Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis.

Since April 2015, whole genome sequencing (WGS) has been the routine test for Salmonella identification, surveillance and outbreak investigation at the national reference laboratory in England and Wales. In May 2015, an outbreak of Salmonella Enteritidis cases was detected using WGS data and investigated. UK cases were interviewed to obtain a food history and links between suppliers were mapped to produce a food chain network for chicken eggs. The association between the food chain network and the phylogeny was explored using a network comparison approach. Food and environmental samples were taken from premises linked to cases and tested for Salmonella. Within the outbreak single nucleotide polymorphism defined cluster, 136 cases were identified in the UK and 18 in Spain. One isolate from a food containing chicken eggs was within the outbreak cluster. There was a significant association between the chicken egg food chain of UK cases and phylogeny of outbreak isolates. This is the first published Salmonella outbreak to be prospectively detected using WGS. This outbreak in the UK was linked with contemporaneous cases in Spain by WGS. We conclude that UK and Spanish cases were exposed to a common source of Salmonella-contaminated chicken eggs.

Economic evaluation of treatment for MRSA complicated skin and soft tissue infections in Glasgow hospitals.

In the UK, methicillin-resistant Staphylococcus aureus (MRSA)-associated skin and soft tissue infections (SSTIs) are predominantly managed in the hospital using intravenous (IV) glycopeptides. We set out to explore the potential for and relative healthcare costs of earlier hospital discharge through switch to oral antibiotic therapy (linezolid or rifampicin and doxycycline) or continuation of IV therapy (teicoplanin) via an outpatient parenteral antimicrobial therapy (OPAT) service. Over 16 months, 173 patients were retrospectively identified with MRSA SSTI, of whom 82.8 % were treated with IV therapy. Thirty-seven patients were potentially suitable for earlier discharge with outpatient therapy. The model assumed 3 days of inpatient management and a maximum of 14 days of outpatient therapy. For the status quo, where patients received only inpatient care with IV therapy, hospital costs were calculated at £12,316 per patient, with 97 % of costs accounted for by direct bed day costs. The mean total cost savings achievable through OPAT or oral therapy was estimated to be £6,136 and £6,159 per patient treated, respectively. A significant proportion of patients with MRSA SSTI may be suitable for outpatient management with either oral therapy or via OPAT, with the potential for significant reduction in healthcare costs.

Investigating the link between the presence of enteroaggregative Escherichia coli and infectious intestinal disease in the United Kingdom, 1993 to 1996 and 2008 to 2009.

There are an estimated 17 million human diarrhoea cases annually in the United Kingdom. In 2008 and 2009, enteroaggregative E. coli (EAEC) were identified in 1.9% of stools. However, it remains unclear whether there is a causal link between presence of EAEC and disease. This study used bacterial load, the presence of co-infections and demographic data to assess if EAEC was independently associated with intestinal infectious disease. Quantitative real-time PCR data (Ct values) generated directly from stool specimens for several pathogen targets were analysed to identify multiple pathogens, including EAEC, in the stools of cases and healthy controls. Sensitivity and specificity using Ct value (60% and 60%) was not useful for identifying cases or controls, but an independent association between disease and EAEC presence was demonstrated: multivariate logistic regression for EAEC presence (odds ratio: 2.41; 95% confidence interval: 1.78­3.26; p<0.001). The population-attributable fraction was 3.3%. The group of bacteria known as EAEC are associated with gastrointestinal disease in at least half of the cases with EAEC positive stools. We conclude that the current definition of EAEC, by plasmid gene detection, includes true pathogens as well as non-pathogenic variants.

Antibiotic stewardship and early discharge from hospital: impact of a structured approach to antimicrobial management.

