Faecal Samples
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2021 ◽  
Sanzhima Garmaeva ◽  
Trishla Sinha ◽  
Anastasia Gulyaeva ◽  
Ranko Gacesa ◽  
Sergio Andreu-Sanchez ◽  

Abstract Seeding and development of the gut ecosystem are crucial for health, both in childhood and later in life. While the composition of infant gut bacterial communities has been described, the composition and origin of the infant gut virome remains under-studied. Here, we explore mother-to-infant transmission of bacteria and viruses in 30 mother–infant pairs in a longitudinal collection of faecal samples taken during pregnancy and the first 3 months after birth. We demonstrate that infant bacterial strains resemble maternal strains more than those of unrelated mothers. We quantify viromes using a complementary approach examining both total metagenomes and viral metagenomes. The virome composition is highly consistent between viral and total metagenomes. The infant gut viromes are dominated by active temperate bacteriophages, which are more abundant in infants than mothers (p-value=7.2e-06). We observe that the proportion of shared viruses between maternal and infant gut is only 11.3% when considering the active virome fraction alone, but increases to 37.6% when taking into account temperate phages in the form of prophages. These findings indicate that viruses are vertically transmitted from mothers to infants early in life and that pioneering phages can reach the infant gut via vertical transmission of their bacterial hosts.

2021 ◽  
Vol 13 (13) ◽  
pp. 20124-20127
Maneesh Sharma ◽  
B.L. Jangir ◽  
D. Lather ◽  
G.A. Chandratre ◽  
V. Nehra ◽  

The present study was conducted on 20 dead carcasses of Nilgai Boselaphus tragocamelus brought to the Department of Veterinary Pathology, Lala Lajpat Rai University of Veterinary and Animal Sciences (LUVAS), Hisar for post mortem examination. Thorough necropsy examinations were conducted and the representative samples for parasitic examination were collected. Most of the carcasses showed varying degrees of traumatic injuries (9), external wounds and haemorrhages (5) along with putrefactive changes (6). Intestinal contents and faecal samples were collected and screened for the presence of any parasite by sedimentation and flotation techniques. Out of 20 faecal samples, overall incidence of parasitic gastrointestinal tract infection was 40% (8/20). Out of 20, eight cases revealed presence of coccidian oocysts, however, among the eight cases, one case also revealed mixed infection of Moneizia andStrongylespp.,andanother case with Strongyle and Trichuris spp. Gross pathology of the intestines revealed varying degrees of vascular changes like petechial haemorrhages and the presence of catarrhal exudate. Histopathological examination revealed mild to moderate congestion, fused villi, desquamated mucosal epithelium in focal areas, and infiltration of mononuclear cells mainly lymphocytes. The different developmental stages of coccidian spp.were also observed in the intestinal mucosa. In conclusion, the preliminary study reported the parasitic load and pathological changes in the intestinal tract which further indicated the parasitism of these wild animals which is of immense significance from the epidemiological point of view.

Sushila Maan ◽  
Kanisht Batra ◽  
Deepika Chaudhary ◽  
Monika Punia ◽  
Vijay Kadian ◽  

Background: Senecavirus A (SVA), is a positive sense small non-enveloped RNA virus which belongs to Picornaviridae family and is responsible for porcine vesicular disease. The disease has been reported in many countries since late 2014, 2015 and 2016 like USA, Canada, Brazil, China and Thailand. Methods: In this study, the metagenomic study was performed on faecal samples of pigs/piglets suffering from diarrhea in Haryana, India with the help of next generation sequencing. The cDNA library was prepared from the faecal samples and run on the Illumina MiSeq instrument followed by identification and genomic characterization. Result: This study revealed the presence of SVA in the samples. The characterization of complete genome sequence of this strain showed complete nucleotide identity (100%) with SVA genomes reported from Canada, however, the polyprotein shares 98-99% amino acid sequence similarity with the genomes currently available in the GenBank. To the best of our knowledge this is the first report of SVA infection in pigs/piglets of Haryana, India. It demonstrates that an active and urgent surveillance of the swine population is required in the region. Additionally, the veterinarians must pay immediate attention to this vesicular disease and adopt preventive measures for its control.

