Clinical and Genomic Investigation of an International Ceftriaxone- and Azithromycin-Resistant Shigella sonnei Cluster among Men Who Have Sex with Men, Montréal, Canada 2017-2019

A case of intercurrent shigellosis and rectal gonorrhea in an acutely unwell febrile returned traveler

Both acute traveler's diarrhea and sexually transmitted infections are common causes of fever in the returned traveler, with the male sex corresponding to two-fold increased odds of a sexually transmitted infection (STI) diagnosis related to travel. Shigella flexneri is the most common cause of shigellosis in low- and middle-income countries, while within the men who have sex with men (MSM) population, outbreaks of S. flexneri 3a, S. flexneri 2a, and S. sonnei have been reported. We herein present a case of a febrile returned MSM traveler with a predominantly gastrointestinal presentation and proctocolitis whose microbiological work-up confirmed coinfection with S. flexneri and rectal gonorrhea. Based on his travel history and epidemiologic risk factors, it is unclear if food- and waterborne shigellosis versus transmission via sexual contact was the major route of acquisition. This case highlights the broad differential for proctocolitis and the importance of consideration of intercurrent infections.

Shigella sonnei: epidemiology, evolution, pathogenesis, resistance and host interactions

Shigella sonnei is a major cause of diarrhoea globally and is increasing in prevalence relative to other Shigella because of multiple demographic and environmental influences. This single-serotype species has traditionally received less attention in comparison to Shigella flexneri and Shigella dysenteriae, which were more common in low-income countries and more tractable in the laboratory. In recent years, we have learned that Shigella are highly complex and highly susceptible to environmental change, as exemplified by epidemiological trends and increasing relevance of S. sonnei. Ultimately, methods, tools and data generated from decades of detailed research into S. flexneri have been used to gain new insights into the epidemiology, microbiology and pathogenesis of S. sonnei. In parallel, widespread adoption of genomic surveillance has yielded insights into antimicrobial resistance, evolution and organism transmission. In this Review, we provide an overview of current knowledge of S. sonnei, highlighting recent insights into this globally disseminated antimicrobial-resistant pathogen and assessing how novel data may impact future vaccine development and implementation.

Genome and antibiotic resistance characteristics of Shigella clinical isolates in Fujian Province, Southeast China, 2005-2019

Shigellosis is a serious public health issue in many developing countries. The emergence of multidrug-resistant (MDR) Shigella isolates has deepened the treatment difficulty and health burden of shigellosis. China is the largest developing country in the world, but so far, the genome of MDR Shigella isolates has not been well characterized. In this study, 60 clinical isolates of Shigella spp. in Fujian Province, southeast China, from 2005 to 2019 were characterized for drug resistance phenotype, whole-genome sequencing and bioinformatics analysis. The results showed that the MDR rate of Shigella isolates was 100%, among which the resistance rates of cefotaxime, ciprofloxacin and azithromycin were 36.67, 21.67 and 10.00 %, respectively. The positive rate of extended-spectrum beta-lactamase (ESBL)-producing strains was 23.33%. The resistance profiles of Shigella flexneri and Shigella sonnei to some antimicrobials differed. The MDR isolates carried multiple antimicrobial resistance genes, among which blaCTX-M-14 and blaCTX-M-15 mediated ESBL resistance. 'ISEcp1 -blaCTX-M -IS903' (type I) and 'ISEcp1 -blaCTX-M' (type II) were the most common genetic environments around the blaCTX-M genes, and plasmids containing these structures included IncFII, IncI1, IncI2 and IncN. The double gene mutation pattern of gyrA and parC resulted in a significant decrease in the sensitivity of S. flexneri to ciprofloxacin. The overall resistance phenotype and genotype concordance rate was 88.50%, and the sensitivity and specificity of the genotype antimicrobial susceptibility test (AST) were 93.35 and 82.53 %, respectively. However, inconsistency occurred between phenotypic and genotype profiles for a few antibiotics. Phylogenomic investigation with core genome multi-locus sequence typing (cgMLST) and SNPs were used to characterize the endemic transmission of these infections in Fujian and their evolutionary origin within the global context. For S. flexneri, Fujian isolates were all limited to PG3 and could be divided into three phylogenetic clusters. The ciprofloxacin-resistant strains were mainly F2a and FXv and assigned to the three clusters with different quinolone resistance-determining region mutation patterns. For S. sonnei, most Fujian strains belonged to Lineage III with genotype 3.7.6, except three isolates of Lineage I with genotype 1.3. The strains carrying the blaCTX-M genes were dispersed, indicating different origins of gene acquisition. Most of the circulating isolates in Fujian Province were not related to major international outbreak lineages and were only endemic to the country. In conclusion, multi-drug resistance of Shigella isolates in Fujian Province was serious, and genome-based laboratory surveillance will be crucial to the clinical treatment and public health measures for shigellosis.

