Whole-Genome Sequencing Reveals the Contribution of Long-Term Carriers in Staphylococcus aureus Outbreak Investigation.

Whole-genome sequencing (WGS) makes it possible to determine the relatedness of bacterial isolates at a high resolution, thereby helping to characterize outbreaks. However, for Staphylococcus aureus, the accumulation of within-host diversity during carriage might limit the interpretation of sequencing data. In this study, we hypothesized the converse, namely, that within-host diversity can in fact be exploited to reveal the involvement of long-term carriers (LTCs) in outbreaks. We analyzed WGS data from 20 historical outbreaks and applied phylogenetic methods to assess genetic relatedness and to estimate the time to most recent common ancestor (TMRCA). The findings were compared with the routine investigation results and epidemiological evidence. Outbreaks with epidemiological evidence for an LTC source had a mean estimated TMRCA (adjusted for outbreak duration) of 243 days (95% highest posterior density interval [HPD], 143 to 343 days) compared with 55 days (95% HPD, 28 to 81 days) for outbreaks lacking epidemiological evidence for an LTC (P = 0.004). A threshold of 156 days predicted LTC involvement with a sensitivity of 0.875 and a specificity of 1. We also found 6/20 outbreaks included isolates with differing antimicrobial susceptibility profiles; however, these had only modestly increased pairwise diversity (mean 17.5 single nucleotide variants [SNVs] [95% confidence interval {CI}, 17.3 to 17.8]) compared with isolates with identical antibiograms (12.7 SNVs [95% CI, 12.5 to 12.8]) (P < 0.0001). Additionally, for 2 outbreaks, WGS identified 1 or more isolates that were genetically distinct despite having the outbreak pulsed-field gel electrophoresis (PFGE) pulsotype. The duration-adjusted TMRCA allowed the involvement of LTCs in outbreaks to be identified and could be used to decide whether screening for long-term carriage (e.g., in health care workers) is warranted. Requiring identical antibiograms to trigger investigation could miss important contributors to outbreaks.

A case of cutaneous Rhodotorula infection mimicking cryptococcosis.

Rhodotorula is a ubiquitous environmental and commensal yeast, and an emerging opportunistic pathogen, particularly in immunocompromised individuals. Clinical infections with Rhodotorula have been increasingly recognized over the past 30 years; however, infections in solid-organ transplant recipients are uncommon, and cutaneous manifestations have rarely been reported. We describe a 59-year-old male renal transplant recipient, who developed cutaneous infection with Rhodotorula upon failure of his graft and commencement of haemodialysis.

Genome sequencing and characterization of an extensively drug-resistant sequence type 111 serotype O12 hospital outbreak strain of Pseudomonas aeruginosa.

A series of extensively drug-resistant isolates of Pseudomonas aeruginosa from two outbreaks in UK hospitals were characterized by whole genome sequencing (WGS). Although these isolates were resistant to antibiotics other than colistin, we confirmed that they are still sensitive to disinfectants. The sequencing confirmed that isolates in the larger outbreak were serotype O12, and also revealed that they belonged to sequence type ST111, which is a major epidemic strain of P. aeruginosa throughout Europe. As this is the first reported sequence of an ST111 strain, the genome was examined in depth, focusing particularly on antibiotic resistance and potential virulence genes, and on the reported regions of genome plasticity. High degrees of sequence similarity were discovered between outbreak isolates collected from recently infected patients, isolates from sinks, an isolate from the sewer, and a historical isolate, suggesting that the ST111 strain has been endemic in the hospital for many years. The ability to translate easily from outbreak investigation to detailed genome biology by use of the same data demonstrates the flexibility of WGS application in a clinical setting.

Multidrug-resistant Pseudomonas aeruginosa outbreaks in two hospitals: association with contaminated hospital waste-water systems.

