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1.
Artículo en Inglés | MEDLINE | ID: mdl-32160143

RESUMEN

A Gram-negative rod from the Yersinia genus was isolated from a clinical case of yersiniosis in the United Kingdom. Long read sequencing data from an Oxford Nanopore Technologies (ONT) MinION in conjunction with Illumina HiSeq reads were used to generate a finished quality genome of this strain. Overall Genome Related Index (OGRI) of the strain was used to determine that it was a novel species within Yersinia, despite biochemical similarities to Yersinia enterocolitica. The 16S ribosomal RNA gene accessions are MN434982-MN434987 and the accession number for the complete and closed chromosome is CP043727. The type strain is SRR7544370T (=NCTC 14382T/=LMG 31573T).

2.
Microb Genom ; 6(3)2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32100710

RESUMEN

Over the last 35 years in the UK, the burden of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infection has, during different periods of time, been associated with five different sub-lineages (1983-1995, Ia, I/IIa and I/IIb; 1996-2014, Ic; and 2015-2018, IIb). The acquisition of a stx2a-encoding bacteriophage by these five sub-lineages appears to have coincided with their respective emergences. The Oxford Nanopore Technologies (ONT) system was used to sequence, characterize and compare the stx-encoding prophages harboured by each sub-lineage to investigate the integration of this key virulence factor. The stx2a-encoding prophages from each of the lineages causing clinical disease in the UK were all different, including the two UK sub-lineages (Ia and I/IIa) circulating concurrently and causing severe disease in the early 1980s. Comparisons between the stx2a-encoding prophage in sub-lineages I/IIb and IIb revealed similarity to the prophage commonly found to encode stx2c, and the same site of bacteriophage integration (sbcB) as stx2c-encoding prophage. These data suggest independent acquisition of previously unobserved stx2a-encoding phage is more likely to have contributed to the emergence of STEC O157:H7 sub-lineages in the UK than intra-UK lineage to lineage phage transmission. In contrast, the stx2c-encoding prophage showed a high level of similarity across lineages and time, consistent with the model of stx2c being present in the common ancestor to extant STEC O157:H7 and maintained by vertical inheritance in the majority of the population. Studying the nature of the stx-encoding bacteriophage contributes to our understanding of the emergence of highly pathogenic strains of STEC O157:H7.

3.
J Med Microbiol ; 69(3): 379-386, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-32101158

RESUMEN

Introduction. Despite many ongoing surveillance projects and the recent focus on the veterinary and clinical 'One Health' aspects of antimicrobial resistance (AMR), evidence of the extent of any public health risk posed by animal reservoirs with respect to the transmission of resistant strains of Escherichia coli to humans remains varied and contentious. In the UK, the main zoonotic reservoir for the foodborne pathogen Shiga toxin-producing E. coli (STEC) is cattle and sheep. In this study, we adopt an alternative approach to the risk assessment of transmission of AMR E. coli from animals to humans, involving monitoring AMR in isolates of STEC, an established zoonotic, foodborne pathogen, from human cases of gastrointestinal disease.Aim. The aim of this study was to determine the genome-derived AMR profiles for STEC from human cases to assess the risk of transmission of multidrug-resistant STEC from ruminants to humans.Methodology. STEC belonging to 10 different clonal complexes (CCs) (n=457) isolated from human faecal specimens were sequenced and genome-derived AMR profiles were determined. Phenotypic susceptibility testing was undertaken on all isolates (n=100) predicted to be resistant to at least one class of antimicrobial.Results. Of the 457 isolates, 332 (72.7 %) lacked identifiable resistance genes and were predicted to be fully susceptible to 11 classes of antimicrobials; 125/332 (27.3 %) carried 1 or more resistance genes, of which 83/125 (66.4 %) were resistant to 3 or more classes of antibiotic. The percentage of isolates harbouring AMR determinants varied between CCs, from 4% in CC25 to 100% in CC504. Forty-six different AMR genes were detected, which conferred resistance to eight different antibiotic classes. Resistance to ampicillin, streptomycin, tetracyclines and sulphonamides was most commonly detected. Four isolates were identified as extended-spectrum ß-lactamase producers. An overall concordance of 97.7 % (n=1075/1100) was demonstrated between the phenotypic and genotypic methods.Conclusion. This analysis provided an indirect assessment of the risk of transmission of AMR gastrointestinal pathogens from animals to humans, and revealed a subset of human isolates of the zoonotic pathogen STEC were resistant to the antimicrobials used in animal husbandry. However, this proportion has not increased over the last three decades, and thismay provide evidence that guidancepromoting responsible practice has been effective.