A Qualitative Evaluation of the Acceptability of Shigellosis Prevention Recommendations Among Gay, Bisexual, and Other Men Who Have Sex With Men

BACKGROUND

Shigellosis is diarrheal disease caused by highly infectious Shigella bacteria. Shigella can spread in multiple ways, including sexual contact. Gay, bisexual, and other men who have sex with men are particularly at risk for shigellosis.

METHODS

To evaluate the acceptability of 3 Centers for Disease Control and Prevention-developed behavioral recommendations for the prevention of sexually transmitted shigellosis, virtual in-depth interviews were conducted among 26 gay or bisexual men in March to May 2021.

RESULTS

Participants had a median age of 25 years; 65% were non-Hispanic White, 12% were Hispanic White, 12% Asian, 4% Hispanic Black, and 8% multiracial/other. Respondents indicated willingness to engage in certain prevention behaviors (e.g., washing hands, genitals, and anus before and after sex), but were less willing to engage in behaviors that were viewed as outside social norms or difficult to practice (e.g., dental dams for oral-anal contact; latex gloves for fingering or fisting). Respondents thought recommendations may be more feasible if knowledge of shigellosis was greater; however, some perceived that the severity of shigellosis is low and did not warrant the effort of engaging in prevention behaviors.

CONCLUSIONS

Educational efforts to increase awareness of shigellosis and other enteric diseases spread through sexual contact are needed and public health practitioners should consider the acceptability of how realistic it is for individuals to engage in certain prevention behaviors. Rather than recommending behaviors that do not have buy-in, it may be more efficacious to focus recommendations on adopting behaviors reported as acceptable to the target audience.

Multidrug-Resistant Shigellosis as a Sexually Transmitted Infection in Advanced HIV: A Case Report

Shigellosis, a significant public health concern, has increasingly been recognized as a sexually transmitted infection (STI) among men who have sex with men (MSM), particularly in those with HIV. This case report describes a 25-year-old MSM with advanced HIV who presented with recurrent multidrug-resistant (MDR) Shigella flexneri infection despite multiple hospitalizations and antibiotic courses. The patient's high-risk sexual behaviors and suboptimal HIV management likely contributed to recurrent exposure to Shigella and the selection of resistant strains. This case highlights the complex interplay of individual behaviors, immune suppression, antimicrobial resistance, and the healthcare system in the context of this emerging STI. It underscores the importance of optimized HIV care, comprehensive patient education, robust healthcare coordination, and strengthened surveillance to effectively combat MDR shigellosis in vulnerable populations.

Risk factors and provider awareness of sexually transmitted enteric pathogens among men who have sex with men

Sexual transmission of enteric pathogens among men who have sex with men (MSM) is well documented, although whether providers are cognizant of this risk when MSM patients present with gastrointestinal symptoms has not been studied. Over 34 months at a major tertiary metropolitan medical system, this study retrospectively analyzed 436 BioFire FilmArray Gastrointestinal results from 361 patients documented as MSM. An extensive chart review was performed, including specific sexual behaviors, socioeconomic risk factors, and whether providers charted a sexual history when a patient presented for care. Overall BioFire positivity rate was 62% with no significant difference in positivity between persons living with HIV and those without. Patients charted as sexually active had a significantly increased odds ratio (OR) of a positive result compared to those who were not. Anilingus had the highest OR. Providers charted any type of sexual history in 40.6% of cases, and HIV/infectious disease providers were significantly more likely to do this compared to other subspecialties. Sexual transmission of enteric pathogens within MSM is ongoing, and patients are at risk regardless of living with HIV. Not all sexual behaviors have the same associated risk, highlighting opportunities to decrease transmission. Increased provider vigilance and better patient education on sexual transmission of enteric pathogens are needed to reduce the disease burden.

