​Faecal Consistency: A Measure of Gastrointestinal Parasitic Infections in Goats

Background: Gastrointestinal (GI) parasitism in goats is a serious and widely distributed problem. Diarrhoea, moderate or severe, though a result of various factors involving feed, fodder, seasons and state of gut physiology of digestion, is a common symptom in goats infested with GI parasites, the nematodes and coccidia. Intensity of diarrhoea corresponds to quantum and type of parasitism. Methods: In the present study, 1451 faecal samples collected from goats of different ages ( less than 3 M, greater than 3-6 M, greater than 6-12 M and greater than 12 M) were categorized as normal, lumpy and diarrheic based on their consistency and were processed for parasitic infections. The GI parasitic load was quantified by faecal eggs/oocysts counting (FEC and FOC) per gram of faeces through the modified Mac-master technique. Identification of parasites was based on the morphology of third-stage larvae procured by coproculture of randomly selected positive samples. FEC/FOC data (strongyle and coccidian), being skewed and uneven, were log-transformed to normalize. The transformed data [loge (100+n)] was analyzed statistically and results were interpreted. Result: Means of FEC and FOC in three type of faecal samples viz. normal, lumpy and diarrheic, were significantly different. Similarly, the effect of age on FEC and FOC was significant. The interaction between animals age × faecal sample type was significant in coccidian and non-significant in strongyle infection. The results were discussed to support the hypothesis that faecal consistency was a measure of coccidian and strongyle worm load in goats and can be a basis of targeted selective treatment.

Molecular Identification and Characterization of a Genotype 3 Hepatitis E Virus (HEV) Strain Detected in a Wolf Faecal Sample, Italy

Hepatitis E virus (HEV) infection is a major health problem worldwide. In developed countries, zoonotic transmission of HEV genotypes (Gt) 3 and 4 is caused by the ingestion of raw or undercooked meat of infected pigs and wild boars, the main reservoirs of HEV. However, additional animals may harbour HEV or HEV-related strains, including carnivores. In this study, we investigated the molecular epidemiology of orthohepeviruses in wild canids by screening a total of 136 archival faecal samples, collected from wolves (42) and red foxes (94) in Northwestern Italy. Orthohepevirus RNA was identified in a faecal specimen, collected from a wolf carcass in the province of La Spezia (Liguria Region, Italy). The nearly full-length (7212 nucleotides) genome of the strain HEV/81236/Wolf/2019/ITA (GenBank accession no. MZ463196) was determined by combining a sequence-independent single-primer amplification (SISPA) approach with the Oxford Nanopore Technologies sequencing platform. Upon phylogenetic analysis, the HEV detected in wolf was segregated into clade HEV-3.1, displaying the highest nucleotide (nt) identity (89.0–93.3%) to Gt3 strains belonging to subtype c. Interestingly, the wolf faecal sample also contained porcine astrovirus sequences, endorsing the hypothesis of a dietary origin of the HEV strain due to preying habits.

1322A pilot study of faecal sample collection from prospective cohort study participants

Background Faecal specimens offer a relatively accessible means of assessing the gut microbial community. We conducted a pilot study to compare the feasibility of different protocols for self-collection of faecal specimens from Australian Breakthrough Cancer (ABC) Study participants. Methods Pilot study participants were randomly selected from ABC Study participants who had not yet been invited to participate in follow-up. All pilot study participants were asked to provide a faecal sample using FOBT cards and complete a ‘day of sample’ questionnaire. Participants were randomised to 1 of 4 groups defined by combination of (i) a request (or not) to also provide a faecal sample using a tube containing 2.5ml of 95% ethanol and (ii) a request (or not) to complete a food frequency questionnaire. Results 1,136 ABC Study participants were invited to participate in the pilot study. Of the 56% that opted in, 88% returned the requested sample. Very few participants (5%) actively opted out. Overall, 49% of invited participants returned a sample. There was no statistically significant difference between the groups in the percentage of participants who completed the pilot study. Conclusions The pilot study demonstrated the feasibility of self-collection of faecal samples. Increasing the time commitment and complexity (through provision of an additional sample suspended in ethanol and a FFQ) did not reduce the likelihood of successful completion. Key messages The findings demonstrate the feasibility of collecting faecal samples both on an FOBT card and in a tube containing ethanol, and a lengthy FFQ, within a prospective cohort study.