BACKGROUND: Multidrug-resistant Pseudomonas aeruginosa (MDR-P) expressing VIM-metallo-beta-lactamase is an emerging infection control problem. The source of many such infections is unclear, though there are reports of hospital outbreaks of P. aeruginosa related to environmental contamination, including tap water. AIM: We describe two outbreaks of MDR-P, sensitive only to colistin, in order to highlight the potential for hospital waste-water systems to harbour this organism. METHODS: The outbreaks were investigated by a combination of descriptive epidemiology, inspection and microbiological sampling of the environment, and molecular strain typing. FINDINGS: The outbreaks occurred in two English hospitals; each involved a distinct genotype of MDR-P. One outbreak was hospital-wide, involving 85 patients, and the other was limited to four cases in one specialized medical unit. Extensive environmental sampling in each outbreak yielded MDR-P only from the waste-water systems. Inspection of the environment and estates records revealed many factors that may have contributed to contamination of clinical areas, including faulty sink, shower and toilet design, clean items stored near sluices, and frequent blockages and leaks from waste pipes. Blockages were due to paper towels, patient wipes, or improper use of bedpan macerators. Control measures included replacing sinks and toilets with easier-to-clean models less prone to splashback, educating staff to reduce blockages and inappropriate storage, reviewing cleaning protocols, and reducing shower flow rates to reduce flooding. These measures were followed by significant reductions in cases. CONCLUSION: The outbreaks highlight the potential of hospital waste systems to act as a reservoir of MDR-P and other nosocomial pathogens.

Impact of an intervention to control Clostridium difficile infection on hospital- and community-onset disease; an interrupted time series analysis.

Strategies to reduce rates of Clostridium difficile infection (CDI) generally recommend isolation or cohorting of active cases and the reduced use of cephalosporin and quinolone antibiotics. Data supporting these recommendations come predominantly from the setting of epidemic disease caused by ribotype 027 strains. We introduced an initiative involving a restrictive antibiotic policy and a CDI-cohort ward at an acute, 820-bed teaching hospital where ribotype 027 strains account for only one quarter of all CDI cases. Antibiotic use and monthly CDI cases in the 12 months before and the 15 months after the initiative were compared using an interrupted time series analysis and segmented regression analysis. The initiative resulted in a reduced level of cephalosporin and quinolone use (22.0% and 38.7%, respectively, both p <0.001) and changes in the trends of antibiotic use such that cephalosporin use decreased by an additional 62.1 defined daily doses (DDD) per month (p <0.001) and antipseudomonal penicillin use increased by 20.7 DDD per month (p = 0.011). There were no significant changes in doxycycline or carbapenem use. Although the number of CDI cases each month was falling before the intervention, there was a significant increase in the rate of reduction after the intervention from 3% to 8% per month (0.92, 95% CI 0.86-0.99, p = 0.03). During the study period, there was no change in the proportion of cases having their onset in the community, nor in the proportion of ribotype 027 cases. CDI cohorting and restriction of cephalosporin and quinolone use are effective in reducing CDI cases in a setting where ribotype 027 is endemic.

Invasive group A streptococcal infection in injecting drug users and non-drug users in a single UK city.

OBJECTIVES: Injecting drug users (IDU) represent an increasing proportion of patients with invasive group A streptococcal (GAS) disease. Our aims were to characterise the clinical presentation and strains causing GAS bacteremia in IDU from a single UK city (Brighton and Hove), and to compare this patient group with non-drug users (non-DU) with GAS bacteremia. METHODS: Consecutive GAS blood culture isolates from twenty-two IDU and twenty-two non-DU presenting to the city hospital were studied. Clinical features, strain emm typing and superantigen toxin genotyping were investigated. RESULTS: GAS invasive disease presented differently in IDU compared to non-DU with a predominance of injection site abscesses and lower mortality in IDU. GAS strains from IDU were predominantly emm82 and emm83 types, which are uncommon in the UK and emm82 strains appeared clonal. The non-DU GAS strains demonstrated a broader range of emm types including most frequently emm1 and emm89. There was no major difference in superantigen gene profile between the isolate groups. CONCLUSION: The distinct presentation of invasive GAS disease in IDU compared with non-DU was associated with distinct emm types, a predominance of abscesses, and low mortality, although the small numbers preclude definitive conclusions. Further study is required to establish if these findings reflect strain differences or epidemiological differences in colonisation patterns and injecting practice.

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.