Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study.

We conducted a feasibility cohort study which aimed to recruit and retain adults from the community to collect saliva (oral) and stool (gut) samples at three time points, at the start of the study (baseline), during a respiratory tract infection (RTI) and post-RTI. Community RTIs place a huge burden on health care services, and a non-invasive microbial diagnostic tool to predict the most vulnerable to respiratory infection would be ideal. To this aim, we analysed oral-gut baseline samples comparing those who reported RTI symptoms to those who remained healthy throughout the study for microbial biomarkers of respiratory susceptibility. Amplicon sequence variants (ASV) were identified by 16S sequence profiling to reveal oral-gut microbes. Reverse transcriptase-polymerase chain reaction (RT-PCR) was applied to target common respiratory microbes. Two general practices were recruited, and the participant recruitment rate was 1.3%. A total of 40 adult participants were retained, of which 19 acquired an RTI whereas 21 remained healthy. In healthy baseline oral and gut samples, ASVs from participants with RTI symptoms compared to those who remained healthy were similar with a high relative abundance of Streptococcus sp., and Blautia sp., respectively. Linear discriminant analysis effect size (LEfSe) revealed baseline oral microbes differed, indicating participants who suffered RTI symptoms had enhanced Streptococcus sobrinus and Megamonas sp., and depletion of Lactobacillus salivarius, Synergistetes, Verrucomicrobia and Dethiosulfovibrio. Furthermore, a random forest model ranked Streptococcus (4.13) as the highest mean decrease in accuracy (MDA) and RT-PCR showed a higher level of carriage of coagulase-negative Staphylococcus. Baseline core gut microbes were similar in both participant groups whereas LEfSe analysis revealed enhanced Veillonella, Rikenellaceae, Enhydobacteria, Eggerthella and Xanthomonsdales and depleted Desulfobulbus and Coprobacillus. Sutterella (4.73) had a high MDA value. Overall, we demonstrated the feasibility of recruiting and retaining adult participants from the community to provide multiple biological samples for microbial profiling. Our analyses identified potential oral-gut microbial biomarkers of respiratory infection susceptibility in otherwise healthy participants.

Which patients received a ReSPECT form, what was documented and what were the patient outcomes? A protocol for a retrospective observational study investigating the impact of the COVID-19 pandemic on the implementation of the ReSPECT process.

INTRODUCTION: Recommended Summary Plan for Emergency Care and Treatment (ReSPECT) is a UK advance care planning (ACP) initiative aiming to standardise the process of creating personalised recommendations for a person's clinical care in a future emergency and therefore improve person-focused care. Implementation of the ReSPECT process across a large geographical area, involving both community and secondary care, has not previously been studied. In particular, it not known whether such implementation is associated with any change in outcomes for those patients with a ReSPECT form.Implementation of ReSPECT in the Bristol, North Somerset and South Gloucestershire (BNSSG) Clinical Commissioning Group (CCG) area overlapped with the first UK COVID-19 wave. It is unclear what impact the pandemic had on the implementation of ReSPECT and if this affected the type of patients who underwent the ReSPECT process, such as those with specific diagnoses or living in care homes. Patterns of clinical recommendations documented on ReSPECT forms during the first year of its implementation may also have changed, particularly with reference to the pandemic.To determine the equity and potential benefits of implementation of the ReSPECT form process in BNSSG and contribute to the ACP evidence base, this study will describe the characteristics of patients in the BNSSG area who had a completed ReSPECT form recorded in their primary care medical records before, during and after the first wave of the COVID-19 pandemic; describe the content of ReSPECT forms; and analyse outcomes for those patients who died with a ReSPECT form. METHODS AND ANALYSIS: We will perform an observational retrospective study on data, collected from October 2019 for 12 months. Data will be exported from the CCG Public Health Management data resource, a pseudonymised database linking data from organisations providing health and social care to people across BNSSG. Descriptive statistics of sociodemographic and health-related variables for those who completed the ReSPECT process with a clinician and had a documented ReSPECT form in their notes, in addition to their ReSPECT form responses, will be compared between before, during and after first COVID-19 wave groups. Additionally, routinely collected outcomes for patients who died in our study period will be compared between those who completed the ReSPECT process with a community clinician, hospital clinician or not at all. These include emergency department attendances, emergency hospital admissions, community nurse home visits, hospice referrals, anticipatory medication prescribing, place of death and if the patient died in preferred place of death. ETHICS AND DISSEMINATION: Approval has been obtained from a National Health Service Research Ethics Committee (20/YH/0185). Findings will be disseminated to policy decision-makers, care providers and the public through scientific meetings and peer-reviewed publication.