Clinical and Microbiological Characteristics of a Community-Acquired Carbapenem-Resistant Escherichia coli ST410 Isolate Harbouring blaNDM-5-Encoding IncX3-Type Plasmid From Blood

Objectives: The aim of this research was to investigate the clinical and microbiological characteristics of a case of community-acquired carbapenem-resistant Escherichia coli isolated from a patient with a bloodstream infection in China.Methods:Escherichia coli Huamei202001 was recovered from the first blood culture from a patient hospitalised in China. An antimicrobial susceptibility test was performed, and the genome was sequenced on an Illumina HiSeq X 10 platform with a 150-bp paired-end approach. The generated sequence reads were assembled using Unicycler, and the whole genome sequence data were analysed using bioinformatics tools. Moreover, the patient and her main family members obtained a faecal sample screening test for CRE, the positive strain was further isolated and the identification and antimicrobial susceptibility testing was performed.Results:Escherichia coli Huamei202001 belonged to sequence type 410. In addition, a blaNDM-5-encoding IncX3-type plasmid was responsible for the spreading of carbapenem resistance. Only the patient was detected as having a positive faecal sample screening test for CRE. Strain Fec01 was identified as E. coli, and the antibiotic susceptibility profile was the same as that of E. coli Huamei202001.Conclusions:Escherichia coli Huamei202001 is defined as community-acquired carbapenem-resistant Enterobacteriaceae. The clone ST410 that harbours the blaNDM-5-encoding IncX3-type plasmid is causing new high-risk clones globally. Thus, infection control measures should be strengthened to curb the dissemination of IncX3.

In vitro Efficacy of Albendazole against Strongyle eggs recovered from Trade Goats slaughtered at the Nsukka Abattoir: A Preliminary Survey of Resistance to Albendazole

The efficacy of Albendazole against trichostrongyle nematode parasites in goats presented for slaughter at the Nsukka municipal abattoir was evaluated using the In vitro Egg hatch assay (EHA) model. The abattoir was visited once every week for 4 consecutive months during which a total of 240 goats were sampled. Fecal samples were collected per rectum from a minimum of 15 goats on each day of the visit. Egg Hatch Assay was performed on strongyle eggs recovered from pooled faecal sample on each day of sampling with a 2.5% W/V Albendazole. Faecal culture was also set up from the pooled faecal sample on each sampling day to recover and identify the nematode parasites present in the goats. Among the 240 goats sampled, the prevalence of trichostrongylosis as observed by the presence of strongyle eggs was 94.6% (227/240). Faecal culture and larval identification revealed 69.8% of the strongyles as Haemonchus contortus, while 25.5 and 4.8% were Trichostrongylus colubriformis and Oesophagostomum species respectively. In the EHA, Albendazole had mean LC50 value of 0.16 µg/ml which is slightly in excess of the discriminating dose of 0.1µg/ml as prescribed by the World Association for the Advancement of Veterinary Parasitology (WAAVP) as an indication of anthelmintic resistance. There is therefore an urgent need to screen the nematode parasite population in the Nigeria for the presence Albendazole resistance genes. Key words: GI nematode; egg hatch assay; goat; Albendazole; Resistance; Nigeria

Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

Background The gut phageome comprises a complex phage community of thousands of individual strains, with a few highly abundant bacteriophages. CrAss-like phages, which infect bacteria of the order Bacteroidales, are the most abundant bacteriophage family in the human gut and make an important contribution to an individual’s core virome. Based on metagenomic data, crAss-like phages form a family, with four sub-families and ten candidate genera. To date, only three representatives isolated in pure culture have been reported: ΦcrAss001 and two closely related phages DAC15 and DAC17; all are members of the less abundant candidate genus VI. The persistence at high levels of both crAss-like phage and their Bacteroidales hosts in the human gut has not been explained mechanistically, and this phage-host relationship can only be properly studied with isolated phage-host pairs from as many genera as possible. Results Faeces from a healthy donor with high levels of crAss-like phage was used to initiate a faecal fermentation in a chemostat, with selected antibiotics chosen to inhibit rapidly growing bacteria and selectively enrich for Gram-negative Bacteroidales. This had the objective of promoting the simultaneous expansion of crAss-like phages on their native hosts. The levels of seven different crAss-like phages expanded during the fermentation, indicating that their hosts were also present in the fermenter. The enriched supernatant was then tested against individual Bacteroidales strains isolated from the same faecal sample. This resulted in the isolation of a previously uncharacterised crAss-like phage of candidate genus IV of the proposed Alphacrassvirinae sub-family, ΦcrAss002, that infects the gut commensal Bacteroides xylanisolvens. ΦcrAss002 does not form plaques or spots on lawns of sensitive cells, nor does it lyse liquid cultures, even at high titres. In keeping with the co-abundance of phage and host in the human gut, ΦcrAss002 and Bacteroides xylanisolvens can also co-exist at high levels when co-cultured in laboratory media. Conclusions We report the isolation and characterisation of ΦcrAss002, the first representative of the proposed Alphacrassvirinae sub-family of crAss-like phages. ΦcrAss002 cannot form plaques or spots on bacterial lawns but can co-exist with its host, Bacteroides xylanisolvens, at very high levels in liquid culture without impacting on bacterial numbers.

