Background: The genus Norovirus comprises large genetic diversity and new GII.4 variants emerge every 2-3 years. It is unknown in which host these new variants originate. Here we study whether prolonged shedders within the immunocompromised population could be a reservoir for newly emerging strains.
Methods: Faecal samples (n=65) from immunocompromised patients (n=16) were retrospectively selected. Isolated viral RNA was enriched by hybridization with a custom norovirus whole-genome RNA bait set and deep sequenced on the Illumina MiSeq platform.
Results: Patients shed virus for average 352 days (range: 76-716 days). Phylogenetic analysis showed distinct GII.4 variants in 3 out of 13 (23%) patients. The viral mutation rates were variable between patients, but did not differ between various immune status groups. All within host GII.4 viral populations showed amino acid changes at blocking epitopes over time and the majority of VP1 amino acid mutations were located at the capsid surface.
Discussion: This study found viruses in the immunocompromised host that are genetically distinct from viruses circulating in the general population and these patients therefore may contain a reservoir for newly emerging strains. Future studies need to determine whether these new strains are of risk for other immunocompromised patients and the general population.
Extended-spectrum cephalosporin (ESC)-resistant Salmonella has been described at low level in EU, nevertheless the increasing importation of poultry meat could be an important source of epidemic strains carrying ESC-resistant genes. We evaluated ESC resistance and characterized genetic platforms as well as the clonal relatedness of Salmonella isolates from poultry meat products imported into Portugal. All Salmonella isolates recovered from samples of fresh meat destined to be imported into the EU in the scope of Portuguese official border control between 2014 and 2015 were studied. Susceptibility to antibiotics and detection of β-lactamase production was performed by disk diffusion/microdilution methods. Molecular studies included detection of genes encoding for qAmpC and extended-spectrum β-lactamases, plasmid-mediated quinolone resistance and other antibiotic resistance by PCR/sequencing and clonality by MLST and XbaI-PFGE. Plasmid characterization was assessed by conjugation assays, replicon typing (PCR-PBRT/pMLST) and hybridization experiments (I-CeuI/S1-PFGE nuclease). Salmonella belonged to S. Heidelberg (n=6; ST15/eBG26) and S. Minnesota (n=1; ST548/eBG77) serotypes and presented multidrug-resistant profiles, including to ESC and/or fluoroquinolones. All but one carried blaCMY-2 gene, located on two epidemic plasmids, IncA/C (ST2-n=5) or a transferable IncI1 (ST12-n=1). S. Heidelberg was associated with 5 PFGE-types, including one similar to an American epidemic clone. This study reveals imported poultry products as a source of uncommon and/or invasive ESC resistant Salmonella strains in EU. The increase of those clinically-relevant poultry-related serotypes in Europe, as described here, must be taken into account in the current monitoring of antibiotic resistance trends and in re-evaluation of food regulations.
BACKGROUND: The importance of biofilms to clinical practice is being increasingly realised. Biofilm tolerance to antibiotics is well described but limited work has been conducted on the efficacy of heat disinfection and sterilization against biofilms.
AIM: To test the susceptibility of planktonic, hydrated biofilm and dry-surface biofilm forms of Staphylococcus aureus, to dry heat and wet heat treatments.
METHODS: S. aureus was grown as both hydrated biofilm and dry-surface biofilm in the CDC biofilm generator. Biofilm was subjected to a range of temperatures in a hot air oven (dry heat), water bath or autoclave (wet heat).
FINDINGS: Dry-surface biofilms remained culture positive even when treated with the harshest dry-heat condition of 100(o)C for 60 minutes. Following autoclaving samples were culture negative but 62-74% of bacteria in dry-surface biofilms remained alive as demonstrated by live/dead staining and confocal microscopy. Dry-surface biofilms subjected to autoclaving at 121(o)C for up to 30 minutes, recovered and released planktonic cells. Recovery didn't occur following autoclaving for longer or at 134(o)C, at least during the time-period tested. Hydrated biofilm recovered following dry heat treatment up to 100(o)C for 10 minutes but failed to recover following autoclaving despite the presence of 43-60% live cells as demonstrated by live/dead staining.
CONCLUSIONS: S. aureus dry-surface biofilms are less susceptible to killing by dry heat and steam autoclaving than hydrated biofilms, which are less susceptible to heat treatment than planktonic suspensions.
