Changes in causes of acute gastroenteritis in the United Kingdom over 15 years: microbiologic findings from 2 prospective, population-based studies of infectious intestinal disease.

BACKGROUND: Large-scale, prospective studies of infectious intestinal disease (IID) in developed countries are uncommon. Two studies of IID incidence and etiology have been conducted in the United Kingdom: the Infectious Intestinal Disease Study in England (IID1) in 1993-1996 and the Second Study of Infectious Intestinal Disease in the Community (IID2) in 2008-2009. We examined changes in etiology and diagnostic yield of IID cases over 15 years. METHODS: Fecal samples submitted by IID cases were examined for a range of bacterial, viral, and protozoal pathogens using traditional and molecular microbiological methods. We calculated the percentage of specimens positive for each organism based on traditional methods and on traditional and molecular methods combined. We compared the distributions of organisms in the 2 studies. RESULTS: For pathogens investigated in both studies, 40% of fecal samples submitted by cases in IID2 were positive compared with 28% in IID1. Viruses were most frequent among community cases in IID2. Campylobacter was the most common bacterial pathogen among cases presenting to healthcare. Major differences between the 2 studies were increases in the detection of norovirus and sapovirus and a decline Salmonella. CONCLUSIONS: Most fecal specimens were negative for the pathogens tested in both studies, so new strategies are needed to close the diagnostic gap. Among known pathogens, effective control of norovirus, rotavirus, and Campylobacter remain high priorities. The reduction in nontyphoidal salmonellosis demonstrates the success of Europe-wide control strategies, notably an industry-led Salmonella control program in poultry in the United Kingdom.

High metabolic potential may contribute to the success of ST131 uropathogenic Escherichia coli.

Uropathogenic Escherichia coli (UPEC) is the predominant cause of urinary tract infection in both hospital and community settings. The recent emergence of multidrug-resistant clones like the O25b:H4-ST131 lineage represents a significant threat to health, and numerous studies have explored the virulence potential of these organisms. Members of the ST131 clone have been described as having variable carriage of key virulence factors, and it has been suggested that additional unidentified factors contribute to virulence. Here we demonstrated that ST131 isolates have high metabolic potential and biochemical profiles that distinguish them from isolates of many other sequence types (STs). A collection of 300 UPEC isolates recovered in 2007 and 2009 in the Northwest region of England were subjected to metabolic profiling using the Vitek2 Advanced Expert System (AES). Of the 47 tests carried out, 30 gave a positive result with at least one of the 300 isolates examined. ST131 isolates demonstrated significant association with eight tests, including those for peptidase, decarboxylase, and alkalinization activity. Metabolic activity also correlated with antibiotic susceptibility profiles, with resistant organisms displaying the highest metabolic potential. This is the first comprehensive study of metabolic potential in the ST131 lineage, and we suggest that high metabolic potential may have contributed to the fitness of members of the ST131 clone, which are able to exploit the available nutrients in both the intestinal and urinary tract environments.

Population structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli from Northwest England.

OBJECTIVES: Multilocus sequence typing (MLST) has been used to characterize diverse pathogens, including uropathogenic Escherichia coli (UPEC). There has been significant interest in the contribution of the O25b:H4-ST131 lineage to UPEC disease, as these isolates are often highly virulent and exhibit multidrug resistance. To reveal the wider impact of sequence type (ST) 131, we have examined its contribution to the overall population structure of UPEC isolates that were not selected on the basis of virulence or antibiotic resistance. METHODS: Three hundred UPEC isolates were recovered from community and hospital urine samples examined by clinical microbiology laboratories in the Northwest region of England in June 2007 and June 2009. They were characterized by susceptibility profiling, MLST and virulence gene PCR. PFGE was used to examine isolates from key clones. RESULTS: The most common lineage was ST73 (16.6%) followed by ST131 (13.3%), ST69 (9%), ST95 (6.3%), ST10 (4.3%) and ST127 (3.6%). ST131 isolates were significantly more likely to exhibit high levels of antibiotic resistance (35% being CTX-M-15 PCR positive) and those of ST127 were the most widely susceptible but carried the highest number of virulence genes. Only when the CTX-M-15-O25b-positive strains were examined was a high level of virulence observed for ST131 isolates. PFGE indicated ongoing local evolution in ST131. CONCLUSIONS: ST131 isolates are well established in the wider UPEC population. This clone is still evolving and we further support suggestions that it represents a real threat to health. We suggest that ST127 is a recently emerged, community-associated, virulent clone that warrants further study.