Patient attitudes towards faecal sampling for gut microbiome studies and clinical care reveal positive engagement and room for improvement

Faecal sample collection is crucial for gut microbiome research and its clinical applications. However, while patients and healthy volunteers are routinely asked to provide stool samples, their attitudes towards sampling remain largely unknown. Here, we investigate the attitudes of 780 Dutch patients, including participants in a large Inflammatory Bowel Disease (IBD) gut microbiome cohort and population controls, in order to identify barriers to sample collection and provide recommendations for gut microbiome researchers and clinicians. We sent questionnaires to 660 IBD patients and 112 patients with other disorders who had previously been approached to participate in gut microbiome studies. We also conducted 478 brief interviews with participants in our general population cohort who had collected stool samples. Statistical analysis of the data was performed using R. 97.4% of respondents reported that they had willingly participated in stool sample collection for gut microbiome research, and most respondents (82.9%) and interviewees (95.6%) indicated willingness to participate again, with their motivations for participating being mainly altruistic (57.0%). Responses indicated that storing stool samples in the home freezer for a prolonged time was the main barrier to participation (52.6%), but clear explanations of the sampling procedures and their purpose increased participant willingness to collect and freeze samples (P = 0.046, P = 0.003). To account for participant concerns, gut microbiome researchers establishing cohorts and clinicians trying new faecal tests should provide clear instructions, explain the rationale behind their protocol, consider providing a small freezer and inform patients about study outcomes. By assessing the attitudes, motives and barriers surrounding participation in faecal sample collection, we provide important information that will contribute to the success of gut microbiome research and its near-future clinical applications.

THE COCCIDIAN SPECIES PARASITIZING THE DOMESTIC GOAT IN NIGERIA

Nine fully recognized and described species of coccidia in goats and also one species not previously described are identified. Size shape, colour, sporulation time, morphology of unsporulated oocysts were the criteria for species identification 30 out of 36 faecal sample were positive form single or mixed infections with 3 samples being pure infections of single species. The unidentified species has a low occurrence and probably is not of importance in clinical coccidiosis in goats. The sporulation time for different species is found to be directly related to the size of the oocysts. As most species sporulate within 48 hours, daily removal of faecal materials form goat pens is recommended

Wide distribution of alternatively coded Lak megaphages in animal microbiomes

Lak phages with alternatively coded ~540 kbp genomes were recently reported to replicate in Prevotella in the gut microbiomes of humans that consume a non-western diet, baboons and some pigs. Here, we investigate the diversity and broader distribution of Lak phages in human and animal microbiomes using diagnostic PCR and genome-resolved metagenomics. Lak phages were detected in 13 different animal types and are particularly prevalent in pigs, with significant enrichment in the hindgut compared to foregut. We reconstructed 34 new Lak genomes, including six curated complete genomes, all of which are alternatively coded. The most deeply branched Lak is from a horse faecal sample and is the largest phage genome from an animal microbiome (~660 kbp). From the Lak genomes, we identified families of hypothetical proteins associated with specific animal types. Overall, we substantially expanded Lak phage diversity and demonstrate their occurrence in a variety of human and animal microbiomes.

Genomic analysis reveals G3P[13] porcine rotavirus A interspecific transmission to human from pigs in a swine farm with diarrhoea outbreak

Rotavirus A (RVA) is a major diarrhoea-causing pathogen in young animals and children. The zoonotic potential of RVA has received extensive attention in recent years. In May 2018, an outbreak of diarrhoea among piglets occurred on a swine farm in Sichuan province, PR China. RVA was detected in 95.7 % (22/23) of piglet samples, 60 % (9/15) of sow samples and 100 % (3/3) of pig-breeder faecal samples. The predominant RVA genotype on this swine farm was G3P[13], and G3P[13] RVA was also detected in the three breeder faecal samples. Three G3P[13] RVA strains were isolated from a piglet faecal sample, a sow faecal sample and a pig-breeder faecal sample, and were named SCLS-X1, SCLS-3 and SCLS-R3, respectively. The complete sequences of 11 gene segments of these three isolates were derived. Phylogenetic analysis showed that ten gene segments (VP7, VP4, VP1–VP3 and NSP1–NSP5) of pig-breeder isolate SCLS-R3 were closely related to pig isolates SCLS-X1 and SCLS-3 from this farm. Only the VP6 gene shared higher homology with human RVA strain I321. Therefore, a G3P[13] porcine RVA strain most likely infected pig breeders. These results provided the first complete epidemiological link demonstrating interspecies transmission of G3P[13] RVA from pigs to human. Our data contribute to an improved understanding of the genetic evolution and interspecies transmission of RVA.