The re-emergence of sexually transmissible multidrug resistant Shigella flexneri 3a, England, United Kingdom

DuPont, H. L., Levine, M. M., Hornick, R. B. & Formal, S. B. Inoculum size in Shigellosis and implications for expected mode of transmission. J. Infect. Dis. 159, 1126–1128 (1989).Article 
CAS 
PubMed 

Google Scholar 
Kotloff, K. L., Riddle, M. S., Platts-Mills, J. A., Pavlinac, P. & Zaidi, A. K. M. Shigellosis. Lancet 391, 801–812 (2018).Article 
PubMed 

Google Scholar 
Joyce, F. B. et al. Shigella is common in symptomatic and asymptomatic men who have sex with men visiting a sexual health clinic in Amsterdam. Sex. Transm. Infect. 98, 564 (2022).Article 

Google Scholar 
Adams, C., Vose, A., Edmond, M. B. & Lyckholm, L. Shigella sonnei and hemolytic uremic syndrome: a case report and literature review. IDCases 8, 6–8 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
McGuire, E., Tiberi, S., Ciesielczuk, H. & Melzer, M. Shigellosis and toxic megacolon secondary to Shigella flexneri serotype 3a: the challenges of laboratory diagnosis. Int. J. Infect. Dis. 70, 104–106 (2018).Article 
PubMed 

Google Scholar 
Morduchowicz, G. et al. Shigella bacteremia in adults. A report of five cases and review of the literature. Arch. Intern. Med. 147, 2034–2037 (1987).Article 
CAS 
PubMed 

Google Scholar 
Kaeley, N., Kumar, M., Bhardwaj, B. & Nagasubramanyam, V. Shigella flexneri associated reactive arthritis – GI transmitted or sexually transmitted? J. Fam. Med. Prim. Care 8, 1250 (2019).Article 

Google Scholar 
Thomas, M. E. & Tillett, H. E. Sonne dysentery in day schools and nurseries: an eighteen-year study in Edmonton. J. Hyg. 71, 593–602 (1973).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Rew, V. et al. Whole-genome sequencing revealed concurrent outbreaks of shigellosis in the English Orthodox Jewish Community caused by multiple importations of Shigella sonnei from Israel. Microb. Genom. 4, e000170 (2018).PubMed 
PubMed Central 

Google Scholar 
Lampel, K. A., Formal, S. B. & Maurelli, A. T. A Brief History of Shigella. EcoSal Plus 8. https://doi.org/10.1128/ecosalplus.ESP-0006-2017 (2018).Bader, M. A. X., Pedersen, A. H. B., Williams, R., Spearman, J. & Anderson, H. Venereal Transmission of Shigellosis in Seattle-King County. Sex. Transm. Dis. 4, 89–91 (1977).Article 
CAS 
PubMed 

Google Scholar 
Dritz, S. K. & Back, A. F. Letter: Shigella enteritis venereally transmitted. N. Engl. J. Med. 291, 1194 (1974).Article 
CAS 
PubMed 

Google Scholar 
Drusin, L. M., Genvert, G., Topf-Olstein, B. & Levy-Zombek, E. Shigellosis. Another sexually transmitted disease? Br. J. Vener. Dis. 52, 348–350 (1976).Morgan, O. et al. Shigella sonnei outbreak among homosexual men, London. Emerg. Infect. Dis. 12, 1458–1460 (2006).Article 
PubMed 
PubMed Central 

Google Scholar 
Mohammed, S., Holly, O., Flanagan, Daniel, R. & Carrie, D. L. Factors associated with sexually transmitted Shigella in men who have sex with men: a systematic review. Sex. Transm. Infect. 99, 58 (2023).Article 

Google Scholar 
Gilbart, V. L. et al. Sex, drugs and smart phone applications: findings from semistructured interviews with men who have sex with men diagnosed with Shigella flexneri 3a in England and Wales. Sex. Transm. Infect. 91, 598–602 (2015).Article 
CAS 
PubMed 

Google Scholar 
Daniel, R., John, D., Colin, F. & Nicolas, P.-S. Sexually transmitted Shigella flexneri and Shigella sonnei in men who have sex with men. Sex. Transm. Infect. 97, 244 (2021).Article 

