Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study.

BACKGROUND: Since June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has, worldwide, caused 104 infections in people including 49 deaths, with 82 cases and 41 deaths reported from Saudi Arabia. In addition to confirming diagnosis, we generated the MERS-CoV genomic sequences obtained directly from patient samples to provide important information on MERS-CoV transmission, evolution, and origin. METHODS: Full genome deep sequencing was done on nucleic acid extracted directly from PCR-confirmed clinical samples. Viral genomes were obtained from 21 MERS cases of which 13 had 100%, four 85-95%, and four 30-50% genome coverage. Phylogenetic analysis of the 21 sequences, combined with nine published MERS-CoV genomes, was done. FINDINGS: Three distinct MERS-CoV genotypes were identified in Riyadh. Phylogeographic analyses suggest the MERS-CoV zoonotic reservoir is geographically disperse. Selection analysis of the MERS-CoV genomes reveals the expected accumulation of genetic diversity including changes in the S protein. The genetic diversity in the Al-Hasa cluster suggests that the hospital outbreak might have had more than one virus introduction. INTERPRETATION: We present the largest number of MERS-CoV genomes (21) described so far. MERS-CoV full genome sequences provide greater detail in tracking transmission. Multiple introductions of MERS-CoV are identified and suggest lower R0 values. Transmission within Saudi Arabia is consistent with either movement of an animal reservoir, animal products, or movement of infected people. Further definition of the exposures responsible for the sporadic introductions of MERS-CoV into human populations is urgently needed. FUNDING: Saudi Arabian Ministry of Health, Wellcome Trust, European Community, and National Institute of Health Research University College London Hospitals Biomedical Research Centre.

Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study.

BACKGROUND: Middle East respiratory syndrome (MERS) is a new human disease caused by a novel coronavirus (CoV). Clinical data on MERS-CoV infections are scarce. We report epidemiological, demographic, clinical, and laboratory characteristics of 47 cases of MERS-CoV infections, identify knowledge gaps, and define research priorities. METHODS: We abstracted and analysed epidemiological, demographic, clinical, and laboratory data from confirmed cases of sporadic, household, community, and health-care-associated MERS-CoV infections reported from Saudi Arabia between Sept 1, 2012, and June 15, 2013. Cases were confirmed as having MERS-CoV by real-time RT-PCR. FINDINGS: 47 individuals (46 adults, one child) with laboratory-confirmed MERS-CoV disease were identified; 36 (77%) were male (male:female ratio 3·3:1). 28 patients died, a 60% case-fatality rate. The case-fatality rate rose with increasing age. Only two of the 47 cases were previously healthy; most patients (45 [96%]) had underlying comorbid medical disorders, including diabetes (32 [68%]), hypertension (16 [34%]), chronic cardiac disease (13 [28%]), and chronic renal disease (23 [49%]). Common symptoms at presentation were fever (46 [98%]), fever with chills or rigors (41 [87%]), cough (39 [83%]), shortness of breath (34 [72%]), and myalgia (15 [32%]). Gastrointestinal symptoms were also frequent, including diarrhoea (12 [26%]), vomiting (ten [21%]), and abdominal pain (eight [17%]). All patients had abnormal findings on chest radiography, ranging from subtle to extensive unilateral and bilateral abnormalities. Laboratory analyses showed raised concentrations of lactate dehydrogenase (23 [49%]) and aspartate aminotransferase (seven [15%]) and thrombocytopenia (17 [36%]) and lymphopenia (16 [34%]). INTERPRETATION: Disease caused by MERS-CoV presents with a wide range of clinical manifestations and is associated with substantial mortality in admitted patients who have medical comorbidities. Major gaps in our knowledge of the epidemiology, community prevalence, and clinical spectrum of infection and disease need urgent definition. FUNDING: None.

Persistence of skin contamination and environmental shedding of Clostridium difficile during and after treatment of C. difficile infection.

BACKGROUND: Current guidelines for control of Clostridium difficile infection (CDI) suggest that contact precautions be discontinued after diarrhea resolves. However, limited information is available regarding the frequency of skin contamination and environmental shedding of C. difficile during and after treatment. DESIGN: We conducted a 9-month prospective, observational study involving 52 patients receiving therapy for CDI. Stool samples, skin (chest and abdomen) samples, and samples from environmental sites were cultured for C. difficile before, during, and after treatment. Polymerase chain reaction ribotyping was performed to determine the relatedness of stool, skin, and environmental isolates. RESULTS: Fifty-two patients with CDI were studied. C. difficile was suppressed to undetectable levels in stool samples from most patients during treatment; however, 1-4 weeks after treatment, 56% of patients who had samples tested were asymptomatic carriers of C. difficile. The frequencies of skin contamination and environmental shedding remained high at the time of resolution of diarrhea (60% and 37%, respectively), were lower at the end of treatment (32% and 14%, respectively), and again increased 1-4 weeks after treatment (58% and 50%, respectively). Skin and environmental contamination after treatment was associated with use of antibiotics for non-CDI indications. Ninety-four percent of skin isolates and 82% of environmental isolates were genetically identical to concurrent stool isolates. CONCLUSIONS: Skin contamination and environmental shedding of C. difficile often persist at the time of resolution of diarrhea, and recurrent shedding is common 1-4 weeks after therapy. These results provide support for the recommendation that contact precautions be continued until hospital discharge if rates of CDI remain high despite implementation of standard infection-control measures.