Asunto(s)
Antibacterianos/farmacología , Reservorios de Enfermedades/microbiología , Farmacorresistencia Bacteriana Múltiple/genética , Infecciones por Escherichia coli/epidemiología , Genoma Bacteriano/genética , Escherichia coli Shiga-Toxigénica/genética , Animales , Bovinos , Inglaterra/epidemiología , Infecciones por Escherichia coli/microbiología , Infecciones por Escherichia coli/transmisión , Heces/microbiología , Genotipo , Humanos , Masculino , Salud Única , Minorías Sexuales y de Género , Ovinos , Escherichia coli Shiga-Toxigénica/aislamiento & purificación , Zoonosis
4.
Spat Spatiotemporal Epidemiol ; 32: 100305, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-32007279

RESUMEN

Identifying geographical areas with significantly higher or lower rates of infectious diseases can provide important aetiological clues to inform the development of public health policy and interventions designed to reduce morbidity. We applied kernel smoothing to estimate the spatial and spatio-temporal variation in risk of STEC O157 infection in England between 2009 and 2015, and to explore differences between the residential locations of cases reporting travel and those not reporting travel. We provide evidence that the distribution of STEC O157 infection in England is non-uniform with respect to the distribution of the at-risk population; that the spatial distribution of the three main genetic lineages infecting humans (I, II and I/II) differs significantly and that the spatio-temporal risk is highly dynamic. Our results also indicate that cases of STEC O157 reporting travel within or outside the UK are more likely to live in the south/south-east of the country, meaning that their residential location may not reflect the location of exposure that led to their infection. We suggest that the observed variation in risk reflects exposure to sources of STEC O157 that are geographically prescribed. These differences may be related to a combination of changes in the strains circulating in the ruminant reservoir, animal movements (livestock, birds or wildlife) or the behavior of individuals prior to infection. Further work to identify the importance of behaviours and exposures reported by cases relative to residential location is needed.

5.
Microb Genom ; 6(2)2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-32003708

RESUMEN

To establish the prevalence of mobile colistin resistance (mcr) genes amongst Salmonella enterica isolates obtained through public health surveillance in England (April 2014 to September 2017), 33 205 S. enterica genome sequences obtained from human, food, animal and environmental isolates were screened for the presence of mcr variants 1 to 8. The mcr-positive genomes were assembled, annotated and characterized according to plasmid type. Nanopore sequencing was performed on six selected isolates with putative novel plasmids, and phylogenetic analysis was used to provide an evolutionary context for the most commonly isolated clones. Fifty-two mcr-positive isolates were identified, of which 32 were positive for mcr-1, 19 for mcr-3 and 1 for mcr-5. The combination of Illumina and Nanopore sequencing identified three novel mcr-3 plasmids and one novel mcr-5 plasmid, as well as the presence of chromosomally integrated mcr-1 and mcr-3. Monophasic S. enterica serovar Typhimurium accounted for 27/52 (52 %) of the mcr-positive isolates, with the majority clustering in clades associated with travel to Southeast Asia. Isolates in these clades were associated with a specific plasmid range and an additional extended-spectrum beta-lactamase genotype. Routine whole-genome sequencing for public health surveillance provides an effective screen for novel and emerging antimicrobial determinants, including mcr. Complementary long-read technologies elucidated the genomic context of resistance determinants, offering insights into plasmid dissemination and linkage to other resistance genes.

