Human transmission and outbreaks of feline-like G6 rotavirus revealed with whole-genome analysis of G6P[9] feline rotavirus.

Group A rotaviruses (RVAs) are generally highly species-specific; however, some strains infect across species. Feline RVAs sporadically infect humans, causing gastroenteritis. In 2012 and 2013, rectal swab samples were collected from 61 asymptomatic shelter cats at a public health center in Mie Prefecture, Japan, to investigate the presence of RVA and any association with human infections. The analysis identified G6P[9] strains in three cats and G3P[9] strains in two cats, although no feline RVA sequence data were available for the former. A whole-genome analysis of these G6P[9] strains identified the genotype constellation G6-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3. The nucleotide identity among these G6P[9] strains exceeded 99.5% across all 11 gene segments, indicating the circulation of this G6P[9] strain among cats. Notably, strain RVA/Human-wt/JPN/KF17/2010/G6P[9], previously detected in a 3-year-old child with gastroenteritis, shares high nucleotide identity (>98%) with Mie20120017f, the representative G6P[9] strain in this study, across all 11 gene segments, confirming feline RVA infection and symptomatic presentation in this child. The VP7 gene of strain Mie20120017f also shares high nucleotide identity with other sporadically reported G6 RVA strains in humans. This suggests that feline-origin G6 strains as the probable source of these sporadic G6 RVA strains causing gastroenteritis in humans globally. Moreover, a feline-like human G6P[8] strain circulating in Brazil in 2022 was identified, emphasizing the importance of ongoing surveillance to monitor potential global human outbreaks of RVA.

Production of OSU G5P[7] Porcine Rotavirus Expressing a Fluorescent Reporter via Reverse Genetics.

Rotaviruses are a significant cause of severe, potentially life-threatening gastroenteritis in infants and the young of many economically important animals. Although vaccines against porcine rotavirus exist, both live oral and inactivated, their effectiveness in preventing gastroenteritis is less than ideal. Thus, there is a need for the development of new generations of porcine rotavirus vaccines. The Ohio State University (OSU) rotavirus strain represents a Rotavirus A species with a G5P[7] genotype, the genotype most frequently associated with rotavirus disease in piglets. Using complete genome sequences that were determined via Nanopore sequencing, we developed a robust reverse genetics system enabling the recovery of recombinant (r)OSU rotavirus. Although rOSU grew to high titers (~107 plaque-forming units/mL), its growth kinetics were modestly decreased in comparison to the laboratory-adapted OSU virus. The reverse genetics system was used to generate the rOSU rotavirus, which served as an expression vector for a foreign protein. Specifically, by engineering a fused NSP3-2A-UnaG open reading frame into the segment 7 RNA, we produced a genetically stable rOSU virus that expressed the fluorescent UnaG protein as a functional separate product. Together, these findings raise the possibility of producing improved live oral porcine rotavirus vaccines through reverse-genetics-based modification or combination porcine rotavirus vaccines that can express neutralizing antigens for other porcine enteric diseases.

The impact and complete genome characterisation of viruses involved in outbreaks of gastroenteritis in a farrow-to-finish holding.

Viral enteric pathogens continuously burden intensive pig farming, causing gastrointestinal diseases of epidemic and endemic nature. The present study investigated two diarrhoea outbreaks on a large farrow-to-finish holding and subsequent circulation of outbreak-related enteric viruses. These viruses were characterised by whole genome sequencing, and statistical evaluation of the impact on specific production metrics was performed. The results provided evidence that the Porcine epidemic diarrhoea virus-swine enteric coronavirus (PEDV-SeCoV) S gene recombinant strain was responsible for the first outbreak, whilst Rotavirus A (RVA) in a mixed infection with Rotavirus B (RVB) and porcine kobuvirus (PKV) probably caused the second diarrhoea outbreak. Whole genome characterisation revealed a porcine origin of all viruses involved and significant heterogeneity of RVB strain, proposing four novel genotypes and changes in RVB VP1 genotype classification. The statistical evaluation confirmed only a minor disturbance in the number of weaned pigs per sow, with statistical forecasting showing positive trends. A follow-up study corroborated the endemicity of RVA and PKV, in contrast to PEDV-SeCoV. Punctual, comprehensive and timely investigation of diarrhoea outbreaks is a prerequisite for applying adequate pig health and biosecurity management. Calculating such outbreaks' impact on production metrics can potentially shape future decisions on management improvements.

