---
title: "Emergence of Multidrug-Resistant, Ciprofloxacin-Resistant Salmonella Typhi Genotype 2.3.1 in West"
id: "cdc-emerging-infectious-diseases-journal-2-emergence-of-genotype-2-3-1-multidrug-resistant-salmonella-enterica-serovar"
canonical_url: "https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-2-emergence-of-genotype-2-3-1-multidrug-resistant-salmonella-enterica-serovar"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "CDC Emerging Infectious Diseases Journal"
source_url: "https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article"
published_at: "2026-09-21T04:00:00.000Z"
evidence_level: "Agency Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Emergence of Multidrug-Resistant, Ciprofloxacin-Resistant Salmonella Typhi Genotype 2.3.1 in West
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-2-emergence-of-genotype-2-3-1-multidrug-resistant-salmonella-enterica-serovar
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** CDC Emerging Infectious Diseases Journal
- **Source URL:** [Original Journal Publication](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article)
- **Published At:** 2026-09-21T04:00:00.000Z
- **Evidence Rating:** Agency Feed
## Executive GIST (TL;DR)
- Surveillance at the Institut Pasteur (France) identified an emerging **genotype 2.3.1** lineage of **Salmonella enterica** serovar **Typhi** linked to West Africa and travellers returning to France. - From 2016–2025 the reference center received 1,603 nonredundant S. Typhi isolates; 167 were genotype 2.3.1 (median patient age 28 years; 80.8% reported travel to Africa). - Beginning 2021, isolates with a combined **multidrug-resistant (MDR) profile A** (blaTEM-1, strA, strB, aadA1, sul1, sul2, dfrA1, tet(B)) and the **gyrA S83F** mutation (explaining **ciprofloxacin resistance**) were increasingly detected. - In 2022, 35 MDR–ciprofloxacin-resistant (CIPR) genotype 2.3.1 isolates from Senegal were identified; the number linked to Senegal fluctuated with a peak of 50 in 2025. - Phylogenetic and genomic analyses indicate this lineage locally acquired two different MDR plasmids over ≈25 years, integrated the **IncHI1** MDR region into the chromosome, and later acquired the **gyrA** mutation leading to CIPR. - Overall, 79 isolates recovered since 2023 were CIPR, 71 of which displayed the MDRA profile; an additional 52 genotype 2.3.1 genomes from databases included 39 with the MDRA–CIPR profile and travel links to West African countries. - The findings document local evolution in West Africa toward stable chromosomal MDR and fluoroquinolone resistance in a non–H58 lineage, with implications for regional surveillance and treatment guidance.
## Clinical Analysis & Structured Key Points
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[EID Journal](https://wwwnc.cdc.gov/eid/) 2. [Volume 32](https://wwwnc.cdc.gov/eid/early-release) 3. [Early Release](https://wwwnc.cdc.gov/eid/early-release#issue-1346) 4. [Main Article](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article) * [Facebook](https://www.facebook.com/sharer/sharer.php?u=%2Feid%2Farticle%2F32%2F10%2F26-0813_article "Share to Facebook") * [Twitter](http://twitter.com/share?url=%2Feid%2Farticle%2F32%2F10%2F26-0813_article&text= "Share to Twitter") * [LinkedIn](https://www.linkedin.com/shareArticle?url=%2Feid%2Farticle%2F32%2F10%2F26-0813_article&title= "Share to LinkedIn") * [Syndicate](https://tools.cdc.gov/medialibrary/index.aspx#/sharecontent//eid/article/32/10/26-0813_article "Embed this Page") [ Emerging Infectious Disease journal ISSN: 1080-6059 ](https://wwwnc.cdc.gov/eid/) _Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released._ #### Volume 32, Number 10—October 2026 ##### _Dispatch_ ### Emergence of Genotype 2.3.1 Multidrug-Resistant _Salmonella enterica_ Serovar Typhi Strain, West Africa, 2021–2025 On This Page [The Study](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article) * * * [Conclusion](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article) * * * [Suggested Citation](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article) Figures [Figure 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0813-f1) * * * [Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0813-f2) * * * [Figure 