofloxacin, and trimethoprim-sulfamethoxazole. Consideration should be given to the first-choice antibiotic used for treatment of typhoid fever. More information about treatment of typhoid fever is available.

Percentage of Salmonella Typhi REPJPP01 isolates from ill people that were antimicrobial resistant, by antibiotic (n = 149), 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

Epidemiology

Information is based on patient interviews conducted by state and local health departments and reported to CDC.

Missing data were excluded from percentage calculations.

Timeline

N = 150 for whom information was reported as of December 31, 2023. Some illness onset dates may have occurred earlier than the month of isolate collection.

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

The map shows the state of residence for people with typhoid fever caused by REPJPP01. However, most patients (92%) traveled internationally in the 30 days before becoming ill and are presumed to have acquired their infection outside of the United States.

Antimicrobial-resistant isolates

Resistance was determined based on the results of antimicrobial susceptibility testing when available (n = 118 isolates); otherwise, resistance was predicted based on whole genome sequencing (n = 31). No isolates were resistant to amoxicillin-clavulanic acid, cefoxitin, colistin, gentamicin, kanamycin, or tetracycline.

Resistance results include isolates with intermediate interpretation to ciprofloxacin (n = 13; 9%) or those carrying a single quinolone-resistance mutation (n = 7; 5%); a single mutation typically results in interpretation of "intermediate" for ciprofloxacin on antimicrobial susceptibility testing.

Resources

About Typhoid Fever and Paratyphoid Fever

Clinical Guidance for Typhoid Fever and Paratyphoid Fever

Food and Drink Considerations When Traveling

Typhoid & Paratyphoid Fever | CDC Yellow Book 2024

Travel Health Notice: Extensively Drug-Resistant Typhoid Fever in Pakistan

Updated Recommendations for the Use of Typhoid Vaccine — Advisory Committee on Immunization Practices, United States, 2015 (cdc.gov)

Suggested citation

Centers for Disease Control and Prevention. (2024). Data Summary: Emerging Strain of Salmonella Typhi (REPJPP01) Linked to Travel to Pakistan.