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.

Prosthetic joint infections: single versus combination therapy.

Prosthetic joint replacement is increasingly used to alleviate pain and increase mobility. Bone and joint infections remain a therapeutic dilemma for healthcare providers in all fields. Antimicrobial agents combined with appropriate surgical techniques play a vital role in eradicating infections associated with prosthetic joints. The question still remains whether monotherapy or combination therapy is effective in this situation because there is a paucity of well-defined comparative studies. We reviewed in vitro and in vivo studies evaluating the effectiveness of various antimicrobial agents either as single agents or in combination.

Impact of rapid microbial identification on clinical outcomes in bloodstream infection: the RAPIDO randomized trial.

OBJECTIVES: Bloodstream infection has a high mortality rate. It is not clear whether laboratory-based rapid identification of the organisms involved would improve outcome. METHODS: The RAPIDO trial was an open parallel-group multicentre randomized controlled trial. We tested all positive blood cultures from hospitalized adults by conventional methods of microbial identification and those from patients randomized (1:1) to rapid diagnosis in addition to matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) performed directly on positive blood cultures. The only primary outcome was 28-day mortality. Clinical advice on patient management was provided to members of both groups by infection specialists. RESULTS: First positive blood culture samples from 8628 patients were randomized, 4312 into rapid diagnosis and 4136 into conventional diagnosis. After prespecified postrandomization exclusions, 2740 in the rapid diagnosis arm and 2810 in the conventional arm were included in the mortality analysis. There was no significant difference in 28-day survival (81.5% 2233/2740 rapid vs. 82.3% 2313/2810 conventional; hazard ratio 1.05, 95% confidence interval 0.93-1.19, p 0.42). Microbial identification was quicker in the rapid diagnosis group (median (interquartile range) 38.5 (26.7-50.3) hours after blood sampling vs. 50.3 (47.1-72.9) hours after blood sampling, p < 0.01), but times to effective antimicrobial therapy were no shorter (respectively median (interquartile range) 24 (2-78) hours vs. 13 (2-69) hours). There were no significant differences in 7-day mortality or total antibiotic consumption; times to resolution of fever, discharge from hospital or de-escalation of broad-spectrum therapy or 28-day Clostridioides difficile incidence. CONCLUSIONS: Rapid identification of bloodstream pathogens by MALDI-TOF MS in this trial did not reduce patient mortality despite delivering laboratory data to clinicians sooner.

Evaluation of chromogenic media for the isolation of vancomycin-resistant enterococci from stool samples.

AIMS: This study sought to evaluate the performance of two chromogenic media designed for the isolation of vancomycin-resistant enterococci (VRE) and compare them with a traditional bile-esculin medium for the isolation of VRE from stool samples. METHODS AND RESULTS: A total of 285 stool samples were inoculated onto Chromogenic VRE Agar (AES VRE agar; AES Chemunex), chromID VRE (bioMérieux) and VRE Agar (Oxoid) both directly and also following broth enrichment. In total 18 strains of vancomycin-resistant Enterococcus faecium were recovered, including 17 harbouring the vanA gene and one with vanB. On direct culture, the sensitivity of the three media was 66.7%, 77.8% and 44.4% and after broth enrichment 66.7%, 83.3% and 77.8% using AES VRE Agar, chromID VRE and Oxoid VRE Agar respectively. CONCLUSIONS: All three media are useful tools for the isolation of VRE from stool samples. AES VRE Agar and bioMérieux chromID VRE are easier to use than Oxoid VRE Agar due to diffusion of black coloration from the latter. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study to evaluate the performance of AES VRE Agar and the first to compare two media containing synthetic chromogens for the isolation of VRE.

Outcomes of lung transplantation for cystic fibrosis in a large UK cohort.

BACKGROUND: Lung transplantation is an important option to treat patients with advanced cystic fibrosis (CF) lung disease. The outcomes of a large UK cohort of CF lung transplantation recipients is reported. METHODS: Retrospective review of case notes and transplantation databases. RESULTS: 176 patients with CF underwent lung transplantation at our centre. The majority (168) had bilateral sequential lung transplantation. Median age at transplantation was 26 years. Diabetes was common pretransplantation (40%). Polymicrobial infection was common in individual recipients. A diverse range of pathogens were encountered, including the Burkholderia cepacia complex (BCC). The bronchial anastomotic complication rate was 2%. Pulmonary function (forced expiratory volume in 1 s % predicted) improved from a pretransplantation median of 0.8 l (21% predicted) to 2.95 l (78% predicted) at 1 year following transplantation. We noted an acute rejection rate of 41% within the first month. Our survival values were 82% survival at 1 year, 70% at 3 years, 62% at 5 years and 51% at 10 years. Patients with BCC infection had poorer outcomes and represented the majority of those who had a septic death. Data are presented on those free from these infections. Bronchiolitis obliterans syndrome (BOS) and sepsis were common causes of death. Freedom from BOS was 74% at 5 years and 38% at 10 years. Biochemical evidence of renal dysfunction was common although renal replacement was infrequently required (<5%). CONCLUSION: Lung transplantation is an important therapeutic option in patients with CF even in those with more complex microbiology. Good functional outcomes are noted although transplantation associated morbidities accrue with time.