6.
J Antimicrob Chemother ; 75(4): 883-889, 2020 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-31943013

RESUMEN

OBJECTIVES: To compare and evaluate phenotypic and genotypic methods for the detection of antimicrobial resistance (AMR) in Campylobacter jejuni and Campylobacter coli in England and Wales. METHODS: WGS data from 528 isolates of Campylobacter spp. (452 C. jejuni and 76 C. coli) from human (494), food (21) and environmental (2) sources, collected between January 2015 and December 2016, and from the PHE culture collection (11) were mapped to genes known to be associated with phenotypic resistance to antimicrobials in the genus. Phenotypic antibiotic susceptibility (erythromycin, ciprofloxacin, tetracycline, gentamicin and streptomycin) testing using an in-agar dilution method was performed on all isolates. RESULTS: Concordance between phenotypic resistance and the presence of corresponding AMR determinants was 97.5% (515/528 isolates). Only 13 out of 528 isolates (10 C. jejuni and 3 C. coli) had discordant interpretations for at least one of the five antibiotics tested, equating to a total of 15 (0.6%) discrepancies out of 2640 isolate/antimicrobial combinations. Seven discrepant results were genotypically resistant but phenotypically susceptible (major errors) and eight discrepant results were genotypically susceptible but phenotypically resistant (very major errors). CONCLUSIONS: The use of this bioinformatics approach for predicting AMR from WGS data for routine public health surveillance is a reliable method for real-time monitoring of changing AMR patterns in isolates of C. jejuni and C. coli.

7.
J Med Microbiol ; 69(3): 487-491, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31935188

RESUMEN

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens that cause symptoms of severe gastrointestinal disease, including haemolytic uraemic syndrome (HUS), in humans. Currently in England, STEC serotypes other than O157:H7 are not cultured at the local hospital laboratories. The aim of this study was to evaluate the utility of CHROMagar STEC for the direct detection of STEC from faecal specimens in a diagnostic setting, compared to the current reference laboratory method using PCR targeting the Shiga-toxin gene (stx) to test multiple colonies cultured on MacConkey agar. Of the 292 consecutive faecal specimens submitted to the Gastrointestinal Bacterial Reference Unit that tested positive for stx by PCR, STEC could not be cultured on MacConkey agar or CHROMagar STEC from 87/292 (29.8 %). Of the 205 that were cultured, 106 (51.7 %) were detected on both MacConkey agar and CHROMagar STEC and 99 (48.3 %) were detected on MacConkey agar only. All 106 (100 %) isolates that grew on CHROMagar STEC had the ter gene cassette, known to be associated with resistance to tellurite, compared to 13/99 (13.1 %) that were not detected on CHROMagar STEC. CHROMagar STEC supported the growth of 36/40 (90 %) isolates harbouring stx2a or stx2d, the subtypes most frequently associated with progression to HUS. Of the 92 isolates harbouring eae, an important STEC virulence marker, 77 (83.7 %) grew on CHROMagar STEC. CHROMagar STEC is a useful selective media for the rapid, near-patient detection of STEC that have the potential to cause HUS.


Asunto(s)
Infecciones por Escherichia coli/diagnóstico , Escherichia coli Shiga-Toxigénica/aislamiento & purificación , Agar , Compuestos Cromogénicos , Infecciones por Escherichia coli/microbiología , Heces/microbiología , Humanos , Toxina Shiga/genética , Escherichia coli Shiga-Toxigénica/genética
8.
J Clin Microbiol ; 58(4)2020 Mar 25.
Artículo en Inglés | MEDLINE | ID: mdl-31969425

RESUMEN

Whole-genome sequencing has enhanced surveillance and facilitated detailed monitoring of the transmission of Shigella species in England. We undertook an epidemiological and phylogenetic analysis of isolates from all cases of shigellosis referred to Public Health England between 2015 and 2018 to explore recent strain characteristics and the transmission dynamics of Shigella species. Of the 4,950 confirmed cases of shigellosis identified during this period, the highest proportion of isolates was Shigella sonnei (54.4%), followed by S. flexneri (39.2%), S. boydii (4.1%), and S. dysenteriae (2.2%). Most cases were adults (82.9%) and male (59.5%), and 34.9% cases reported recent travel outside the United Kingdom. Throughout the study period, diagnoses of S. flexneri and S. sonnei infections were most common in men with no history of recent travel abroad. The species prevalence was not static, with cases of S. flexneri infection in men decreasing between 2015 and 2016 and the number of cases of S. sonnei infection increasing from 2017. Phylogenetic analysis showed this recent increase in S. sonnei infections was attributed to a novel clade that emerged from a Central Asia sublineage exhibiting resistance to ciprofloxacin and azithromycin. Despite changes in species prevalence, diagnoses of Shigella infections in England are persistently most common in adult males without a reported travel history, consistent with sexual transmission among men who have sex with men. The trend toward increasing rates of ciprofloxacin resistance in S. sonnei, in addition to plasmid-mediated azithromycin resistance, is of significant public health concern with respect to the transmission of multidrug-resistant gastrointestinal pathogens and the risk of treatment failures.

