Protecting the Microbiota.

We examine 3 different approaches to protecting the gut microbiome: highly targeted antibiotics, antibiotic destruction, and antibiotic binding. Each approach shows promise to prevent the off-target effects of antibiotics on the gut microbiome.

Dissemination of multiple carbapenem resistance genes in an in vitro gut model simulating the human colon.

BACKGROUND: Carbapenemase-producing Enterobacteriaceae (CPE) pose a major global health risk. Mobile genetic elements account for much of the increasing CPE burden. OBJECTIVES: To investigate CPE colonization and the impact of antibiotic exposure on subsequent resistance gene dissemination within the gut microbiota using a model to simulate the human colon. METHODS: Gut models seeded with CPE-negative human faeces [screened with BioMérieux chromID® CARBA-SMART (Carba-Smart), Cepheid Xpert® Carba-R assay (XCR)] were inoculated with distinct carbapenemase-producing Klebsiella pneumoniae strains (KPC, NDM) and challenged with imipenem or piperacillin/tazobactam then meropenem. Resistant populations were enumerated daily on selective agars (Carba-Smart); CPE genes were confirmed by PCR (XCR, Check-Direct CPE Screen for BD MAX™). CPE gene dissemination was tracked using PacBio long-read sequencing. RESULTS: CPE populations increased during inoculation, plateauing at ∼105 log10 cfu/mL in both models and persisting throughout the experiments (>65 days), with no evidence of CPE 'washout'. After antibiotic administration, there was evidence of interspecies plasmid transfer of blaKPC-2 (111742 bp IncFII/IncR plasmid, 99% identity to pKpQIL-D2) and blaNDM-1 (∼170 kb IncFIB/IncFII plasmid), and CPE populations rose from <0.01% to >45% of the total lactose-fermenting populations in the KPC model. Isolation of a blaNDM-1K. pneumoniae with one chromosomal single-nucleotide variant compared with the inoculated strain indicated clonal expansion within the model. Antibiotic administration exposed a previously undetected K. pneumoniae encoding blaOXA-232 (KPC model). CONCLUSIONS: CPE exposure can lead to colonization, clonal expansion and resistance gene transfer within intact human colonic microbiota. Furthermore, under antibiotic selective pressure, new resistant populations emerge, emphasizing the need to control exposure to antimicrobials.

Low fruit and vegetable consumption is associated with low knowledge of the details of the 5-a-day fruit and vegetable message in the UK: findings from two cross-sectional questionnaire studies.

BACKGROUND: This project aimed to understand the details of the 5-a-day fruit and vegetable (FV) message (which foods are included, portion sizes, the need for variety, reasons for consumption) least known by UK consumers, and most associated with low FV consumption. METHODS: Study 1 assessed FV consumption, knowledge of the details of the message, and relationships between these, using a short questionnaire administered face-to-face to an opportunity sample of one large UK city. Study 2 assessed the same variables using a comprehensive postal questionnaire administered across the UK to a representative population sample. RESULTS: Five hundred and seven respondents completed Study 1 and 247 respondents completed Study 2. The majority of individuals in both studies were aware of the 5-a-day message and could recount this correctly. In both studies, however, knowledge of the details of the message was low, and lower knowledge was associated with lower FV consumption. Respondents had lowest knowledge of the details of the message related to portion sizes and the need for variety. However, FV consumption was not independently associated with knowledge of any one aspect of the message. CONCLUSIONS: These findings suggest that, although most of the UK population sampled were aware of the 5-a-day FV message and could recount this correctly, details of the 5-a-day FV message were not well known, and that FV consumption was related to this knowledge. These findings suggest that strategies to increase FV consumption will benefit from increasing UK consumers' knowledge of the details of the 5-a-day FV message.

How much is '5-a-day'? A qualitative investigation into consumer understanding of fruit and vegetable intake guidelines.