Respiratory tract infections and gut microbiome modifications: A systematic review.

Respiratory tract infections (RTIs) are extremely common and can cause gastrointestinal tract symptoms and changes to the gut microbiota, yet these effects are poorly understood. We conducted a systematic review to evaluate the reported evidence of gut microbiome alterations in patients with a RTI compared to healthy controls (PROSPERO: CRD42019138853). We systematically searched Medline, Embase, Web of Science, Cochrane and the Clinical Trial Database for studies published between January 2015 and June 2021. Studies were eligible for inclusion if they were human cohorts describing the gut microbiome in patients with an RTI compared to healthy controls and the infection was caused by a viral or bacterial pathogen. Dual data screening and extraction with narrative synthesis was performed. We identified 1,593 articles and assessed 11 full texts for inclusion. Included studies (some nested) reported gut microbiome changes in the context of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (n = 5), influenza (H1N1 and H7N9) (n = 2), Tuberculosis (TB) (n = 4), Community-Acquired Pneumonia CAP (n = 2) and recurrent RTIs (rRTI) (n = 1) infections. We found studies of patients with an RTI compared to controls reported a decrease in gut microbiome diversity (Shannon) of 1.45 units (95% CI, 0.15-2.50 [p, <0.0001]) and a lower abundance of taxa (p, 0.0086). Meta-analysis of the Shannon value showed considerable heterogeneity between studies (I2, 94.42). Unbiased analysis displayed as a funnel plot revealed a depletion of Lachnospiraceae, Ruminococcaceae and Ruminococcus and enrichment of Enterococcus. There was an important absence in the lack of cohort studies reporting gut microbiome changes and high heterogeneity between studies may be explained by variations in microbiome methods and confounder effects. Further human cohort studies are needed to understand RTI-induced gut microbiome changes to better understand interplay between microbes and respiratory health.

Prospective Study of the Performance of Parent-Collected Nasal and Saliva Swab Samples, Compared with Nurse-Collected Swab Samples, for the Molecular Detection of Respiratory Microorganisms.

Respiratory tract infections (RTIs) are ubiquitous among children in the community. A prospective observational study was performed to evaluate the diagnostic performance and quality of at-home parent-collected (PC) nasal and saliva swab samples, compared to nurse-collected (NC) swab samples, from children with RTI symptoms. Children with RTI symptoms were swabbed at home on the same day by a parent and a nurse. We compared the performance of PC swab samples as the test with NC swab samples as the reference for the detection of respiratory pathogen gene targets by reverse transcriptase PCR, with quality assessment using a human gene. PC and NC paired nasal and saliva swab samples were collected from 91 and 92 children, respectively. Performance and interrater agreement (Cohen's κ) of PC versus NC nasal swab samples for viruses combined showed sensitivity of 91.6% (95% confidence interval [CI], 85.47 to 95.73%) and κ of 0.84 (95% CI, 0.79 to 0.88), respectively; the respective values for bacteria combined were 91.4% (95% CI, 86.85 to 94.87%) and κ of 0.85 (95% CI, 0.80 to 0.89). In saliva samples, viral and bacterial sensitivities were lower at 69.0% (95% CI, 57.47 to 79.76%) and 78.1% (95% CI, 71.60 to 83.76%), as were κ values at 0.64 (95% CI, 0.53 to 0.72) and 0.70 (95% CI, 0.65 to 0.76), respectively. Quality assessment for human biological material (18S rRNA) indicated perfect interrater agreement. At-home PC nasal swab samples performed comparably to NC swab samples, whereas PC saliva swab samples lacked sensitivity for the detection of respiratory microbes. IMPORTANCE RTIs are ubiquitous among children. Diagnosis involves a swab sample being taken by a health professional, which places a considerable burden on community health care systems, given the number of cases involved. The coronavirus disease 2019 (COVID-19) pandemic has seen an increase in the at-home self-collection of upper respiratory tract swab samples without the involvement of health professionals. It is advised that parents conduct or supervise swabbing of children. Surprisingly, few studies have addressed the quality of PC swab samples for subsequent identification of respiratory pathogens. We compared NC and PC nasal and saliva swab samples taken from the same child with RTI symptoms, for detection of respiratory pathogens. The PC nasal swab samples performed comparably to NC samples, whereas saliva swab samples lacked sensitivity for the detection of respiratory microbes. Collection of swab samples by parents would greatly reduce the burden on community nurses without reducing the effectiveness of diagnoses.