Google Scholar 
Farrar, W. E. Jr. & Eidson, M. Antibiotic resistance in Shigella mediated by R Factors. J. Infect. Dis. 123, 477–484 (1971).Article 
CAS 
PubMed 

Google Scholar 
Davies, J. R., Farrant, W. N. & Tomlinson, A. J. Further studies on the antibiotic resistance of Shigella sonnei. II. The acquisition of transferable antibiotic resistance in vivo. J. Hyg. 66, 479–487 (1968).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chung The, H. et al. South Asia as a reservoir for the global spread of Ciprofloxacin-Resistant Shigella sonnei: a cross-sectional study. PLOS Med. 13, e1002055 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Baker, K. S. et al. Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species. Nat. Commun. 9, 1462 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Mason, L. C. E. et al. The evolution and international spread of extensively drug resistant Shigella sonnei. Nat. Commun. 14, 1983 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Mook, P. et al. ESBL-producing and macrolide-resistant Shigella sonnei infections among men who have sex with men, England, 2015. Emerg. Infect. Dis. J. 22, 1948 (2016).Article 
CAS 

Google Scholar 
World Health Organization (WHO). Guidelines for the control of shigellosis, including epidemics due to Shigella dysenteriae type 1. Report No. 924159330X, https://appls.who.int/iris/handle/20665/43252, Geneva, 2005).Simms, I. et al. Intensified shigellosis epidemic associated with sexual transmission in men who have sex with men – Shigella flexneri and S. sonnei in England, 2004 to end of February 2015. Eurosurveillance 20, 21097 (2015).Article 
PubMed 

Google Scholar 
Bardsley, M. et al. Persistent transmission of Shigellosis in England is associated with a recently emerged multidrug-resistant strain of Shigella sonnei. J. Clin. Microbiol. 58, e01692–19 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Charles, H. et al. Outbreak of sexually transmitted, extensively drug-resistant Shigella sonnei in the UK, 2021-22: a descriptive epidemiological study. Lancet Infect. Dis. 22, 1503–1510 (2022).Article 
CAS 
PubMed 

Google Scholar 
Thorley, K. et al. Emergence of extensively drug-resistant and multidrug-resistant Shigella flexneri serotype 2a associated with sexual transmission among gay, bisexual, and other men who have sex with men, in England: a descriptive epidemiological study. Lancet Infect. Dis. 23, 732–739 (2023).Article 
CAS 
PubMed 

Google Scholar 
Nicola, K. L. et al. Impact of the COVID-19 pandemic on gastrointestinal infection trends in England, February–July 2020. Br. Med. J. Open 12, e050469 (2022).
Google Scholar 
Baker, K. S. et al. Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study. Lancet Infect. Dis. 15, 913–921 (2015).Article 
PubMed 

Google Scholar 
De Silva, P. M. et al. Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins. eBioMedicine 97, 104822 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80–92 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Tedijanto, C., Olesen, S. W., Grad, Y. H. & Lipsitch, M. Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora. Proc. Natl Acad. Sci. 115, E11988–E11995 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bignell, C. & FitzGerald, M. UK national guideline for the management of gonorrhoea in adults, 2011. Int. J. STD AIDS 22, 541–547 (2011).Article 
CAS 
PubMed 

Google Scholar 
Fifer, H., Saunders, J., Soni, S., Sadiq, S. T. & FitzGerald, M. 2018 UK national guideline for the management of infection with Neisseria gonorrhoeae. Int. J. STD AIDS 31, 4–15 (2020).Article 
PubMed 

Google Scholar 
Siu, L. K. et al. beta-lactamases in Shigella flexneri isolates from Hong Kong and Shanghai and a novel OXA-1-like beta-lactamase, OXA-30. Antimicrob. Agents Chemother. 44, 2034–2038 (2000).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Al-Marzooq, F., Ghazawi, A., Daoud, L. & Tariq, S. Boosting the antibacterial activity of Azithromycin on Multidrug-Resistant Escherichia coli by Efflux pump inhibition coupled with outer membrane permeabilization induced by Phenylalanine-Arginine β-Naphthylamide. Int. J. Mol. Sci. 24, 8662 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Laurenson-Schafer, H. et al. Description of the first global outbreak of mpox: an analysis of global surveillance data. Lancet Glob. Health 11, e1012–e1023 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cohen, D. et al. Recent trends in the epidemiology of shigellosis in Israel. Epidemiol. Infect. 142, 2583–2594 (2014).Article 
CAS 
PubMed 

