Letter: faecal microbiota transplantation for irritable bowel syndrome

his article is linked to Lahtinen et al papers. To view these articles, visit https://doi.org/10.1111/apt.15810 and https://doi.org/10.1111/apt.15875

Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts

The gut microbiota is a reservoir for antimicrobial resistance genes (ARGs). With current sequencing methods, it is difficult to assign ARGs to their microbial hosts, particularly if these ARGs are located on plasmids. Metagenomic chromosome conformation capture approaches (meta3C and Hi-C) have recently been developed to link bacterial genes to phylogenetic markers, thus potentially allowing the assignment of ARGs to their hosts on a microbiome-wide scale. Here, we generated a meta3C dataset of a human stool sample and used previously published meta3C and Hi-C datasets to investigate bacterial hosts of ARGs in the human gut microbiome. Sequence reads mapping to repetitive elements were found to cause problematic noise in, and may importantly skew interpretation of, meta3C and Hi-C data. We provide a strategy to improve the signal-to-noise ratio by discarding reads that map to insertion sequence elements and to the end of contigs. We also show the importance of using spike-in controls to quantify whether the cross-linking step in meta3C and Hi-C protocols has been successful. After filtering to remove artefactual links, 87 ARGs were assigned to their bacterial hosts across all datasets, including 27 ARGs in the meta3C dataset we generated. We show that commensal gut bacteria are an important reservoir for ARGs, with genes coding for aminoglycoside and tetracycline resistance being widespread in anaerobic commensals of the human gut

Optimising triage of urgent referrals for suspected IBD: results from the Birmingham IBD inception study

Objective: Diagnostic delays in inflammatory bowel disease (IBD) result in adverse outcomes. We report a bespoke diagnostic pathway to assess how best to combine clinical history and faecal calprotectin (FCP) for early diagnosis and efficient resource utilisation. Methods: A rapid-access pathway was implemented for suspected IBD patients referred outside urgent ‘two-week wait’ criteria. Patients were triaged using symptoms and FCP. A 13-point symptom history was taken prediagnosis and clinical indices, including repeat FCP, collected prospectively. Results: Of 767 patients (January 2021–August 2023), 423 were diagnosed with IBD (208 Crohn’s disease (CD), 215 ulcerative colitis (UC)). Most common symptoms in CD were abdominal pain (84%), looser stools (84%) and fatigue (79%) and in UC per-rectal bleeding (94%), urgency (82%) and looser stools (81%). Strongest IBD predictors were blood mixed with stools (CD OR 4.38; 95% CI 2.40–7.98, UC OR 33.68; 15.47–73.33) and weight loss (CD OR 3.39; 2.14–5.38, UC OR 2.33; 1.37–4.00). Repeat FCP testing showed reduction from baseline in non-IBD. Both measurements >100 µg/g (area under the curve (AUC) 0.800) and >200 µg/g (AUC 0.834) collectively predicted IBD. However, a second value ≥220 µg/g considered alone, regardless of the first result, was more accurate (Youden’s index 0.735, AUC 0.923). Modelling symptoms with FCP increased AUC to 0.947. Conclusion: Serial FCP measurement prevents unnecessary colonoscopy. Two FCPs >200 µg/g could stream patients direct to colonoscopy, with two >100 µg/g prompting clinic review. A second result ≥220 µg/g was more accurate than dual-result thresholds. Coupling home FCP testing with key symptoms may form the basis of effective self-referral pathways

The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease

The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex interaction between a patient’s genetic predisposition, environment, gut microbiota and immune system. Currently, however, it is not known if the distinctive perturbations of the gut microbiota that appear to accompany both Crohn’s disease and ulcerative colitis are the cause of, or the result of, the intestinal inflammation that characterizes IBD. With the utilization of novel systems biology technologies, we can now begin to understand not only details about compositional changes in the gut microbiota in IBD, but increasingly also the alterations in microbiota function that accompany these. Technologies such as metagenomics, metataxomics, metatranscriptomics, metaproteomics and metabonomics are therefore allowing us a deeper understanding of the role of the microbiota in IBD. Furthermore, the integration of these systems biology technologies through advancing computational and statistical techniques are beginning to understand the microbiome interactions that both contribute to health and diseased states in IBD. This review aims to explore how such systems biology technologies are advancing our understanding of the gut microbiota, and their potential role in delineating the aetiology, development and clinical care of IBD

Fertility Levels, Trends and Differentials in Pakistan: Evidence from the Population, Labour Force and Migration Survey 1979-80

The objectives of the present report are two fold: (1) to analyse in some detail the fertility data collected in "Population, Labour Force and Migration" (PLM) Survey of 1979; and (2) to compare its findings, wherever necessary, with those of PFS (particularly for current fertility) and other surveys. The report is organized into eight sections, Section 2 is a brief review of earlier fertility levels and trends. Discussion of the PLM Survey and its methodology finds its place in section 3. In Section 4, we have discussed the current parity (children ever born to women at the time of the survey ) by age, marriage duration and age at marriage, as well as differentials in current parity. Early, marital fertility is discussed in section 5. The next two sections provide brief accounts of current fertility. In order to structure our analysis we have identified the women either through their birth cohorts ( current age ) or their marriage cohorts ( years since first marriage ). Realizing that the two fundamental aspects of a woman's chlld bearing life - the number of children she has had and the tempo of her having had them - cannot be fully separated as the results based on one type of measure do not always correspond to those obtained through another. We have, therefore, presented a brief synthesis of various findings in the concluding section

Fertility Levels, Trends and Differentials in Pakistan: Evidence from the Population, Labour Force and Migration Survey 1979-80