Development of a multiplex primer extension assay for rapid detection of Salmonella isolates of diverse serotypes.

Food-borne salmonellosis is a major manifestation of gastrointestinal disease in humans across the globe. Accurate and rapid identification methods could positively impact the identification of isolates, enhance outbreak investigation, and aid infection control. The SNaPshot multiplex system is a primer extension-based method that enables multiplexing of single nucleotide polymorphisms (SNPs). Here the method has been developed for the identification of five Salmonella serotypes, commonly detected in the United Kingdom, based on serotype-specific SNPs identified in the multilocus sequence typing (MLST) database of Salmonella enterica. The SNPs, in genes hemD, thrA, purE, and sucA, acted as surrogate markers for S. enterica serovars Typhimurium, Enteritidis, Virchow, Infantis, and Braenderup. The multiplex primer extension assay (MPEA) was conducted in two separate panels and evaluated using 152 Salmonella enterica isolates that were characterized by MLST. The MPEA was shown to be 100% specific and sensitive, within this collection of isolates. The MPEA is a sensitive and specific method for the identification and detection of Salmonella serotypes based upon SNPs seen in MLST data. The method can be applied in less than 6 h and has the potential to improve patient care and source tracing. The utility of the assay for identification of Salmonella serotypes directly from clinical specimens and food samples warrants further investigation.

Methods for determining disease burden and calibrating national surveillance data in the United Kingdom: the second study of infectious intestinal disease in the community (IID2 study).

BACKGROUND: Infectious intestinal disease (IID), usually presenting as diarrhoea and vomiting, is frequently preventable. Though often mild and self-limiting, its commonness makes IID an important public health problem. In the mid 1990s around 1 in 5 people in England suffered from IID a year, costing around pound0.75 billion. No routine information source describes the UK's current community burden of IID. We present here the methods for a study to determine rates and aetiology of IID in the community, presenting to primary care and recorded in national surveillance statistics. We will also outline methods to determine whether or not incidence has declined since the mid-1990s. METHODS/DESIGN: The Second Study of Infectious Intestinal Disease in the Community (IID2 Study) comprises several separate but related studies. We use two methods to describe IID burden in the community - a retrospective telephone survey of self-reported illness and a prospective, all-age, population-based cohort study with weekly follow-up over a calendar year. Results from the two methods will be compared. To determine IID burden presenting to primary care we perform a prospective study of people presenting to their General Practitioner with symptoms of IID, in which we intervene in clinical and laboratory practice, and an audit of routine clinical and laboratory practice in primary care. We determine aetiology of IID using molecular methods for a wide range of gastrointestinal pathogens, in addition to conventional diagnostic microbiological techniques, and characterise isolates further through reference typing. Finally, we combine all our results to calibrate national surveillance data. DISCUSSION: Researchers disagree about the best method(s) to ascertain disease burden. Our study will allow an evaluation of methods to determine the community burden of IID by comparing the different approaches to estimate IID incidence in its linked components.

Increasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom.

BACKGROUND: Campylobacter jejuni is the most common bacterial cause of human infectious intestinal disease. METHODS: We genome sequenced 601 human C. jejuni isolates, obtained from two large prospective studies of infectious intestinal disease (IID1 [isolates from 1993-1996; n = 293] and IID2 [isolates from 2008-2009; n = 93]), the INTEGRATE project [isolates from 2016-2017; n = 52] and the ENIGMA project [isolates from 2017; n = 163]. RESULTS: There was a significant increase in the prevalence of the T86I mutation conferring resistance to fluoroquinolone between each of the three later studies (IID2, INTEGRATE and ENIGMA) and IID1. Although the distribution of major multilocus sequence types (STs) was similar between the studies, there were changes in both the abundance of minority STs associated with the T86I mutation, and the abundance of clones within single STs associated with the T86I mutation. DISCUSSION: Four population-based studies of community diarrhoea over a 25 year period revealed an increase over time in the prevalence of the T86I amongst isolates of C. jejuni associated with human gastrointestinal disease in the UK. Although associated with many STs, much of the increase is due to the expansion of clones associated with the resistance mutation.