Google Scholar 
Ratnayake, R., Allard, R. & Pilon, P. A. Shifting dominance of Shigella species in men who have sex with men. Epidemiol. Infect. 140, 2082–2086 (2012).Article 
CAS 
PubMed 

Google Scholar 
Harrow, G. L. et al. Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. Int. Soc. Microb. Ecol. J. 15, 1523–1538 (2021).CAS 

Google Scholar 
Hay, J., Routledge, I., & Takahashi, S. Serodynamics: a review of methods for epidemiological inference using serological data. OSF Preprints. https://doi.org/10.31219/osf.io/kqdsn (2023).Mitchell, H. D. et al. 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. Microb. Genom. 5, e000311 (2019).PubMed 
PubMed Central 

Google Scholar 
SRAToolkitDevelopmentTeam. SRA Toolkit, https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit (Github Repository, 2020).Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Broad Institute. Picard Toolkit v. 2.27.2, https://broadinstitute.github.io/picard/ (GitHub Repository, 2019).García-Alcalde, F. et al. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics 28, 2678–2679 (2012).Article 
PubMed 

Google Scholar 
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).Article 
PubMed 
PubMed Central 

Google Scholar 
Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Page, A. J. et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb. Genom. 2, e000056 (2016).PubMed 
PubMed Central 

Google Scholar 
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Croucher, N. J. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 43, e15 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Comput. Biol. 13, e1005595 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. & Korobeynikov, A. Using SPAdes De Novo Assembler. Curr. Protoc. Bioinforma. 70, e102 (2020).Article 
CAS 

Google Scholar 
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Permana, B., Beatson, S. A. & Forde, B. M. GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach. BMC Bioinforma. 24, 209 (2023).Article 

Google Scholar 
Feldgarden, M. et al. AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci. Rep. 11, 12728 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ashton, P. M. et al. Identification of Salmonella for public health surveillance using whole genome sequencing. PeerJ 4, e1752 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Seemann T., Abricate https://github.com/tseemann/abricate (Github Repository, 2024).Chen, L., Zheng, D., Liu, B., Yang, J. & Jin, Q. VFDB 2016: hierarchical and refined dataset for big data analysis-10 years on. Nucleic Acids Res. 44, D694–D697 (2016).Article 
CAS 
PubMed 

Google Scholar 
European Committee on Antimicrobial Susceptibility Testing (EUCAST). Clinical Breakpoints and Dosing of Antibiotics-Bacteria (V 12.0) Vaxjo, 2022. https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.pdf. Accessed 6 Sep. 2023 (EUCAST, 2022).Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).Article 
CAS 
PubMed 

Google Scholar 
Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wick, R. R. & Holt, K. E. Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLOS Comput. Biol. 18, e1009802 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Tatusova, T. et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614–6624 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gilchrist, C. L. M. & Chooi, Y.-H. clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics 37, 2473–2475 (2021).Article 
CAS 
PubMed 

Google Scholar 
Carattoli, A. et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895–3903 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).Article 
CAS 
PubMed 

Google Scholar 
Carver, T., Harris, S. R., Berriman, M., Parkhill, J. & McQuillan, J. A. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28, 464–469 (2011).Article 
PubMed 
PubMed Central 

Google Scholar 
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).Article 
CAS 
PubMed 

Google Scholar 
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Sagulenko, P., Puller, V. & Neher, R. A. TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evol. 4, vex042 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 52, W78–W82 (2024).Article 
PubMed 
PubMed Central 

Google Scholar 
Consortium, T. U. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 51, D523–D531 (2022).Article 

Google Scholar 
Henikoff, S. & Henikoff, J. G. Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA 89, 10915–10919 (1992).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar