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

2020 ◽  
Author(s):  
Nan Yan ◽  
Hua Yue ◽  
Yuanwei Wang ◽  
Bin Zhang ◽  
Cheng Tang
Keyword(s):  
Faecal Sample ◽  
Genomic Analysis ◽  
Interspecies Transmission ◽  
Swine Farm ◽  
Rotavirus A ◽  
Faecal Samples ◽  
Complete Sequences ◽  
Pr China ◽  
Porcine Rotavirus ◽  
Epidemiological Link

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.

scholarly journals Multiple Types of Novel Enteric Bopiviruses (Picornaviridae) with the Possibility of Interspecies Transmission Identified from Cloven-Hoofed Domestic Livestock (Ovine, Caprine and Bovine) in Hungary

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 66
Author(s):  
Zoltán László ◽  
Péter Pankovics ◽  
Gábor Reuter ◽  
Attila Cságola ◽  
Ádám Bálint ◽  
...  
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Background Information ◽  
Type Ii ◽  
Rt Pcr ◽  
Faecal Samples ◽  
The Family ◽  
Domestic Livestock

Most picornaviruses of the family Picornaviridae are relatively well known, but there are certain “neglected” genera like Bopivirus, containing a single uncharacterised sequence (bopivirus A1, KM589358) with very limited background information. In this study, three novel picornaviruses provisionally called ovipi-, gopi- and bopivirus/Hun (MW298057-MW298059) from enteric samples of asymptomatic ovine, caprine and bovine respectively, were determined using RT-PCR and dye-terminator sequencing techniques. These monophyletic viruses share the same type II-like IRES, NPGP-type 2A, similar genome layout (4-3-4) and cre-localisations. Culture attempts of the study viruses, using six different cell lines, yielded no evidence of viral growth in vitro. Genomic and phylogenetic analyses show that bopivirus/Hun of bovine belongs to the species Bopivirus A, while the closely related ovine-origin ovipi- and caprine-origin gopivirus could belong to a novel species “Bopivirus B” in the genus Bopivirus. Epidemiological investigation of N = 269 faecal samples of livestock (ovine, caprine, bovine, swine and rabbit) from different farms in Hungary showed that bopiviruses were most prevalent among <12-month-old ovine, caprine and bovine, but undetectable in swine and rabbit. VP1 capsid-based phylogenetic analyses revealed the presence of multiple lineages/genotypes, including closely related ovine/caprine strains, suggesting the possibility of ovine–caprine interspecies transmission of certain bopiviruses.

scholarly journals Genomic analysis of group B Streptococcus from milk demonstrates the need for improved biosecurity: a cross-sectional study of pastoralist camels in Kenya

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dinah Seligsohn ◽  
Chiara Crestani ◽  
Taya L. Forde ◽  
Erika Chenais ◽  
Ruth N. Zadoks
Keyword(s):  
Public Health ◽  
Milk Production ◽  
Disease Transmission ◽  
Tetracycline Resistance ◽  
Genomic Analysis ◽  
Sub Saharan Africa ◽  
Camel Milk ◽  
Interspecies Transmission ◽  
Cross Sectional ◽  
Group B

Abstract Background Streptococcus agalactiae (Group B Streptococcus, (GBS)) is the leading cause of mastitis (inflammation of the mammary gland) among dairy camels in Sub-Saharan Africa, with negative implications for milk production and quality and animal welfare. Camel milk is often consumed raw and presence of GBS in milk may pose a public health threat. Little is known about the population structure or virulence factors of camel GBS. We investigated the molecular epidemiology of camel GBS and its implications for mastitis control and public health. Results Using whole genome sequencing, we analysed 65 camel milk GBS isolates from 19 herds in Isiolo, Kenya. Six sequence types (STs) were identified, mostly belonging to previously described camel-specific STs. One isolate belonged to ST1, a predominantly human-associated lineage, possibly as a result of interspecies transmission. Most (54/65) isolates belonged to ST616, indicative of contagious transmission. Phylogenetic analysis of GBS core genomes showed similar levels of heterogeneity within- and between herds, suggesting ongoing between-herd transmission. The lactose operon, a marker of GBS adaptation to the mammary niche, was found in 75 % of the isolates, and tetracycline resistance gene tet(M) in all but two isolates. Only the ST1 isolate harboured virulence genes scpB and lmb, which are associated with human host adaptation. Conclusions GBS in milk from Kenyan camel herds largely belongs to ST616 and shows signatures of adaptation to the udder. The finding of similar levels of within- and between herd heterogeneity of GBS in camel herds, as well as potential human-camel transmission highlights the need for improved internal as well as external biosecurity to curb disease transmission and increase milk production.

scholarly journals Evaluation of rapid assays for the detection of bovine coronavirus, rotavirus A and Cryptosporidium parvum in faecal samples of calves