9.
J Med Microbiol ; 69(3): 419-426, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31999240

RESUMEN

Introduction. Current testing practices for yersiniosis mean that its true incidence and epidemiology are not well understood. In mid-2016, the introduction of testing via a multiplex gastrointestinal PCR panel at Portsmouth hospital laboratory in Hampshire, UK, resulted in a marked increase in the number of Yersinia cases identified locally.Aim. Here we describe the epidemiology and microbiology of Yersinia cases identified at Portsmouth laboratory following the introduction of PCR testing.Methodology. A case was defined as a person with a stool specimen in which Yersinia was detected by PCR and/or culture at Portsmouth NHS Trust laboratory between 1 January 2014 and 31 December 2018. A case list was created from laboratory data submitted by Portsmouth laboratory to Public Health England (PHE), updated with speciation and serotyping data from the PHE reference laboratory. Descriptive analysis was performed.Results. Over 30 months following introduction of PCR testing, 199 cases were confirmed with Yersinia, compared to two cases in the preceding 30 months. This corresponds to a rate of 13.8 and 0.1 per 100 000 population per year respectively (P<0.0001). In total, 85% of tested isolates were Y. enterocolitica, belonging to multiple serotypes, and the rest belonged to a range of Y. enterocolitica-like species.Conclusions. Introduction of PCR testing led to the identification of a previously unrecognized burden of yersiniosis in Hampshire. The diversity of species and serotypes suggests heterogeneity in sources and transmission routes. Further research on exposures, risk factors and clinical sequalae is needed to improve our understanding of the clinical and public health impact.


Asunto(s)
Brotes de Enfermedades , Gastroenteritis/epidemiología , Yersiniosis/epidemiología , Yersinia enterocolitica/aislamiento & purificación , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Niño , Preescolar , Inglaterra/epidemiología , Femenino , Gastroenteritis/microbiología , Humanos , Incidencia , Lactante , Recién Nacido , Masculino , Persona de Mediana Edad , Reacción en Cadena de la Polimerasa , Salud Pública , Yersiniosis/microbiología , Yersinia enterocolitica/genética , Adulto Joven
10.
Microb Genom ; 5(11)2019 11.
Artículo en Inglés | MEDLINE | ID: mdl-31682221

RESUMEN

Since the 1970s, shigellosis has been reported as a sexually transmissible infection, and in recent years, genomic data have revealed the breadth of Shigella spp. transmission among global networks of men who have sex with men (MSM). In 2015, Public Health England (PHE) introduced routine whole-genome sequencing (WGS) of Shigella spp. to identify transmission clusters. However, limited behavioural information for the cases hampers interpretation. We investigated whether WGS can distinguish between clusters representing sexual transmission in MSM and clusters representing community (non-sexual) transmission to inform infection control. WGS data for Shigella flexneri from August 2015 to July 2017 were aggregated into single linkage clusters based on SNP typing using a range of SNP distances (the standard for Shigella surveillance at PHE is 10 SNPs). Clusters were classified as 'adult male', 'household', 'travel-associated' or 'community' using routine demographic data submitted alongside laboratory cultures. From August 2015 to March 2017, PHE contacted those with shigellosis as part of routine public-health follow-up and collected exposure data on a structured questionnaire, which for the first time included questions about sexual identity and behaviour. The questionnaire data were used to determine whether clusters classified as 'adult male' represented likely sexual transmission between men, thereby validating the use of the SNP clustering tool for informing appropriate public-health responses. Overall, 1006 S. flexneri cases were reported, of which 563 clustered with at least one other case (10-SNP threshold). Linked questionnaire data were available for 106 clustered cases, of which 84.0 % belonged to an 'adult male' cluster. At the 10-SNP threshold, 95.1 % [95 % confidence interval (CI) 88.0-98.1%] of MSM belonged to an 'adult male' cluster, while 73.2 % (95 % CI 49.1-87.5%) of non-MSM belonged to a 'community' or 'travel-associated' cluster. At the 25-SNP threshold, all MSM (95 % CI 96.0-100%) belonged to an 'adult male' cluster and 77.8 % (95 % CI 59.2-89.4%) of non-MSM belonged to a 'community' or 'travel-associated' cluster. Within one phylogenetic clade of S. flexneri, 9 clusters were identified (7 'adult male'; 2 'community') using a 10-SNP threshold, while a single 'adult male' cluster was identified using a 25-SNP threshold. Genotypic markers of azithromycin resistance were detected in 84.5 % (294/348) of 'adult male' cases and 20.9 % (9/43) of cases in other clusters (10-SNP threshold), the latter of which contained gay-identifying men who reported recent same-sex sexual contact. Our study suggests that SNP clustering can be used to identify Shigella clusters representing likely sexual transmission in MSM to inform infection control. Defining clusters requires a flexible approach in terms of genetic relatedness to ensure a clear understanding of underlying transmission networks.