Age patterns of persons with campylobacteriosis, England and Wales, 1990-2007.

To explore hypotheses for age-related changes in the incidence of Campylobacter infections in England and Wales during 1990-2007, we analyzed electronic laboratory data. Disease incidence was reduced among children, and the greatest increase in risk was for those >/=60 years of age. Risk factors for campylobacteriosis in the elderly population should be identified.

A Fully Integrated Real-Time Detection, Diagnosis, and Control of Community Diarrheal Disease Clusters and Outbreaks (the INTEGRATE Project): Protocol for an Enhanced Surveillance System.

BACKGROUND: Diarrheal disease, which affects 1 in 4 people in the United Kingdom annually, is the most common cause of outbreaks in community and health care settings. Traditional surveillance methods tend to detect point-source outbreaks of diarrhea and vomiting; they are less effective at identifying low-level and intermittent food supply contamination. Furthermore, it can take up to 9 weeks for infections to be confirmed, reducing slow-burn outbreak recognition, potentially impacting hundreds or thousands of people over wide geographical areas. There is a need to address fundamental problems in traditional diarrheal disease surveillance because of underreporting and subsequent unconfirmed infection by patients and general practitioners (GPs); varying submission practices and selective testing of samples in laboratories; limitations in traditional microbiological diagnostics, meaning that the timeliness of sample testing and etiology of most cases remains unknown; and poorly integrated human and animal surveillance systems, meaning that identification of zoonoses is delayed or missed. OBJECTIVE: This study aims to detect anomalous patterns in the incidence of gastrointestinal disease in the (human) community; to target sampling; to test traditional diagnostic methods against rapid, modern, and sensitive molecular and genomic microbiology methods that identify and characterize responsible pathogens rapidly and more completely; and to determine the cost-effectiveness of rapid, modern, sensitive molecular and genomic microbiology methods. METHODS: Syndromic surveillance will be used to aid identification of anomalous patterns in microbiological events based on temporal associations, demographic similarities among patients and animals, and changes in trends in acute gastroenteritis cases using a point process statistical model. Stool samples will be obtained from patients' consulting GPs, to improve the timeliness of cluster detection and characterize the pathogens responsible, allowing health protection professionals to investigate and control outbreaks quickly, limiting their size and impact. The cost-effectiveness of the proposed system will be examined using formal cost-utility analysis to inform decisions on national implementation. RESULTS: The project commenced on April 1, 2013. Favorable approval was obtained from the Research Ethics Committee on June 15, 2015, and the first patient was recruited on October 13, 2015, with 1407 patients recruited and samples processed using traditional laboratory techniques as of March 2017. CONCLUSIONS: The overall aim of this study is to create a new One Health paradigm for detecting and investigating diarrhea and vomiting in the community in near-real time, shifting from passive human surveillance and management of laboratory-confirmed infection toward an integrated, interdisciplinary enhanced surveillance system including management of people with symptoms. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/13941.

Major uropathogenic Escherichia coli strain isolated in the northwest of England identified by multilocus sequence typing.

A total of 88 uropathogenic Escherichia coli isolates, including 68 isolates from urine and 20 isolates from blood, were characterized by multilocus sequence typing (MLST). MLST has identified an important genetic lineage of E. coli, designated sequence type 131 (ST-131), represented by 52 of these isolates, 51 of which were resistant to extended-spectrum cephalosporins. ST-131 appears to be a drug-resistant uropathogenic strain of E. coli responsible for causing urinary tract infections and bacteremia and is widely disseminated among both community and hospital patients from different geographical areas in the northwest of England. Application of MLST has helped to define the population biology which may underpin the epidemiology of pathogenic E. coli strains. The portability of MLST allows the accurate monitoring of this antibiotic-resistant uropathogenic strain of E. coli and will enhance surveillance for this important group of organisms.

UK epidemic Escherichia coli strains A-E, with CTX-M-15 beta-lactamase, all belong to the international O25:H4-ST131 clone.