Should homes and workplaces purchase portable air filters to reduce the transmission of SARS-CoV-2 and other respiratory infections? A systematic review.

Respiratory infections, including SARS-CoV-2, are spread via inhalation or ingestion of airborne pathogens. Airborne transmission is difficult to control, particularly indoors. Manufacturers of high efficiency particulate air (HEPA) filters claim they remove almost all small particles including airborne bacteria and viruses. This study investigates whether modern portable, commercially available air filters reduce the incidence of respiratory infections and/or remove bacteria and viruses from indoor air. We systematically searched Medline, Embase and Cochrane for studies published between January 2000 and September 2020. Studies were eligible for inclusion if they included a portable, commercially available air filter in any indoor setting including care homes, schools or healthcare settings, investigating either associations with incidence of respiratory infections or removal and/or capture of aerosolised bacteria and viruses from the air within the filters. Dual data screening and extraction with narrative synthesis. No studies were found investigating the effects of air filters on the incidence of respiratory infections. Two studies investigated bacterial capture within filters and bacterial load in indoor air. One reported higher numbers of viable bacteria in the HEPA filter than in floor dust samples. The other reported HEPA filtration combined with ultraviolet light reduced bacterial load in the air by 41% (sampling time not reported). Neither paper investigated effects on viruses. There is an important absence of evidence regarding the effectiveness of a potentially cost-efficient intervention for indoor transmission of respiratory infections, including SARS-CoV-2. Two studies provide 'proof of principle' that air filters can capture airborne bacteria in an indoor setting. Randomised controlled trials are urgently needed to investigate effects of portable HEPA filters on incidence of respiratory infections.

Evaluation of an Inexpensive Growth Medium for Direct Detection of Escherichia coli in Temperate and Sub-Tropical Waters.

The cost and complexity of traditional methods for the detection of faecal indicator bacteria, including E. coli, hinder widespread monitoring of drinking water quality, especially in low-income countries and outside controlled laboratory settings. In these settings the problem is exacerbated by the lack of inexpensive media for the detection of E. coli in drinking water. We developed a new low-cost growth medium, aquatest (AT), and validated its use for the direct detection of E. coli in temperate and sub-tropical drinking waters using IDEXX Quanti-Tray®. AT was compared with IDEXX Colilert-18® and either EC-MUG or MLSB for detecting low levels of E. coli from water samples from temperate (n = 140; Bristol, UK) and subtropical regions (n = 50, Pretoria/Tshwane, South Africa). Confirmatory testing (n = 418 and 588, respectively) and the comparison of quantitative results were used to assess performance. Sensitivity of AT was higher than Colilert-18® for water samples in the UK [98.0% vs. 86.9%; p<0.0001] and South Africa [99.5% vs. 93.2%; p = 0.0030]. There was no significant difference in specificity, which was high for both media (>95% in both settings). Quantitative results were comparable and within expected limits. AT is reliable and accurate for the detection of E. coli in temperate and subtropical drinking water. The composition of the new medium is reported herein and can be used freely.

Synthesis and application of resorufin ß-D-glucuronide, a low-cost chromogenic substrate for detecting Escherichia coli in drinking water.