OBJECTIVES: To assess the impact of an infection team review of patients receiving antibiotics in six hospitals across the UK and to establish the suitability of these patients for continued care in the community. METHODS: An evaluation audit tool was used to assess all patients on antibiotic treatment on acute wards on a given day. Clinical and antibiotic use data were collected by an infection team (doctor, nurse and antibiotic pharmacist). Assessments were made of the requirement for continuing antibiotic treatment, route and duration [including intravenous (iv)/oral switch] and of the suitability of the patients for discharge from hospital and their requirement for community support. RESULTS: Of 1356 patients reviewed, 429 (32%) were on systemic antibiotics, comprising 165 (38%) on iv ±â€Šoral antibiotics and 264 (62%) on oral antibiotics alone. Ninety-nine (23%) patients (including 26 on iv antibiotics) had their antibiotics stopped immediately on clinical grounds. The other 330 (77%) patients (including 139 on iv antibiotics) needed to continue antibiotics, although 47 (34%) could be switched to oral. Eighty-nine (21%) patients were considered eligible for discharge, comprising 10 who would have required outpatient parenteral antibiotic therapy (OPAT), 55 who were suitable for oral outpatient treatment and 24 who had their antibiotics stopped. CONCLUSIONS: Infection team review had a significant impact on antimicrobial use, facilitating iv to oral switch and a reduction in the volume of antibiotic use, possibly reducing the risk of healthcare-associated complications and infections. It identified many patients who could potentially have been managed in the community with appropriate resources, saving 481 bed-days. The health economics are reported in a companion paper.

A foodborne outbreak of Salmonella Bareilly in the United Kingdom, 2010.

We report the preliminary findings of the investigation of an outbreak of foodborne Salmonella Bareilly. Between August and November 2010, there were 231 laboratory-confirmed reports of S. Bareilly in the United Kingdom. A case­control study showed that consumption of bean sprouts was significantly associated with illness. The investigation concluded that raising public awareness to ensure the correct preparation of raw bean sprouts during cooking was the principal means of preventing further cases.

Description of demographic and clinical characteristics of extrapulmonary tuberculosis in Shandong, China.

BACKGROUND: According to the clinical manifestation, tuberculosis (TB) is divided into pulmonary tuberculosis (PTB) and extrapulmonary tuberculosis (EPTB). The incidence rate of EPTB has increased in many countries. The demographic and clinical characteristics of EPTB in China remain still unclear. MATERIALS AND METHODS: We retrospectively analyzed the medical records of 5,624 hospitalized patients with positive M. tuberculosis culture between January 2008 and June 2013 in Shandong province. We investigated the epidemiological, demographic, and clinical characteristics of patients with EPTB. RESULTS: Among 5,624 hospitalized TB patients with positive M. tuberculosis culture, 4,277 (76.05 %) had PTB, 618 (10.99 %) had EPTB, and 729 (12.96 %) had both PTB and EPTB. The proportion of EPTB increased significantly from 6.97 % in 2008 to 19.98 % in 2012 (p <0.001).  The most frequent sites or foci of EPTB were pleura (63.27 %), followed by bone/joint (13.75 %), and lymph nodes (8.9 %). The mean duration of treatment for pleural TB was eight months and for EPTB in the other foci was more than 15 months. CONCLUSION: The proportion of EPTB in Shandong province has significantly increased. Clinicians need to be aware of the trend and remain vigilant against EPTB. EPTB requires prolonged treatment, and clinical supervision should be strengthened to prevent drug resistance. HIPPOKRATIA 2020, 24(1): 27-32.

Update of Clostridium difficile infection due to PCR ribotype 027 in Europe, 2008.

Outbreaks of Clostridium difficile infections (CDI) with increased severity, high relapse rate and significant mortality have been related to the emergence of a new, hypervirulent C. difficile strain in North America and Europe. This emerging strain is referred to as PCR ribotype 027 (Type 027). Since 2005, individual countries have developed surveillance studies about the spread of type 027.C. difficile Type 027 has been reported in 16 European countries. It has been responsible for outbreaks in Belgium, Germany, Finland, France, Ireland, Luxembourg, The Netherlands, Switzerland and the United Kingdom (England, Wales, Northern Ireland and Scotland). It has also been detected in Austria, Denmark, Sweden, Norway, Hungary, Poland and Spain. Three countries experienced imported patients with CDI due to Type 027 who acquired the infection abroad.The antimicrobial resistance pattern is changing, and outbreaks due to clindamycin-resistant ermB positive Type 027 strains have occurred in three European countries. Ongoing epidemiological surveillance of cases of CDI, with periodic characterisation of the strains involved, is required to detect clustering of cases in time and space and to monitor the emergence of new, highly virulent clones.

How to: diagnose infection caused by Clostridium difficile.