Use of real-time PCR to measure Epstein-Barr virus genomes in whole blood.

The measurement of the Epstein-Barr viral load in peripheral blood has been recognised as an important way of monitoring the response to treatment in patients with Epstein-Barr virus (EBV)-related malignancies. In particular, EBV load in transplant recipients can be used as a predictive parameter for Post-transplant Lymphoproliferative Disorder (PTLD). The aim was to develop a rapid and reliable PCR protocol for the quantification of the cell-associated EBV genome. Real-time PCR using TaqMan methodology was established. This technique was applied to determine the EBV load in various study groups including healthy controls, transplant recipients, patients on haemodialysis, and patients with infectious mononucleosis. The baseline level of EBV genomes in the immunosuppressed renal transplant recipients was significantly different from that in the healthy controls.

Donor organ transmission of varicella zoster due to cardiac transplantation.

BACKGROUND: We report a case of donor-transmitted varicella zoster viral (VZV) infection in a cardiac transplant recipient. A 15-month-old girl developed primary VZV infection 12 days after cardiac transplantation. The donor suffered from varicella 2 weeks before death from pneumococcal meningitis. METHODS: Despite treatment of the seronegative recipient with intravenous acyclovir from the time of surgery, she developed symptoms of fever, a nonspecific macular rash, and small palatal vesicles. RESULTS: After rapid diagnostic confirmation by direct immunofluorescence on vesicular fluid, high-dose intravenous acyclovir was commenced. In addition, the cyclosporine dose was reduced by 25%. The child made a quick and uncomplicated recovery. CONCLUSIONS: Donor organ transmission of VZV has not, to our knowledge, been previously reported. It occurred despite treatment with acyclovir and resulted in an atypical cutaneous eruption. It responded to an increased dose of acyclovir and a reduced level of immunosuppression.

Prophylaxis and management of cytomegalovirus pneumonitis after lung transplantation: a review of experience in one center.

Our experience was reviewed to assess the incidence and severity of cytomegalovirus disease after lung transplantation. Between 1987 and 1992, 74 lung transplantations were performed. Donor and recipient sera were tested for cytomegalovirus immunoglobulin G at the time of transplantation; in the event that an organ from a positive donor was transplanted into a negative recipient, a course of hyperimmune globulin was given. Significant pyrexial episodes were thoroughly investigated by bronchioalveolar lavage and transbronchial biopsy, where appropriate. Antiviral therapy was given only if progressive pneumonitis or a disease affecting more than one organ system was present. Fifty-nine patients survived more than 28 days after transplantation; organs from antibody-positive donors were transplanted into nine sero-negative recipients. Cytomegalovirus pneumonitis was diagnosed histologically in five of these patients; four were treated with ganciclovir therapy, and two underwent reventilation. All but one patient survived; the role of cytomegalovirus in the outcome of this patient remains uncertain. No recurrent infections have been seen. Of these nine patients, all but one was seroconverted to immunoglobulin M. Although frequently found to be excreting virus, of the 35 patients who were antibody positive before transplantation, pneumonitis was diagnosed histologically in five patients, two of whom required both treatment and reventilation and who subsequently died despite early treatment. Our findings, compared with historical data, suggest that the prophylactic use of high-titer immunoglobulin may reduce the incidence of pneumonitis in the mismatch group. The role of specific prophylaxis in patients who were antibody positive before transplantation requires further evaluation.

Single lung transplantation with simultaneous contralateral pneumonectomy for cystic fibrosis.

A 24-year-old man with cystic fibrosis and marked reduction of volume of the left hemithorax caused by skeletal asymmetry and mediastinal shift underwent successful right single lung transplantation with simultaneous left pneumonectomy. Despite significant preoperative microbiologic contamination, it proved possible to sterilize the pneumonectomy space and no airway complications occurred. Good long-term results have been achieved, and the historic assumption that single lung transplantation is unsuitable for patients with septic lung disease is challenged.

