Epidemiologic and Genomic Investigation of Sexually Transmitted Shigella sonnei, England

Abstract

Shigellosis is a bacterial infection that causes enteric illness and can be sexually transmitted, particularly among gay, bisexual, and other men who have sex with men. Multiple extensively drug-resistant Shigella strains have been detected through genomic surveillance and are associated with plasmids carrying the gene variant bla_CTX-M-27 in the United Kingdom. We report an increase in possible sexually transmitted cases of Shigella bacteria carrying the bla_CTX-M-15 gene variant, which was previously associated with travel. In 2023, there were 117 cases belonging to the 10 single-nucleotide polymorphism linkage cluster t10.1814. Although this cluster has been documented in England since August 2019, genetic analyses revealed that the bla_CTX-M-15 gene variant entered the lineage on a novel resistance plasmid coinciding with the first outbreak case. Our analysis highlights the shifting antimicrobial resistance landscape of sexually transmitted Shigella bacteria. Parallel emergence of resistance determinants against third-generation cephalosporins in sexual transmission networks suggests high levels of antimicrobial selection pressure.

Keywords: England; S. sonnei; S. sonnei blaCTXM-15; Shigella; antimicrobial resistance; bacteria; enteric infections; sexually transmitted infections; shigellosis.

Figure 1

Epidemiologic and genomic investigation of sexually transmitted Shigella sonnei diagnoses in presumptive MSM classification, England, 2016–2023. Presumptive MSM category was defined as cases among male adults (>16 years of age) without a history of travel or where travel history was unknown. MSM, men who have sex with men.

Figure 2

Sexually transmitted Shigella sonnei isolates among presumptive men who have sex with men by the presence of the bla_CTX-M-15 or bla_CTX-M-27 gene variant from an epidemiologic and genomic investigation, England, 2016–2023. Presumptive men who have sex with men category was defined as cases among male adults (>16 years of age) without a history of travel or where travel history was unknown.

Figure 3

Shigella sonnei isolates with the bla_CTX-M-15 gene variant among presumptive men who have sex with men compared with nonpresumptive men who have sex with men from an epidemiologic and genomic investigation, England, 2016–2023. Presumptive MSM was defined as cases among male adults (>16 years of age) without a history of travel or where travel history was unknown. MSM, men who have sex with men.

Figure 4

Maximum-likelihood phylogenetic tree of the Shigella sonnei clonal complex 152 within the 10 single-nucleotide polymorphism linkage cluster t10.1814 (n = 125) found during an epidemiologic and genomic investigation of sexually transmitted S. sonnei from presumptive men who have sex with men, England, 2016–2023. A total of 125 isolates included in tree. Sequence read run accession is sample identification, additional information provided is gender, presence of bla_CTX-M gene variants, and association with travel. Presumptive men who have sex with men was defined as cases among male adults (>16 years of age) without a history of travel or where travel history was unknown.

Figure 5

Maximum-likelihood phylogenetic tree of clonal complex 152 within nucleotide cluster t25:1 found during an epidemiologic and genomic investigation of sexually transmitted Shigella sonnei from presumptive men who have sex with men, England, 2016–2023. Included in the tree were 1,325 isolates. Blue, t10.377 cluster; green, t10.2218 cluster; red, t10.1814. The outer ring indicates presence of bla_CTX-M; red, bla_CTX-M-15; blue, bla_CTX-M-27; orange, bla_CTX-M-134; green, bla_CTX-M-55. Presumptive men who have sex with men was defined as cases among male adults (>16 years of age) without a history of travel or where travel history was unknown.

Figure 6

Diagnoses of Shigella sonnei in cluster t10.1814 by the bla_CTX-M-15 gene variant status from an epidemiologic and genomic investigation, England, 2016–2023.

Figure 7

Diagnoses of Shigella sonnei in the t10.377 cluster compared with the t10.1814 cluster among presumptive men who have sex with men from an epidemiologic and genomic investigation, England, 2016–2023. Presumptive MSM was defined as cases among male adults (>16 years of age) without a history of travel or where travel history was unknown.

Figure 8

Alignment of IncFII plasmids in samples selected for Nanopore sequencing during an epidemiologic and genomic investigation of sexually transmitted Shigella sonnei from presumptive men who have sex with men, England, 2016–2023. Red gene is the bla_CTX-M variant. Presumptive men who have sex with men was defined as cases among male adults (>16 years of age) without a history of travel or where travel history was unknown.

Figure 9

Alignment of exemplar IncFII plasmid from a Shigella sonnei strain during an epidemiologic and genomic investigation of sexually transmitted Shigella sonnei from presumptive men who have sex with men, England, 2016–2023. The strain fell within the 10 single-nucleotide polymorphism linkage cluster t10.1814 and strain 01233204 (GenBank accession no. SRR29176725), showing the cassette containing bla_CTX-M-15 (highlighted in red) has moved to the chromosome. Presumptive men who have sex with men was defined as cases among male adults (>16 years of age) without a history of travel or where travel history was unknown.