Research and analysis

Sexually transmitted Shigella spp. in England: 2016 to 2023

Updated 16 May 2024

Applies to England

Background

Shigella spp. (S. dysenteriae, S. flexneri, S. boydii and S. sonnei) are bacterial enteric pathogens, transmitted through faecal-oral contact, which can cause dysentery. Historically, the majority of the burden of shigellosis has been associated with exposure to contaminated food or water during travel to endemic countries (1, 2, 3),

However, in England shigellosis is increasingly acquired domestically by men who have sex with men (MSM) (4). Here, trends of Shigella spp. diagnoses are explored using laboratory surveillance data. Throughout this report, adult men not reporting travel, or where travel is unknown, are assumed to most likely have acquired their infection through sexual transmission and are described as “presumptive MSM” (5).

Whole genome sequencing (WGS) data for shigellosis has been explored (6). WGS data is available for a subset of the data presented here and this information has been submitted for peer review publication (7).

Main messages

The key observations from this report are that:

• following the COVID-19 pandemic, reported diagnoses of Shigella spp. related to both travel and presumed sexual transmission increased and returned to pre-pandemic 2019 levels, and have substantially exceeded pre-pandemic levels among presumptive MSM

• in 2023, most diagnoses of Shigella spp. were seen in London (46%), Greater Manchester (7%) and Surrey and Sussex (8%); this reflects variations in the population of MSM across the country

• cases of sexually transmitted S. sonnei increased substantially from Q3 2021 onwards, 230 and 432 diagnoses being reported in 2022 and 2023 respectively; notable within this increase was the re-emergence of a S. sonnei CipR.MSM5 (Clade 5) outbreak strain in late 2021, which subsequently became extensively drug-resistant (XDR) (8)

• very high levels of antimicrobial resistance among Shigella spp. isolates continue to be a significant public health concern; the increase in XDR in S. sonnei isolates with resistance to ceftriaxone (a key second-line treatment for shigellosis) is being monitored to ensure that present cases of shigellosis are treated effectively and that antimicrobial treatment continues to be effective (see the Conclusions section of this report for recommended actions)

Data sources

Two sources of data were used (see technical notes): the Second Generation Surveillance System (SGSS) provides the total number of Shigella spp. diagnoses reported from diagnostic laboratories in England. Local laboratories refer specimens to the UK Health Security Agency (UKHSA) Gastrointestinal Bacteria Reference Laboratory (GBRU) for further testing, information that is captured in the Gastrointestinal Data Warehouse (GDW) dataset. The GDW, which is a subset of the SGSS dataset, contains detailed information on the antimicrobial profile of isolates.

Overall trends

Trends in diagnoses recorded in SGSS and GDW surveillance systems

After a steady increase between 2016 and 2019, in early 2020 there was a steep decline, and subsequent low plateau in diagnoses of Shigella spp. reported to both surveillance systems (Figure 1). This was likely to have been influenced by COVID-19 related control measures restricting both international travel and social mixing within England. Diagnoses reported to both SGSS and GDW increased rapidly after Q3 2021 and reached pre-COVID-19 pandemic levels in Q4 2022. Between 2022 and 2023 reported diagnoses further increased by 38% (3,224 to 4,441) in SGSS and 38% (1,252 to 1,724) in GDW.

The disparity between diagnoses reported in SGSS and GDW is due to the incomplete referral of specimens from local laboratories to the UKHSA GBRU. In addition, S. flexneri isolates are more likely to be referred to the GBRU than isolates of S. sonnei. Variations in the prevalence of species over time also influences the level of reporting.

Figure 1. Diagnoses of Shigella spp. among all persons (adults and children) by surveillance system, England: 2016 to 2023

Data source: GDW and SGSS.

Variations in diagnostic trends associated with factors related to infection

Shigella spp. infection varies by age, gender, and travel history. Reported diagnoses among adult males not reporting travel or where travel history is unknown (presumptive MSM) have been consistently higher, and increasing at a faster rate compared to females, children, or males reporting recent travel (Figure 2). The decline in diagnoses seen in 2020 was largely explained by a fall in travel-associated diagnoses. Reported diagnoses among presumptive MSM also declined, but to a lesser extent. During this period around 75% of all shigella reports were presumed to be sexually transmitted (Figure 3), indicating that transmission between MSM persisted during the pandemic. The proportion has since declined but, in 2023, still accounted for as much as 51% of all diagnoses.

Following the easing of COVID-19 restrictions from Q2 2021, both travel-associated and non-travel associated diagnoses increased. This was more pronounced among presumptive MSM, with diagnoses increasing by 280% between Q3 2021 and Q4 2023 (from 66 to 251).

