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.

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.

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.

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.

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.

Plasmid profiles and restriction enzyme fragmentation patterns of plasmids of methicillin-sensitive and methicillin-resistant isolates of Staphylococcus aureus from hospital and the community.

The number, frequency distribution and restriction enzyme fragmentation patterns of plasmids harboured by 163 methicillin-sensitive isolates of Staphylococcus aureus (MSSA) and 53 methicillin-resistant isolates (MRSA) were compared. Plasmids were demonstrated in less than half of the MSSA isolates; their frequency distribution did not differ from that predicted by a simple model of plasmid distributions. In contrast, all the MRSA isolates harboured plasmids, their distribution suggesting dissemination of a limited number of clones within the hospital. Among 72 MSSA isolates harbouring plasmids, 38 different restriction patterns were identified. There were fewer patterns among MRSA isolates; 11 were observed, and two predominant patterns accounted for 68% of those identified. These restriction patterns correlated with the presence or absence of aminoglycoside resistance. A multicopy plasmid of 2.6 kb was present in both MSSA and MRSA isolates that harboured more than one plasmid; it had the same restriction pattern irrespective of its source. The importance of these results in choosing a method of studying the spread of staphylococci is discussed.

Characterisation of methicillin-resistant Staphylococcus aureus by biotyping, immunoblotting and restriction enzyme fragmentation patterns.

We have characterised 45 isolates of methicillin-resistant Staphylococcus aureus (MRSA) from Glasgow Royal Infirmary by means of simple biotyping, immunoblotting of exported proteins and restriction enzyme fragmentation patterns (REFP) of plasmid DNA. The strains were subdivided into four groups (A-D) on the basis of biotype. Immunoblotting and restriction enzyme fragmentation generated a number of unique patterns. Analysis of these patterns by means of Dice coefficients of similarity separated them into two major immunoblot groups (Blot1 and Blot2) and two major REFP groups (FP1 and FP2). There was strong positive correlation between Blot1 and FP1 groups and between Blot2 and FP2 groups. In addition, Blot1-FP1 isolates were almost exclusively of biotypes A or C, whereas Blot2-FP2 isolates were of biotypes B or D. The methods described here have provided comprehensive epidemiological information which has been valuable in studying the origin and spread of MRSA.

Comparison of enterotoxins and haemolysins produced by methicillin-resistant (MRSA) and sensitive (MSSA) Staphylococcus aureus.

A collection of 201 isolates of Staphylococcus aureus was examined: 152 methicillin-sensitive S. aureus (MSSA) comprised 48 blood culture isolates (BC) and 58 isolates from routine diagnostic specimens (RD) from Glasgow Royal Infirmary (GRI), and 46 strains from nasal swabs of patients attending a general practitioner (GP); 49 isolates were of methicillin-resistant S. aureus (MRSA) from GRI. We have previously shown that the MRSA could be divided into two sub-groups on the basis of sensitivity or resistance to aminoglycoside antibiotics. Production of enterotoxins A, B, C and D, and alpha-, beta-, gamma- and delta- haemolysins was detected by reverse passive latex agglutination (RPLA) and agar overlay methods respectively: 60% of BC MSSA and a similar proportion of MSSA from other sources produced enterotoxin; 87% of aminoglycoside-sensitive MRSA produced enterotoxin (89% of these produced enterotoxin A alone) whereas only 27% of aminoglycoside-resistant MRSA were enterotoxin-positive, significantly less than either MSSA or aminoglycoside-sensitive MRSA. The proportion of haemolysin-producing isolates did not differ amongst the isolates of MSSA and MRSA; there was no difference in the distributions of haemolysins between aminoglycoside-sensitive and -resistant strains of MRSA. GP MSSA had higher and lower numbers of gamma- and delta-haemolysin producers respectively than other S. aureus isolates. alpha-Haemolysin producers were commoner amongst MRSA isolates, which were also more likely than MSSA isolates to produce several haemolysins. Differences in enterotoxin production between aminoglycoside-sensitive and -resistant MRSA isolates reflect subgroups previously defined by biotype, phage type, immunoblot and restriction enzyme fragmentation pattern data, and provide further evidence for the existence of two major MRSA clones in GRI.

