Multidrug-resistant Escherichia coli soft tissue infection investigated with bacterial whole genome sequencing.

A 45-year-old man with dilated cardiomyopathy presented with acute leg pain and erythema suggestive of necrotising fasciitis. Initial surgical exploration revealed no necrosis and treatment for a soft tissue infection was started. Blood and tissue cultures unexpectedly grew a Gram-negative bacillus, subsequently identified by an automated broth microdilution phenotyping system as an extended-spectrum ß-lactamase producing Escherichia coli. The patient was treated with a 3-week course of antibiotics (ertapenem followed by ciprofloxacin) and debridement for small areas of necrosis, followed by skin grafting. The presence of E. coli triggered investigation of both host and pathogen. The patient was found to have previously undiagnosed liver disease, a risk factor for E. coli soft tissue infection. Whole genome sequencing of isolates from all specimens confirmed they were clonal, of sequence type ST131 and associated with a likely plasmid-associated AmpC (CMY-2), several other resistance genes and a number of virulence factors.

Use of an automated blood culture system (BD BACTEC™) for diagnosis of prosthetic joint infections: easy and fast.

BACKGROUND: For the diagnosis of prosthetic joint infection (PJI) automated BACTEC™ blood culture bottle methods have comparable sensitivity, specificity and a shorter time to positivity than traditional cooked meat enrichment broth methods. We evaluate the culture incubation period required to maximise sensitivity and specificity of microbiological diagnosis, and the ability of BACTEC™ to detect slow growing Propionibacteria spp. METHODS: Multiple periprosthetic tissue samples taken by a standardised method from 332 patients undergoing prosthetic joint revision arthroplasty were cultured for 14 days, using a BD BACTEC™ instrumented blood culture system, in a prospective study from 1st January to 31st August 2012. The "gold standard" definition for PJI was the presence of at least one histological criterion, the presence of a sinus tract or purulence around the device. Cases where > =2 samples yielded indistinguishable isolates were considered culture-positive. 1000 BACTEC™ bottle cultures which were negative after 14 days incubation were sub-cultured for Propionibacteria spp. RESULTS: 79 patients fulfilled the definition for PJI, and 66 of these were culture-positive. All but 1 of these 66 culture-positive cases of PJI were detected within 3 days of incubation. Only one additional (clinically-insignificant) Propionibacterium spp. was identified on terminal subculture of 1000 bottles. CONCLUSIONS: Prolonged microbiological culture for 2 weeks is unnecessary when using BACTEC™ culture methods. The majority of clinically significant organisms grow within 3 days, and Propionibacteria spp. are identified without the need for terminal subculture. These findings should facilitate earlier decisions on final antimicrobial prescribing.

Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study.

BACKGROUND: Patients born outside the UK have contributed to a 20% rise in the UK's tuberculosis incidence since 2000, but their effect on domestic transmission is not known. Here we use whole-genome sequencing to investigate the epidemiology of tuberculosis transmission in an unselected population over 6 years. METHODS: We identified all residents with Oxfordshire postcodes with a Mycobacterium tuberculosis culture or a clinical diagnosis of tuberculosis between Jan 1, 2007, and Dec 31, 2012, using local databases and checking against the national Enhanced Tuberculosis Surveillance database. We used Illumina technology to sequence all available M tuberculosis cultures from identified cases. Sequences were clustered by genetic relatedness and compared retrospectively with contact investigations. The first patient diagnosed in each cluster was defined as the index case, with links to subsequent cases assigned first by use of any epidemiological linkage, then by genetic distance, and then by timing of diagnosis. FINDINGS: Although we identified 384 patients with a diagnosis of tuberculosis, country of birth was known for 380 and we sequenced isolates from 247 of 269 cases with culture-confirmed disease. 39 cases were genomically linked within 13 clusters, implying 26 local transmission events. Only 11 of 26 possible transmissions had been previously identified through contact tracing. Of seven genomically confirmed household clusters, five contained additional genomic links to epidemiologically unidentified non-household members. 255 (67%) patients were born in a country with high tuberculosis incidence, conferring a local incidence of 109 cases per 100,000 population per year in Oxfordshire, compared with 3·5 cases per 100,000 per year for those born in low-incidence countries. However, patients born in the low-incidence countries, predominantly UK, were more likely to have pulmonary disease (adjusted odds ratio 1·8 [95% CI 1·2-2·9]; p=0·009), social risk factors (4·4 [2·0-9·4]; p<0·0001), and be part of a local transmission cluster (4·8 [1·6-14·8]; p=0·006). INTERPRETATION: Although inward migration has contributed to the overall tuberculosis incidence, our findings suggest that most patients born in high-incidence countries reactivate latent infection acquired abroad and are not involved in local onward transmission. Systematic screening of new entrants could further improve tuberculosis control, but it is important that health care remains accessible to all individuals, especially high-risk groups, if tuberculosis control is not to be jeopardised. FUNDING: UK Clinical Research Collaboration (Wellcome Trust, Medical Research Council, National Institute for Health Research [NIHR]), and NIHR Oxford Biomedical Research Centre.

Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing.

Sequence-based typing is essential for understanding the epidemiology of Campylobacter infections, a major worldwide cause of bacterial gastroenteritis. We demonstrate the practical and rapid exploitation of whole-genome sequencing to provide routine definitive characterization of Campylobacter jejuni and Campylobacter coli for clinical and public health purposes. Short-read data from 384 Campylobacter clinical isolates collected over 4 months in Oxford, United Kingdom, were assembled de novo. Contigs were deposited at the pubMLST.org/campylobacter website and automatically annotated for 1,667 loci. Typing and phylogenetic information was extracted and comparative analyses were performed for various subsets of loci, up to the level of the whole genome, using the Genome Comparator and Neighbor-net algorithms. The assembled sequences (for 379 isolates) were diverse and resembled collections from previous studies of human campylobacteriosis. Small subsets of very closely related isolates originated mainly from repeated sampling from the same patients and, in one case, likely laboratory contamination. Much of the within-patient variation occurred in phase-variable genes. Clinically and epidemiologically informative data can be extracted from whole-genome sequence data in real time with straightforward, publicly available tools. These analyses are highly scalable, are transparent, do not require closely related genome reference sequences, and provide improved resolution (i) among Campylobacter clonal complexes and (ii) between very closely related isolates. Additionally, these analyses rapidly differentiated unrelated isolates, allowing the detection of single-strain clusters. The approach is widely applicable to analyses of human bacterial pathogens in real time in clinical laboratories, with little specialist training required.

High-dose daptomycin monotherapy cures Staphylococcus epidermidis 'endotipsitis' after failure of conventional therapy.

A 67-year-old gentleman developed persistent Staphylococcus epidermidis bacteraemia following transjugular intrahepatic portal shunting. 'Endotipsitis' was diagnosed. Conventional therapy with a vancomycin infusion, amikacin and rifampicin failed after 17 days. He was cured with a 6-week course of high-dose (8 mg/kg) daptomycin monotherapy.

Endovascular stent-associated infection with Staphylococcus lugdunensis.

An elderly woman presented febrile 5 days after stenting of multiple coronary arteries. Echocardiography showed a thickening of the aortic root, raising the possibility of stent infection. Four  of four blood culture bottles grew Staphylococcus lugdunensis and repeat echo showed an aortic root abscess. Despite appropriate antibiotic treatment, the patient died. A 24-year-old man with a ventricular septal defect presented febrile 4 weeks after stenting of an aortic coarctation. Initial transoesophageal echo found no vegetations around the stent or elsewhere. Four of six blood culture bottles grew S lugdunensis. Following an episode of hypoxia, the imaging was repeated and a new large vegetation was seen on the pulmonary valve with two thin-walled cavities in the lungs on a CT pulmonary angiogram. The patient was treated with a long course of appropriate antibiotic therapy and discharged from hospital 6 weeks later.

Clostridium septicum sepsis and its implications.

An elderly gentleman, who had 12 years earlier been successfully treated for colon cancer, presented with fever, rigours, right upper quadrant abdominal pain and tenderness. A CT of the abdomen revealed a colonic mass distal to the hepatic flexure with multiple gas locules and a walled off perforation. He underwent a right hemicolectomy. Histology confirmed multifocal colonic adenocarcinoma. His admission blood cultures grew Clostridium septicum. A week postoperatively he developed intermittent fevers and abdominal pain. Repeat CT revealed an abdominal collection adjacent to the new anastomosis, but more importantly, a sharply shouldered aneurysmal dilation of the infra-renal abdominal aorta. These findings prompted immediate surgical drainage of the collection, repair of the anastomostic leak, resection of the infected aortic aneurysm and replacement with a tube graft. This case highlights the clinical significance of C septicum bacteraemia: its association with occult colonic malignancy and with mycotic aneurysm formation. Clostridia isolated from blood cultures should not be dismissed as contaminants but fully identified to ensure appropriate patient management.

A longitudinal 6-year study of the molecular epidemiology of clinical campylobacter isolates in Oxfordshire, United kingdom.