BACKGROUND: Clostridium difficile is recognized as the major agent responsible for nosocomial diarrhoea. In the context of recent increase in the incidence and severity of C. difficile infections (CDI), an accurate diagnosis is essential for optimal treatment and prevention, but continues to be challenging. AIMS: The present article reviews each key step of CDI diagnosis including stool selection, methods and strategies used, and interpretation of the results. SOURCES: The most recent guidelines for CDI diagnosis published by scientific societies were reviewed. CONTENT: CDI diagnosis is based on clinical presentation and laboratory tests confirming the presence of toxigenic strain or toxins in stools. Stool selection is crucial and can be improved by implementing rejection criteria and a strict policy for appropriate testing. Multiple laboratory tests detecting different targets (free toxin or presence of a potentially toxigenic strain) are commercially available. However, none of these tests combine high sensitivity and specificity to diagnose CDI, low hands-on time and low cost. An optimized diagnosis can be achieved by implementing a two- or three-step algorithm. Algorithms currently recommended by the ESCMID comprise a screening test with high sensitivity followed by a more specific test to detect free toxins. Presence of free toxins in stools has been shown to better correlate with severe outcome whereas nucleic acid amplification tests may lead to an over-diagnosis by detecting asymptomatic carriers of a toxigenic strain. IMPLICATION: To date, no single test can accurately diagnose CDI. Guidelines from the ESCMID recommend a two- or three-step algorithm for optimal CDI detection.

Trends in mortality following Clostridium difficile infection in Scotland, 2010-2016: a retrospective cohort and case-control study.

BACKGROUND: National surveillance of Clostridium difficile infection (CDI) in Scotland enables the monitoring of trends in incidence rates but not mortality. AIM: To assess factors associated with mortality for all CDI cases aged ≥15 years in Scotland between 2010 and 2016. METHODS: All CDI cases aged ≥15 years in Scotland between 2010 and 2016 were linked to hospital admission and mortality datasets. Logistic regression was used to assess factors associated with mortality (30-day all-cause). A case-control study of a hospitalized subset of cases and matched hospitalized controls assessed the impact of CDI on mortality and length of stay. FINDINGS: Thirty-day all-cause mortality decreased over the seven-year period (from 20.5% to 15.6%; P < 0.001), mainly among healthcare-associated CDI (HA-CDI). Increased age, higher Charlson score, HA-CDI, as well as liver, heart and malignancy comorbidities were associated with higher mortality. No association was observed between polymerase chain reaction ribotype and higher mortality, though 015 and 078 were associated with lower mortality. Adjusted odds ratio (OR) for 30-day mortality in hospitalized CDI cases compared to controls was 2.67 (95% confidence interval (CI): 2.42-2.94; P < 0.001). Whereas mortality declined over time in cases and controls, the trend in ORs remained relatively stable. Having CDI increased additional mean length of stay beyond infection by 22.3% (95% CI: 18.0-26.8%; P < 0.001). CONCLUSION: CDI is associated with an almost three-fold increase in 30-day mortality and places an increased burden on hospital resources by increasing mean LOS beyond the infection date by 22.3%. The decreasing CDI mortality trends may be due to overall improvements in mortality among the general and hospital population of Scotland. Therefore, despite large declines in incidence rates, CDI remains a serious healthcare problem.

Guidance document for prevention of Clostridium difficile infection in acute healthcare settings.

SCOPE: Clostridium difficile infection (CDI) is the most important infective cause of healthcare-associated diarrhoea in high income countries and one of the most important healthcare-associated pathogens in both Europe and the United States. It is associated with high morbidity and mortality resulting in both societal and financial burden. A significant proportion of this burden is potentially preventable by a combination of targeted infection prevention and control measures and antimicrobial stewardship. The aim of this guidance document is to provide an update on recommendations for prevention of CDI in acute care settings to provide guidance to those responsible for institutional infection prevention and control programmes. METHODS: An expert group was set up by the European society of clinical microbiology and infectious diseases (ESCMID) Study Group for C. difficile (ESGCD), which performed a systematic review of the literature on prevention of CDI in adults hospitalized in acute care settings and derived respective recommendations according to the GRADE approach. Recommendations are stratified for both outbreak and endemic settings. QUESTIONS ADDRESSED BY THE GUIDELINE AND RECOMMENDATIONS: This guidance document provides thirty-six statements on strategies to prevent CDI in acute care settings, including 18 strong recommendations. No recommendation was provided for three questions.

Investigation of outbreaks of Pneumocystis jirovecii pneumonia in two Scottish renal units.

Pneumocystis jirovecii is recognized as an opportunistic pathogen. In recent years, human-to-human transmission of P. jirovecii has been demonstrated. However, outbreaks of P. jirovecii infections are not well defined because the epidemiological setting that facilitates transmission is not fully understood. This article describes two outbreaks of P. jirovecii pneumonia (PCP) in renal transplant patients in the West of Scotland. In total, 25 patients in two geographically contiguous locations were affected. Allele B was identified as the dominant type, along with allele A3. It was not possible to determine the exact reason for clustering of cases, although the outpatient clinic setting featured in one of the outbreaks. The outbreaks ceased with the use of trimethoprim-sulphamethoxazole prophylaxis; the target populations that received prophylaxis were different in the two outbreaks. Infection control teams should be alert to the possibility of outbreaks of PCP.

First outbreak of colonization by linezolid- and glycopeptide-resistant Enterococcus faecium harbouring the cfr gene in a UK nephrology unit.

AIM: To describe an outbreak of colonization by linezolid- and glycopeptide-resistant Enterococcus faecium harbouring the cfr gene in a UK nephrology unit. METHODS: Isolates of linezolid-resistant E. faecium were typed by pulsed-field gel electrophoresis (PFGE), and examined by polymerase chain reaction (PCR) and sequencing for the transmissible cfr gene that confers resistance to linezolid. Enhanced environmental cleaning, initial and weekly screening of all patients, and monitoring of adherence to standard infection control precautions were implemented. FINDINGS: Five patients with pre-existing renal disease were found to have rectal colonization with linezolid-resistant E. faecium over a two-week period. The index case was a 57-year-old male from India who had travelled to the UK. One patient also had a linezolid-resistant E. faecium of a different PFGE profile isolated from a heel wound. All isolates were confirmed to harbour the cfr gene by PCR and Sanger sequencing, and all were resistant to glycopeptides (VanA phenotype). CONCLUSIONS: This article describes the first UK outbreak with a single strain of linezolid- and glycopeptide-resistant E. faecium harbouring the cfr gene, affecting five patients in a nephrology unit. Following the implementation of aggressive infection control measures, no further cases were detected beyond a two-week period.

Guidelines for the control and prevention of meticillin-resistant Staphylococcus aureus (MRSA) in healthcare facilities.

Meticillin-resistant Staphylococcus aureus (MRSA) remains endemic in many UK hospitals. Specific guidelines for control and prevention are justified because MRSA causes serious illness and results in significant additional healthcare costs. Guidelines were drafted by a multi-disciplinary group and these have been finalised following extensive consultation. The recommendations have been graded according to the strength of evidence. Surveillance of MRSA should be undertaken in a systematic way and should be fed back routinely to healthcare staff. The inappropriate or unnecessary use of antibiotics should be avoided, and this will also reduce the likelihood of the emergence and spread of strains with reduced susceptibility to glycopeptides, i.e. vancomycin-intermediate S. aureus/glycopeptide-intermediate S. aureus (VISA/GISA) and vancomycin-resistant S. aureus (VRSA). Screening for MRSA carriage in selected patients and clinical areas should be performed according to locally agreed criteria based upon assessment of the risks and consequences of transmission and infection. Nasal and skin decolonization should be considered in certain categories of patients. The general principles of infection control should be adopted for patients with MRSA, including patient isolation and the appropriate cleaning and decontamination of clinical areas. Inadequate staffing, especially amongst nurses, contributes to the increased prevalence of MRSA. Laboratories should notify the relevant national authorities if VISA/GISA or VRSA isolates are identified.

Development of a sporicidal test method for Clostridium difficile.

BACKGROUND: Disinfectants with claimed activity against Clostridium difficile must be evaluated to ensure efficacy against the spores that comprise an environmental source of patient infection. Unfortunately there is, at present, no generally accepted method for evaluating these disinfectants. In the absence of such a method, laboratories have to adapt protocols that were not designed for products used in medical environments and consequently may use inappropriate test organisms, exposure times, and pass criteria. AIM: To develop and evaluate a method for testing the activity of disinfectants against C. difficile spores using exposure times and pass criteria which are relevant to clinical application. METHODS: A Joint Working Party of the Healthcare Infection Society (HIS) and the Advisory Committee on Antimicrobial Resistance and Healthcare Associated Infections (ARHAI) of the Department of Health in England was assembled. The Working Party adapted a previously described enzyme-based method for spore purification (the Clospore method) using an exposure time of 5 min and a 5 log10 kill as a pass criterion. FINDINGS: Evaluation of the method by three laboratories demonstrated that the method is simple to follow and that the results are repeatable and reproducible. CONCLUSION: The method described by the Working Party produces a clean suspension with a high titre of spores. It is recommended that, for a disinfectant used in the environment, the product should demonstrate a 5 log10 reduction in 5 min under clean or dirty conditions to fulfil the requirements of the test.