2021 ◽  
Vol 11 (1) ◽  
Sara Albuixech-Martí ◽  
Sharon A. Lynch ◽  
Sarah C. Culloty

AbstractShellfish, including the key species the common cockle Cerastoderma edule, living and feeding in waters contaminated by infectious agents can accumulate them within their tissues. It is unknown if microbial pathogens and microparasites can subsequently be transmitted via concomitant predation to their consumers, including shorebirds. The objective of this study was to assess if pathogens associated with C. edule could be detected seasonally in the faeces of shorebirds that feed on C. edule and in the physical environment (sediment) in which C. edule reside, along the Irish and Celtic Seas. Two potentially pathogenic global groups, Vibrio and Haplosporidia, were detected in C. edule. Although Haplosporidia were not detected in the bird faeces nor in the sediment, identical strains of Vibrio splendidus were detected in C. edule and bird faecal samples at sites where the oystercatcher Haematopus ostralegus and other waders were observed to be feeding on cockles. Vibrio spp. prevalence was seasonal and increased in C. edule and bird faecal samples during the warmer months, possibly due to higher seawater temperatures that promote the replication of this bacteria. The sediment samples showed an overall higher prevalence of Vibrio spp. than the bird faecal and C. edule samples, and its detection remained consistently high through the sites and throughout the seasons, which further supports the role of the sediment as a Vibrio reservoir. Our findings shed light on the fact that not all pathogen groups are transmitted from prey to predator via feeding but bacteria such as V. splendidus can be. As most of the wading birds observed in this study are migratory, the results also indicate the potential for this bacterium to be dispersed over greater geographic distances, which will have consequences for areas where it may be introduced.

2021 ◽  
Andrea Turner ◽  
Hannah Schubert ◽  
Emma F Puddy ◽  
Jordan E Sealey ◽  
Virginia C Gould ◽  

Aims To investigate whether on-farm antibacterial usage (ABU), environmental antibacterial resistant (ABR) Escherichia coli prevalence, and sampling and sample handling methodologies are associated with ABR E. coli positivity in individual faecal samples from dairy heifers. Methods and Results Three hundred and sixty-four heifers from 37 farms were sampled via rectal or faecal pat sampling. Samples were stored at -80 C for variable periods before microbiological analysis. Data analysis was through a multilevel, multivariable logistic regression approach. Individual rectal samples had increased odds of positivity for amoxicillin, cefalexin and tetracycline-resistant E. coli. Sample storage for 6-12 month was associated with decreased odds of finding amoxicillin and tetracycline-resistant E. coli. On-farm ABU had little influence, and environmental ABR E. coli prevalence had no significant influence on on the odds of sample-level positivity for ABR E. coli. Conclusions Sampling methodology and sample handling have a greater association than on-farm factors with the detection of ABR E. coli in individual faecal samples from dairy heifers. Significance and Impact of the Study Sampling and storage methodologies should be considered carefully at the point of designing ABR surveillance studies in livestock and their environments and, where possible, standardised between and within future studies.

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3201
Hannah Joan Jørgensen ◽  
Mette Valheim ◽  
Camilla Sekse ◽  
Bjarne Asbjørn Bergsjø ◽  
Helene Wisløff ◽  

An outbreak investigation was initiated in September 2019, following a notification to the Norwegian Food Safety Authority (NFSA) of an unusually high number of dogs with acute haemorrhagic diarrhoea (AHD) in Oslo. Diagnostic testing by reporting veterinarians had not detected a cause. The official investigation sought to identify a possible common cause, the extent of the outbreak and prevent spread. Epidemiological data were collected through a survey to veterinarians and interviews with dog owners. Diagnostic investigations included necropsies and microbiological, parasitological and toxicological analysis of faecal samples and food. In total, 511 dogs with acute haemorrhagic diarrhoea were registered between 1 August and 1 October. Results indicated a common point source for affected dogs, but were inconclusive with regard to common exposures. A notable finding was that 134 of 325 faecal samples (41%) cultured positive for Providencia alcalifaciens. Whole genome sequencing (WGS) of 75 P. alcalifaciens isolates from 73 dogs revealed that strains from 51 dogs belonged to the same WGS clone. Findings point to P. alcalifaciens as implicated in the outbreak, but investigations are needed to reveal the pathogenic potential of P. alcalifaciens in dogs and its epidemiology.

2021 ◽  
Vol 8 (11) ◽  
pp. 249
Michal Babják ◽  
Alžbeta Königová ◽  
Ľudmila Burcáková ◽  
Michaela Komáromyová ◽  
Michaela Urda Dolinská ◽  

This study was performed on a cattle farm with a long-term use of albendazole (ABZ) and a permanent history of fasciolosis for comparing in vivo and in vitro methods for the detection of anthelmintic resistance and drug efficacy. A selected group of 10 Charolais cows was treated in autumn 2020 with ABZ at a dose of 7.5 mg/kg body weight. Another group of 10 cows remained untreated as a control. The faecal egg count reduction test was used to determine in vivo efficacy. The percentage reduction of eggs on day 14 after treatment ranged from 77 to 81.8%, depending on the formula used for calculation. The in vitro egg hatch test (EHT) was used as a second diagnostic method. F. hepatica eggs for the EHT were isolated from faecal samples. The test was performed in two versions differing in the length of incubation with ABZ (12 h and 15 d). The percentage of eggs with inhibited development at a concentration of 0.5 μM in both versions of the EHT agreed with the in vivo results. Ovicidal activity at a concentration of 0.5 μM in the 12-h version suggested a reduced efficacy of ABZ (65.40%). An EHT prepared using pooled faecal samples was a prospective method for the detection of efficacy and ABZ resistance in F. hepatica.

