Association between lung function and dyspnoea and its variation in the multinational Burden of Obstructive Lung Disease (BOLD) study

BACKGROUND

Dyspnoea is a common symptom of respiratory disease. However, data on its prevalence in general populations and its association with lung function are limited and are mainly from high-income countries. The aims of this study were to estimate the prevalence of dyspnoea across several world regions, and to investigate the association of dyspnoea with lung function.

METHODS

Dyspnoea was assessed, and lung function measured in 25,806 adult participants of the multinational Burden of Obstructive Lung Disease study. Dyspnoea was defined as ≥2 on the modified Medical Research Council (mMRC) dyspnoea scale. The prevalence of dyspnoea was estimated for each of the study sites and compared across countries and world regions. Multivariable logistic regression was used to assess the association of dyspnoea with lung function in each site. Results were then pooled using random-effects meta-analysis.

RESULTS

The prevalence of dyspnoea varied widely across sites without a clear geographical pattern. The mean prevalence of dyspnoea was 13.7 % (SD=8.2 %), ranging from 0 % in Mysore (India) to 28.8 % in Nampicuan-Talugtug (Philippines). Dyspnoea was strongly associated with both spirometry restriction (FVC

CONCLUSION

The prevalence of dyspnoea varies substantially across the world and is strongly associated with lung function impairment. Using the mMRC scale in epidemiological research should be discussed.

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Key Words

• Breathlessness
• Dyspnoea
• Lung function
• Spirometry

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Affiliation(s)

A Müller Ludwig Boltzmann Institute for Lung Health, Vienna, Austria; Care and Public Health Research Institute, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands.
E F Wouters Ludwig Boltzmann Institute for Lung Health, Vienna, Austria; Sigmund Freud University, Faculty of Medicine, Vienna, Austria; Department of Respiratory Medicine, Maastricht University Medical Center, Maastricht, the Netherlands
P Koul Department of Pulmonary Medicine, Sheri Kashmir Institute of Medical Sciences, Srinagar, India
T Welte Department of Respiratory Medicine/Infectious Disease, Member of the German Centre for Lung Research, Hannover School of Medicine, Hannover, Germany
I Harrabi Faculté de Médecine, Sousse, Tunisia
A Rashid RCSI and UCD Malaysia Campus, Penang, Malaysia
L C Loh RUMC, Penang, Malaysia
M Al Ghobain King Abdullah International Medical Research Center, King Saud ben Abdulaziz University for Health Science, Riyadh, Saudi Arabia
A Elsony The Epidemiological Laboratory, Khartoum, Sudan
R Ahmed The Epidemiological Laboratory, Khartoum, Sudan
J Potts National Heart and Lung Institute, Imperial College London, London, UK
K Mortimer University of Cambridge, Cambridge, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
F Rodrigues Pulmonology Department, Lisbon North Hospital Centre, Lisbon, Portugal; Institute of Environmental Health, Associate Laboratory TERRA, Lisbon Medical School, Lisbon University, Lisbon, Portugal
S N Paraguas Philippine College of Chest Physicians, Manila, Philippines
S Juvekar KEM Hospital Research Centre, Pune, India
D Agarwal KEM Hospital Research Centre, Pune, India
D Obaseki Department of Medicine, Obafemi Awolowo University, Nigeria; Faculty of Medicine, University of British Columbia, Canada
T Gislason Faculty of Medicine, University of Iceland, Reykjavik, Iceland; Department of Sleep, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
T Seemungal Faculty of Medical Sciences, University of West Indies, St Augustine, Trinidad and Tobago
A A Nafees Aga Khan University, Karachi, Pakistan
C Jenkins Woolcock Institute of Medical Research, Sydney, Australia
H B Dias Escola Superior de Tecnologia da Saúde de Lisboa, Politecnico de Lisboa, Lisbon, Portugal
F M E Franssen Department of Respiratory Medicine, Maastricht University Medical Center, Maastricht, the Netherlands; Department of Research and Development, Ciro, Horn, the Netherlands
M Studnicka Department of Pulmonary Medicine, Paracelsus Medical University, Salzburg, Austria
C Janson Department of Medical Sciences: Respiratory, Allergy and Sleep Research, Uppsala University, Uppsala, Sweden
H H Cherkaski Faculty of Medicine, University Badji Mokhtar, Annaba, Algeria
M El Biaze Department of Respiratory Medicine, Faculty of Medicine, Mohammed Ben Abdellah University, Fes, Morocco
P A Mahesh Department of Respiratory Medicine, JSS Medical College and Hospital, Mysore, Karnataka, India
J Cardoso Pulmonology Department, Centro Hospitalar Universitário de Lisboa Central, Lisboa, Portugal; NOVA Medical School, Nova University Lisbon, Lisboa, Portugal
P Burney National Heart and Lung Institute, Imperial College London, London, UK
S Hartl Ludwig Boltzmann Institute for Lung Health, Vienna, Austria; Sigmund Freud University, Faculty of Medicine, Vienna, Austria
D J A Janssen Care and Public Health Research Institute, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; Department of Research and Development, Ciro, Horn, the Netherlands
A F S Amaral National Heart and Lung Institute, Imperial College London, London, UK; NIHR Imperial Biomedical Research Centre, London, UK

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Re-analysis of an outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with raw drinking milk using Nanopore sequencing

The aim of this study was to compare Illumina and Oxford Nanopore Technology (ONT) sequencing data to quantify genetic variation to assess within-outbreak strain relatedness and characterise microevolutionary events in the accessory genomes of a cluster of 23 genetically and epidemiologically linked isolates related to an outbreak of Shiga toxin-producing Escherichia coli O157:H7 caused by the consumption of raw drinking milk. There were seven discrepant variants called between the two technologies, five were false-negative or false-positive variants in the Illumina data and two were false-negative calls in ONT data. After masking horizontally acquired sequences such as prophages, analysis of both short and long-read sequences revealed the 20 isolates linked to the outbreak in 2017 had a maximum SNP distance of one SNP between each other, and a maximum of five SNPs when including three additional strains identified in 2019. Analysis of the ONT data revealed a 47 kbp deletion event in a terminal compound prophage within one sample relative to the remaining samples, and a 0.65 Mbp large chromosomal rearrangement (inversion), within one sample relative to the remaining samples. Furthermore, we detected two bacteriophages encoding the highly pathogenic Shiga toxin (Stx) subtype, Stx2a. One was typical of Stx2a-phage in this sub-lineage (Ic), the other was atypical and inserted into a site usually occupied by Stx2c-encoding phage. Finally, we observed an increase in the size of the pO157 IncFIB plasmid (1.6 kbp) in isolates from 2019 compared to those from 2017, due to the duplication of insertion elements within the plasmids from the more recently isolated strains. The ability to characterize the accessory genome in this way is the first step to understanding the significance of these microevolutionary events and their impact on the genome plasticity and virulence between strains of this zoonotic, foodborne pathogen.

Sporadic bovine encephalopathy caused by Chlamydia pecorum secondary to bovine viral diarrhoea virus infection in calves in South Australia

BACKGROUND

Despite bovine viral diarrhoea virus and Chlamydia pecorum being important endemic diseases of cattle, there are limited reports of theirco-occurrence.

CASE REPORT

Several 12-18-week-old, weaned Hereford calves presented with ill-thriftiness and neurological signs on a mixed cattle and sheep farm in South Australia in July 2021. Immune suppression resulting from transient infection with bovine viral diarrhoea virus (BVDV) is implicated in predisposing to infection with Chlamydia pecorum, the causative agent of sporadic bovine encephalopathy (SBE). Chlamydia spp. are difficult to culture in vitro or definitively identify based on current standard molecular based tests. In this case, diagnosis was confirmed by immunohistochemistry.

CONCLUSION

To the authors' knowledge, this case report is the first to document BVDV transient infection occurring in conjunction with SBE. Given the current high prevalence of BVDV on Australian farms, such co-infections may have significant future clinical relevance. This case also highlights the need for appropriate tests, such as immunohistochemistry to demonstrate the causative organism in histological lesions and thus reduce the occurrence of false negative diagnosis.

Listeria monocytogenes: the silent assassin

Listeriosis is a foodborne infection in humans caused by Listeria monocytogenes. Consumption of contaminated food can lead to severe infection in vulnerable patients, that can be fatal. Clinical manifestations include sepsis and meningitis, and in pregnancy-associated infection, miscarriage and stillbirth. Diagnosis is confirmed by culture and identification of the pathogen from blood, cerebrospinal fluid, vaginal swab, placenta or amniotic fluid. Treatment regimens recommend amoxicillin, ampicillin or an aminoglycoside. Virulence factors mediate bacterial adhesion and invasion of gut epithelial cells. Other factors mediate biofilm formation and tolerance to low temperatures and high salt concentrations facilitating persistence and survival in the environment.