While the reported number of Shigella spp. diagnoses among females, children and males who reported travel is slightly lower than that seen in presumptive MSM, the burden of infection is significant and likely influences the transmission dynamics of shigellosis overall.

Figure 2. Number of Shigella spp. diagnoses among all persons (adults and children) by sex and travel association: 2016 to 2023 (‡)

Data Source: GDW

‡ Excludes the 80 (0.88%) diagnoses for which sex was not known.

Figure 3. Diagnoses of Shigella spp. in presumptive MSM and the proportion of all diagnoses that were seen in presumptive MSM: 2016 to 2023 (‡)

Data Source: GDW.

‡ Excludes the 80 (0.88%) diagnoses for which sex was not known.

Diagnoses trends by species among presumptive MSM

Following an increase in S. sonnei diagnoses between 2016 and 2018, diagnoses among presumptive MSM started to decline from Q4 2019 to Q1 2020. A further fall was seen in 2020, accounting for much of the overall fall in shigellosis during the COVID-19 pandemic and remaining low until Q3 2021 (Figure 4). Subsequently, diagnoses rebounded and increased by more than 10-fold (from 11 to 133) between Q3 2021 and Q4 2023.

Conversely, reported diagnoses of S. flexneri were decreasing among presumptive MSM between 2016 and 2018, before increasing in 2019. Whilst reported S. flexneri diagnoses did decline in 2020 and 2021, this was not as large of a decrease compared to S. sonnei, and transmission appears to have continued, albeit at a lower level, during the COVID-19 pandemic (Figure 4).

Figure 4. Diagnoses of S. sonnei and S. flexneri among presumptive MSM, England: 2016 to 2023

Data Source: GDW.

Regional distribution of diagnoses among presumptive MSM

In 2023, 45% (397/863) of diagnoses among presumptive MSM were reported from London followed by Greater Manchester HPT (7%), and Surrey and Sussex HPT (8%) respectively (Figure 5).

Figure 5. Diagnoses of Shigella spp. among presumptive MSM by Health Protection Team (‡), England: 2023

Data source: GDW 

‡ Where patient residence was not known, the HPT of the reporting laboratory was used. The North London HPT was created in April 2024 through the amalgamation of two existing HPTs.

Antimicrobial resistance among sexually transmitted Shigella spp.

The World Health Organization recommends ciprofloxacin (a fluoroquinolone) as a first-line treatment for shigellosis. The recommended second line therapies are azithromycin (a macrolide), ceftriaxone (third-generation cephalosporin), or pivmecillinam (an extended-spectrum penicillin) (9). Isolates are classified as multidrug-resistant (MDR) or extensively drug-resistant (XDR) based on the presence of genetic markers of resistance (see technical notes). In 2023, among presumptive MSM, antimicrobial resistance (classified as MDR or XDR) was consistently high in isolates of both S. sonnei (97%) and S. flexneri (93%) (Figure 6).

Over half of S. sonnei isolates are now extensively drug resistant to 8 classes of antibiotics (Figure 5a). Between 2020 and 2021 resistance to third-generation cephalosporins increased sharply from 24% of isolates in 2020 to 71% and was associated with the resurgence of a large cluster of Clade 5 which had acquired markers of resistance to this antibiotic class 6).

While the proportion of S. flexneri isolates that are XDR is smaller compared to S. sonnei, isolates of S. flexneri that had markers of resistance to third-generation cephalosporins increased 8-fold from 2% in 2021 to 15% in 2022 and 16% in 2023 (Figure 5b).

In terms of the recommended first and second line treatments, in 2023, markers of resistance to fluoroquinolones, including ciprofloxacin, were present in 93% of S. sonnei and 39% of S. flexneri isolates among presumptive MSM (Figure 6). Furthermore, 63% of S. sonnei and 44% of S. flexneri isolates had resistance markers to macrolides, such as azithromycin.

Figure 6a. Patterns of antimicrobial resistance detected in S. sonnei isolates among presumptive MSM by antimicrobial resistance and MDR and XDR classification, England: 2016 to 2023 (‡)

Data source: GDW

‡ Antimicrobial resistance is based on the presence of genetic markers. Only those isolates for which information on antimicrobial resistance markers and the overall classification (MDR or XDR) were available have been included.