Skin and environmental contamination with vancomycin-resistant Enterococci in patients receiving oral metronidazole or oral vancomycin treatment for Clostridium difficile-associated disease.

BACKGROUND: Oral metronidazole has been recommended for treatment of mild-to-moderate Clostridium difficile-associated disease (CDAD), in part because of concern that use of vancomycin may be more likely to promote colonization and transmission of vancomycin-resistant enterococci (VRE). The objective of our study was to compare the frequency of skin and environmental VRE contamination associated with metronidazole treatment for CDAD with such frequency associated with vancomycin treatment for CDAD. DESIGN: Prospective, observational study. This study was performed at the Cleveland Veterans Affairs Medical Center (Cleveland, OH). For patients with CDAD who had concurrent VRE colonization, stool, skin, and environmental samples were cultured for VRE before, during, and up to 3 weeks after therapy with metronidazole or vancomycin. The proportions of skin and environmental contamination were compared before and after resolution of diarrhea and during treatment with metronidazole or vancomycin. RESULTS: Of the 34 patients, 17 were treated with vancomycin and 17 were treated with metronidazole. The proportion of environmental cultures that were positive for VRE was significantly higher during resolution of diarrhea than it was after resolution of diarrhea (38% vs 28%; P=.025), whereas the proportion of skin cultures positive was not different during and after resolution of diarrhea (78% vs 71%; P=.60). There were no differences between patients who received metronidazole and patients who received vancomycin in the proportions of skin culture results (73% vs 77%; P=.80) or environmental culture results (37% vs 32%; P=.359) that were positive for VRE. Eleven patients (32%) had chronic fecal incontinence, and 28 (82%) had incontinence at least once during their CDAD episode. CONCLUSIONS: In VRE-colonized patients with CDAD who experienced frequent fecal incontinence, skin and environmental VRE contamination was common during and after resolution of diarrhea. The frequency of VRE contamination was similar between patients treated with metronidazole and patients treated with vancomycin.

Comparison of clinical and microbiological response to treatment of Clostridium difficile-associated disease with metronidazole and vancomycin.

BACKGROUND: There have been recent reports of frequent treatment failure associated with the use of metronidazole for treatment of Clostridium difficile-associated disease. We tested the hypothesis that treatment failure with metronidazole is associated with a suboptimal microbiological response in comparison with that of vancomycin. METHODS: We conducted a 9-month prospective observational study of patients with C. difficile-associated disease. Cox proportional hazards models were used to compare metronidazole-treated and vancomycin-treated patients in terms of time to resolution of diarrhea and time to reduction of C. difficile in stool to an undetectable level. RESULTS: Of 52 study patients with C. difficile-associated disease, 34 (65%) received initial therapy with oral metronidazole, and 18 (35%) received initial therapy with oral vancomycin. Diarrhea resolved in >90% of patients who completed 10 days of treatment with either agent. However, vancomycin-treated patients were more likely to develop undetectable levels of C. difficile (adjusted hazard ratio, 3.99; 95% confidence interval, 1.41-11.3;P = .009) and to have resolution of diarrhea (adjusted hazard ratio, 4.17; 95% confidence interval, 1.53-11.40;P = .005) during the first 5 days of therapy. Ten metronidazole-treated patients (29%) had their treatment changed to oral vancomycin because of persistent symptoms. Seven (70%) of these 10 patients had <1 log reduction in C.difficile concentration; however, only 4 had completed > or = 6 days of metronidazole treatment at the time of the treatment change. CONCLUSION: In an observational study with a limited number of subjects, a majority of patients with C. difficile-associated disease responded to therapy with metronidazole or vancomycin. Failure with metronidazole treatment may be attributable to a slower and less consistent microbiological response than that with oral vancomycin treatment.

Both oral metronidazole and oral vancomycin promote persistent overgrowth of vancomycin-resistant enterococci during treatment of Clostridium difficile-associated disease.

For treatment of mild to moderate Clostridium difficile-associated disease (CDAD), oral metronidazole has been recommended as the preferred agent, in part due to concern that vancomycin may be more likely to promote colonization by vancomycin-resistant enterococci (VRE). We performed a prospective observational study to examine the effects of oral metronidazole or vancomycin treatment of CDAD on acquisition and concentration of VRE stool colonization. Before, during, and after 90 courses of CDAD therapy, stool samples were cultured for VRE, and the concentrations were quantified. Eighty-seven subjects (97%) had received antibiotics within the past month. For 56 treatment courses in which preexisting VRE colonization was present, metronidazole (n = 37 courses) and vancomycin (n = 19 courses), each promoted persistent VRE overgrowth during therapy, and the concentration decreased significantly in both groups by approximately 2 weeks after completion of treatment (P <0.049). For 34 treatment courses in which baseline cultures were negative for VRE, new detection of VRE stool colonization occurred during 3 (14%) of the 22 courses of metronidazole and 1 (8%) of the 12 courses of vancomycin (P = 1.0). These results demonstrate that both oral metronidazole and oral vancomycin promote the overgrowth of VRE during treatment of CDAD. New CDAD treatments are needed that are less likely to disrupt the intestinal microflora and promote overgrowth of healthcare-associated pathogens.

Clostridium difficile skin contamination in patients with C. difficile-associated disease.

In a prospective study of 27 patients with Clostridium difficile-associated disease, we found that C. difficile frequently contaminated multiple skin sites, including groin, chest, abdomen, forearms, and hands, and was easily acquired on investigators' hands. Skin contamination often persisted on patients' chest and abdomen after resolution of diarrhea.