Shedding and exclusion from childcare in children with Shiga toxin-producing Escherichia coli, 2018-2022

Excluding children with Shiga toxin-producing Escherichia coli (STEC) from childcare until microbiologically clear of the pathogen, disrupts families, education, and earnings. Since PCR introduction, non-O157 STEC serotype detections in England have increased. We examined shedding duration by serotype and transmission risk, to guide exclusion advice. We investigated STEC cases aged <6 years, residing in England and attending childcare, with diarrhoea onset or sample date from 31 March 2018 to 30 March 2022. Duration of shedding was the interval between date of onset or date first positive specimen and earliest available negative specimen date. Transmission risk was estimated from proportions with secondary cases in settings attended by infectious cases. There were 367 cases (STEC O157 n = 243, 66.2%; STEC non-O157 n = 124, 33.8%). Median shedding duration was 32 days (IQR 20-44) with no significant difference between O157 and non-O157; 2% (n = 6) of cases shed for ≥100 days. Duration of shedding was reduced by 17% (95% CI 4-29) among cases reporting bloody diarrhoea. Sixteen settings underwent screening; four had secondary cases (close contacts' secondary transmission rate = 13%). Shedding duration estimates were consistent with previous studies (median 31 days, IQR 17-41). Findings do not warrant guidance changes regarding exclusion and supervised return of prolonged shedders, despite serotype changes.

Yersinia enterocolitica biovar 1A: An underappreciated potential pathogen in the food chain

Yersinia enterocolitica is an underreported cause of foodborne gastroenteritis. Little is known of the diversity of Y. enterocolitica isolated from food and which food commodities contribute to human disease. In this study, Y. enterocolitica was isolated from 37/50 raw chicken, 8/10 pork, 8/10 salmon and 1/10 leafy green samples collected at retail in the UK. Up to 10 presumptive Y. enterocolitica isolates per positive sample underwent whole genome sequencing (WGS) and were compared with publicly available genomes. In total, 207 Y. enterocolitica isolates were analyzed and belonged to 38 sequence types (STs). Up to five STs of Y. enterocolitica were isolated from individual food samples and isolates belonging to the same sample and ST differed by 0-74 single nucleotide polymorphisms (SNPs). Biotype was predicted for 205 (99 %) genomes that all belonged to biotype 1A, previously described as non-pathogenic. However, around half (51 %) of food samples contained isolates belonging to the same ST as previously isolated from UK human cases. The closest human-derived isolates shared between 17 and 7978 single nucleotide polymorphisms (SNPs) with the food isolates. Extensive food surveillance is required to determine what food sources are responsible for Y. enterocolitica infections and to re-examine the role of biotype 1A as a human pathogen.

Clinical and public health implications of increasing notifications of LEE-negative Shiga toxin-producing Escherichia coli in England, 2014-2022

Introduction. Shiga toxin-producing Escherichia coli (STEC) belong to a diverse group of gastrointestinal pathogens. The pathogenic potential of STEC is enhanced by the presence of the pathogenicity island called the Locus of Enterocyte Effacement (LEE), including the intimin encoding gene eae.Gap statement. STEC serotypes O128:H2 (Clonal Complex [CC]25), O91:H14 (CC33), and O146:H21 (CC442) are consistently in the top five STEC serotypes isolated from patients reporting gastrointestinal symptoms in England. However, they are eae/LEE-negative and perceived to be a low risk to public health, and we know little about their microbiology and epidemiology.Aim. We analysed clinical outcomes and genome sequencing data linked to patients infected with LEE-negative STEC belonging to CC25 (O128:H2, O21:H2), CC33 (O91:H14) and, and CC442 (O146:H21, O174:H21) in England to assess the risk to public health.Results. There was an almost ten-fold increase between 2014 and 2022 in the detection of all STEC belonging to CC25, CC33 and CC442 (2014 n=38, 2022 n=336), and a total of 1417 cases. There was a higher proportion of female cases (55-70 %) and more adults than children, with patients aged between 20-40 and >70 most at risk across the different serotypes. Symptoms were consistent across the three dominant serotypes O91:H14 (CC33), O146:H21 (CC442) and O128:H2 (CC25) (diarrhoea >75 %; bloody diarrhoea 25-32 %; abdominal pain 64-72 %; nausea 37-45 %; vomiting 10-24 %; and fever 27-30 %). Phylogenetic analyses revealed multiple events of acquisition and loss of different stx-encoding prophage. Additional putative virulence genes were identified including iha, agn43 and subA.Conclusions. Continued monitoring and surveillance of LEE-negative STEC infections is essential due to the increasing burden of infectious intestinal disease, and the risk that highly pathogenic strains may emerge following acquisition of the Shiga toxin subtypes associated with the most severe clinical outcomes.

Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK

Listeria monocytogenes is a food-borne pathogen, typically affecting the elderly, immunocompromised patients and pregnant women. The aim of this study was to determine the population structure of L. monocytogenes clonal complex 1 (CC1) in the UK and describe the genomic epidemiology of this clinically significant CC. We interrogated a working dataset of 4073 sequences of L. monocytogenes isolated between January 2015 and December 2020 from human clinical specimens, food and/or food-production environments. A minimum spanning tree was reconstructed to determine the population structure of L. monocytogenes in the UK. Subsequent analysis focused on L. monocytogenes CC1, as the cause of the highest proportion of invasive listeriosis in humans. Sequencing data was integrated with metadata on food and environmental isolates, and information from patient questionnaires, including age, sex and clinical outcomes. All isolates either belonged to lineage I (n=1299/4073, 32%) or lineage II (n=2774/4073, 68%), with clinical isolates from human cases more likely to belong to lineage I (n=546/928, 59%) and food isolates more likely to belong to lineage II (n=2352/3067, 77%). Of the four largest CCs, CC1 (n=237) had the highest proportion of isolates from human cases of disease (CC1 n=160/237, 67.5 %; CC121 n=13/843, 2 %; CC9 n=53/360, 15 %; CC2 n=69/339, 20%). Within CC1, most cases were female (n=95/160, 59%, P=0.01771) and the highest proportion of cases were in people >60 years old (39/95, 41%, P=1.314×10-6) with a high number of them aged 20-39 years old (n=35/95, 37%) most linked to pregnancy-related listeriosis (n=29/35, 83%). Most of the male cases were in men aged over 60 years old (40/65, 62%), and most of the fatal cases in both males and females were identified in this age group (42/55, 76%). Phylogenetic analysis revealed 23 5 SNP single linkage clusters comprising 80/237 (34 %) isolates with cluster sizes ranging from 2 to 19. Five 5 SNP clusters comprised isolates from human cases and an implicated food item. Expanding the analysis to 25 SNP single linkage clusters resolved an additional two clusters linking human cases to a potential food vehicle. Analysis of demographic and clinical outcome data identified CC1 as a clinically significant cause of invasive listeriosis in the elderly population and in women of child-bearing age. Phylogenetic analysis revealed the population structure of CC1 in the UK comprised small, sparsely populated genomic clusters. Only clusters containing isolates from an implicated food vehicle, or food processing or farming environments, were resolved, emphasizing the need for clinical, food and animal-health agencies to share sequencing data in real time, and the importance of a One Health approach to public-health surveillance of listeriosis.

Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins

BACKGROUND

Shigella sp. are enteric pathogens which causes >125 million cases of shigellosis annually. S. sonnei accounts for about a quarter of those cases and is increasingly prevalent in industrialising nations. Being an enteric pathogen, S. sonnei benefits from outcompeting gut commensals such as Escherichia coli to establish itself and cause disease. There are numerous mechanisms that bacterial pathogens use to outcompete its rivals including molecules called colicins. A Type 6 Secretion System (T6SS) was recently described as contributing to E. coli killing in S. sonnei.

METHODS

We used Bulk Phenotyping of Epidemiological Replicates (BPER) which combined bacterial Genome Wide Association Studies (bGWAS) and high throughput phenotyping on a collection of S. sonnei surveillance isolates to identify the genetic features associated with E. coli killing and explore their relationship with epidemiological behaviour. We further explored the presence of colicins and T6SS components in the isolates using genomics, laboratory experimentation, and proteomics.

FINDINGS

Our bGWAS analysis returned known and novel colicin and colicin related genes as significantly associated with E. coli killing. In silico analyses identified key colicin clusters responsible for the killing phenotype associated with epidemiologically successful sub-lineages. The killing phenotype was not associated with the presence of a T6SS. Laboratory analyses confirmed the presence of the key colicin clusters and that killing was contact-independent.

INTERPRETATION

Colicins are responsible for E. coli killing by S. sonnei, not a T6SS. This phenotype contributes to shaping the observed epidemiology of S. sonnei and may contribute to its increasing prevalence globally. BPER is an epidemiologically relevant approach to phenotypic testing that enables the rapid identification of genetic drivers of phenotypic changes, and assessment of their relevance to epidemiology in natural settings.

FUNDING

Biotechnology and Biological Sciences Research Council, Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship, Wellcome Trust, Medical Research Council (UK), French National Research Agency.