IMPORTANCE

Our work adds several key findings to the growing body of literature describing the epidemiology of enteric pathogens as sexually transmitted infections among men who have sex with men (MSM). We analyzed clinical test results, housing status, provider awareness, sexual behaviors, and symptoms for 361 patients. We found that any sexual activity was associated with an increased risk of diarrheal pathogen detection, whereas being unhoused was not a risk factor. These findings suggest separate transmission networks between unhoused persons, who are also at risk of infectious diarrhea, and MSM. Moreover, our study suggested low awareness among patient-facing clinicians that diarrheal pathogens can be sexually transmitted. Together, our findings indicate an important opportunity to disrupt transmission cycles by educating clinicians on how to assess and counsel MSM patients.

Pathogenicity and virulence of Shigella sonnei: A highly drug-resistant pathogen of increasing prevalence

Shigella spp. are the causative agent of shigellosis (or bacillary dysentery), a diarrhoeal disease characterized for the bacterial invasion of gut epithelial cells. Among the 4 species included in the genus, Shigella flexneri is principally responsible for the disease in the developing world while Shigella sonnei is the main causative agent in high-income countries. Remarkably, as more countries improve their socioeconomic conditions, we observe an increase in the relative prevalence of S. sonnei. To date, the reasons behind this change in aetiology depending on economic growth are not understood. S. flexneri has been widely used as a model to study the pathogenesis of the genus, but as more research data are collected, important discrepancies with S. sonnei have come to light. In comparison to S. flexneri, S. sonnei can be differentiated in numerous aspects; it presents a characteristic O-antigen identical to that of one serogroup of the environmental bacterium Plesiomonas shigelloides, a group 4 capsule, antibacterial mechanisms to outcompete and displace gut commensal bacteria, and a poorer adaptation to an intracellular lifestyle. In addition, the World Health Organization (WHO) have recognized the significant threat posed by antibiotic-resistant strains of S. sonnei, demanding new approaches. This review gathers knowledge on what is known about S. sonnei within the context of other Shigella spp. and aims to open the door for future research on understanding the increasing spread of this pathogen.

Genomics for public health and international surveillance of antimicrobial resistance

Historically, epidemiological investigation and surveillance for bacterial antimicrobial resistance (AMR) has relied on low-resolution isolate-based phenotypic analyses undertaken at local and national reference laboratories. Genomic sequencing has the potential to provide a far more high-resolution picture of AMR evolution and transmission, and is already beginning to revolutionise how public health surveillance networks monitor and tackle bacterial AMR. However, the routine integration of genomics in surveillance pipelines still has considerable barriers to overcome. In 2022, a workshop series and online consultation brought together international experts in AMR and pathogen genomics to assess the status of genomic applications for AMR surveillance in a range of settings. Here we focus on discussions around the use of genomics for public health and international AMR surveillance, noting the potential advantages of, and barriers to, implementation, and proposing recommendations from the working group to help to drive the adoption of genomics in public health AMR surveillance. These recommendations include the need to build capacity for genome sequencing and analysis, harmonising and standardising surveillance systems, developing equitable data sharing and governance frameworks, and strengthening interactions and relationships among stakeholders at multiple levels.

The genomic epidemiology of shigellosis in South Africa

Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.

Resistance in Enteric Shigella and nontyphoidal Salmonella : emerging concepts

PURPOSE OF REVIEW

The emergence of globally resistant enteric Shigella and nontyphoidal Salmonella strains (NTS) has limited the selection of effective drugs, which has become a major challenge for the treatment of infections. The purpose of this review is to provide the current opinion on the antimicrobial-resistant enteric Shigella and nontyphoidal Salmonella .

RECENT FINDINGS

Enteric Shigella and NTS are resistant to almost all classes of antimicrobials in recent years. Those with co-resistance to ciprofloxacin, azithromycin and ceftriaxone, the first-line antibiotics for the treatment of infectious diarrhoea have emerged worldwide. Some of them have caused interregional and international spread by travel, trade, MSM, and polluted water sources. Several strains have even developed resistance to colistin, the last-resort antibiotic used for treatment of multidrug-resistant Gram-negative bacteria infections.