OBJECTIVES: Uropathogenic and invasive Escherichia coli O25:H4-ST131 isolates producing CTX-M-15 extended-spectrum beta-lactamase (ESBL) enzymes have recently been shown to be disseminated across the globe. In the UK, many CTX-M-15 ESBL-producing E. coli strains have been previously defined as belonging to the epidemic strains A-E, as determined by PFGE. The present study was carried out to define the relationship between these two groups of pathogenic E. coli. METHODS: Multilocus sequence typing and PFGE were used for molecular characterization of a collection of 61 ESBL-producing E. coli isolates from across the UK. RESULTS: Strains A to E all belonged to the ST131 clone, further underscoring the epidemiological importance of this lineage. CONCLUSIONS: The future spread of the ST131 clone, and its UK variants, should be monitored closely and the pathogenic mechanisms explaining their success should be investigated.

Molecular epidemiology of Campylobacter jejuni populations in dairy cattle, wildlife, and the environment in a farmland area.

We describe a cross-sectional study of the molecular epidemiology of Campylobacter jejuni in a dairy farmland environment, with the aim of elucidating the dynamics of horizontal transmission of C. jejuni genotypes among sources in the area. A collection of 327 C. jejuni isolates from cattle, wildlife, and environmental sources in a 100-km(2) area of farmland in northwest England was characterized by multilocus sequence typing. A total of 91 sequence types and 18 clonal complexes were identified. Clonal complexes ST-21, ST-45, and ST-61, which have been frequently associated with human disease, were the most commonly recovered genotypes in this study. In addition, widely distributed genotypes as well as potentially host-associated genotypes have been identified, which suggests that both restricted and interconnecting pathways of transmission may be operating in the dairy farmland environment. In particular, the ST-61 complex and the ST-21 complex were significantly associated with cattle. In contrast, complex strains ST-45, ST-952, and ST-677 were isolated predominantly from wild birds, wild rabbits, and environmental water. A considerable number of novel sequence types have also been identified, which were unassigned to existing clonal complexes and were frequently isolated from wildlife and environmental sources. The segregated distribution of genotypes among samples from different sources suggests that their transmission to humans is perhaps via independent routes. Insight into the dynamics and interactions of C. jejuni populations between important animal reservoirs and their surrounding environment would improve the identification of sources of Campylobacter infection and the design of control strategies.

Longitudinal study of the molecular epidemiology of Campylobacter jejuni in cattle on dairy farms.

Multilocus sequence typing (MLST), an accurate and phylogenetically robust characterization method for population studies of Campylobacter, was applied to Campylobacter jejuni isolates (n = 297) from the fecal samples of cattle from five dairy farms in Cheshire, United Kingdom, collected throughout 2003. The population dynamics of the C. jejuni strains, as identified by the occurrence of sequence types and clonal complexes, demonstrated variations within and between cattle populations over time. Three clonal lineages have emerged to predominate among the cattle isolates, namely, the ST-61 complex (24.2%), ST-21 complex (23.6%), and ST-42 complex (20.5%). This provided further evidence that the ST-61 clonal complex may present a cattle-adapted C. jejuni genotype. In addition, the ST-42 clonal complex may also represent an important cattle-associated genotype. Strong geographical associations for these genotypes were also found among the farms. This is the first longitudinal study and the largest study to date for C. jejuni involving cattle populations using MLST for accurate strain characterization. This study shows the important associations between cattle and C. jejuni clonal complexes ST-61, ST-21, and ST-42, and it suggests that cattle and/or dairy products are likely to be a source of the human Campylobacter gastroenteritis caused by such genotypes. The reported findings have significant implications for the design of effective intervention strategies for disease control and prevention.

An Ontology to Improve Transparency in Case Definition and Increase Case Finding of Infectious Intestinal Disease: Database Study in English General Practice.