Shigella Serotypes Associated With Carriage in Humans Establish Persistent Infection in Zebrafish

Shigella represents a paraphyletic group of enteroinvasive Escherichia coli. More than 40 Shigella serotypes have been reported. However, most cases within the men who have sex with men (MSM) community are attributed to 3 serotypes: Shigella sonnei unique serotype and Shigella flexneri 2a and 3a serotypes. Using the zebrafish model, we demonstrate that Shigella can establish persistent infection in vivo. Bacteria are not cleared by the immune system and become antibiotic tolerant. Establishment of persistent infection depends on the O-antigen, a key constituent of the bacterial surface and a serotype determinant. Representative isolates associated with MSM transmission persist in zebrafish, while representative isolates of a serotype not associated with MSM transmission do not. Isolates of a Shigella serotype establishing persistent infections elicited significantly less macrophage death in vivo than isolates of a serotype unable to persist. We conclude that zebrafish are a valuable platform to illuminate factors underlying establishment of Shigella persistent infection in humans.

Animal and environmental risk factors for sporadic Shiga toxin-producing Escherichia coli (STEC) infection in England: a case control study for O157, O26 and other STEC serotypes

Most Shiga toxin-producing E. coli (STEC) infections are sporadic. Routine enhanced surveillance questionnaires of confirmed STEC cases in England contained promising data to conduct a case-control study to identify non-food exposures linked to the risk of becoming infected with different STEC serotypes, including O157, O26 and all others; this study pulled eligible cases from the recorded enhanced surveillance data. Controls were recruited from the general population and answered a comparable postal questionnaire. Logistic regression was performed to identify risk factors associated with STEC infection for O157, O26 and other serotype cases. In adjusted models, travel outside of the U.K. and childcare occupations raised the risk of infection for all serotypes. Day trips within the UK, exposure to dogs and contact with soil were linked to lower infection risk. Resident region within England was often linked to decreased risk. Summer season was linked to O157 and O26, but not other STEC. Swimming in the sea was linked to increased risk of infection by O157, but not other types of STEC. Correlations between exposures and infection were similar when the analysis was repeated excluding participants with a history of foreign travel. As the first case-control study in England to include sporadic non-O157 STEC, the varying risk factors between O157 and non-O157 cases suggest there are potentially unique reservoirs for different serotypes.

Initial Experience with the Commercial Electron FLASH Research Extension

PURPOSE/OBJECTIVE(S)

The purpose of this study was to introduce a new commercial electron FLASH system that has the potential to become widely available for FLASH researchers globally. In this study, we first present the initial acceptance and commissioning tests for the FLASH system, and second, we highlight preliminary FLASH effect results from our cell studies.

MATERIALS/METHODS

A linear accelerator was converted into a commercial research platform with the FLASH Research Extension, enabling the generation of a powerful 16 MeV electron FLASH beam. The dosimetric and stability tests were conducted using various dosimeters (i.e., radiochromic film, optically stimulated luminescent dosimeters (OSLDs), and a plane-parallel ionization chamber). To evaluate the FLASH effect, normal and cancer cell lines were FLASH irradiated using different pulse repetition frequencies (PRF) of 18 pulses/s and 180 pulses/s.

RESULTS

The electron FLASH mode was able to generate over 1 Gy per pulse at the isocenter and a dose rate of up to 690 Gy/s near the accessory mount of the Linac gantry head. The charge collected by the plane-parallel ionization chamber at the highest PRF (i.e., 180 pulses/s) showed a linear relationship with the delivered number of pulses (i.e., 1 to 99 pulses) with a coefficient of determination (R2) of 0.9996. The absorbed dose measured using radiochromic film and OSLDs agreed within 3%, on average, and followed an inverse square law as the source-to-axis distance (SAD) varied for which the R2 values were 0.9972 and 0.9955 for radiochromic film and OSLDs, respectively. The profile of the FLASH beam was symmetrical but was not as flat as the conventional 16 MeV electron beam due to the use of a thinner custom scattering foil to reduce the degradation of the ultra-high dose rate. The depth-dose curve beyond the build-up region for the FLASH beam was similar to the conventional 16 MeV electron beam for which the range at 50% the maximum dose (R50) agreed within 0.5 mm. The FLASH beam output remained consistent over a 4-month period with a variation of 2.5%, on average. The FLASH sparing effect was observed in vitro for healthy human pancreatic cells. Furthermore, we observed that the highest PRF beam (180 pulses/s) was more effective at destroying pancreatic cancerous cells while minimizing damage to healthy cells compared to the lowest PRF beam (18 pulses/s).

CONCLUSION

The novel commercial FLASH Research Extension system was dosimetrically characterized for pre-clinical FLASH research, and preliminary in vitro results demonstrated the FLASH effect. Given the prevalence of linear accelerators, this new commercial system has the potential to greatly increase the access to FLASH research.

Commissioning and Initial Validation of Commercial Treatment Planning System for the Electron FLASH Research Extension

PURPOSE/OBJECTIVE(S)

The aim of this study was to investigate the feasibility of commissioning the 16 MeV electron FLASH beam in a commercial treatment planning system (TPS) for pre-clinical research purposes. The delivery system consisted of a new commercial solution for which a linear accelerator was modified into a FLASH Research Extension platform. Additionally, preliminary radiation biology results were highlighted to showcase the future use of this system.

MATERIALS/METHODS

To commission a commercial electron Monte Carlo (MC) for dose calculation of a 16 MeV FLASH beam in the TPS, radiochromic film was used to measure the vendor-required beam data, e.g., profiles and percent depth dose (PDD) curves for cone sizes of 6 × 6 cm2, 10 × 10 cm2, and 15 × 15 cm2 as well as an in-air profile for a 40 × 40 cm2 open field (no cone). Once the electron MC beam model was generated, additional measurements were collected for validation and compared against the calculated dose from the TPS. A treatment planning comparison between the newly commissioned FLASH beam and the conventional electron beam was conducted. Specifically, the dose-volume histograms (DVHs) for target volumes and organs at risk were investigated for skin cancer cases previously treated with conventional electron beams. Lastly, the FLASH dose distribution predicted by the electron MC for an in vitro cell study setup was validated with radiochromic film measurements, and initial radiobiology tests were conducted using FLASH and conventional dose-rate electron beams.

RESULTS

The electron MC calculated dose for the 16 MeV electron FLASH beam agreed with measured PDDs within 1% for all field sizes. The beam profile characteristics, such as penumbra, shape, and full width at half maximum, demonstrated good agreement with less than 0.5 mm difference between the TPS and measurements. There were noticeable differences in the profiles of large fields between the FLASH and conventional dose-rate beam models due to the more forward-peaked FLASH beam. For treatment planning, Regarding DVH, the FLASH dose-rate plan provided comparable plan quality to the conventional dose-rate plan, achieving adequate coverage for the target volumes and sparing the healthy organs and tissues. The electron MC dose prediction for the FLASH beam was also found to be in good agreement with the film measurements of the in vitro cell study setup. Furthermore, the FLASH beam was observed to be more effective with a 20 % increase in killing pancreatic cancer cells compared to the conventional dose rate.

CONCLUSION

The study successfully incorporated the 16 MeV electron FLASH Research Extension into the commercial TPS using electron Monte Carlo for dose calculation. This will be valuable for pre-clinical cell and animal studies. This research also enables FLASH treatment planning studies, a key component for the future implementation of FLASH into clinical care. Further research is necessary to incorporate the radiation biology effect of FLASH into the treatment planning system.

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes

Background

The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000).

Methods

This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch.

Results

Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes.

Conclusions

The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies.

Funding

No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).

Surveillance of antimicrobial resistant Shiga toxin-producing E. coli O157:H7 in England, 2016-2020

OBJECTIVES

Shiga toxin-producing Escherichia coli (STEC) O157:H7 are zoonotic pathogens and transmission to humans occurs via contaminated food or contact with infected animals. The aim of this study was to describe the frequency, and distribution across the phylogeny, of antimicrobial resistance (AMR) determinants in STEC O157:H7 isolated from human cases in England.

METHODS

Short-read whole-genome sequencing data from 1473 isolates of STEC O157:H7 from all seven sub-lineages (Ia-Ic, IIa-IIc and I/II) were mapped to genes known to confer phenotypic resistance to 10 different classes of antibiotic. Long-read sequencing was used to determine the location and genomic architecture of the AMR determinants within phylogenetic clusters exhibiting multidrug resistance.

RESULTS

Overall, 216/1473 (14.7%) isolates had at least one AMR determinant, although the proportion of isolates exhibiting AMR varied by sub-lineage. The highest proportion of AMR determinants were detected in sub-lineages Ib (28/64, 43.7%), I/II (18/51, 35.3%) and IIc (122/440, 27.7%). In all sub-lineages, the most commonly detected AMR determinants conferred resistance to the aminoglycosides, tetracyclines and sulphonamides, while AMR determinants conferring resistance to fluroquinolones, macrolides and third-generation cephalosporins were rarely detected. Long-read sequencing analysis showed that the AMR determinants were co-located on the chromosome in sub-lineages Ib and lineage I/II, whereas those associated with sub-lineage IIc were encoded on the chromosome and/or large plasmids.