Prevalence of transmissible gastroenteritis among swine populations in China during 1983-2022: A systematic review and meta-analysis.

BACKGROUND: Transmissible gastroenteritis virus (TGEV), which belongs to the coronaviruses (CoVs), causes diarrhea and high mortality rates in piglets and poses a huge threat and loss to the pig industry in China. METHOD: We estimated the prevalence of TGEV in Chinese pig animals from 1983 to 2022 by screening 36 papers on TGEV investigations in China from databases such as China Knowledge Network (CNKI), Wanfang Database, Science and Technology Journal Repository (VIP), PubMed, and ScienceDirect, excluding duplicate literature and other host studies according to the exclusion criteria we developed, and excluding literature with incomplete data to extract information from studies that could estimate the prevalence of TGEV infection in pigs in mainland China. RESULTS: A total of 36 studies (including data from 50,403 pigs) met our evaluation criteria. The overall estimated prevalence of TGEV infection in pigs in China is 10% (3887/50403), and the prevalence of TGEV in northeast China is 38% (2582/3078700) is significantly higher than the rest of China. The prevalence of TGEV infection was related to the sampling season and region. CONCLUSION: The results of the study show that the prevalence of TGEV is clearly seasonal and regional. Therefore, further research and monitoring of the prevalence of TGEV infection and the development of control programs based on different conditions are essential. In addition, effective and robust regulatory measures should be taken in colder regions to prevent the spread and transmission of TGEV in pigs.

A multi-strain probiotic promoted recovery of puppies from gastroenteritis in a randomized, double-blind, placebo-controlled study.

Objective and animals: Acute diarrhea is among the most common causes of veterinary consultations for dogs. A double-blind, placebocontrolled intervention trial was done with 120 puppies with gastroenteritis. These dogs were 1 to 4 mo old, male and female, of various breeds and sizes. Procedure: Dogs were randomly allocated into 2 groups: Those in the treated group (TG) received a multi-strain probiotic with Lactobacillus johnsonii CRL1693, Ligilactobacillus murinus CRL1695, Limosilactobacillus mucosae CRL1696, and Ligilactobacillus salivarius CRL1702 (1 × 109 CFU/mL) daily for 7 d, whereas those in the control group (CG) received a placebo. All puppies received intravenous fluids, an antiparasitic, amoxicillin PO, and enrofloxacin SC. Results: At the start of the trial, the 2 groups were similar. Probiotic administration for 7 d normalized fecal consistency, with 69, 50, and 80% of small, medium, and large puppies in the TG achieving a fecal score of 1 (separate hard lumps) at 7 d, significantly better than puppies in the CG. After 7 d of treatment, most puppies (70%) in the TG had an excellent recovery, whereas in the CG, recoveries were 35.7% "bad" and 30.4% "fair." Therefore, treatment with probiotics hastened recovery (P < 0.0001). At the end of the trial, there was a significant increase of cultivable lactobacilli in the feces of TG puppies, but no significant differences between the 2 groups in numbers of total mesophylls, enterobacteria, or Gram-positive cocci. Total mortality was 5.8%, including 4 puppies from the CG and 3 from the TG. Conclusion: In a randomized, double-blind, placebo-controlled study, puppies with gastroenteritis symptoms receiving a multi-strain probiotic had rapid improvement, implying beneficial effects on the microbiota and its functionality.