Does the mode of donor death influence the early outcome of lung transplantation? A review of lung transplantation from donors involved in major trauma.

BACKGROUND: Pulmonary dysfunction, often delayed in presentation, is among the sequelae of major trauma. Transplantation of lungs from donors involved in major trauma therefore carries a risk of early graft dysfunction. This study was conducted to assess this risk. METHODS: A retrospective comparison of the outcome from 123 donors (57 donors resulting from major trauma, group T, and 66 donors with nontraumatic origin, group NT) in 125 consecutive technically successful lung or heart-lung transplantations. Variables analyzed included the following: clinical and bacteriologic details of donors and indexes of early graft dysfunction in the recipients. RESULTS: Group T donors were more likely to be younger and male (p < 0.05) and more likely to have had lung ventilation for over 48 hours (p < 0.05) than group NT donors. Microbial contamination of routine donor bronchial lavage (72 of 122, 61%) was no higher in group T (34 of 57, 60%), but, in this group, enteric gram-negative bacilli were more common (30% versus 7%; p < 0.05). Male patients were more likely to receive lungs from group T donors (35 male, 23 female), and female patients were more likely to receive lungs from group NT donors (27 male, 40 female). Mode of donor death did not affect the following indexes of early graft function: length of postoperative ventilation, ratio of arterial oxygen tension to fractional concentration of inspired oxygen at 1 or 24 hours after transplantation, or the incidence of diffuse alveolar damage in lung biopsy specimens at 7 days. Thirty-day mortality (28%) was no higher among recipients of group T lungs, but six recipient deaths were donor-related (donor-transmitted pneumonia in five and donor acquired fat embolism in one case). CONCLUSION: The use of donors involved in major trauma does not increase the risk of early complications after lung transplantation providing their specific characteristics are recognized.

Incidence and significance of noncytomegalovirus viral respiratory infection after adult lung transplantation.

Lower respiratory tract infection is a major cause of morbidity and death after lung transplantation. The incidence and significance of noncytomegalovirus viral respiratory tract infections has not been reported to date. We report our center's experience with these infections.

Management of cytomegalovirus antibody negative patients undergoing heart transplantation.

In a series of 61 consecutive patients undergoing heart, heart and lung, and lung transplantation, 24 patients were known to be cytomegalovirus (CMV) antibody negative on the day of transplantation. Enzyme linked immunosorbent assays (ELISA) for CMV IgG were performed on donor samples on the day of operation. In 16 of the 24 susceptible patients the test was negative and the only preventive measure taken was the use of blood and blood products from CMV-antibody negative blood donors. None of these patients acquired primary infection with CMV. In another six patients the donor serum was found to contain CMV specific IgG, and in these patients, including one heart and lung transplant recipient, prophylaxis with CMV specific hyperimmune globulin was given. All six patients developed CMV IgM antibodies and in five there was an associated but clinically mild illness. None of these patients required treatment. In the remaining two patients ELISA tests on the donor sera gave equivocal results and hyperimmune globulin was withheld. Both patients developed primary CMV infection of greater severity than those given hyperimmune globulin and one required treatment. Reference tests confirmed that the donor sera contained CMV antibodies. Primary CMV infection in susceptible patients after heart transplantation can be avoided by the use of screened blood and blood products where the organ donor is seronegative to CMV and it can be improved by the use of prophylactic hyperimmune globulin where the donor is CMV antibody positive.

Rapid conventional scheme for biochemical identification of antibiotic resistant enterobacteriaceae isolates from urine.

Six conventional biochemical tests were combined to produce an identification scheme. These tests included decarboxylation of lysine and ornithine, fermentation of glucose and cellobiose, indole production and urease production. Three hundred antibiotic resistant coliforms from urine specimens were tested by this scheme and also by the API 20E for comparison. Two hundred and seventy nine (93%) of organisms were correctly identified using the six tests, 17 (5.7%) were referred for further study, and four (1.3%) were misidentified. It is concluded that this combination of tests provides an inexpensive, accurate, and rapid tool for identification.

Does storage of sputum specimens adversely affect culture results?

It has been recommended that samples submitted for microbiological examination should be retained for 48 hours after issue of the final report. In order to ascertain whether reproducible results could be achieved following storage of sputum specimens, two laboratories each re-cultured 100 samples 48 hours after their report had been issued and a further laboratory re-cultured 100 samples 48 hours after receipt. Discordant results were obtained in only 5-25% of specimens, indicating that potential respiratory pathogens could survive storage.