11.
J Food Prot ; 82(11): 1950-1958, 2019 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-31638410

RESUMEN

Shiga toxin-producing Escherichia coli (STEC) outbreaks involving ready-to-eat salad products have been described in the scientific literature since 1995. These products typically do not undergo a definitive control step such as cooking to eliminate pathogens. To reduce the number of STEC infections from salad products, efforts will need to focus on preventing and reducing contamination throughout the food chain. We performed a systematic review of STEC outbreaks involving sprouted seeds, salad, or leafy green products to determine whether there were recurrent features, such as availability of microbiological evidence or identification of the contamination event, which may inform future investigations and prevention and control strategies. Thirty-five STEC outbreaks linked to contaminated leafy greens were identified for inclusion. The outbreaks occurred from 1995 to 2018 and ranged from 8 to more than 8,500 cases. Detection of STEC in the food product was rare (4 of 35 outbreaks). For the remaining outbreaks, the determination of leafy greens as the source of the outbreak mainly relied on analytical epidemiology (20 of 35) or descriptive evidence (11 of 35). The traceback investigation in 21 of 32 outbreaks was not able to identify possible routes leading to where the STEC bacteria came from or how the leaves were contaminated. Investigations in eight outbreaks found poor practice during processing that may have contributed to the outbreak, such as insufficient postharvest disinfection of the product. Six outbreak investigations were able to identify the outbreak strain in animal feces near the growing fields; two of these were also able to find it in irrigation water on the farms, providing a likely route of contamination. These results highlight the limitations of relying on microbiological confirmation as a basis to initiate investigations of upstream production to understand the source of contamination. This review also demonstrates the importance of, and difficulties associated with, food-chain traceback studies to inform control measures and future prevention.

12.
Nat Commun ; 10(1): 4828, 2019 10 23.
Artículo en Inglés | MEDLINE | ID: mdl-31645551

RESUMEN

Shigella sonnei increasingly dominates the international epidemiological landscape of shigellosis. Treatment options for S. sonnei are dwindling due to resistance to several key antimicrobials, including the fluoroquinolones. Here we analyse nearly 400 S. sonnei whole genome sequences from both endemic and non-endemic regions to delineate the evolutionary history of the recently emergent fluoroquinolone-resistant S. sonnei. We reaffirm that extant resistant organisms belong to a single clonal expansion event. Our results indicate that sequential accumulation of defining mutations (gyrA-S83L, parC-S80I, and gyrA-D87G) led to the emergence of the fluoroquinolone-resistant S. sonnei population around 2007 in South Asia. This clone was then transmitted globally, resulting in establishments in Southeast Asia and Europe. Mutation analysis suggests that the clone became dominant through enhanced adaptation to oxidative stress. Experimental evolution reveals that under fluoroquinolone exposure in vitro, resistant S. sonnei develops further intolerance to the antimicrobial while the susceptible counterpart fails to attain complete resistance.