An increase in the number of staphylococcal infections and carriers among medical staff has forced us to seek more and more effective antibacterial agents. Bacteria from the Staphylococcus genus possessing different mechanisms of resistance are the cause of nosocomial infections. The objective of our investigations was susceptibility of S. aureus strains isolated from nasal vestibule of medical students to fennel essential oil. The GC-MS analysis of fennel essential oil revealed eleven constituents among which a majority of trans-anethole (80%) was found. The D-tests showed iMLSB (80%), cMLSB and MSB (10%) resistant phenotypes of S. aureus. The S. aureus isolates were intermediate to mupirocin (45%). Fennel essential oil increased the inhibition zone around cefoxitin, mupirocin, co-trimoxazole and ciprofloxacin with statistical significance. Our research showed that the fennel essential oil in combination with mupirocin may be considered as a natural alternative in eradication of S. aureus with iMLSB, cMLSB, MSB resistant phenotypes and is able to decrease the growth rate of antibiotic resistance.
Norovirus is the leading cause of acute gastroenteritis. In older adults, it is responsible for an estimated 3.7 million illnesses; 320,000 outpatient visits; 69,000 emergency department visits; 39,000 hospitalizations; and 960 deaths annually in the United States. Older adults are particularly at risk for severe outcomes, including prolonged symptoms and death. Long-term care facilities and hospitals are the most common settings for norovirus outbreaks in developed countries. Diagnostic platforms are expanding. Several norovirus vaccines in clinical trials have the potential to reap benefits. This review summarizes current knowledge on norovirus infection in older adults.
OBJECTIVE: Proton pump inhibitors (PPIs) can kill some human protozoan parasites in cell culture better than the drug metronidazole. Clinical data showing an antiprotozoal effect for PPIs are lacking. The objective of the study is to determine if PPI use is associated with a reduced risk of having intestinal parasites.
METHODS: We obtained electronic medical record data for all persons who received a stool ova and parasite (O & P) examination at our tertiary care academic medical center in Cleveland, Ohio, between January 2000 and September 2014. We obtained the person's age, whether they were taking a PPI at the time of the O & P examination, and whether the pathology report indicated the presence of any parasites. χ(2) with Yates correction was used to determine if PPI use was associated with stool protozoa.
RESULTS: Three intestinal protozoa were identified in 1199 patients taking a PPI (0.3%), and 551 intestinal parasites were identified in the 14,287 patients not taking a PPI (3.9%). There was a statistically significant lower likelihood of finding protozoa in the stool of a person taking a PPI compared with those not taking a PPI (P < .0001).
CONCLUSIONS: Patients taking a PPI were statistically less likely to have an intestinal protozoa reported on stool O & P examination compared with those not taking a PPI.
Gene delivery vectors that do not rely on host cell genome integration offer several advantages for gene transfer, chiefly the avoidance of insertional mutagenesis and position effect variegation. However, unless engineered for replication and segregation, nonintegrating vectors will dilute progressively in proliferating cells, and are not exempt of epigenetic effects. This article provides an overview of the main nonintegrating viral (adenoviral, adeno-associated viral, integration-deficient retro-lentiviral, poxviral), and nonviral (plasmid vectors, artificial chromosomes) vectors used for preclinical and clinical cell and gene therapy applications. Particular emphasis is placed on their use in hematologic disease.
The paper entitled "Rosacea and demodicidosis with gain of function mutation in STAT1″ by Second et al.(1) is of indubitable interest and prompted us to make some observations. The Authors described a patient with cutaneous and ocular rosacea that they related to demodicidosis since oral ivermectin improved the cutaneous lesions(1) . However, the Authors did not demonstrate by skin scraping nor by standardized skin surface biopsy (SSSB) an excessive number of Demodex folliculorum (DF) mites in the pilosebaceous units to justify an oral antiparasitic treatment as a drug of first choice(1) . This article is protected by copyright. All rights reserved.
In April 2016, an outbreak of gastrointestinal illness (4,136 cases) occurred in Catalonia, Spain. We detected high levels of norovirus genotypes I and II in office water coolers associated with the outbreak. Infectious viral titer estimates were 33-49 genome copies/L for genotype I and 327-660 genome copies/L for genotype II.
BACKGROUND: In June 2015, a local public health laboratory was notified that students had developed gastroenteritis symptoms after participating in a camp. An outbreak investigation was conducted to determine the extent and cause of the outbreak.
METHOD: We conducted a retrospective cohort study to determine the correlations between the illness and specific exposures at the school camp. All attendees were interviewed with a standard questionnaire that addressed clinical symptoms, food consumption and environmental exposures. Clinical specimens were cultured using standard microbiological methods for bacterial or viral pathogens. The genetic relationships of all isolates were determined using pulsed-field gel electrophoresis (PFGE).