BACKGROUND: Infectious intestinal disease (IID) has considerable health impact; there are 2 billion cases worldwide resulting in 1 million deaths and 78.7 million disability-adjusted life years lost. Reported IID incidence rates vary and this is partly because terms such as "diarrheal disease" and "acute infectious gastroenteritis" are used interchangeably. Ontologies provide a method of transparently comparing case definitions and disease incidence rates. OBJECTIVE: This study sought to show how differences in case definition in part account for variation in incidence estimates for IID and how an ontological approach provides greater transparency to IID case finding. METHODS: We compared three IID case definitions: (1) Royal College of General Practitioners Research and Surveillance Centre (RCGP RSC) definition based on mapping to the Ninth International Classification of Disease (ICD-9), (2) newer ICD-10 definition, and (3) ontological case definition. We calculated incidence rates and examined the contribution of four supporting concepts related to IID: symptoms, investigations, process of care (eg, notification to public health authorities), and therapies. We created a formal ontology using ontology Web language. RESULTS: The ontological approach identified 5712 more cases of IID than the ICD-10 definition and 4482 more than the RCGP RSC definition from an initial cohort of 1,120,490. Weekly incidence using the ontological definition was 17.93/100,000 (95% CI 15.63-20.41), whereas for the ICD-10 definition the rate was 8.13/100,000 (95% CI 6.70-9.87), and for the RSC definition the rate was 10.24/100,000 (95% CI 8.55-12.12). Codes from the four supporting concepts were generally consistent across our three IID case definitions: 37.38% (3905/10,448) (95% CI 36.16-38.5) for the ontological definition, 38.33% (2287/5966) (95% CI 36.79-39.93) for the RSC definition, and 40.82% (1933/4736) (95% CI 39.03-42.66) for the ICD-10 definition. The proportion of laboratory results associated with a positive test result was 19.68% (546/2775). CONCLUSIONS: The standard RCGP RSC definition of IID, and its mapping to ICD-10, underestimates disease incidence. The ontological approach identified a larger proportion of new IID cases; the ontology divides contributory elements and enables transparency and comparison of rates. Results illustrate how improved diagnostic coding of IID combined with an ontological approach to case definition would provide a clearer picture of IID in the community, better inform GPs and public health services about circulating disease, and empower them to respond. We need to improve the Pathology Bounded Code List (PBCL) currently used by laboratories to electronically report results. Given advances in stool microbiology testing with a move to nonculture, PCR-based methods, the way microbiology results are reported and coded via PBCL needs to be reviewed and modernized.

Validation of three rapid screening methods for detection of verotoxin-producing Escherichia coli in foods: interlaboratory study.

An interlaboratory study was conducted for the validation of 3 methods for the detection of all verotoxin-producing Escherichia coli (VTEC) in foods. The methods were a multi-analyte 1-step lateral flow immunoassay (LFIA) for detection of E. coli O157 and verotoxin (VT); an enzyme-linked immunosorbent assay targeted against VT1, VT2, and VT2c (VT-ELISA); and a polymerase chain reaction (PCR) method for detection of VT genes (VT-PCR). Aliquots (25 g or 25 mL) of 4 food types (raw minced [ground] beef, unpasteurized milk, unpasteurized apple juice [cider], and salami) were individually inoculated with low numbers (<9 to 375 cells/25 g) of 6 test strains of E. coli (serogroups O26, O103, O111, O145, and O157) with differing VT-producing capabilities. Five replicates for each test strain and 5 uninoculated samples were prepared for each food type. Fourteen participating laboratories analyzed samples using the LFIA, 9 analyzed the samples by ELISA, and 9 by PCR. The LFIA for O157 and VT had a specificity (correct identification of negative samples) of 92 and 94%, respectively, and a sensitivity (correct identification of positive samples) of 94 and 55%, respectively. The VT-ELISA and VT-PCR had a specificity of 98 and 99%, respectively, and a sensitivity of 89 and 72%, respectively.

Antimicrobial activity of novel nanostructured Cu-SiO2 coatings prepared by chemical vapour deposition against hospital related pathogens.