Asunto(s)
Farmacorresistencia Bacteriana/genética , Disentería Bacilar/microbiología , Fluoroquinolonas , Genoma Bacteriano/genética , Shigella sonnei/genética , Antibacterianos/uso terapéutico , Asia Sudoriental/epidemiología , Asia Occidental/epidemiología , Teorema de Bayes , Ciprofloxacino/uso terapéutico , Girasa de ADN/genética , Topoisomerasa de ADN IV/genética , Evolución Molecular Dirigida , Disentería Bacilar/tratamiento farmacológico , Disentería Bacilar/epidemiología , Europa (Continente)/epidemiología , Evolución Molecular , Humanos , Epidemiología Molecular , Mutación , Filogenia , Polimorfismo de Nucleótido Simple , Shigella sonnei/fisiología
13.
Front Genet ; 10: 763, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31543896

RESUMEN

Bacterial-host interactions are non-linear and actually threefold, involving significant selection through predatory lytic bacteriophages in the host environment. In studies of human and animal gut microbiome bacteria, it is important to consider phage in all host-pathogen interactions. We use an important zoonotic pathogen, Shiga toxigenic Escherichia coli (STEC) O157:H7, to investigate this. Our study provides evidence that phage resistance profiles are well maintained at the sub-lineage level with variation in profiles within sub-lineages uncommon. This indicates that phage resistance heterogeneity happened early on in the STEC O157:H7 natural history and that occasional "wobbles" do not often outcompete the stable lineage unless combined with a competitive advantage. We discuss an example of this in the acquisition of stx2a that, while an important virulence factor, also conveys increased phage cross-resistance. We also discuss the role of phage resistance in co-occurrence of the three stable lineages worldwide and whether differing phage resistance is maintaining diversity.

14.
Gigascience ; 8(8)2019 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-31433830

RESUMEN

BACKGROUND: We aimed to compare Illumina and Oxford Nanopore Technology sequencing data from the 2 isolates of Shiga toxin-producing Escherichia coli (STEC) O157:H7 to determine whether concordant single-nucleotide variants were identified and whether inference of relatedness was consistent with the 2 technologies. RESULTS: For the Illumina workflow, the time from DNA extraction to availability of results was ∼40 hours, whereas with the ONT workflow serotyping and Shiga toxin subtyping variant identification were available within 7 hours. After optimization of the ONT variant filtering, on average 95% of the discrepant positions between the technologies were accounted for by methylated positions found in the described 5-methylcytosine motif sequences, CC(A/T)GG. Of the few discrepant variants (6 and 7 difference for the 2 isolates) identified by the 2 technologies, it is likely that both methodologies contain false calls. CONCLUSIONS: Despite these discrepancies, Illumina and Oxford Nanopore Technology sequences from the same case were placed on the same phylogenetic location against a dense reference database of STEC O157:H7 genomes sequenced using the Illumina workflow. Robust single-nucleotide polymorphism typing using MinION-based variant calling is possible, and we provide evidence that the 2 technologies can be used interchangeably to type STEC O157:H7 in a public health setting.


Asunto(s)
Infecciones por Escherichia coli/microbiología , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Nanotecnología , Polimorfismo de Nucleótido Simple , Escherichia coli Shiga-Toxigénica/genética , Alelos , Biología Computacional/métodos , Brotes de Enfermedades , Infecciones por Escherichia coli/epidemiología , Genoma Bacteriano , Genómica/métodos , Genotipo , Humanos , Nanoporos , Filogenia , Escherichia coli Shiga-Toxigénica/clasificación , Flujo de Trabajo
15.
Euro Surveill ; 24(16)2019 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-31014418

RESUMEN

An outbreak of Shiga toxin-producing Escherichia coli (STEC) O157:H7 occurred on the Isle of Wight between August and October 2017. Of the seven cases linked to the outbreak, five were identified through the statutory notification process and two were identified through national surveillance of whole genome sequencing data. Enhanced surveillance questionnaires established a common link to a farm, and link to the likely food vehicle, raw drinking milk (RDM). Microbiological investigations, including PCR, identified the presence of STEC O157:H7 in samples of RDM. Analysis of core genome single nucleotide polymorphism (SNP) data of STEC O157:H7 from human stool specimens, animal faecal samples and RDM demonstrated a one SNP difference between isolates, and therefore close genetic relatedness. Control measures that were put in place included suspension of sales and recall of RDM, as well as restrictions on public access to parts of the farm. Successful integration of traditional epidemiological surveillance and advanced laboratory methods for the detection and characterisation of STEC O157:H7 from human, animal and environmental samples enabled prompt identification of the outbreak vehicle and provided evidence to support the outbreak control team's decision-making, leading to implementation of effective control measures in a timely manner.