2009 ◽  
Vol 182 (3) ◽  
pp. 484-486 ◽  
Author(s):  
Daniela Klein ◽  
Angela Kern ◽  
Gudrun Lapan ◽  
Viviane Benetka ◽  
Karin Möstl ◽  
...  
Keyword(s):  
Cryptosporidium Parvum ◽  
Bovine Coronavirus ◽  
Rotavirus A ◽  
Rapid Assays ◽  
Faecal Samples

scholarly journals Phylogenetic Analyses of Rotavirus A from Cattle in Uruguay Reveal the Circulation of Common and Uncommon Genotypes and Suggest Interspecies Transmission

Pathogens ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 570
Author(s):  
Matías Castells ◽  
Rubén Darío Caffarena ◽  
María Laura Casaux ◽  
Carlos Schild ◽  
Samuel Miño ◽  
...  
Keyword(s):  
Dairy Products ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Economic Losses ◽  
Cattle Production ◽  
Economic Sectors ◽  
Beef Calves ◽  
Rotavirus A ◽  
P Type ◽  
Neonatal Calf Diarrhea

Uruguay is one of the main exporters of beef and dairy products, and cattle production is one of the main economic sectors in this country. Rotavirus A (RVA) is the main pathogen associated with neonatal calf diarrhea (NCD), a syndrome that leads to significant economic losses to the livestock industry. The aims of this study are to determine the frequency of RVA infections, and to analyze the genetic diversity of RVA strains in calves in Uruguay. A total of 833 samples from dairy and beef calves were analyzed through RT-qPCR and sequencing. RVA was detected in 57.0% of the samples. The frequency of detection was significantly higher in dairy (59.5%) than beef (28.4%) calves (p < 0.001), while it did not differ significantly among calves born in herds that were vaccinated (64.0%) or not vaccinated (66.7%) against NCD. The frequency of RVA detection and the viral load were significantly higher in samples from diarrheic (72.1%, 7.99 log10 genome copies/mL of feces) than non-diarrheic (59.9%, 7.35 log10 genome copies/mL of feces) calves (p < 0.005 and p = 0.007, respectively). The observed G-types (VP7) were G6 (77.6%), G10 (20.7%), and G24 (1.7%), while the P-types were P[5] (28.4%), P[11] (70.7%), and P[33] (0.9%). The G-type and P-type combinations were G6P[11] (40.4%), G6P[5] (38.6%), G10P[11] (19.3%), and the uncommon genotype G24P[33] (1.8%). VP6 and NSP1-5 genotyping were performed to better characterize some strains. The phylogenetic analyses suggested interspecies transmission, including transmission between animals and humans.

Resistance to critically important antimicrobials in Australian silver gulls (Chroicocephalus novaehollandiae) and evidence of anthropogenic origins

2019 ◽  
Vol 74 (9) ◽  
pp. 2566-2574 ◽  
Author(s):  
Shewli Mukerji ◽  
Marc Stegger ◽  
Alec Vincent Truswell ◽  
Tanya Laird ◽  
David Jordan ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Resistant Bacteria ◽  
Molecular Characteristics ◽  
Widespread Occurrence ◽  
E Coli ◽  
Human Contact ◽  
Carbapenem Resistant ◽  
Sampling Locations ◽  
Faecal Samples ◽  
Australian Continent

Abstract Objectives Antimicrobial resistance (AMR) to critically important antimicrobials (CIAs) amongst Gram-negative bacteria can feasibly be transferred amongst wildlife, humans and domestic animals. This study investigated the ecology, epidemiology and origins of CIA-resistant Escherichia coli carried by Australian silver gulls (Chroicocephalus novaehollandiae), a gregarious avian wildlife species that is a common inhabitant of coastal areas with high levels of human contact. Methods Sampling locations were widely dispersed around the perimeter of the Australian continent, with sites separated by up to 3500 km. WGS was used to study the diversity and molecular characteristics of resistant isolates to ascertain their epidemiological origin. Results Investigation of 562 faecal samples revealed widespread occurrence of extended-spectrum cephalosporin-resistant (21.7%) and fluoroquinolone-resistant (23.8%) E. coli. Genome sequencing revealed that CIA-resistant E. coli isolates (n = 284) from gulls predominantly belonged to human-associated extra-intestinal pathogenic E. coli (ExPEC) clones, including ST131 (17%), ST10 (8%), ST1193 (6%), ST69 (5%) and ST38 (4%). Genomic analysis revealed that gulls carry pandemic ExPEC-ST131 clades (O25:H4 H30-R and H30-Rx) and globally emerging fluoroquinolone-resistant ST1193 identified among humans worldwide. Comparative analysis revealed that ST131 and ST1193 isolates from gulls overlapped extensively with human clinical isolates from Australia and overseas. The present study also detected single isolates of carbapenem-resistant E. coli (ST410-blaOXA-48) and colistin-resistant E. coli (ST345-mcr-1). Conclusions The carriage of diverse CIA-resistant E. coli clones that strongly resemble pathogenic clones from humans suggests that gulls can act as ecological sponges indiscriminately accumulating and disseminating CIA-resistant bacteria over vast distances.