CONCLUSIONS

AMR genes were unevenly distributed across the different sub-lineages of STEC O157:H7 and between different clades within the same sub-lineage. Long-read sequencing facilitates tracking the transmission of AMR at the pathogen and mobile genetic element level.

Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health

For the last two decades, the human infection frequency of Escherichia coli O157 (O157) in Scotland has been 2.5-fold higher than in England and Wales. Results from national cattle surveys conducted in Scotland and England and Wales in 2014/2015 were combined with data on reported human clinical cases from the same time frame to determine if strain differences in national populations of O157 in cattle could be associated with higher human infection rates in Scotland. Shiga toxin subtype (Stx) and phage type (PT) were examined within and between host (cattle vs human) and nation (Scotland vs England and Wales). For a subset of the strains, whole genome sequencing (WGS) provided further insights into geographical and host association. All three major O157 lineages (I, II, I/II) and most sub-lineages (Ia, Ib, Ic, IIa, IIb, IIc) were represented in cattle and humans in both nations. While the relative contribution of different reservoir hosts to human infection is unknown, WGS analysis indicated that the majority of O157 diversity in human cases was captured by isolates from cattle. Despite comparable cattle O157 prevalence between nations, strain types were localized. PT21/28 (sub-lineage Ic, Stx2a+) was significantly more prevalent in Scottish cattle [odds ratio (OR) 8.7 (2.3-33.7; P<0.001] and humans [OR 2.2 (1.5-3.2); P<0.001]. In England and Wales, cattle had a significantly higher association with sub-lineage IIa strains [PT54, Stx2c; OR 5.6 (1.27-33.3); P=0.011] while humans were significantly more closely associated with sub-lineage IIb [PT8, Stx1 and Stx2c; OR 29 (4.9-1161); P<0.001]. Therefore, cattle farms in Scotland were more likely to harbour Stx2a+O157 strains compared to farms in E and W (P<0.001). There was evidence of limited cattle strain migration between nations and clinical isolates from one nation were more similar to cattle isolates from the same nation, with sub-lineage Ic (mainly PT21/28) exhibiting clear national association and evidence of local transmission in Scotland. While we propose the higher rate of O157 clinical cases in Scotland, compared to England and Wales, is a consequence of the nationally higher level of Stx2a+O157 strains in Scottish cattle, we discuss the multiple additional factors that may also contribute to the different infection rates between these nations.

Haemolytic uraemic syndrome in children England, Wales, Northern Ireland, and Ireland: A prospective cohort study

Haemolytic uraemic syndrome (HUS) caused by infection with Shiga toxin-producing Escherichia coli (STEC) is a relatively rare but potentially fatal multisystem syndrome clinically characterised by acute kidney injury. This study aimed to provide robust estimates of paediatric HUS incidence in England, Wales, Northern Ireland, and the Republic of Ireland by using data linkage and case reconciliation with existing surveillance systems, and to describe the characteristics of the condition. Between 2011 and 2014, 288 HUS patients were included in the study, of which 256 (89.5%) were diagnosed as typical HUS. The crude incidence of paediatric typical HUS was 0.78 per 100,000 person-years, although this varied by country, age, gender, and ethnicity. The majority of typical HUS cases were 1 to 4 years old (53.7%) and female (54.0%). Clinical symptoms included diarrhoea (96.5%) and/or bloody diarrhoea (71.9%), abdominal pain (68.4%), and fever (41.4%). Where STEC was isolated (59.3%), 92.8% of strains were STEC O157 and 7.2% were STEC O26. Comparison of the HUS case ascertainment to existing STEC surveillance data indicated an additional 166 HUS cases were captured during this study, highlighting the limitations of the current surveillance system for STEC for monitoring the clinical burden of STEC and capturing HUS cases.

Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive Escherichia coli

Enteroinvasive Escherichia coli (EIEC) and Shigella are closely related agents of bacillary dysentery. It is widely viewed that EIEC and Shigella species evolved from E. coli via independent acquisitions of a large virulence plasmid (pINV) encoding a type 3 secretion system (T3SS). Sequence Type (ST)99 O96:H19 E. coli is a novel clone of EIEC responsible for recent outbreaks in Europe and South America. Here, we use 92 whole genome sequences to reconstruct a dated phylogeny of ST99 E. coli, revealing distinct phylogenomic clusters of pINV-positive and -negative isolates. To study the impact of pINV acquisition on the virulence of this clone, we developed an EIEC-zebrafish infection model showing that virulence of ST99 EIEC is thermoregulated. Strikingly, zebrafish infection using a T3SS-deficient ST99 EIEC strain and the oldest available pINV-negative isolate reveals a separate, temperature-independent mechanism of virulence, indicating that ST99 non-EIEC strains were virulent before pINV acquisition. Taken together, these results suggest that an already pathogenic E. coli acquired pINV and that virulence of ST99 isolates became thermoregulated once pINV was acquired. IMPORTANCE Enteroinvasive Escherichia coli (EIEC) and Shigella are etiological agents of bacillary dysentery. Sequence Type (ST)99 is a clone of EIEC hypothesized to cause human disease by the recent acquisition of pINV, a large plasmid encoding a type 3 secretion system (T3SS) that confers the ability to invade human cells. Using Bayesian analysis and zebrafish larvae infection, we show that the virulence of ST99 EIEC isolates is highly dependent on temperature, while T3SS-deficient isolates encode a separate temperature-independent mechanism of virulence. These results indicate that ST99 non-EIEC isolates may have been virulent before pINV acquisition and highlight an important role of pINV acquisition in the dispersal of ST99 EIEC in humans, allowing wider dissemination across Europe and South America.

Prevalence and Persistence of Antibiotic Resistance Determinants in the Gut of Travelers Returning to the United Kingdom is Associated with Colonization by Pathogenic Escherichia coli

The gut microbiota constitutes an ideal environment for the selection, exchange, and carriage of antibiotic resistance determinants (ARDs), and international travel has been identified as a risk factor for acquisition of resistant organisms. Here, we present a longitudinal metagenomic analysis of the gut resistome in travellers to "high-risk" countries (Gutback). Fifty volunteers, recruited at a travel clinic in London, United Kingdom, provided stool samples before (pre-travel), immediately after (post-travel), and 6 months after their return (follow-up) from a high-risk destination. Fecal DNA was extracted, metagenomic sequencing performed and the resistome profiled. An increase in abundance and diversity of resistome was observed after travel. Significant increases in abundance were seen in antimicrobial genes conferring resistance to macrolides, third-generation cephalosporins, aminoglycosides, and sulfonamides. There was a significant association with increased resistome abundance if the participant experienced diarrhea during travel or took antibiotics, but these two variables were co-correlated. The resistome abundance returned to pre-travel levels by the 6-month sample point but there was evidence of persistence of several ARDs. The post-travel samples had an increase in abundance Escherichia coli which was positively associated with many acquired resistant determinants. Virulence and phylogenetic profiling revealed pathogenic E. coli significantly contributed to this increase abundance. In summary, in this study, foreign travel remains a significant risk factor for acquisition of microbes conferring resistance to multiple classes of antibiotics, often associated with symptomatic exposure to diarrhoeagenic E. coli. IMPORTANCE A future where antimicrobial therapy is severely compromised by the increase in resistant organisms is of grave concern. Given the variability in prevalence and diversity of antimicrobial resistance determinants in different geographical settings, international travel is a known risk factor for acquisition of resistant organisms into the gut microbiota. In this study, we show the utility of metagenomic approaches to quantify the levels of acquisition and carriage of resistance determinants after travel to a "high-risk" setting. Significant modulation to the resistome was seen after travel that is largely resolved within 6 months, although evidence of persistence of several ARDs was observed. Risk factors for acquisition included experiencing a diarrheal episode and the use of antibiotics. Colonization by pathogenic Escherichia coli was correlated with an increase in acquisition of antimicrobial resistance determinants, and as such established public health guidance to travelers on food and water safety remain an important message to reduce the spread of antibiotic resistance.

O-Antigen Diversification Masks Identification of Highly Pathogenic Shiga Toxin-Producing Escherichia coli O104:H4-Like Strains

Shiga toxin-producing Escherichia coli (STEC) can give rise to a range of clinical outcomes from diarrhea to the life-threatening systemic condition hemolytic-uremic syndrome (HUS). Although STEC O157:H7 is the serotype most frequently associated with HUS, a major outbreak of HUS occurred in 2011 in Germany and was caused by a rare serotype, STEC O104:H4. Prior to 2011 and since the outbreak, STEC O104:H4 strains have only rarely been associated with human infections. From 2012 to 2020, intensified STEC surveillance was performed in Germany where the subtyping of ~8,000 clinical isolates by molecular methods, including whole-genome sequencing, was carried out. A rare STEC serotype, O181:H4, associated with HUS was identified, and like the STEC O104:H4 outbreak strain, this strain belongs to sequence type 678 (ST678). Genomic and virulence comparisons revealed that the two strains are phylogenetically related and differ principally in the gene cluster encoding their respective lipopolysaccharide O-antigens but exhibit similar virulence phenotypes. In addition, five other serotypes belonging to ST678 from human clinical infection, such as OX13:H4, O127:H4, OgN-RKI9:H4, O131:H4, and O69:H4, were identified from diverse locations worldwide. IMPORTANCE Our data suggest that the high-virulence ensemble of the STEC O104:H4 outbreak strain remains a global threat because genomically similar strains cause disease worldwide but that the horizontal acquisition of O-antigen gene clusters has diversified the O-antigens of strains belonging to ST678. Thus, the identification of these highly pathogenic strains is masked by diverse and rare O-antigens, thereby confounding the interpretation of their potential risk.