Typing of Clostridium difficile causing diarrhoea in an orthopaedic ward.

In an outbreak of diarrhoeal disease in an orthopaedic ward Clostridium difficile was isolated from all six patients with diarrhoea. Attempts were made to type these isolates by means of antibiogram, detection of pre-formed enzymes, analysis of surface proteins by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting, and plasmid profile analysis. This showed that a single strain (type E) indistinguishable by the four distinct methods of typing, was isolated from all six patients at some time during their episodes of diarrhoea. Relapse was caused by the acquisition of a new strain in two patients, and by re-emergence or reacquisition of the original strain in two patients. The immunochemical method was the most sensitive and discriminatory of the typing strategies adopted.

Use of bar code readers and programmable keypads to improve the speed and accuracy of manual data entry in the clinical microbiology laboratory: experience of two laboratories.

AIM: To assess the effect of the use of bar code readers and programmable keypads for entry of specimen details and results in two microbiology laboratories. METHODS: The solutions selected in each laboratory are described. The benefits resulting from the implementation were measured in two ways. The speed of data entry and error reduction were measured by observation. A questionnaire was completed by users of bar codes. RESULTS: There were savings in time and in reduced data entry errors. Average time to enter a report by keyboard was 21.1 s v 14.1 s for bar coded results entry. There were no observed errors with the bar code readers but 55 errors with keystroke entries. The laboratory staff of all grades found the system fast, easy to use, and less stressful than conventional keyboard entry. CONCLUSIONS: Indirect time savings should accrue from the observed reduction in incorrectly entered data. Any microbiology laboratory seeking to improve the accuracy and efficiency of data entry into their laboratory information systems should consider the adoption of this technology which can be readily interfaced to existing terminals.

Comparison of two automated quantitative immunoassays for the determination of C reactive protein concentrations.

Two quantitative, automated methods for the determination of C reactive protein (CRP) were compared: turbidimetry (Cobas Fara II, Roche, Welwyn Garden City, UK) and fluorescence polarisation TDx, Abbott, Wokingham, UK). One hundred and twenty routine serum samples submitted for measurement of CRP were tested using both procedures. The results were compared using regression line analysis and showed a high degree of correlation (r2 = 0.99, X coefficient = 1.01, constant = 0.11). C reactive protein can be accurately measured using the automated turbidimetric method which can be recommended as an alternative to fluorescence polarisation.

The diagnostic value of anti-neutrophil cytoplasmic antibody testing in a routine clinical setting.

Anti-neutrophil cytoplasmic antibody (ANCA) tests are a routine clinical assay in most UK hospitals. We examined the role of routine ANCA testing in achieving a diagnosis of systemic vasculitis in a routine clinical setting. From April 1996 to March 2000, 2734 samples from five hospital departments were tested for ANCA by indirect immunofluorescence (IIF) at a single laboratory. After April 1999, enzyme-linked immunosorbent assays (ELISAs) were performed on all IIF-positive samples. Clinical diagnosis was determined for all patients with a positive IIF ANCA, and a sample of the ANCA-negative patients. Some 2-18% of patients with suspected ANCA-associated systemic vasculitis (AASV) had positive IIF ANCA. The AASV diagnosis was confirmed in 0-56% of these cases. Analysis by department suggested that 88-100% of patients with a positive IIF ANCA did not have AASV, except in the Rheumatology department. The positive predictive value (PPV) of IIF ANCA for AASV was 59% and the negative predictive value (NPV) was 84%. Of the patients with proven AASV, 41% did not have ANCA on IIF. Combined ANCA testing by IIF/ELISA had a higher sensitivity and PPV but lower specificity than IIF alone for AASV. For the combined IIF/ELISA test, only the Rheumatology department had a sensitivity or PPV >0% for AASV. The PPV of ANCA by IIF/ELISA for AASV was 79% and the NPV was 63%. The ANCA test is being widely applied with very poor return. Guidelines for more effective usage are proposed.