There is increasing recognition that the healthcare environment acts as an important reservoir for transmission of healthcare acquired infections (HCAI). One method of reducing environmental contamination would be use of antimicrobial materials. The antimicrobial activity of thin silica-copper films prepared by chemical vapour deposition was evaluated against standard strains of bacteria used for disinfectant testing and bacteria of current interest in HCAI. The structure of the coatings was determined using Scanning Electron Microscopy and their hardness and adhesion to the substrate determined. Antimicrobial activity was tested using a method based on BS ISO 22196:2007. The coatings had a pale green-brown colour and had a similar hardness to steel. SEM showed nano-structured aggregates of Cu within a silica matrix. A log10 reduction in viability of >5 could be obtained within 4 h for the disinfectant test strains and within 6 h for producing Acinetobacter baumannii, Klebsiella pneumoniae and Stenotrophomonas maltophilia. Activity against the other hospital isolates was slower but still gave log10 reduction factors of >5 for extended spectrum ß-lactamase producing Escherichia coli and >3 for vancomycin resistant Enterococcus faecium, methicillin resistant Staphylococcus aureus and Pseudomonas aeruginosa within 24 h. The results demonstrate the importance of testing antimicrobial materials destined for healthcare use against isolates of current interest in hospitals as well as standard test strains. The coatings used here can also be applied to substrates such as metals and ceramics and have potential applications where reduction of microbial environmental contamination is desirable.

Universal extraction method for gastrointestinal pathogens.

A universal stool extraction method for recovery of nucleic acids (NAs) from gastrointestinal pathogens was developed to support rapid diagnostics for the London 2012 Olympics. The method involved mechanical disruption (bead beating) of the stools, followed by automated extraction and detection using real-time PCR. This method had been used extensively in the Second Infectious Intestinal Disease Study (IID2) for the isolation of NA from bacteria and parasites (and was effective for the robust recovery of Cryptosporidium spp.) but had not been used for enteric viruses. To ensure this method was universally suitable, panels of samples known to contain target bacteria, viruses or parasites were processed in triplicate using the pre-treatment method routinely used for each target and the new extraction method (bead beating). The extracts were tested using real-time PCR and the cycle threshold values were compared. The results from this study showed that bead beating improved yields for the bacterial and parasitic targets and was suitable for the viral targets. The implementation of this universal method should confer cost- and time-saving benefits and streamline the processes required for the characterization of an array of pathogens from faecal samples.

A real-time PCR assay for the detection of Campylobacter jejuni in foods after enrichment culture.

A real-time PCR assay was developed for the quantitative detection of Campylobacter jejuni in foods after enrichment culture. The specificity of the assay for C. jejuni was demonstrated with a diverse range of Campylobacter species, related organisms, and unrelated genera. The assay had a linear range of quantification over six orders of magnitude, and the limit of detection was approximately 12 genome equivalents. The assay was used to detect C. jejuni in both naturally and artificially contaminated food samples. Ninety-seven foods, including raw poultry meat, offal, raw shellfish, and milk samples, were enriched in blood-free Campylobacter enrichment broth at 37 degrees C for 24 h, followed by 42 degrees C for 24 h. Enrichment cultures were subcultured to Campylobacter charcoal-cefoperazone-deoxycholate blood-free selective agar, and presumptive Campylobacter isolates were identified with phenotypic methods. DNA was extracted from enrichment cultures with a rapid lysis method and used as the template in the real-time PCR assay. A total of 66 samples were positive for C. jejuni by either method, with 57 samples positive for C. jejuni by subculture to selective agar medium and 63 samples positive in the real-time PCR assay. The results of both methods were concordant for 84 of the samples. The total time taken for detection from enrichment broth samples was approximately 3 h for the real-time PCR assay, with the results being available immediately at the end of PCR cycling, compared to 48 h for subculture to selective agar. This assay significantly reduces the total time taken for the detection of C. jejuni in foods and is an important model for other food-borne pathogens.

Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation.

A total of 814 isolates of the foodborne pathogen Campylobacter jejuni were characterized by multilocus sequence typing (MLST) and analysis of the variation of two cell-surface components: the heat-stable (HS) serotyping antigen and the flagella protein FlaA short variable region. We identified 379 combinations of the MLST loci (sequence types) and 215 combinations of the cell-surface components among these isolates, which had been obtained from human disease, animals, food, and the environment. Despite this diversity, 748 (92%) of the isolates belonged to one of 17 clonal complexes, 6 of which contained many (318, 63%) of the human disease isolates. Several clonal complexes exhibited associations with isolation source or particular cell-surface components; however, the latter were poorly predictive of clonal complex. These data demonstrate that the clonal complex, as defined by MLST, is an epidemiologically relevant unit for both long and short-term investigations of C. jejuni epidemiology.