BACKGROUND: Despite the known health benefits of fruit and vegetables (FV), population intakes remain low. One potential contributing factor may be a lack of understanding surrounding recommended intakes. The present study aimed to explore the understanding of FV intake guidelines among a sample of low FV consumers. METHODS: Six semi-structured focus groups were held with low FV consumers (n = 28, age range 19-55 years). Focus groups were recorded digitally, transcribed verbatim and analysed thematically using nvivo (QSR International, Melbourne, Australia) to manage the coded data. Participants also completed a short questionnaire assessing knowledge on FV intake guidelines. Descriptive statistics were used to analyse responses. RESULTS: The discussions highlighted that, although participants were aware of FV intake guidelines, they lacked clarity with regard to the meaning of the '5-a-day' message, including what foods are included in the guideline, as well as what constitutes a portion of FV. There was also a sense of confusion surrounding the concept of achieving variety with regard to FV intake. The sample highlighted a lack of previous education on FV portion sizes and put forward suggestions for improving knowledge, including increased information on food packaging and through health campaigns. Questionnaire findings were generally congruent with the qualitative findings, showing high awareness of the '5-a-day' message but a lack of knowledge surrounding FV portion sizes. CONCLUSIONS: Future public health campaigns should consider how best to address the gaps in knowledge identified in the present study, and incorporate evaluations that will allow the impact of future initiatives on knowledge, and ultimately behaviour, to be investigated.

Robust T cell responses to aspergillosis in chronic granulomatous disease: implications for immunotherapy.

Chronic granulomatous disease (CGD) patients are highly susceptible to invasive aspergillosis and might benefit from aspergillus-specific T cell immunotherapy, which has shown promise in treating those with known T cell defects such as haematopoietic stem cell transplant (HSCT) recipients. But whether such T cell defects contribute to increased risks for aspergillus infection in CGD is unclear. Hence, we set out to characterize the aspergillus-specific T cell response in CGD. In murine CGD models and in patients with CGD we showed that the CD4(+) T cell responses to aspergillus were unimpaired: aspergillus-specific T cell frequencies were even elevated in CGD mice (P < 0·01) and humans (P = 0·02), compared to their healthy counterparts. CD4-depleted murine models suggested that the role of T cells might be redundant because resistance to aspergillus infection was conserved in CD4(+) T cell-depleted mice, similar to wild-type animals. In contrast, mice depleted of neutrophils alone or neutrophils and CD4(+) T cells developed clinical and pathological evidence of pulmonary aspergillosis and increased mortality (P < 0·05 compared to non-depleted animals). Our findings that T cells in CGD have a robust aspergillus CD4(+) T cell response suggest that CD4(+) T cell-based immunotherapy for this disease is unlikely to be beneficial.

A Practical Guide to 16S rRNA Microbiome Analysis in Musculoskeletal Disorders.

Microbial taxonomic assignment based on 16S marker gene amplification requires multiple data transformations, often encompassing the use of a variety of computational platforms. Bioinformatics analysis may represent a bottleneck for researchers as many tools require programmatic access in order to implement the software. Here we describe a step-by-step approach for taxonomic assignment using QIIME2 and highlight the utility of graphical-based microbiome tools for further analysis and identification of biological relevant taxa with reference to an outcome of interest.

The United Kingdom public health response to an imported laboratory confirmed case of a novel coronavirus in September 2012.

On 22 September 2012, a novel coronavirus, very closely related to that from a fatal case in Saudi Arabia three months previously, was detected in a previously well adult transferred to intensive care in London from Qatar with severe respiratory illness. Strict respiratory isolation was instituted. Ten days after last exposure, none of 64 close contacts had developed severe disease, with 13 of 64 reporting mild respiratory symptoms. The novel coronavirus was not detected in 10 of 10 symptomatic contacts tested.

Long-term restoration of immunity against Epstein-Barr virus infection by adoptive transfer of gene-modified virus-specific T lymphocytes.