Temporal and seasonal trends in Campylobacter genotypes causing human gastroenteritis were investigated in a 6-year study of 3,300 recent isolates from Oxfordshire, United Kingdom. Genotypes (sequence types [ST]) were defined using multilocus sequence typing and assigned to a clonal complex (a cluster of related strains that share four or more identical alleles with a previously defined central genotype). A previously undescribed clonal complex (ST-464) was identified which, together with ST-42, ST-45, and ST-52 complexes, showed increasing incidence. Concurrently, the incidence of ST-574, ST-607, and ST-658 complexes declined. The relative frequencies of three clonal complexes (ST-45, ST-283, and ST-42) peaked during summer and those of two (ST-353 and ST-403) peaked during winter. Nine clonal complexes (ST-22, ST-45, ST-48, ST-61, ST-257, ST-283, ST-403, ST-658, and ST-677) were significantly associated with ciprofloxacin sensitivity (P < 0.05). Seven clonal complexes (ST-49, ST-206, ST-354, ST-446, ST-460, ST-464, and ST-607) were associated with ciprofloxacin resistance (P < 0.05). Clonal complexes exhibited changing incidence and differences in seasonality and antibiotic resistance phenotype. These data also demonstrated that detailed surveillance at a single site captures information which reflects that observed nationally.

Acute necrotizing sinusitis caused by Staphylococcus lugdunensis.

Staphylococcus lugdunensis is most commonly associated with infections arising from the inguinal region, but here we report this organism as a cause of bacterial sinusitis, highlighting its potential niche as a commensal of the upper airways. The severity of necrosis demonstrates the potential for destructive pathology mimicking Staphylococcus aureus disease.

Streptococcus mutans infective endocarditis complicated by vertebral discitis following dental treatment without antibiotic prophylaxis.

We report what we believe is the first reported case of Streptococcus mutans endocarditis complicated by vertebral discitis. The case is particularly interesting and topical as it occurred in a patient with pre-existing cardiac valvular disease who had recently had a dental procedure without antibiotic prophylaxis following a dramatic shift in the UK guidelines.

Risk factors for recurrence after Staphylococcus aureus bacteraemia. A retrospective matched case-control study.

OBJECTIVES: We sought to identify risk factors for recurrence of Staphylococcus aureus bacteraemia (SAB) by auditing compliance with guidelines on its treatment in our hospital. METHODS: We retrospectively identified patients over the preceding 8 years whose SAB had recurred, matching each to a control patient with non-recurrent SAB. RESULTS: 40/1870 patients with SAB had suffered recurrent disease (2.1%), 33 of whom were available for study. Where 2, 4 and 6 weeks of intravenous therapy were recommended, 78%, 29% and 25% of patients received it, and there was no association with recurrence. Glycopeptide use in patients with methicillin sensitive SAB (MSSA) was significantly associated with recurrence (p=0.015). Where the source of the bacteraemia was a peripheral venous catheter the odds of recurrence were less than where an SAB originated at another site (p=0.047). All patients with SAB in whom a central venous catheter was not removed suffered recurrence. CONCLUSIONS: We found the recurrence rate after SAB was low despite poor compliance with guidelines on treatment duration. Glycopeptide therapy for MSSA bacteraemia was more likely to result in recurrent SAB than beta-lactam therapy. Recurrence was significantly less likely in patients where the source of the SAB was a peripheral line than in those with another source.

Native valve endocarditis due to Streptococcus vestibularis and Streptococcus oralis.

Viridans streptococci are the commonest cause of native valve infective endocarditis (IE). The taxonomy of this group is evolving allowing new disease associations to be made. Streptococcus vestibularis is a recently described member of the viridans group, first isolated from the vestibular mucosa of the human oral cavity. It has rarely been associated with human disease. Streptococcus oralis, another member of the viridans group resident in the human oral cavity is a well known cause of IE and bacteraemia in neutropenic patients. We report the first case of native mitral valve endocarditis due to S. vestibularis in a patient with co-existing S. oralis endocarditis.

Do the new lipid formulations of amphotericin B really work?

Over the past two years, there has been a dramatic rise in the prescription of lipid formulations of amphotericin B at our hospital. These compounds now account for a significant proportion of all expenditure on antimicrobial agents. We therefore conducted a review of the efficacy of the lipid formulations of amphotericin B. Only one randomized controlled trial has assessed the efficacy of any of these formulations in treating proven fungal infections, and this is only available in abstract form. Most of the available evidence on the use of lipid formulations is in the form of case series. There are therefore limited data to justify the widespread use of these compounds, and we believe that there are few circumstances when their administration is warranted. We suggest that local policies should be drawn up for the prescription of lipid formulations of amphotericin B, and, until more compelling data are available, that these drugs only be administered after discussion with microbiologists or infectious diseases physicians.