16.
J Med Microbiol ; 68(6): 930-939, 2019 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-30994441

RESUMEN

PURPOSE: This study describes the epidemiology of Shiga toxin-producing Escherichia coli (STEC) infections in a population in the South East of England. METHODS: From 1 November 2013 to 31 March 2017 participating diagnostic laboratories reported Shiga toxin gene (stx) positive real-time PCR results to local public health teams. Stx positive faecal samples/isolates were referred to the Gastrointestinal Bacteria Reference Unit (GBRU) for confirmation by culture and typing by whole genome sequencing (WGS). Key clinical information was collected by public health teams.Results/Key findings. Altogether, 548 faecal specimens (420 were non-travel associated) were stx positive locally, 535 were submitted to the GBRU. STEC were isolated from 42 %, confirmed by stx PCR in 21 % and 37 % were PCR negative. The most common non-travel associated STEC serogroups were O157, O26, O146 and O91. The annualized incidence of confirmed STEC infections (PCR or culture) was 5.8 per 100 000. The ratio of O157 to non-O157 STEC serogroups was 1:7. The annualized incidence of non-O157 haemolytic uraemic syndrome-associated Escherichia coli (HUSEC) strains was 0.4 per 100 000. Bloody diarrhoea was reported by 58 % of cases infected with E. coli O157, 33 % of cases infected with non-O157 HUSEC strains and 12 % of other lower risk non-O157 strains. Overall, 76 % of non-O157 HUSEC isolates possessed the eae virulence gene. CONCLUSIONS: HUSEC including serogroup O157 were uncommon and more likely to cause bloody diarrhoea than other STEC. The routine use of stx PCR testing can influence clinical management. Understanding the local epidemiology facilitates a proportionate public health response to STEC, based on clinical and microbiological characteristics including stx subtype(s).


Asunto(s)
Infecciones por Escherichia coli/epidemiología , Síndrome Hemolítico-Urémico/epidemiología , Toxina Shiga/metabolismo , Escherichia coli Shiga-Toxigénica/inmunología , Diarrea/epidemiología , Diarrea/microbiología , Inglaterra/epidemiología , Infecciones por Escherichia coli/microbiología , Heces/microbiología , Síndrome Hemolítico-Urémico/microbiología , Humanos , Incidencia , Salud Pública , Serogrupo , Escherichia coli Shiga-Toxigénica/aislamiento & purificación , Escherichia coli Shiga-Toxigénica/patogenicidad , Virulencia
17.
J Med Microbiol ; 68(4): 538-548, 2019 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-30888316

RESUMEN

PurposeandMethodology. Epidemiological and microbiological data on Yersinia enterocolitica (n=699) and Yersinia pseudotuberculosis (n=35) isolated from human clinical specimens in England between April 2004 and March 2018 were reviewed. Traditional biochemical species identification and serological typing results were compared with species identifications and serotypes derived from whole-genome sequencing (WGS) data for a sub-set of these isolates (n=179).Results. Most Y. enterocolitica isolates were from faecal specimens (74.4%) from adults (80.7%) and 50.7  % of isolates were from male patients. Most Y. pseudotuberculosis isolates were from blood cultures (68.6%) from adults (91%) and 60.0  % of isolates were from male patients. All sequenced isolates of Y. enterocolitica (n=158) and Y. pseudotuberculosis (n=21), as well as isolates belonging to other Yersinia species (n=21), were correctly identified from genomic data using a kmer-based identification approach. Traditional phenotypic serotyping typed 82/158 and 12/21 isolates of Y. enterocolitica and Y. pseudotuberculosis, respectively, while 118/158 and 21/21 isolates of Y. enterocolitica and Y. pseudotuberculosis, respectively, were typed by the genome-derived serotyping method. In addition, WGS data provided a multi-locus sequence type profile and virulence gene profile for all isolates.Conclusion. The use of WGS for typing Y. enterocolitica and Y. pseudotuberculosis at Public Health England will facilitate the monitoring of animal-to-human transmission of these important foodborne pathogens in the UK and improve public health surveillance of the pathogenic lineages.