Adoptive transfer of antigen-specific cytotoxic T lymphocytes (CTLs) offers safe and effective therapy for certain viral infections and could prove useful in the eradication of tumor cells. Whether or not the infused T cells persist for extended periods, retaining their ability to expand in response to antigenic stimulation, is not known. We now report long-term detection of gene-marked Epstein-Barr virus (EBV)-specific CTLs in immunocompromised patients at risk for the development of EBV lymphoproliferative disease. Infusions of CTLs not only restored cellular immune responses against EBV, but also established populations of CTL precursors that could respond to in vivo or ex vivo challenge with the virus for as long as 18 months. Our findings support wider use of antigen-specific CTLs in adoptive immunotherapy.

Evidence review of physical distancing and partition screens to reduce healthcare acquired SARS-CoV-2.

We review the evidence base for two newly introduced Infection prevention and control strategies within UK hospitals. The new standard infection control precaution of 2 metres physical distancing and the use of partition screens as a means of source control of infection for SARS-CoV-2. Following review of Ovid-MEDLINE and governmental SAGE outputs there is limited evidence to support the use of 2 metres physical distancing and partition screens within healthcare.

Trends in Parkinson's disease related mortality in England and Wales, 1993-2006.

BACKGROUND: This paper describes changes in Parkinson's disease (PD) mortality in England and Wales between 1993 and 2006 using all information on death certificates. METHODS: Information on deaths was obtained from the Office for National Statistics. Mortality rates for any mention of PD on death certificates were directly age-standardized using the European standard population. Average yearly changes in mortality rates were estimated using linear regression. The underlying cause of death on death certificates where PD was mentioned was examined by sex and calendar period. RESULTS: Male PD age-standardized mortality rates for any mention of PD decreased from 15.0 to 11.7 per 100 000 between 1993 and 2006. Female PD mortality rates fell from 6.3 to 4.9 per 100 000. Decreases were greater for older age-groups. The proportion of deaths with PD recorded as the underlying cause increased by 50% in 2001 following implementation of the 10th revision of the International Classification of Diseases (ICD). CONCLUSION: Parkinson's disease mortality rates in England and Wales are decreasing, especially for men and for older age-groups. Because of data limitations we are unable to ascertain whether the decrease of PD recorded on death certificates is because of a reduction in PD incidence, or to improved survival for PD patients resulting from advancements in PD treatments or to improvements in general medical care. The dramatic increase in PD as the underlying cause of death following ICD revision in 2001 demonstrates the dangers of using underlying cause of death to investigate mortality trends without being aware of the potential for artifacts.

Adoptive cellular immunotherapy for viral diseases.

Viral infections remain a major cause of morbidity and mortality after pediatric hematopoietic stem cell transplantation. Adoptive transfer of donor-derived virus-specific T cells can reconstitute antiviral immunity in recipients and be effective both in preventing and treating cytomegalovirus, Epstein-Barr virus and adenovirus infection. Current efforts are focused on providing protection toward a broader range of viruses safely, rapidly and effectively.

Reconstitution of adenovirus-specific cell-mediated immunity in pediatric patients after hematopoietic stem cell transplantation.

Adenovirus (adv) is a significant cause of morbidity and mortality in pediatric hematopoietic stem cell transplant recipients, and control of infection seems to require antigen-specific T cells. We evaluated the recovery of adv-specific cellular immunity in this patient population related to degree of T-cell immunosuppressive therapy and compared this to adv cellular immunity of normal donors. Over 12 months, we monitored for adv DNA in stool and blood of patients and in the blood of a normal donor group. Twenty-two pediatric hematopoietic stem cell transplant (HSCT) patients (14 months-20 years) who received matched-related (MRD n=6), mismatched related (Haplo n=6) or matched unrelated donor (MUD n=10) grafts, were followed and results compared to healthy controls (n=8). Adv was detected by polymerase chain reaction in blood and/or stool from 81.8% of patients on at least one occasion post-HSCT, but only 68% of patients developed symptomatic adv infections. Recovery of adv-specific T cells was significantly delayed in the MUD and Haplo recipients, whereas recovery in the MRD group was similar to levels detected in healthy donors within 30 days post-transplant. In conclusion, recipients of alternative donor transplants at our institution have significantly delayed adv-specific cellular immune recovery, which correlates to an increased risk of adv-associated morbidity and mortality.