Figure 6b. Patterns of antimicrobial resistance detected in S. flexneri isolates among presumptive MSM by antimicrobial resistance and MDR and XDR classification, England: 2016 to 2023 (‡)

Data source: GDW

‡ Antimicrobial resistance is based on the presence of genetic markers. Only those isolates for which information on antimicrobial resistance markers and the overall classification (MDR or XDR) were available have been included.

Conclusions

Following a decline in reports in 2020, diagnoses of Shigella spp. rebounded and returned to pre-pandemic 2019 levels among females, children, and males with a recent history of foreign travel. By 2023 diagnoses of Shigella spp. had substantially exceeded the pre-pandemic 2019 level among presumptive MSM. For sexually transmitted shigellosis, focal areas continued to be London, Greater Manchester, and Surrey and Sussex. The proportion of isolates that are XDR continues to increase among S. flexneri and, particularly, S. sonnei isolates which raises concern that there are very few therapeutic options available for patients with complications.

Diagnostic laboratories should continue to refer isolates from high risk populations so as to monitor emergence of pan-resistance. Clinicians should take a sexual history in males cases presenting with diarrhoeal illness and be aware that first or second-line antibiotics may fail in severe shigellosis.

Acknowledgements

The authors acknowledge support of reporting laboratories, the local Health Protection Teams and the Gastrointestinal Bacteria Research Unit (GBRU, UKHSA).

Contributors

Ian Simms, Hannah Charles, Gauri Godbole, Claire Jenkins, Katy Sinka.

Technical notes

Data sources

Second Generation Surveillance System (SGSS)

This dataset includes primary laboratory-based diagnostic data and has the advantages of automated reporting and national coverage, so provides the total number of Shigella spp. diagnoses reported in England from diagnostic laboratories.

Gastro Data Warehouse (GDW)

Faecal specimens from cases with gastrointestinal symptoms are sent to local hospital, private and regional laboratories in England for culture. Local hospital laboratories are recommended to submit presumptive Shigella spp. samples to Gastrointestinal Bacterial Reference Unit (GBRU) at UKHSA for confirmation and typing. Approximately two thirds of Shigella spp. samples are submitted to the GBRU.

Data is updated on an annual or biannual basis and subject to current extraction and cleaning procedures. Therefore, it is possible data may differ from previous publications.

Presumptive men who have sex with men

Data obtained from GDW does not include information on the sexual orientation or sexual behaviour of reported cases. These analyses consider adult males with no recent foreign travel history or where travel history is unknown as a proxy for men who have sex with men (MSM), in alignment with research on the transmission of Shigella spp. in England (5).

Multidrug-resistant

Multidrug-resistant (MDR) is defined as non-susceptibility to at least 1 agent in 3 or more antimicrobial categories (10).

Extensively drug-resistant

Extensively drug-resistant (XDR) is defined as non-susceptibility to at least 1 agent in all but 2 or fewer antimicrobial categories (10).

References

1. Public Health England (2017) ‘Travel-associated Shigella spp. in England, Wales and Northern Ireland: 2014’

2. European Centre for Disease Prevention and Control (2023). ‘Outbreak of Shigella sonnei in the EU/EEA, the United Kingdom and the United States among travellers returning from Cape Verde.‘

3. Mikhail AFW and others (2021). ‘Utility of whole-genome sequencing during an investigation of multiple foodborne outbreaks of Shigella sonnei.‘ Epidemiology and infection of Shigella sonnei. Epidemiology and Infection: volume 149

4. Mitchell H and Hughes G (2018). ‘Recent epidemiology of sexually transmissible enteric infections in men who have sex with men’. Current Opinion in Infectious Diseases: volume 31, issue 1, pages 50 to 56

5. Mitchell HD and others (2019). ‘Use of whole-genome sequencing to identify clusters of Shigella flexneri associated with sexual transmission in men who have sex with men in England: a validation study using linked behavioural data.’ Microbiology Society: volume 5, issue 11

6. Baker KS and others (2015). ‘Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study.‘ Lancet Infectious Diseases; volume 15, pages 913 to 921

7. Charles H and others. ‘Trends in shigellosis notifications in England, January 2016 to March 2023’. Paper submitted to Epidemiology and Infection

8. Charles H and others (2022). ‘Outbreak of sexually transmitted, extensively drug-resistant Shigella sonnei in the UK, 2021 to 2022: a descriptive epidemiological study’. The Lancet Infectious Diseases

9. World Health Organization (2005). ‘Guidelines for the control of shigellosis, including epidemics due to Shigella dysenteriae type 1’.

10. Magiorakos AP and others (2012). ‘Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.’ Clinical Microbiology and Infection: volume 18, issue 3, pages 268 to 281