The iron uptake mechanisms of enteropathogenic Escherichia coli: the use of haem and haemoglobin during growth in an iron-limited environment.

The iron uptake mechanisms of enteropathogenic Escherichia coli (EPEC) were examined and compared with those of control E. coli strains. The incidence of aerobactin production was similar (39% and 37% respectively) in the two groups. The quantities of enterochelin produced by aerobactin-negative EPEC and control strains were similar, as were the quantities of enterochelin produced by aerobactin-positive EPEC and control strains. The ability to use haem or haemoglobin as an iron source in an iron-restricted environment was found in 80.4% and 60.8% of EPEC strains respectively, and in 76.6% and 56.6% of control E. coli strains. The ability of E. coli strains to use these compounds was not related to the production of enterochelin or aerobactin or to the production of haemolysins, and may be an important characteristic of bowel organisms. When growing in an iron-limited environment, the iron contained in haemoglobin was used in preference to ovotransferrin-bound iron. During periods of haemoglobin-stimulated growth, the enterochelin uptake system was shown to be fully expressed and may be involved in transport of haemoglobin-derived iron into the cell. Uptake of ovotransferrin-bound iron took place immediately upon exhaustion of haemoglobin-derived iron. The ability to use iron derived from haem compounds represents an alternative iron uptake mechanism for organisms growing in an iron-limited environment and allows greater flexibility during growth in vivo.

Epidemiological typing of coagulase-negative staphylococci by pyrolysis mass spectrometry.

Pyrolysis mass spectrometry (PMS) was evaluated for the epidemiological typing of coagulase-negative staphylococci (CNS) in situations in which it was necessary to distinguish between repeated isolation of the same strain from a single patient (genuine infection) and coincidental isolation of unrelated strains (contamination). Thirteen CNS isolates were examined, consisting of five pairs, each pair isolated from a single patient, and three unrelated strains. PMS analysis gave results equivalent to a conventional typing system comprising antibiogram, biotype and plasmid profile analysis. Both methods facilitate differentiation between genuine infection with CNS and the isolation of contaminants. The speed, reproducibility, versatility and relatively low cost of PMS suggest that it may be a valuable new technique for the epidemiological typing of CNS in routine clinical settings.

Pyrolysis-mass spectrometry (Py-MS) for the rapid epidemiological typing of clinically significant bacterial pathogens.

Fresh clinical isolates of Salmonella spp. and Streptococcus pyogenes were analysed by pyrolysis-mass spectrometry (Py-MS). The results formed the basis of mathematically derived characterizations of individual strains and these were compared with the results of phage typing for the salmonellas and M protein typing for the streptococci. Py-MS was shown to be a rapid and reproducible method for inter-strain comparisons, giving evidence of identity and non-identity between strains that agreed well with the results of conventional tests. Py-MS has potential value as a rapid, relatively inexpensive and highly discriminatory method of epidemiological analysis in bacterial disease.

Prevention of nosocomial infection in solid organ transplantation.

Despite improvements in survival rates, infection remains an important cause of morbidity and mortality following solid organ transplantation. Prevention of infection and, failing this, prompt diagnosis and treatment remain the cornerstones of management. During the peri-operative admission, when the level of immunosuppression is at its height, nosocomial infection accounts for the majority of infective morbidity. Although the measures taken to prevent nosocomial infection may vary, centres undertaking such procedures must ensure that strategies are in place to protect patients. The importance of basic infection control measures cannot be over-emphasised. In addition, appropriate prophylactic agents, rapid diagnostic techniques and the early institution of appropriate therapy are essential. As developments in this field advance, the epidemiology of infection will continue to change, demanding an ongoing assessment of preventative, diagnostic and therapeutic strategies.

Strain differentiation of nosocomial isolates of Pseudomonas aeruginosa by pyrolysis mass spectrometry.

Pyrolysis mass spectrometry (PyMS) was used for rapid interstrain comparison of Pseudomonas aeruginosa isolates from a small outbreak of sternal wound infections in a cardiothoracic surgical ward. The PyMS results were compared with those obtained by conventional O-serotyping. All the isolates were phage non-typable. Evidence obtained from PyMS of identity/non-identity between isolates correlated completely with that obtained by O-typing and correctly identified those isolates comprising the epidemic strain, in one instance in advance of O-serotyping. The speed and versatility of PyMS make it an attractive technique for the initial screening of isolates from nosocomial outbreaks of infection with P. aeruginosa and other organisms.