The objectives of the present report are two fold: (1) to analyse in some detail the fertility data collected in "Population, Labour Force and Migration" (PLM) Survey of 1979; and (2) to compare its findings, wherever necessary, with those of PFS (particularly for current fertility) and other surveys. The report is organized into eight sections, Section 2 is a brief review of earlier fertility levels and trends. Discussion of the PLM Survey and its methodology finds its place in section 3. In Section 4, we have discussed the current parity (children ever born to women at the time of the survey ) by age, marriage duration and age at marriage, as well as differentials in current parity. Early, marital fertility is discussed in section 5. The next two sections provide brief accounts of current fertility. In order to structure our analysis we have identified the women either through their birth cohorts ( current age ) or their marriage cohorts ( years since first marriage ). Realizing that the two fundamental aspects of a woman's chlld bearing life - the number of children she has had and the tempo of her having had them - cannot be fully separated as the results based on one type of measure do not always correspond to those obtained through another. We have, therefore, presented a brief synthesis of various findings in the concluding section

Infekcija vrstom Ornithobacterium rhinotracheale u crvenolikih vivaka (Vanellus indicus) u Pakistanu - prikaz slučaja

Respiratory infections are of major concern in the poultry industry in Pakistan. Previously, wild birds have been reported to transmit respiratory infections. The Red Wattled Lapwing (RWL) is a wild bird prevalent in the Indus basin and the wetlands of Punjab, Pakistan. Out of total of eighteen RWL birds housed at Lahore Zoo, Pakistan, three birds died after showing signs of respiratory distress and paralysis, in August, 2014. Postmortem examination revealed air sacculitis and pneumonia. Microbiological examination revealed Ornithobacterium rhinotracheale (ORT) as the causative agent, which was later confirmed by Polymerase Chain Reaction (PCR). The isolate was found to be susceptible to amoxicillin, erythromycin, tetracycline and enrofloxacin, and resistant to gentamycin, neomycin and sulfamethoxazole/trimethoprim. All the remaining birds were treated with long acting tetracycline, and diseased birds eventually recovered. No further mortality was declared. This is the first report of its kind which demonstrates ORT infection in RWL in Punjab, Pakistan.Dišne infekcije od velike su važnosti za peradarsku industriju u Pakistanu. Znano je da ih mogu prenositi divlje ptice. Crvenoliki vivak nastanjuje bazen Indus i močvarna područja Pendžaba u Pakistanu. Od ukupno 18 crvenolikih vivaka iz Zoološkog vrta Lahore, tri su uginula nakon pojave znakova dišnog poremećaja i paralize u kolovozu 2014. Razudbom je utvrđen sacculitis i pneumonija. Mikrobiološkom pretragom dokazan je Ornithobacterium rhinotracheale što je bilo potvrđeno lančanom reakcijom polimerazom. Izolat je bio osjetljiv na amoksicilin, eritromicin, tetraciklin i enrofloksacin, a otporan na gentamicin, neomicin i sulfametoksazol/trimetoprim. Sve preživjele ptice bile su liječene tetraciklinom s produženim djelovanjem i ozdravile. Novi slučajevi uginuća nisu bili primijećeni. Ovo je prvo izvješće o pojavi infekcije vrstom Ornithobacterium rhinotracheale u crvenolikog vivka u Pendžabu u Pakistan

SARS-CoV-2 vaccines and donor recruitment for FMT

Non peer reviewe

Epidemiology of the human immunodeficiency virus in Saudi Arabia; 18-year surveillance results and prevention from an Islamic perspective

BACKGROUND: data on HIV epidemiology and preventive measures in Islamic countries is limited. This study describes the results of 18-year of HIV surveillance in Saudi Arabia (SA) and the preventive measures implemented from an Islamic perspective. METHODS: surveillance for HIV has been underway in SA since 1984. Indications for HIV testing include clinical suspicion, screening of contacts of HIV-infected patients, and routine screening of blood and organ donors, prisoners, intravenous drug users, patients with other sexually transmitted infections, and expatriates pre-employment. This is a case series descriptive study of all confirmed HIV infections diagnosed in SA from 1984 through 2001. RESULTS: a total of 6046 HIV infections were diagnosed, of which 1285 (21.3%) cases were Saudi citizens. Over the 18-year surveillance period the number of HIV infections diagnosed annually among Saudi citizens gradually increased and, over the period 1997–2001, it reached to 84 to 142 cases per year. The number of cases per 100,000 population varied widely between regions with a maximum of 74 cases and a minimum of 2 cases. The infection was most common in the age group 20–40 years (74.6%) and predominantly affected men (71.6%). The modes of transmission among Saudi citizens and expatriates, respectively, were as follows: heterosexual contact, 487 (37.9%) and 1352 (28.4%) cases; blood transfusion, 322 (25.0%) and 186 (3.9%) cases; perinatal transmission, 83 (6.5%) and 19 (0.4%) cases; homosexual contact, 32 (2.5%) and 38 (0.8%) cases; intravenous drug use, 17 (1.3%) and 33 (0.7%) cases; bisexual contact, 10 (0.8%) and 14 (0.3%) cases; unknown, 334 (26.0%) and 3119 (65.5%) cases. The number of HIV infections transmitted by blood or blood products transfusion declined to zero by year 2001 and all such infections occurred due to transfusions administered before 1986. At HIV diagnosis, 4502/6046 (74.5%) patients had no symptoms, 787 (13.0%) patients had non-AIDS defining manifestations, and 757 (12.5%) patients had AIDS. A total of 514/1285 (40%) Saudi patients died by year 2001. CONCLUSIONS: the number of HIV cases in SA is limited with heterosexual contact being the main mode of transmission. From an Islamic perspective, preventive strategies include prevention of non-marital sex and intravenous drug use with encouragement of "safe sex" through legal marriage