SUMMARY

The drug resistance of enteric Shigella and NTS is largely driven by the use of antibiotics and horizontal gene transfer of mobile genetic elements. These two species show various drug resistance patterns in different regions and serotypes. Hence treatment decisions for Shigella and Salmonella infections need to take into consideration prevalent antimicrobial drug resistance patterns. It is worth noting that the resistance genes such as blaCTX,mph, ermB , qnr and mcr , which can cause resistance to ciprofloxacin, cephalosporin, azithromycin and colistin are widespread because of transmission by IncFII, IncI1, IncI2 and IncB/O/K/Z plasmids. Therefore, continuous global monitoring of resistance in Shigella and Salmonella is imperative.

Genomic reconstruction and directed interventions in a multidrug-resistant Shigellosis outbreak in Seattle, WA, USA: a genomic surveillance study

BACKGROUND

Shigella spp have been associated with community-wide outbreaks in urban settings. We analysed a sustained shigellosis outbreak in Seattle, WA, USA, to understand its origins and mechanisms of antimicrobial resistance, define ongoing transmission patterns, and optimise strategies for treatment and infection control.

METHODS

We did a retrospective study of all Shigella isolates identified from stool samples at the clinical laboratories at Harborview Medical Center and University of Washington Medical Center (Seattle, WA, USA) from May 1, 2017, to Feb 28, 2022. We characterised isolates by species identification, phenotypic susceptibility testing, and whole-genome sequencing. Demographic characteristics and clinical outcomes of the patients were retrospectively examined.

FINDINGS

171 cases of shigellosis were included. 78 (46%) patients were men who have sex with men (MSM), and 88 (52%) were people experiencing homelessness (PEH). Although 84 (51%) isolates were multidrug resistant, 100 (70%) of 143 patients with data on antimicrobial therapy received appropriate empirical therapy. Phylogenomic analysis identified sequential outbreaks of multiple distinct lineages of Shigella flexneri and Shigella sonnei. Discrete clonal lineages (ten in S flexneri and nine in S sonnei) and resistance traits were responsible for infection in different at-risk populations (ie, MSM, PEH), enabling development of effective guidelines for empirical treatment. The most prevalent lineage in Seattle was probably introduced to Washington State via international travel, with subsequent domestic transmission between at-risk groups.

INTERPRETATION

An outbreak in Seattle was driven by parallel emergence of multidrug-resistant strains involving international transmission networks and domestic transmission between at-risk populations. Genomic analysis elucidated not only outbreak origin, but directed optimal approaches to testing, treatment, and public health response. Rapid diagnostics combined with detailed knowledge of local epidemiology can enable high rates of appropriate empirical therapy even in multidrug-resistant infection.

FUNDING

None.

Increasing trend of antimicrobial resistance in Shigella associated with MSM transmission in Barcelona, 2020-21: outbreak of XRD Shigella sonnei and dissemination of ESBL-producing Shigella flexneri

BACKGROUND

Several countries have recently reported the detection of ESBL-producing Shigella sonnei associated with transmission among MSM. In a previous study by our group, 2.8% of Shigella spp. obtained from MSM in Barcelona between 2015 and 2019 were ESBL producers.

OBJECTIVES

To describe and characterize the emerging ESBL-producing Shigella spp. associated with sexual transmission among MSM detected from 2020 to 2021 in Barcelona, elucidating their connectivity with contemporaneous ESBL-producing Shigella spp. from other countries.

RESULTS

From 2020 to 2021, we identified that among MSM, 68% of S. sonnei were XDR harbouring blaCTX-M-27 and 14% of Shigella flexneri were MDR harbouring blaCTX-M-27. WGS analysis showed that the ESBL-producing S. sonnei were part of a monophyletic cluster, which included isolates responsible for the prolonged outbreak occurring in the UK. Our data also reveal the first emergence and clonal dissemination of ESBL-producing and fluoroquinolone-resistant S. flexneri 2a among MSM.

CONCLUSIONS

We report an increasing trend of antimicrobial resistance in Shigella spp. among MSM in Barcelona since 2021, mainly as a consequence of the dissemination of XDR ESBL-producing S. sonnei, previously reported in the UK. These results highlight the importance of international collaborative surveillance of MDR/XDR S. sonnei and S. flexneri for rapid identification of their emergence and the prevention of the transmission of these pathogens.