3](https://wwwnc.cdc.gov/eid/article/32/10/26-0813-f3) Downloads [Appendix 1 ](https://wwwnc.cdc.gov/eid/article/32/10/26-0813-app1.pdf) * * * [Appendix 2 ](https://wwwnc.cdc.gov/eid/article/32/10/26-0813-app2.xlsx) * * * [RIS [TXT - 2 KB] ](https://wwwnc.cdc.gov/eid/article/32/10/26-0813.ris) Article Metrics [Metric Details](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article) Related Articles [Macrolide-Resistant _Bordetella pertussis_ , Peru](https://wwwnc.cdc.gov/eid/article/32/10/25-1477_article) * * * [Multidrug-Resistant _C. coli_ ST10042 Lineage](https://wwwnc.cdc.gov/eid/article/32/10/26-0512_article) * * * [_Salmonella_ Infantis Carrying _bla_ CTX-M-65 Gene](https://wwwnc.cdc.gov/eid/article/32/10/25-1758_article) * * * [More articles on Antimicrobial Resistance](https://wwwnc.cdc.gov/eid/spotlight/antimicrobial-resistance) Elisabeth Njamkepo, Maria Pardos de la Gandara, Carolina Silva Nodari, Alexandra Moura, and François-Xavier Weill[![Comments to Author](https://wwwnc.cdc.gov/eid/content/images/icon/email.gif)](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#comment) Author affiliation: Institut Pasteur, Université Paris Cité, Paris, France [Suggested citation for this article](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#suggestedcitation) ### Abstract Since 2021, a genotype 2.3.1, ciprofloxacin-resistant, multidrug-resistant (MDR) _Salmonella enterica_ serovar Typhi strain increasingly has been detected in persons returning from West Africa. This strain locally acquired 2 different MDR plasmids over a ≈25-year period, underwent chromosomal integration of the IncHI1 plasmid MDR region, and finally acquired a _gyrA_ mutation. _Salmonella enterica_ serovar Typhi is a human-restricted pathogen causing typhoid fever through fecally contaminated food or water ([_1_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r1 "1")). In 2021, an estimated 7.1 million typhoid fever cases caused 93,300 deaths worldwide ([_2_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r2 "2")). Sporadic antimicrobial resistance (AMR) was first detected in _Salmonella_ Typhi in the 1950s, followed by epidemic multidrug-resistant (MDR) populations in the Americas and South/Southeast Asia during the 1970s–1980s. Those populations initially displayed resistance to chloramphenicol, streptomycin, tetracycline, and sulfonamides and then became resistant to ampicillin and cotrimoxazole, after the acquisition of large IncHI1 plasmids ([_3_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r3 "3")–[ _7_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r7 "7")). One such MDR population, H58 ([_3_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r3 "3")), now genotype 4.3.1 ([_8_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r8 "8")), emerged in South Asia in the late 1980s and spread across Southeast Asia, Oceania, and East Africa ([_9_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r9 "9"),[_10_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r10 "10")). This H58 lineage first acquired an IncHI1 MDR plasmid (belonging to plasmid multilocus sequence type [pST] 6), followed by, during the 1990s, a point mutation in the chromosomal DNA gyrase gene, _gyrA_ (often _gyrA_ _S83F), which encodes resistance to nalidixic acid (NALR) and has decreased susceptibility to ciprofloxacin (now categorized as resistant to ciprofloxacin (CIPR) according to established guidelines ([Appendix 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0813-app1.pdf)). The MDR region initially located on the IncHI1 plasmid became stably integrated into the bacterial chromosome over time in lineage H58, and the IncHI1 plasmid was lost ([_9_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r9 "9")). This lineage subsequently became extensively drug-resistant after the acquisition of a new IncY plasmid carrying the extended-spectrum β-lactamase _bla_ CTX-M-15 gene in Pakistan in 2016 ([_11_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r11 "11")). In the 2000s, MDR _Salmonella_ Typhi strains of non–4.3.1 genotypes emerged in West and Central Africa. In West Africa and neighboring Cameroon, the MDR genotypes were 3.1.1 (corresponding to haplotypes H56 and H42 [[_3_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r3 "3")] or cluster A [[_12_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r12 "12")]) and 2.3.1 (corresponding to H77 [[_3_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r3 "3")] or cluster C [[_12_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r12 "12")]). Both genotypes had predominantly acquired MDR plasmids of incompatibility group IncHI1 (pST2 with _dfrA15_ as the class 1 integron gene cassette for 3.1.1 isolates and pST2 with _dfrA1-aadA1_ for 2.3.1 isolates) ([_12_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r12 "12"),[_13_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r13 "13")). IncY plasmids in genotype 3.1.1 isolates and IncN (pST3) plasmids in 2.3.1 isolates were less frequent ([_13_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r13 "13"),[_14_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r14 "14")). Quinolone resistance was initially rare in these MDR genotypes; only 6 (4.7%) NALR isolates (all genotype 3.1.1) were found among 128 _Salmonella_ Typhi isolates that were collected in Nigeria during 2008–2013 ([_13_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r13 "13")). However, a recent study showed that the proportion of genotype 3.1.1 NALR isolates reached >75% in Nigeria after 2015 ([_15_](https://wwwnc.cdc.gov/eid/article/32/10/26-0813_article#r15 "15")). A similar trend has not been documented for genotype 2.3.1. In France, enteric fevers have been notifiable diseases since 1903. In addition to mandatory reporting, clinical laboratories forward the isolates to the National Reference Center for _Escherichia coli_ , _Shigella_ , and _Salmonella_ at the Institut Pasteur (Paris, France) on a voluntary basis. Most _Salmonella_ Typhi isolates are obtained from travelers or immigrants, most of whom were infected in Asia and Africa. During 2016–2025, the center received 1,603 _Salmonella_ Typhi isolates (1 per patient) for expert analysis ([Appendix 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0813-app1.pdf)), including 167 of genotype 2.3.1. The median age for those 167 patients was 28 years (range 2–85 years); 64.7% were women and girls and 35.3% men and boys, and 135 (80.8%) had reported traveling to Africa. We used conventional microbiologic examination and whole-genome sequencing to characterize an emerging MDR-CIPR _S._ Typhi strain of genotype 2.3.1 isolated from travelers returning to France from West Africa. We also reconstructed its evolutionary history. ### The Study Figure 1 ![Distribution and genotype of Salmonella enterica serovar Typhi isolates in persons returning to France from Senegal in study of emergence of genotype 2.3.1 multidrug-resistant Salmonella Typhi strain, West Africa, 2016–2025. A\) Total number of nonredundant Salmonella Typhi isolates received each year by France’s National Reference Center for Escherichia coli, Shigella, and Salmonella at the Institut Pasteur and percentage of those associated with Senegal. The unusually small number of Salmonella Typhi isolates received in 2020 and 2021 \( 98%. Light orange rectangle indicates emerging MDR strain. Year of isolation is indicated, together with the travel information \(when available\) for the isolate, to the right of the tree, because those parameters serve as a proxy for the probable origin of the isolates. Resistance to certain antimicrobial drugs and the presence \(black\) or absence \(white\) of antimicrobial-resistance genes \(names given along bottom of tree\) also are indicated to the right of the tree. The MDR profiles are indicated in red \(for profile A; blaTEM-1, strA, strB, aadA1, sul1, sul2, dfrA1, and tet\(B\)\) or blue \(for profile B; blaTEM-1–like, strA, strB, sul2, dfrA14, and tet\(A\)\). The presence of plasmid markers is indicated in blue \(for IncN\) or red \(for IncHI1\). Scale bar indicates number of nucleotide substitutions per variable site. Information displayed in this figure can be found for each individual strain in Appendix 2 \(https://wwwnc.cdc.gov/EID/article/32/10/26-0813-App2.xlsx\). AG, aminoglycosides; MDR, multidrug-resistant; PEN, penicillins; QUI, quinolones; SUL, sulfonamides; TET, tetracyclines; TMP, trimethoprim.](https://wwwnc.cdc.gov/eid/images/26-0813-F2-tn.jpg) [Figure 2](https://wwwnc.cdc.gov/e
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