The development of low-cost tests for Escherichia coli is hampered by the expense and limited choice of enzyme substrates. Most chromogenic substrates are required in costly amounts, while fluorogenic substrates require an additional apparatus (e.g., an ultraviolet lamp) to be detected. Herein, we propose an alternative chromogenic substrate, resorufin ß-d-glucuronide (REG), which is exceptionally sensitive and may be employed in very small amounts. We show that REG can be produced similarly to other simple glucuronides and should therefore be no more expensive. The compound is used by both healthy and injured E. coli, resulting in a pronounced color change from orange to a bright pink. Because the released dye (resorufin) has a high extinction coefficient, substantially lower amounts are needed than for commercially available substrates. The potential of this substrate is demonstrated by a presence/absence test requiring just 0.1 mg of REG/100 mL of water sample, one hundredth of the quantity needed for common chromogenic substrates, with an estimated bulk cost of ≤0.1 U.S. cents/test. REG shows promise as a chromogenic substrate for E. coli detection and should be considered in the development of new water tests, especially for low-income settings.

Signature-tagged transposon mutagenesis studies demonstrate the dynamic nature of cecal colonization of 2-week-old chickens by Campylobacter jejuni.

We have constructed plasmids to be used for in vitro signature-tagged mutagenesis (STM) of Campylobacter jejuni and used these to generate STM libraries in three different strains. Statistical analysis of the transposon insertion sites in the C. jejuni NCTC 11168 chromosome and the plasmids of strain 81-176 indicated that their distribution was not uniform. Visual inspection of the distribution suggested that deviation from uniformity was not due to preferential integration of the transposon into a limited number of hot spots but rather that there was a bias towards insertions around the origin. We screened pools of mutants from the STM libraries for their ability to colonize the ceca of 2-week-old chickens harboring a standardized gut flora. We observed high-frequency random loss of colonization proficient mutants. When cohoused birds were individually inoculated with different tagged mutants, random loss of colonization-proficient mutants was similarly observed, as was extensive bird-to-bird transmission of mutants. This indicates that the nature of campylobacter colonization in chickens is complex and dynamic, and we hypothesize that bottlenecks in the colonization process and between-bird transmission account for these observations.

Halothiobacillus neapolitanus strain OSWA isolated from "The Old Sulphur Well" at Harrogate (Yorkshire, England).

The "Old Sulphur Well" has a subterranean input of water containing 5.5mM total sulfide, which would be inhibitory to the growth of most bacteria. The obligately chemolithoautotrophic Halothiobacillus neapolitanus is a sulfur bacterium known to tolerate and metabolize high sulfide concentrations, and we report the isolation of H. neapolitanus strain OSWA from this source. Strain OSWA grows well on thiosulfate and tetrathionate as energy sources, and tolerates at least 5mM sulfide. Its specific growth rates and yields in batch culture were 0.22h(-1) and 5.3 gmol(-1) (thiosulfate), and 0.23 h(-1) and 9.5 gmol(-1) (tetrathionate). Its 16S rRNA gene sequence shows >99% identity to reference sequences of H. neapolitanus, and it shares morphological and physiological characteristics typical of the species. It is one of a very small number of strains of H. neapolitanus described to date, and the first to be isolated from an ancient sulfide-rich natural spa.

Adaptation of Campylobacter jejuni NCTC11168 to high-level colonization of the avian gastrointestinal tract.

The genome sequence of the human pathogen Campylobacter jejuni NCTC11168 has been determined recently, but studies on colonization and persistence in chickens have been limited due to reports that this strain is a poor colonizer. Experimental colonization and persistence studies were carried out with C. jejuni NCTC11168 by using 2-week-old Light Sussex chickens possessing an acquired natural gut flora. After inoculation, NCTC11168 initially colonized the intestine poorly. However, after 5 weeks we observed adaptation to high-level colonization, which was maintained after in vitro passage. The adapted strain exhibited greatly increased motility. A second strain, C. jejuni 11168H, which had been selected under in vitro conditions for increased motility (A. V. Karlyshev, D. Linton, N. A. Gregson, and B. W. Wren, Microbiology 148:473-480, 2002), also showed high-level intestinal colonization. The levels of colonization were equivalent to those of six other strains, assessed under the same conditions. There were four mutations in C. jejuni 11168H that reduced colonization; maf5, flaA (motility and flagellation), and kpsM (capsule deficiency) eliminated colonization, whereas pglH (general glycosylation system deficient) reduced but did not eliminate colonization. This study showed that there was colonization of the avian intestinal tract by a Campylobacter strain having a known genome sequence, and it provides a model for colonization and persistence studies with specific mutations.