Phylogenetic inference of the porcine Rotavirus A origin of the human G1 VP7 gene

2016 ◽  
Vol 40 ◽  
pp. 205-213 ◽  
Author(s):  
Loan Phuong Do ◽  
Toyoko Nakagomi ◽  
Hiroki Otaki ◽  
Chantal Ama Agbemabiese ◽  
Osamu Nakagomi ◽  
...  
Keyword(s):  
Phylogenetic Inference ◽  
Rotavirus A ◽  
Porcine Rotavirus ◽  
Vp7 Gene

Waterborne gastroenteritis outbreak in Albania

2004 ◽  
Vol 50 (1) ◽  
pp. 57-61 ◽  
Author(s):  
M. Divizia ◽  
R. Gabrieli ◽  
D. Donia ◽  
A. Macaluso ◽  
A. Bosch ◽  
...  
Keyword(s):  
Hepatitis A Virus ◽  
Point Mutations ◽  
Genomic Analysis ◽  
Capital City ◽  
Age Group ◽  
Paediatric Unit ◽  
Faecal Samples ◽  
High Incidence ◽  
Group 5 ◽  
The City

Three different studies are reported concerning the environmental pollution caused by viruses in Albania. The first study describes an outbreak of gastroenteritis in the capital city, involving 2,722 children attending the Paediatric Unit of Tirana Hospital. The age group with the highest morbidity was 0-5 years, with 89.5%; no fatalities were recorded during the outbreak. Rotavirus was detected in 26/28 faecal samples by RT-PCR, although astrovirus, adenovirus and calicivirus were also present. The second study describes an outbreak of hepatitis A virus involving the city of Lac. Two hundred cases were recorded, with the highest incidence in the age-group 5-9 years. Phylogenetic analysis of the VP1/2A region showed the presence of a unique sequence: genotype IA. Rotavirus was identified in drinking-water samples collected during the outbreak. The third study describes the prevalence of HAV and HEV in 202 sera randomly collected from 12 different cities in Albania. HAV showed a high incidence (66.2%), whereas none was positive for HEV. The genomic analysis of the VP1/2A junction revealed the presence of only one genotype (IA) with few point mutations and just two amino acid substitutions at codons 22 and 34. Additionally, two potential antigenic variants were detected, the first at position 46 of VP3 and the second at position 23 of VP1.

scholarly journals Whole genomic analysis of a porcine-like human G5P[6] rotavirus strain isolated from a child with diarrhoea and encephalopathy in Japan

2013 ◽  
Vol 94 (7) ◽  
pp. 1568-1575 ◽  
Author(s):  
Satoshi Komoto ◽  
Yoshimasa Maeno ◽  
Mayuko Tomita ◽  
Tsuyoshi Matsuoka ◽  
Masaharu Ohfu ◽  
...  
Keyword(s):  
Stool Specimen ◽  
Genomic Analysis ◽  
Whole Genome ◽  
Asian Countries ◽  
Dynamic Interactions ◽  
Genotype Constellation ◽  
Porcine Rotavirus ◽  
Porcine Origin ◽  
Unique Genotype

An unusual rotavirus strain, Ryukyu-1120, with G5P[6] genotypes (RVA/Human-wt/JPN/Ryukyu-1120/2011/G5P[6]) was identified in a stool specimen from a hospitalized child aged 4 years who showed diarrhoea and encephalopathy. In this study, we sequenced and characterized the complete genome of strain Ryukyu-1120. On whole genomic analysis, this strain was found to have a unique genotype constellation: G5-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1. The VP6 and NSP1 genotypes I5 and A8 are those commonly found in porcine strains. Furthermore, phylogenetic analysis indicated that each of the 11 genes of strain Ryukyu-1120 appeared to be of porcine origin. Thus, strain Ryukyu-1120 was found to have a porcine rotavirus genetic backbone and is likely to be of porcine origin. To our knowledge, this is the first report of whole-genome-based characterization of the emerging G5P[6] strains in Asian countries. Our observations will provide important insights into the origin of G5P[6] strains and the dynamic interactions between human and porcine rotavirus strains.

Epidemiological analysis of porcine rotavirus A genotypes in Germany

2018 ◽  
Vol 214 ◽  
pp. 93-98 ◽  
Author(s):  
Oliver Wenske ◽  
Antje Rückner ◽  
Daniel Piehler ◽  
Bernd-Andreas Schwarz ◽  
Thomas W. Vahlenkamp
Keyword(s):  
Epidemiological Analysis ◽  
Rotavirus A ◽  
Porcine Rotavirus
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