RESULTS: We identified 188 patients with symptoms of diarrhoea, abdominal pain and nausea. Their completed questionnaires suggested that the consumption of drinking water was likely to be linked to this outbreak. Using microbiological methods, we isolated enterohemorrhagic Escherichia coli, enteropathogenic E. coli and enteroaggregative E. coli, and the isolates from both patient stools and environmental water samples displayed indistinguishable XbaI-PFGE patterns. The water system in the camp used groundwater drawn from a private underground reservoir for cooking and drinking. The environmental investigation revealed some problems with the water supply system, such as the use of inappropriate filters in the water purifier and a defect in the pipeline between the reservoir and the chlorination device.
CONCLUSIONS: This outbreak points to the importance of drinking water quality management in group facilities using underground water and emphasizes the need for periodic sanitation and inspection to prevent possible waterborne outbreaks.
Escherichia coli Infections (1), Gastroenteritis (1), more mentions
More from International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases:
BACKGROUND/AIMS: Clostridium difficile infection (CDI) frequently complicates ulcerative colitis (UC) and can mimic disease flare. Differentiating UC flare from CDI remains a clinical challenge, particularly due to C. difficile colonization. Procalcitonin (PCT) is a serum biomarker for bacterial infections. We hypothesized that PCT would differentiate acute CDI from UC flare and C. difficile colonization.
METHODS: A single-center prospective cohort study was conducted from 2013 to 2016. All UC patients with a stool sample for C. difficile testing were eligible. A total of 117 patients were enrolled, while 20 were excluded. Chart review was performed.
RESULTS: Among 27 patients with CDI, median PCT was 60.7 (range 26-560.6) pg/mL, while among 90 patients without CDI, median PCT was 56.7 (range 25.1-2,252) pg/mL (p = 0.9). It was found that 14 patients with CDI responded completely to C. difficile treatment (CDI-R), while 8 patients did not and were diagnosed with UC flare (CDI-NR). For CDI-R, median PCT was 104.5 (range 26.3-560.6), compared to 40.3 (range 26.0-116.3) for CDI-NR (p = 0.036).
CONCLUSIONS: In UC patients presenting with diarrhea, serum PCT was not significantly higher in UC patients with positive C. difficile testing. However, PCT was significantly elevated in CDI-R versus CDI-NR, suggesting that PCT may have utility in making this discrimination.
The ability of bacteria to respond to environmental change is based on the ability to coordinate, redirect and fine-tune their genetic repertoire as and when required. While we can learn a great deal from reductive analysis of individual pathways and global approaches to gene regulation, a deeper understanding of these complex signaling networks requires the simultaneous consideration of several regulatory layers at the genome scale. To highlight the power of this approach we analyzed the Hfq transcriptional/translational regulatory network in the model bacterium Pseudomonas fluorescens. We first used extensive 'omics' analyses to assess how hfq deletion affects mRNA abundance, mRNA translation and protein abundance. The subsequent, multi-level integration of these datasets allows us to highlight the discrete contributions by Hfq to gene regulation at different levels. The integrative approach to regulatory analysis we describe here has significant potential, for both dissecting individual signaling pathways and understanding the strategies bacteria use to cope with external challenges.
OBJECTIVES: Shiga toxin-producing Escherichia coli (STEC) causes diarrhoeal disease, bloody diarrhoea and haemolytic uraemic syndrome. The aim of this study was to describe the incidence of STEC and the clinical features of STEC patients from a well-defined Danish population in which all fecal samples of patients with suspected infective gastroenteritis were analysed for STEC.
METHODS: In this population-based cohort study, all stool samples referred to two clinical microbiology laboratories, were screened for STEC by culture and/or PCR. Epidemiological (n=170) and clinical (n=209) characteristics were analysed using data from local and national registries.
RESULTS: Overall 75,132 samples from 30,073 patients were screened resulting in 217 unique STEC-isolates. The epidemiological analysis showed an incidence of 10.1 cases per 100,000 person-years, which was more than two-fold higher than the incidence in the rest of Denmark (3.4 cases per 100.000 person-years, p<0.001). Three groups were associated with a higher incidence: age <5 years (n=28, p<0.001), age ≥65 years (n=38, p=0.045) and foreign ethnicity (n=27, p=0.003). In the clinical analysis patients with STEC harboring only the Shiga toxin 1 gene (stx1-only isolates) showed a lower frequency of acute (n=11, p<0.05) and bloody diarrhoea (n=5, p<0.05) and a higher frequency of gastrointestinal symptoms for ≥3 months (n=8, p<0.05) than the other STEC patients.