A comparison of immunomagnetic separation, direct culture and polymerase chain reaction for the detection of verocytotoxin-producing Escherichia coli O157 in human faeces.

Verocytotoxin-producing Escherichia coli O157 (O157 VTEC) has become well recognized as an important enteric pathogen. The number of organisms present in environmental and clinical samples may be low and efforts have been made to increase the sensitivity of O157 VTEC detection. Immunomagnetic seperation (IMS) has been shown to improve O157 VTEC detection in bovine faeces and food samples. A milkborne outbreak of O157 VTEC infection allowed us to compare the isolation rates from human faeces by IMS, direct faecal culture on sorbitol-MacConkey agar and a PCR test for verotoxin gene carriage. Of 142 faecal samples examined, 20 were positive on both direct culture and IMS and a further 13 on IMS alone. Therefore, IMS increased the detection rate of individual cases of O157 VTEC infection and also compared well with PCR. We recommend IMS for use in routine diagnostic laboratories where a more sensitive method than direct faecal culture is required for O157 VTEC isolation.

Eradication of a resistant Pseudomonas aeruginosa strain after a cluster of infections in a hematology/oncology unit.

OBJECTIVES: This report chronicles an outbreak of a multiply resistant strain of Pseudomonas aeruginosa and the measures required to contain this outbreak. METHODS: Laboratory-based ward-liaison surveillance allowed the detection of a multiply resistant strain of P. aeruginosa infecting patients in our hematology/oncology unit. Sampling of the immediate environment was carried out. Pulsed field gel electrophoresis was used to compare the patients' organisms with those found in the environment. Extensive dismantling of the drainage system, repeated cleaning and disinfection, and a review of the departmental antibiotic policy were some of the infection control measures instigated. RESULTS: During a period of 11 months, three patients in the hematology department and two patients in the oncology department were infected with multiply resistant P. aeruginosa. There were two cases of pneumonia, one of which was fatal, and two cases of neutropenic septicaemia. Pulsed field gel electrophoresis performed on the isolates showed that the isolates from geographically separate areas could be divided into two strains that were closely related but distinct. Two genotypically identical strains were also isolated from the plumbing systems in the areas of each ward where patients had been treated. CONCLUSIONS: The potential for serious nosocomial infections with P. aeruginosa is well recognized. Eradication of the organism from the environment may require the co-ordinated efforts of clinicians, nurses, pharmacy and hospital engineers, working in collaboration with the hospital infection control team. To date, the same strains have not been isolated despite repeated surveillance over the past 18 months and therefore these measures have, in our opinion, successfully removed the potential for nosocomial infection with this resistant organism in our hospital.

Clinical, microbiological and epidemiological aspects of Escherichia coli O157 infection.

In the last decade infections caused by Escherichia coli O157:H7 and other verocytotoxigenic E. coli (VTEC) have emerged as a major public health concern in North America and in Europe, and increasingly in other areas of the world. Although absolute numbers of infections are low in comparison with other enteric pathogens such as Salmonella or Campylobacter, it is well-recognised that E. coli O157 can produce severe, potentially life-threatening, illness. As a consequence of this awareness, there has been a rapid expansion of our knowledge about these organisms and the diseases which they cause. In this article, the clinical, microbiological and epidemiological features of VTEC O157 infection are reviewed.

Nosocomial and laboratory-acquired infection with Escherichia coli O157.

Infections caused by verocytotoxigenic Escherichia coli O157 (VTEC O157) have emerged as a major public health concern. The nature and severity of associated clinical sequelae are such that symptomatic cases often require hospitalization, with possible exposure to other patients and healthcare workers, including laboratory personnel, to the risk of acquiring VTEC O157. The occurrence of such episodes of hospital- and laboratory-acquired infections has demonstrated that these concerns are justified. Hospital infection control teams must ensure that staff are aware of this potential hazard, and laboratories must review their operating procedures to ensure that their personnel are not unnecessarily exposed, particularly in the light of revised guidance on the safe handling of these organisms.