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2093
Shen-Yuan Hsieh ◽  
Mohammad A. Tariq ◽  
Andrea Telatin ◽  
Rebecca Ansorge ◽  
Evelien M. Adriaenssens ◽  

The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as “viral dark matter”. However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating “rare” members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.

2021 ◽  
Vol 12 ◽  
Brendha Truccollo ◽  
Paul Whyte ◽  
Catherine M. Burgess ◽  
Declan J. Bolton

Background:Campylobacter is commonly transmitted to humans from chickens. Campylobacter jejuni is the species most frequently associated with human illness, and the most prevalent species recovered from poultry.Objective: The objective of this study was to analyse a sub-population of C. jejuni from two broiler flocks on the farm and at slaughter using whole-genome sequencing to gain insights into the changes in the Campylobacter population during broiler production, including changes in virulence and antimicrobial resistance profiles.Methods: In this study, ten composite faecal samples (n=10), obtained by pooling ten fresh faecal samples (n=10), were collected in the broiler house on two farms on days 14, 21, 28, and 34 (n=80) and ten composite (n=10) caecal samples were collected at the time of slaughter for each flock (n=20). These were tested for C. jejuni using the ISO 10272-2:2016 method. Seven isolates were randomly selected from each of the nine Campylobacter-positive sampling points (n=63) and were subjected to antimicrobial susceptibility tests. Their genomes were sequenced and the data obtained was used to characterise the population structure, virulence, antimicrobial resistance determinants and inter-strain variation.Results: The Farm 1 isolates had three MLST types (ST257-257, ST814-661 and ST48-48) while those on Farm 2 were ST6209-464 and ST9401. Interestingly, only the MLST types positive for most of the virulence genes tested in this study persisted throughout the production cycle, and the detection of antimicrobial resistance determinants (gyrA T86I and tetO) increased after thinning and at slaughter, with the detection of new strains.Conclusion: The persistence of the most virulent strains detected in this study throughout the production cycle has important implications for the risk to consumers and requires further investigation. The detection of new strains within the population corresponding with the time of thinning and transportation reflects previous reports and provides further evidence that these activities pose a risk of introducing new Campylobacter strains to broiler batches.

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 550
Carlo Brogna ◽  
Simone Cristoni ◽  
Mauro Petrillo ◽  
Maddalena Querci ◽  
Ornella Piazza ◽  

Background: SARS-CoV-2 that causes COVID-19 disease and led to the pandemic currently affecting the world has been broadly investigated. Different studies have been performed to understand the infection mechanism, and the involved human genes, transcripts and proteins. In parallel, numerous clinical extra-pulmonary manifestations co-occurring with COVID-19 disease have been reported and evidence of their severity and persistence is increasing. Whether these manifestations are linked to other disorders co-occurring with SARS-CoV-2 infection, is under discussion. In this work, we report the identification of toxin-like peptides in COVID-19 patients by application of the Liquid Chromatography Surface-Activated Chemical Ionization – Cloud Ion Mobility Mass Spectrometry.   Methods: Plasma, urine and faecal samples from COVID-19 patients and control individuals were analysed to study peptidomic toxins’ profiles. Protein precipitation preparation procedure was used for plasma, to remove high molecular weight proteins and efficiently solubilize the peptide fraction; in the case of faeces and urine, direct peptide solubilization was employed.   Results: Toxin-like peptides, almost identical to toxic components of venoms from animals, like conotoxins, phospholipases, phosphodiesterases, zinc metal proteinases, and bradykinins, were identified in samples from COVID-19 patients, but not in control samples.  Conclusions: The presence of toxin-like peptides could potentially be connected to SARS-CoV-2 infection. Their presence suggests a possible association between COVID-19 disease and the release in the body of (oligo-)peptides almost identical to toxic components of venoms from animals. Their involvement in a large set of heterogeneous extra-pulmonary COVID-19 clinical manifestations, like neurological ones, cannot be excluded. Although the presence of each individual symptom is not selective of the disease, their combination might be related to COVID-19 by the coexistence of the panel of the here detected toxin-like peptides. The presence of these peptides opens new scenarios on the aetiology of the COVID-19 clinical symptoms observed up to now, including neurological manifestations.

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