Association between socioeconomic deprivation and incidence of Infectious Intestinal Disease by pathogen and linked transmission route: An ecological analysis in the UK

Infectious intestinal disease (IID) studies conducted at different levels of the surveillance pyramid have found heterogeneity in the association of socioeconomic deprivation with illness. The aim of this study was to analyse the association between socioeconomic deprivation and incidence of IID by certain gastrointestinal pathogens reported to UKHSA. Data were extracted from 2015 to 2018 for Salmonella, Campylobacter, Shigella, Giardia species, and norovirus. Rates were calculated per 100,000 person-years by the index of multiple deprivation quintile, and an ecological analysis was conducted using univariant and multvariable regression models for each pathogen. Incidence of Campylobacter, and Giardia species decreased with increasing deprivation. Conversely, the incidence of norovirus, non-typhoidal Salmonella, Salmonella typhi/paratyphi, Shigella species increased with increasing deprivation. Multivariable analysis results showed that higher deprivation was significantly associated with higher odds of higher number of cases for Shigella flexneri, norovirus and S. typhi/paratyphi. Infections most associated with deprivation were those transmitted by person-to-person spread, and least associated were those transmitted by zoonotic contamination of the environment. Person-to-person transmission can be contained by implementing policies targeting over-crowding and poor hygiene. This approach is likely to be the most effective solution for the reduction of IID.

Escherichia coli encoding Shiga toxin subtype Stx2f causing human infections in England, 2015-2022

Introduction. Shiga toxin-producing Escherichia coli (STEC) belong to a diverse group of gastrointestinal pathogens defined by the presence of Shiga toxin genes (stx) of which there are at least ten subtypes (Stx1a-Stx1d and Stx2a-Stx2g).Gap Statement. Initially thought to be associated with mild symptoms, more recently STEC encoding stx2f have been isolated from cases of haemolytic uraemic syndrome (HUS) and the clinical significance and public health burden require further investigation.Aim. We analysed clinical outcomes and genome-sequencing data linked to patients infected with STEC encoding-stx2f in England to assess the risk to public health.Methodology. One hundred and twelve E. coli (n=58 isolates encoded stx2f; n=54 isolates E. coli belonging to CC122 or CC722 that had eae but were negative for stx) isolated from patients' faecal specimens between 2015 and 2022 were genome sequenced and linked to epidemiological and clinical outcome data. All isolates were investigated for the presence of virulence genes and a maximum-likelihood phylogeny of isolates belonging to CC122 and CC722 was constructed.Results. There were 52 cases infected with STEC harbouring stx2f between 2015 and 2022, with the majority identified in 2022. Most cases resided in the North of England (n=39/52, 75 %), were female (n=31, 59.6 %) and/or aged five and under (n=29, 55.8 %). Clinical outcome data were available for 40/52 cases (76.9 %) and 7/40(17.5 %) were diagnosed with STEC-HUS. In the two most common clonal complexes, CC122 and CC722, the presence of the stx2f-encoding prophage correlated with the presence of additional virulence genes, astA, bfpA and cdt, located on an 85kbp IncFIB plasmid.Conclusions. Certain serotypes of E. coli harbouring stx2f cause severe clinical outcomes, including STEC-HUS. Public health advice and possible interventions are limited, as little is known about the animal and environmental reservoirs and transmission routes. We recommend more comprehensive and standardized collection of microbiological and epidemiological data, and routine sharing of sequencing data between public health agencies worldwide.

The epidemiology of Shiga toxin-producing Escherichia coli O26:H11 (clonal complex 29) in England, 2014-2021

OBJECTIVES

We aimed to describe the genomic epidemiology of the foodborne gastrointestinal pathogen, Shiga toxin-producing Escherichia coli (STEC) serotype O26:H11 belonging to clonal complex 29 (CC29) in England.

METHODS

Between 01 January 2014 and 31 December 2021, 834 human isolates belonging to CC29 were sequenced at the UK Health Security Agency, and the genomic data was integrated with epidemiological data.

RESULTS

Diagnoses of STEC O26:H11 in England have increased each year from 19 in 2014 to 144 in 2021. Most isolates had the Shiga toxin subtype profiles stx1a (47%), stx1a,stx2a (n=24%) or stx2a (n=28%). Most cases were female (57%), and the highest proportion of cases belonged to the 0-5 age group (38%). Clinical symptoms included diarrhoea (93%), blood-stained stool (48%), and abdominal pain (74%). Haemolytic Uraemic Syndrome (HUS) was diagnosed in 40/459 (9%) cases and three children died. All isolates causing STEC-HUS had stx2a either alone (n=33) or in combination with stx1a (n=7).

CONCLUSIONS

STEC O26:H11 are a clinically significant, emerging threat to public health in England. Determining the true incidence and prevalence is challenging due to inconsistent national surveillance strategies. Improved diagnostics and surveillance algorithms are required to monitor the true burden, detect outbreaks and to implement effective interventions.

Rapid geographical source attribution of Salmonella enterica serovar Enteritidis genomes using hierarchical machine learning

Salmonella enterica serovar Enteritidis is one of the most frequent causes of Salmonellosis globally and is commonly transmitted from animals to humans by the consumption of contaminated foodstuffs. In the UK and many other countries in the Global North, a significant proportion of cases are caused by consumption of imported food products or contracted during foreign travel, therefore making the rapid identification of the geographical source of new infections a requirement for robust public health outbreak investigations. Herein, we detail the development and application of a hierarchical machine learning model to rapidly identify and trace the geographical source of S. Enteritidis infections from whole genome sequencing data. 2,313 S. Enteritidis genomes, collected by the UKHSA between 2014-2019, were used to train a 'local classifier per node' hierarchical classifier to attribute isolates to 4 continents, 11 sub-regions and 38 countries (53 classes). The highest classification accuracy was achieved at the continental level followed by the sub-regional and country levels (macro F1: 0.954, 0.718, 0.661 respectively). A number of countries commonly visited by UK travellers were predicted with high accuracy (hF1: >0.9). Longitudinal analysis and validation with publicly accessible international samples indicated that predictions were robust to prospective external datasets. The hierarchical machine learning framework provided granular geographical source prediction directly from sequencing reads in <4 minutes per sample, facilitating rapid outbreak resolution and real-time genomic epidemiology. The results suggest additional application to a broader range of pathogens and other geographically structured problems, such as antimicrobial resistance prediction, is warranted.

The evolution and international spread of extensively drug resistant Shigella sonnei

Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with men (MSM). Multidrug resistance in S. sonnei is common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant S. sonnei was reported in the United Kingdom. Here, we aimed to identify the genetic basis, evolutionary history, and international dissemination of the outbreak strain. Our genomic epidemiological analyses of 3,304 isolates from the United Kingdom, Australia, Belgium, France, and the United States of America revealed an internationally connected outbreak with a most recent common ancestor in 2018 carrying a low-fitness cost resistance plasmid, previously observed in travel associated sublineages of S. flexneri. Our results highlight the persistent threat of horizontally transmitted antimicrobial resistance and the value of continuing to work towards early and open international sharing of genomic surveillance data.

Foodborne outbreak of extended spectrum beta lactamase producing Shigella sonnei associated with contaminated spring onions in the United Kingdom

Globalization of the food supply chain has created conditions favourable for emergence and spread of multidrug resistant (MDR) foodborne pathogens. In November 2021, the UK Health Security Agency detected an outbreak of 17 cases infected with the same strain of MDR extended spectrum beta-lactamase (ESBL)-producing Shigella sonnei. Phylogenetic analysis of whole genome sequencing data revealed the outbreak was closely related to strains of S. sonnei isolated from travellers returning to the UK from Egypt. None of the outbreak cases reported travel and all 17 cases reported eating food from a restaurant/food outlet in the week prior to symptom onset, of which 11/17 (64.7%) ate at branches of the same national restaurant franchise. All 17 cases were adults and 14/17 (82.4%) were female. Ingredient-level analyses of the meals consumed by the cases identified spring onions as the common ingredient. Food chain investigations revealed that the spring onions served at the implicated restaurants could be traced back to a single Egyptian producer. The foodborne transmission of ESBL-producing bacteria is an emerging global health concern, and concerted action from all stakeholders is required to ensure an effective response to mitigate the risks to public health.