CONCLUSIONS: We report a more than two-fold higher incidence in the project area compared with the rest of Denmark, indicating that patients remain undiagnosed when selective STEC screening is used. We found an association between patients with stx1-only isolates and long-term gastrointestinal symptoms.
The theory of species coexistence is a key concept in ecology that has received much attention. The role of rapid evolution for determining species coexistence is still poorly understood although evolutionary change on ecological time-scales has the potential to change almost any ecological process. The influence of evolution on coexistence can be especially pronounced in microbial communities where organisms often have large population sizes and short generation times. Previous work on coexistence has assumed that traits involved in resource use and species interactions are constant or change very slowly in terms of ecological time-scales. However, recent work suggests that these traits can evolve rapidly. Nevertheless, the importance of rapid evolution to coexistence has not been tested experimentally. Here, we show how rapid evolution alters the frequency of two bacterial competitors over time when grown together with specialist consumers (bacteriophages), a generalist consumer (protozoan) and all in combination. We find that consumers facilitate coexistence in a manner consistent with classic ecological theory. However, through disentangling the relative contributions of ecology (changes in consumer abundance) and evolution (changes in traits mediating species interactions) on the frequency of the two competitors over time, we find differences between the consumer types and combinations. Overall, our results indicate that the influence of evolution on species coexistence strongly depends on the traits and species interactions considered.
Background: Data on the use of ceftolozane-tazobactam and emergence of ceftolozane-tazobactam resistance during multidrug resistant (MDR)-Pseudomonas aeruginosa infections are limited.
Methods: We performed a retrospective study of 21 patients treated with ceftolozane-tazobactam for MDR-P. aeruginosa infections. Whole genome sequencing and quantitative real-time polymerase chain reaction were performed on longitudinal isolates.
Results: Median age was 58 years; 9 patients (43%) were transplant recipients. Median simplified acute physiology score-II (SAPS-II) was 26. Eighteen (86%) patients were treated for respiratory tract infections; others were treated for bloodstream, complicated intraabdominal infections, or complicated urinary tract infections. Ceftolozane-tazobactam was discontinued in 1 patient (rash). Thirty-day all-cause and attributable mortality rates were 10% (2/21) and 5% (1/21), respectively; corresponding 90-day mortality rates were 48% (10/21) and 19% (4/21). The ceftolozane-tazobactam failure rate was 29% (6/21). SAPS-II score was the sole predictor of failure. Ceftolozane-tazobactam resistance emerged in 3 (14%) patients. Resistance was associated with de novo mutations, rather than acquisition of resistant nosocomial isolates. ampC overexpression and mutations were identified as potential resistance determinants.
Conclusions: In this small study, ceftolozane-tazobactam was successful in treating 71% of patients with MDR-P. aeruginosa infections, most of whom had pneumonia. The emergence of ceftolozane-tazobactam resistance in 3 patients is worrisome and may be mediated in part by AmpC-related mechanisms. More research on treatment responses and resistance during various types of MDR-P. aeruginosa infections is needed to define ceftolozane-tazobactam's place in the armamentarium.
The pathogenesis of gastrointestinal tract involvement in SSc is not fully understood. However, gastrointestinal signs and symptoms are very common. Trials to test therapies, with rare exceptions, should be double-blind, randomized trials with either active therapy or placebo as comparators. Trial duration will vary dependent on the anticipated therapy and should usually be 6-24 weeks long, although some motility trials may need to be 52 weeks. As in any well-controlled trial, inclusion and exclusion criteria should encourage relatively uniform patients with sufficiently active disease to discern response, importantly considering disease duration. Previous therapy, co-morbid conditions, potentially confounding and/or concomitant therapy should be considered. Outcome measures should include both objective/semi-objective and subjective measures, although validated measures are not frequent and design needs to consider using only validated measures. Unvalidated measures can be included to validate them for future use. A full analysis plan should be completed before study commencement, including the method to account for missing data.
Synthetic biology designed cell-free biosensors are a promising new tool for the detection of clinically relevant biomarkers in infectious diseases. Here, we report that a modular DNA-encoded biosensor in cell-free protein expression systems can be used to measure a bacterial biomarker of Pseudomonas aeruginosa infection from human sputum samples. By optimizing the cell-free system and sample extraction, we demonstrate that the quorum sensing molecule 3-oxo-C12-HSL in sputum samples from cystic fibrosis lungs can be quantitatively measured at nanomolar levels using our cell-free biosensor system, and is comparable to LC-MS measurements of the same samples. This study further illustrates the potential of modular cell-free biosensors as rapid, low-cost detection assays that can inform clinical practice.