Asunto(s)
Yersiniosis/epidemiología , Yersinia enterocolitica/clasificación , Infecciones por Yersinia pseudotuberculosis/epidemiología , Yersinia pseudotuberculosis/clasificación , Adulto , Técnicas de Tipificación Bacteriana , Inglaterra/epidemiología , Monitoreo Epidemiológico , Heces/microbiología , Femenino , Genoma Bacteriano , Humanos , Masculino , Salud Pública , Serotipificación , Virulencia , Secuenciación Completa del Genoma , Yersinia enterocolitica/aislamiento & purificación , Yersinia pseudotuberculosis/aislamiento & purificación
18.
J Clin Microbiol ; 57(4)2019 04.
Artículo en Inglés | MEDLINE | ID: mdl-30700505

RESUMEN

Shigella spp. are a leading cause of human diarrheal disease worldwide, with Shigella flexneri being the most frequently isolated species in developing countries. This serogroup is presently classified into 19 serotypes worldwide. We report here a multicenter validation of a multiplex-PCR-based strategy previously developed by Q. Sun, R. Lan, Y. Wang, A. Zhao, et al. (J Clin Microbiol 49:3766-3770, 2011) for molecular serotyping of S. flexneri This study was performed by seven international laboratories, with a panel of 71 strains (researchers were blind to their identity) as well as 279 strains collected from each laboratory's own local culture collections. This collaborative work found a high extent of agreement among laboratories, calculated through interrater reliability (IRR) measures for the PCR test that proved its robustness. Agreement with the traditional method (serology) was also observed in all laboratories for 14 serotypes studied, while specific genetic events could be responsible for the discrepancies among methodologies in the other 5 serotypes, as determined by PCR product sequencing in most of the cases. This work provided an empirical framework that allowed the use of this molecular method to serotype S. flexneri and showed several advantages over the traditional method of serological typing. These advantages included overcoming the problem of availability of suitable antisera in testing laboratories as well as facilitating the analysis of multiple samples at the same time. The method is also less time-consuming for completion and easier to implement in routine laboratories. We recommend that this PCR be adopted, as it is a reliable diagnostic and characterization methodology that can be used globally for laboratory-based shigella surveillance.

19.
Euro Surveill ; 24(4)2019 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-30696532

RESUMEN

We aim to provide insight and guidance on the utility of whole genome sequencing (WGS) data for investigating food-borne outbreaks of Shiga toxin-producing Escherichia coli (STEC) O157:H7 in England between 2013 and 2017. Analysis of WGS data delivered an unprecedented level of strain discrimination when compared with multilocus variable number tandem repeat analysis. The robustness of the WGS method ensured confidence in the microbiological identification of linked cases, even when epidemiological links were obscured. There was evidence that phylogeny derived from WGS data can be used to trace the geographical origin of an isolate. Further analysis of the phylogenetic data provided insight on the evolutionary context of emerging pathogenic strains. Publically available WGS data linked to the clinical, epidemiological and environmental context of the sequenced strain has improved trace back investigations during outbreaks. Expanding the use of WGS-based typing analysis globally will ensure the rapid implementation of interventions to protect public health, inform risk assessment and facilitate the management of national and international food-borne outbreaks of STEC O157:H7.

20.
Behav Modif ; 43(3): 389-412, 2019 05.
Artículo en Inglés | MEDLINE | ID: mdl-29457465

RESUMEN

Cook et al. recently described a progressive model for teaching children with autism spectrum disorder (ASD) to provide eye contact with an instructor following a name call. The model included the following phases: contingent praise only, contingent edibles plus praise, stimulus prompts plus contingent edibles and praise, contingent video and praise, schedule thinning, generalization assessments, and maintenance evaluations. In the present study, we evaluated the extent to which modifications to the model were needed to train 15 children with ASD to engage in eye contact. Results show that 11 of 15 participants acquired eye contact with the progressive model; however, eight participants required one or more procedural modifications to the model to acquire eye contact. In addition, the four participants who did not acquire eye contact received one or more modifications. Results also show that participants who acquired eye contact with or without modifications continued to display high levels of the behavior during follow-up probes. We discuss directions for future research with and limitations of this progressive model.


Asunto(s)
Trastorno del Espectro Autista/fisiopatología , Trastorno del Espectro Autista/psicología , Condicionamiento Operante , Fijación Ocular , Niño , Preescolar , Femenino , Fijación Ocular/fisiología , Humanos , Masculino
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