Forgotten but not gone: Yersinia infections in England, 1975 to 2020

BackgroundYersiniosis is one of the most common food-borne zoonoses in Europe, but there are large variations in the reported incidence between different countries.AimWe aimed to describe the trends and epidemiology of laboratory-confirmed Yersinia infections in England and estimate the average annual number of undiagnosed Yersinia enterocolitica cases, accounting for under-ascertainment.MethodsWe analysed national surveillance data on Yersinia cases reported by laboratories in England between 1975 and 2020 and enhanced surveillance questionnaires from patients diagnosed in a laboratory that has implemented routine Yersinia testing of diarrhoeic samples since 2016.ResultsThe highest incidence of Yersinia infections in England (1.4 cases per 100,000 population) was recorded in 1988 and 1989, with Y. enterocolitica being the predominant species. The reported incidence of Yersinia infections declined during the 1990s and remained low until 2016. Following introduction of commercial PCR at a single laboratory in the South East, the annual incidence increased markedly (13.6 cases per 100,000 population in the catchment area between 2017 and 2020). There were notable changes in age and seasonal distribution of cases over time. The majority of infections were not linked to foreign travel and one in five patients was admitted to hospital. We estimate that around 7,500 Y. enterocolitica infections may be undiagnosed in England annually.ConclusionsFindings suggest a considerable number of undiagnosed yersiniosis cases in England, with possibly important changes in the epidemiology. The apparently low incidence of yersiniosis in England is probably due to limited laboratory testing.

The genomic epidemiology of Escherichia albertii infecting humans and birds in Great Britain

Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and animals which is typically misidentified as pathotypes of diarrhoeagenic Escherichia coli or Shigella species and is generally only detected during genomic surveillance of other Enterobacteriaceae. The incidence of E. albertii is likely underestimated, and its epidemiology and clinical relevance are poorly characterised. Here, we whole genome sequenced E. albertii isolates from humans (n = 83) and birds (n = 79) isolated in Great Britain between 2000 and 2021 and analysed these alongside a broader public dataset (n = 475) to address these gaps. We found human and avian isolates typically (90%; 148/164) belonged to host-associated monophyletic groups with distinct virulence and antimicrobial resistance profiles. Overlaid patient epidemiological data suggested that human infection was likely related to travel and possibly foodborne transmission. The Shiga toxin encoding stx2f gene was associated with clinical disease (OR = 10.27, 95% CI = 2.98-35.45 p = 0.0002) in finches. Our results suggest that improved future surveillance will further elucidate disease ecology and public and animal health risks associated with E. albertii.

Isolation of Salmonella species of public health concern from commonly fed dried meat dog treats

BACKGROUND

Dried non-heat-treated meat treats, such as ears, skin and tails, are popular supplementary dog foods. Previous studies have demonstrated Salmonella spp. contamination on treats, particularly in pig ears and chicken products. This small, exploratory, cross-sectional study investigated Salmonella spp. presence in dried treats available in the UK.

METHODS

A selection of dried treats from local pet shops and online retailers underwent bacterial culture for Salmonella spp. and subsequent antimicrobial susceptibility testing, with Salmonella serotype determined by whole genome sequencing.

RESULTS

Eighty-four samples were tested, with 16% being Salmonella spp. positive. Five Salmonella serotypes were identified, each associated with specific treat types. An antimicrobial-resistant phenotype was identified in 39% of isolates. All serotypes identified are known to cause human infection.

LIMITATIONS

This study was limited by a small sample size and limited number of retail sources.

CONCLUSION

Salmonella spp. of public health concern were present in some dried dog treats in this study. Dog owners, pet food retailers and veterinary professionals should be aware of the potential zoonotic disease risk associated with these treats, and appropriate hygiene measures, including thorough hand washing, should be utilised if they are fed.

Prevalence and risk factors of bacterial enteric pathogens in men who have sex with men: A cross-sectional study at the UK's largest sexual health service

OBJECTIVES

Outbreaks of bacterial enteric pathogens (BEPs) in men who have sex with men (MSM) associated with antimicrobial resistance are a public health concern. We investigated the prevalence and risk factors of BEPs in MSM to inform infection control.

METHODS

We conducted a cross-sectional study at a London sexual health clinic between 20/12/2017 and 06/02/2018. Residual rectal swabs from MSM attending for sexually transmitted infection (STI) testing were anonymously tested for a range of BEPs using real-time PCR. A sub-set of samples were tested for the mphA gene (a marker of azithromycin resistance). Results were linked to electronic health records.

RESULTS

BEPs were detected in 207 of 2116 participants, giving an overall prevalence of 9.8% (95% CI 8.5%-11.1%) ranging from 0.8% (0.4%-1.2%) for Shigella to 4.9% (4.0%-5.9%) for Enteroaggregative E. coli. MSM with BEPs were more likely to have a history of bacterial STIs (p = 0.010), to report more sexual partners (p<0.001), and among HIV-negative MSM, to report current HIV pre-exposure prophylaxis use (p<0.001). Gastrointestinal symptoms were rare (1.7%) and not associated with BEPs. 41.3% of MSM with BEPs and 14.1% of those without BEPs carried mphA (p<0.001). Among the former, this was associated with a history of bacterial STIs (51.5% vs 31.1%, p = 0.003).

CONCLUSIONS

One in ten MSM had a BEP detected and most did not report symptoms. MphA carriage was common, particularly among those with BEPs. Bacterial STI treatment might contribute to selection of resistant gut organisms, emphasising the need for better antimicrobial stewardship.

Two Outbreaks of Foodborne Gastrointestinal Infection Linked to Consumption of Imported Melons, United Kingdom, March to August 2021

The aim of this study was to describe two foodborne outbreaks caused by contaminated imported melon and make recommendations for future practice. Between March and July 2021, there was an outbreak of 113 cases of Salmonella Braenderup in the UK (62% female, median age 61 years, 33% hospitalized). Analytical epidemiological studies identified Galia melons as the vehicle of infection (OR 671.9, 95% CI 39.0-58,074.0, p < 0.001). Subsequently, the outbreak strain was isolated from two samples of Galia melon imported from Latin America. In July and August 2021, there was an outbreak of 17 cases of Shiga toxin-producing Escherichia coli (STEC) O157:H7 in the UK (53% female, median age 21 years, 35% were hospitalized). Review of the STEC surveillance questionnaire data, followed by the analysis of responses from a modified hypothesis-generating questionnaire, implicated eating precut watermelon from retailer B sourced from Europe as the vehicle of infection. Outbreaks of gastrointestinal pathogens caused by contaminated food of nonanimal origin are a global public health concern. Given the difficulty in removing pathogens from the flesh of ready-to-eat fruit and vegetables, public health interventions should target all steps of the food chain prior to consumption, from cultivation on the farm to processing/packing and distribution.

Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouring bla CTX-M-15 in Salmonella enterica serovar Typhi

Antimicrobial-resistance (AMR) genes can be transferred between microbial cells via horizontal gene transfer (HGT), which involves mobile and integrative elements such as plasmids, bacteriophages, transposons, integrons and pathogenicity islands. Bacteriophages are found in abundance in the microbial world, but their role in virulence and AMR has not fully been elucidated in the Enterobacterales. With short-read sequencing paving the way to systematic high-throughput AMR gene detection, long-read sequencing technologies now enable us to establish how such genes are structurally connected into meaningful genomic units, raising questions about how they might cooperate to achieve their biological function. Here, we describe a novel ~98 kbp circular P1-bacteriophage-like plasmid termed ph681355 isolated from a clinical Salmonella enterica serovar Typhi isolate. It carries bla _CTX-M-15, an IncY plasmid replicon (repY gene) and the ISEcP1 mobile element and is, to our knowledge, the first reported P1-bacteriophage-like plasmid (phage-plasmid) in S. enterica Typhi. We compared ph681355 to two previously described phage-plasmids, pSJ46 from S. enterica serovar Indiana and pMCR-1-P3 from Escherichia coli, and found high nucleotide similarity across the backbone. However, we saw low ph681355 backbone similarity to plasmid p60006 associated with the extensively drug-resistant S. enterica Typhi outbreak isolate in Pakistan, providing evidence of an alternative route for bla _CTX-M-15 transmission. Our discovery highlights the importance of utilizing long-read sequencing in interrogating bacterial genomic architecture to fully understand AMR mechanisms and their clinical relevance. It also raises questions regarding how widespread bacteriophage-mediated HGT might be, suggesting that the resulting genomic plasticity might be higher than previously thought.

Microbiological Quality of Ready-to-Eat Salad Products Collected from Retail and Catering Settings in England during 2020 to 2021

ABSTRACT

Salad and other fresh produce were collected in England from retail and catering businesses during 2020 to 2021 and were tested for Salmonella, Shiga toxin-producing Escherichia coli (STEC), Listeria, Bacillus cereus, and E. coli. Of the 604 samples collected, 57% were from retail settings and 43% were from catering settings; 61% were either salad leaves or salad leaves mixed with other products. Equal numbers of samples were prepacked or loose, and 50% were refrigerated at the time of sampling. Combining results for all microbiological parameters, 84% were interpreted as satisfactory, 12% were interpreted as borderline, and 4% were interpreted as unsatisfactory. One sample (prepacked leaves, cucumber, and tomato from a caterer) was categorized as unacceptable and potentially injurious because of detection of STEC O76; no STEC from human infections in the United Kingdom matched this isolate. No Salmonella enterica was detected, but Listeria monocytogenes was recovered from 11 samples: 1 at 20 CFU/g and the remainder at <20 CFU/g. B. cereus was detected at borderline levels (103 to ≤105 CFU/g) in 9% of samples and at an unsatisfactory level (>105 CFU/g) in one sample. E. coli was detected in 3% of samples at borderline levels (20 to ≤102 CFU/g) and in 4% at unsatisfactory levels (>102 CFU/g). There was a significant association between detection of L. monocytogenes and borderline or unsatisfactory levels of E. coli. There were no specific risk profiles associated with products with the higher levels of B. cereus, STEC, or Listeria, but elevated levels of E. coli were predominantly confined to loose products from the United Kingdom collected from caterers in summer or autumn 2021 and may have resulted from relaxation of COVID-19 restrictions. Among the L. monocytogenes isolates, only one matched those from human cases and was recovered from a prepacked mixed salad from a catering business in 2021. This isolate was the same strain as that responsible for a multicountry outbreak (2015 to 2018) associated with Hungarian-produced frozen sweet corn; no link to the outbreak food chain was established.

HIGHLIGHTS

Suspected chlamydial foetal loss highlights the need for standardised on-farm protocols

Chlamydia psittaci is a recognised cause of late-term equine foetal loss and poses a zoonotic risk in Australia. However, a management strategy is lacking to protect at-risk humans handling infected aborted material and pregnant mares. This study proposes a protocol for approaching C. psittaci foetal loss after investigating four foetal losses that occurred on a horse stud in the Hunter Valley, Australia in 2021. Swabs from the foetal loss cases (n = 4), close contact mares (n = 59), and foals of the close contact mares (n = 33) were collected and tested for C. psittaci using both isothermal points of care and quantitative polymerase chain reaction (qPCR) laboratory-based testing. Genotyping was performed utilising C. psittaci multilocus sequence typing and ompA sequencing from C. psittaci positive pooled foetal and placental (n = 3) DNA. Foetal and placental samples from the four foetal loss cases were all positive for C. psittaci with 100% agreement between the isothermal swab testing on the farm and qPCR DNA testing at an external laboratory. Genotyping revealed the clonal and identical sequence type 24 (ST24) C. psittaci strains in all samples. C. psittaci was not detected in close contact with mares or their foals. There was no statistically significant difference in foal survival between the close contact mare groups that did and did not receive antimicrobial intervention (P > 0.05). The proposed protocol is intended to raise awareness and begin a discussion for guidelines around handling of chlamydial foetal loss cases in late pregnant mares which pose a zoonotic threat to farm workers and veterinarians.

Variations in Tobacco Retailer Type Across Community Characteristics: Place Matters

Introduction

The density of tobacco retailers varies by community characteristics such as poverty levels or racial and ethnic composition. However, few studies have investigated how specific types of tobacco retailers vary by community characteristics. Our objective was to assess how the types of tobacco retailers in Ohio varied by the characteristics of the communities in which they were located.

Results

For all US Census tracts, convenience stores were the most common type of retailer selling tobacco. Yet, the prevalence of convenience stores was higher in high-poverty urban tracts than in low-poverty urban tracts. Discount stores were the second-most common type of tobacco retailer and were most prevalent in rural tracts and high-racial and ethnic minority urban tracts. Grocery stores, pharmacies, and vape or hookah shops typically had the highest prevalence in more advantaged tracts.

Conclusion

Our findings demonstrate that the distribution of specific retailer types varies by community characteristics. The distribution of these retailer types has implications for product availability and price, which may subsequently affect tobacco use and cessation. To create equitable outcomes, policies should focus on retailers such as convenience and discount stores, which are heavily located in communities experiencing tobacco-related health disparities.

A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella

Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two Shigella plasmids (pKSR100 and pAPR100) that circulated in the same transmission network but had starkly contrasting epidemiological outcomes to identify plasmid features that may have contributed to the differences. We used plasmid comparative genomics to reveal divergence between the two plasmids in genes encoding AMR, SOS response alleviation and conjugation. Experimental analyses revealed that these genomic differences corresponded with reduced conjugation efficiencies for the epidemiologically successful pKSR100, but more extensive AMR, reduced fitness costs, and a reduced SOS response in the presence of antimicrobials, compared with the less successful pAPR100. The discrepant phenotypes between the two plasmids are consistent with the hypothesis that plasmid-associated phenotypes contribute to determining the epidemiological outcome of AMR HGT and suggest that phenotypes relevant in responding to antimicrobial pressure and fitness impact may be more important than those around conjugation in this setting. Plasmid phenotypes could thus be valuable tools in conjunction with genomic epidemiology for predicting AMR dissemination.

Wide distribution of Escherichia coli carrying IncF plasmids containing bla NDM-5 and rmtB resistance genes from hospitalized patients in England

Introduction. The New Delhi metallo-β-lactamase (NDM) variant NDM-5 was first described in 2011 in an isolate of Escherichia coli. We noted that a high proportion of isolates of E. coli positive for bla _NDM carbapenemase genes submitted to the UK Health Security Agency (formerly Public Health England) between 2019 and mid-2021 carried the bla _NDM-5 allele, with many co-harbouring rmtB, rendering them highly resistant to aminoglycosides as well as to most β-lactams.Hypothesis/Gap Statement. This observation suggested that a common plasmid may be circulating.Aim. To compare these isolates and describe the plasmids carrying these resistance elements.Methodology. All isolates were sequenced on an Illumina platform, with five also subjected to long-read nanopore sequencing to provide complete assemblies. The locations of bla _NDM-5, rmtB and other associated genetic elements were identified. Susceptibility testing to a wide range of antibiotics was carried out on representative isolates.Results. The 34 isolates co-harbouring bla _NDM-5 and rmtB were from 14 hospital groups and six different regions across England and consisted of 11 distinct sequence types. All carried IncF plasmids. Assembly of the NDM plasmids in five isolates revealed that they carried rmtB and bla _NDM-5 in an IncF conjugative plasmid ranging in size from 85.5 to 161 kb. All carried a highly conserved region, previously described in E. coli plasmid pHC105-NDM, that included bla _TEM-1B and rmtB followed by sequence bounded by two IS26 elements containing ΔISAba125, bla _NDM-5, ble, trpF and tat followed by ISCR1 and an integron with sul1, aadA2 and dfrA12 cassettes. This arrangement has been described in isolates from other countries and continents, suggesting that such plasmids are widely distributed, at least in E. coli, with similar plasmids also found in Klebsiella pneumoniae. Tested isolates were resistant to most antibiotics except colistin, fosfomycin and tigecycline.Conclusion. These observations suggest that conjugative plasmids carrying a highly conserved resistance gene segment have become widespread in England and elsewhere. This study highlights the value of routine whole-genome sequencing in identifying genetic elements responsible for resistance dissemination.

Shiga toxin-producing Escherichia coli clonal complex 32, including serotype O145:H28, in the UK and Ireland

Introduction. Shiga toxin-producing Escherichia coli (STEC) O157:H7 has been the most clinically significant STEC serotype in the UK for over four decades. Over the last 10 years we have observed a decrease in STEC O157:H7 and an increase in non-O157 STEC serotypes, such as O145:H28.Gap Statement. Little is known about the microbiology and epidemiology of STEC belonging to CC32 (including O145:H28) in the UK. The aim of this study was to integrate genomic data with patient information to gain a better understanding of the virulence, disease severity, epidemic risk assessment and population structure of this clinically significant clonal complex.Methodology. Isolates of E. coli belonging to CC32 (n=309) in the archives of public health agencies in the UK and Ireland were whole-genome-sequenced, virulence-profiled and integrated with enhanced surveillance questionnaire (ESQ) data, including exposures and disease severity.Results. Overall, diagnoses of STEC belonging to CC32 (290/309, 94 %) in the UK have increased every year since 2014. Most cases were female (61 %), and the highest proportion of cases belonged to the 0-4 age group (53/211,25 %). The frequency of symptoms of diarrhoea (92 %), abdominal pain (84 %), blood in stool (71 %) and nausea (51 %) was similar to that reported in cases of STEC O157:H7, although cases of STEC CC32 were more frequently admitted to hospital (STEC CC32 48 % vs O157:H7  34 %) and/or developed haemolytic uraemic syndrome (HUS) (STEC CC32 9 % vs O157:H7 4 %).The majority of STEC isolates (268/290, 92 %) had the stx2a/eae virulence gene combination, most commonly associated with progression to STEC HUS. There was evidence of person-to-person transmission and small, temporally related, geographically dispersed outbreaks, characteristic of foodborne outbreaks linked to nationally distributed products.Conclusion. We recommend more widespread use of polymerase chain reaction (PCR) for the detection of all STEC serogroups, the development of consistent strategies for the follow-up testing of PCR-positive faecal specimens, the implementation of more comprehensive and standardized collection of epidemiological data, and routine sharing of sequencing data between public health agencies worldwide.

Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study

BACKGROUND

Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications.

METHODS

We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC).

FINDINGS

In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]).

INTERPRETATION

In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required.

FUNDING

British Journal of Surgery Society.

Comparison of genome-derived and phenotypic antimicrobial resistance profiles of Shigella species isolated from patients with symptoms of gastrointestinal disease in England, 2015-2020

Increasing antimicrobial resistance (AMR) in Shigellaspecies is a global public health problem. We compared genotypic and phenotypic methods for the detection of AMR in Shigellaspecies to evaluate the use of genome data for surveillance and monitoring of emerging AMR.

Whole genome sequencing (WGS) data from 388 isolates of all four Shigella species were analysed for the presence/absence of specific AMR determinants and selected accordingly. Phenotypic antimicrobial susceptibility testing was performed using in-agar dilution on all viable and pure isolates (n=358). The genotypic and phenotypic AMR profiles were then compared.

There were 335 (93.6%) isolates resistant to at least one antimicrobial and 222 (62%) isolates were multi-drug resistant, of which the majority (77%) were associated with foreign travel. Out of a possible 2864 isolate/antimicrobial class combinations, we identified 119 unexpected results, giving an overall concordance of 96.8% between the two methods. There were 54 samples that had an AMR determinant expected to confer resistance that were phenotypically susceptible, of which 31/54 (57.4%) were associated with tetracycline resistance and trimethoprim-sulfamethoxazole resistance. There were 65 that were phenotypically resistant to a specific antimicrobial class, but no AMR determinant was detected, of which 32/65 (49.2%) were associated with isolates harbouring a single gyrA mutation and exhibiting an unexpectedly high minimum inhibitory concentration (MIC) to ciprofloxacin.

Although comparisons between both methods showed good correlation between the genotypic and phenotypic AMR profiles, phenotypic monitoring is required to identify novel AMR mechanisms and to update reference database used for WGS analysis.

Genomic epidemiology of the first London outbreak of antimicrobial resistant sexually transmitted shigellosis

Shigellosis is an intestinal infection caused by Shigella bacteria. Shigella cause an estimated ~200,000 global deaths annually. Antimicrobial resistant (AMR) shigellosis is a significant cause of morbidity in high-income nations, with both multidrug resistant (MDR) and extensively drug resistant (XDR) cases being increasingly reported in Australia, England, and the USA. Sexually transmissible shigellosis was first described in San Francisco, 1974, but it would be a further 30 years before its first description in England. In 2004, London experienced an outbreak of Shigella sonnei (S. sonnei) mediated sexually transmitted shigellosis, associated with men-who-have-sex-with-men (MSM). Since then, sexually transmissible shigellosis has become endemic in England, with a greater than two-fold increase in Shigella diagnoses within sexual health services from 2015 to 2019. Through genomic exploration of samples from the original 2004 outbreak (provided by Public Health England (PHE)), we identified that the 2004 London outbreak isolates clustered within the base of genotype 3.1, lineage III, a lineage which has since gone on to dominate the global epidemiology of S. sonnei. The isolates displayed early evidence of varying degrees of antimicrobial resistance to several drug classes: macrolides, tetracyclines, beta-lactams and sulphonamides. Reconstructing the chronological process of how shigellosis has arrived at its current position in AMR and transmissibility is critical. Further investigation is underway to link this outbreak with MSM-associated shigellosis outbreaks occurring in the early 2000s in other countries to establish whether this lineage globally disseminated; determine the timeframe for global connectivity of shigellosis; and examine the outbreak isolates for virulence determinants.

Use of long read sequencing to characterise the genomic architecture of mobile genetic elements encoding blaCTX-M-15 in Escherichia coli causing travellers’ diarrhoea

Increasing levels of antimicrobial resistance (AMR) have been documented in Escherichia colicausing travellers’ diarrhoea, particularly to the third-generation cephalosporins. Diarrhoeagenic E. coli (DEC) can act as a reservoir for the exchange of AMR genes between bacteria residing in the human gut, enabling them to survive and flourish through the selective pressures of antibiotic treatments.

Using Oxford Nanopore Technology (ONT), we sequenced eight different sequence types (ST) belonging to five different pathotypes of extended-beta-lactamase-producing DEC harbouring blaCTX-M-15from four patients recently returned to the UK from Pakistan. The aim of the study was to determine whether blaCTX-M-15 was chromosome or plasmid-encoded to better understand the mechanisms of onward transmission of AMR determinants.

In Patient A, blaCTX-M-15was plasmid-encoded in both DEC isolates (ST504/ST3032), whereas in Patient B blaCTX-M-15was located on the chromosome in both DEC isolates (ST227/1283). Patients C and D both had one isolate where blaCTX-M-15 was located on the plasmid and one chromosomally encoded (ST443/182 and ST38/99, respectively). The two plasmids associated with Patient A were different although one exhibited high similarity to the plasmid from Patient C. In the four isolates where blaCTX-M-15 was chromosomally encoded, the site of insertion and the characteristics of the inserted plasmid segment differed.

Analysis of long-read sequencing data enables us to characterise the genomic architecture of mobile genetic elements encoding AMR determinants. These data may contribute to a better understanding of persistence and onward transmission of AMR determinants in MDR E. coli causing gastrointestinal and extra-intestinal infections.

Use of Nanopore Sequencing to Characterise the Genomic Architecture of Mobile Genetic Elements Encoding bla CTX-M-15 in Escherichia coli Causing Travellers' Diarrhoea

Increasing levels of antimicrobial resistance (AMR) have been documented in Escherichia coli causing travellers’ diarrhoea, particularly to the third-generation cephalosporins. Diarrhoeagenic E. coli (DEC) can act as a reservoir for the exchange of AMR genes between bacteria residing in the human gut, enabling them to survive and flourish through the selective pressures of antibiotic treatments. Using Oxford Nanopore Technology (ONT), we sequenced eight isolates of DEC from four patients’ specimens who had all recently returned to the United Kingdome from Pakistan. Sequencing yielded two DEC harbouring bla_CTX-M-15 per patient, all with different sequence types (ST) and belonging to five different pathotypes. The study aimed to determine whether bla_CTX-M-15 was located on the chromosome or plasmid and to characterise the drug-resistant regions to better understand the mechanisms of onward transmission of AMR determinants. Patients A and C both had one isolate where bla_CTX-M-15 was located on the plasmid (899037 & 623213, respectively) and one chromosomally encoded (899091 & 623214, respectively). In patient B, bla_CTX-M-15 was plasmid-encoded in both DEC isolates (786605 & 7883090), whereas in patient D, bla_CTX-M-15 was located on the chromosome in both DEC isolates (542093 & 542099). The two bla_CTX-M-15-encoding plasmids associated with patient B were different although the bla_CTX-M-15-encoding plasmid isolated from 788309 (IncFIB) exhibited high nucleotide similarity to the bla_CTX-M-15-encoding plasmid isolated from 899037 (patient A). In the four isolates where bla_CTX-M-15 was chromosomally encoded, two isolates (899091 & 542099) shared the same insertion site. The bla_CTX-M-15 insertion site in isolate 623214 was described previously, whereas that of isolate 542093 was unique to this study. Analysis of Nanopore sequencing data enables us to characterise the genomic architecture of mobile genetic elements encoding AMR determinants. These data may contribute to a better understanding of persistence and onward transmission of AMR determinants in multidrug-resistant (MDR) E. coli causing gastrointestinal and extra-intestinal infections.

Lessons learned from the investigation and management of an outbreak of Shigella flexneri associated with a restaurant in London, 2019-2020

BACKGROUND

Foodborne outbreaks of Shigella flexneri infection are uncommon in the UK. In November 2019, the United Kingdom Health Security Agency investigated an outbreak of S. flexneri associated with a fast-food restaurant in London.

METHODS

Epidemiological investigations included case ascertainment and interviewing suspected cases using enhanced surveillance questionnaires. Whole-genome sequencing (WGS) was used for characterisation of human isolates. Environmental investigations included a review of food safety processes at the implicated restaurant, administration of exposure questionnaires and stool sampling of staff.

RESULTS

Between November 2019 and February 2020, 17 cases were confirmed as part of the outbreak by WGS in London. Among these, 15 were linked to the implicated restaurant. A review of the food safety processes at the restaurant was satisfactory. Despite initial suboptimal coverage of stool screening of staff, all staff members working at the restaurant during the sampling period were screened and an asymptomatic food handler tested positive for S.flexneri with the outbreak WGS profile. The individual underwent microbiological clearance, and no further cases were reported. It was not possible to confirm the direction of transmission for the community cases or the staff member.

CONCLUSION

We report an outbreak of S. flexneri in a fast-food restaurant in London with previous inspection ratings indicating good compliance with food safety and hygiene standards. WGS was crucial in identifying cases linked to the outbreak. This outbreak highlights the importance of prompt testing of food handlers in outbreaks suspected to be associated with food businesses.