Un probiotique multi-souches a favorisé la guérison des chiots de la gastro-entérite dans une étude randomisée, en double aveugle et vérifiée par placebo. Objectif et animaux: La diarrhée aiguë fait partie des causes les plus fréquentes de consultations vétérinaires pour les chiens. Un essai d'intervention en double aveugle et vérifié par placebo a été réalisé avec 120 chiots atteints de gastro-entérite. Ces chiens étaient âgés de 1 à 4 mois, mâles et femelles, de différentes races et tailles. Procédure: Les chiens ont été répartis au hasard en 2 groupes : ceux du groupe traité (TG) ont reçu un probiotique multisouches contenant Lactobacillus johnsonii CRL1693, Ligilactobacillus murinus CRL1695, Limosilactobacillus mucosae CRL1696 et Ligilactobacillus salivarius CRL1702 (1 × 109 UFC/mL) quotidiennement pendant 7 j, tandis que ceux du groupe témoin (CG) ont reçu un placebo. Tous les chiots ont reçu des liquides intraveineux, un antiparasitaire, de l'amoxicilline PO et de l'enrofloxacine SC. Résultats: Au début de l'essai, les 2 groupes étaient similaires. L'administration de probiotiques pour une durée de 7 j a normalisé la consistance fécale, avec 69, 50 et 80 % des chiots petits, moyens et grands dans le TG obtenant un score fécal de 1 (morceaux durs séparés) à 7 jours, ce qui était significativement meilleur que les chiots dans le CG. Après 7 jours de traitement, la plupart des chiots (70 %) dans le TG ont eu une excellente récupération, alors que dans le CG, les récupérations étaient de 35,7 % « mauvaises ¼ et 30,4 % « passables ¼. Par conséquent, le traitement avec des probiotiques a accéléré la récupération (P < 0,0001). À la fin de l'essai, il y avait une augmentation significative des lactobacilles cultivables dans les fèces des chiots TG, mais aucune différence significative entre les 2 groupes en nombre de mésophylles totaux, d'entérobactéries ou de coques à Gram positif. La mortalité totale était de 5,8 %, dont 4 chiots du CG et 3 du TG. Conclusion: Dans une étude randomisée, en double aveugle et vérifiée par placebo, des chiots présentant des symptômes de gastro-entérite recevant un probiotique multi-souches ont présenté une amélioration rapide, impliquant des effets bénéfiques sur le microbiote et sa fonctionnalité.(Traduit par Dr Serge Messier).

Avian campylobacteriosis, prevalence, sources, hazards, antibiotic resistance, poultry meat contamination, and control measures: a comprehensive review.

Avian campylobacteriosis is a vandal infection that poses human health hazards. Campylobacter is usually colonized in the avian gut revealing mild signs in the infected birds, but retail chicken carcasses have high contamination levels of Campylobacter spp. Consequently, the contaminated avian products constitute the main source of human infection with campylobacteriosis and result in severe clinical symptoms such as diarrhea, abdominal pain, spasm, and deaths in sensitive cases. Thus, the current review aims to shed light on the prevalence of Campylobacter in broiler chickens, Campylobacter colonization, bird immunity against Campylobacter, sources of poultry infection, antibiotic resistance, poultry meat contamination, human health hazard, and the use of standard antimicrobial technology during the chicken processing of possible control strategies to overcome such problems.

Detection of G3 human-like rotavirus in institutionalized dogs from Brazil.

Viral gastroenteritis is a common clinical problem in dogs and group A rotavirus (RVA) is one of the agents involved in this etiology. It mainly affects dogs in the first 6 months of life, and these animals are considered an important reservoir and potential transmitters of the virus to other susceptible hosts, such as humans. Among the different types of RVA, G3 is the most detected in dogs, and this genotype is also involved in infections in other animals, including humans. Thus, the present study aims to investigate the presence of RVA in samples of dogs from a public kennel. A total of 64 fecal samples from dogs with diarrhea were analyzed, collected from April 2019 to March 2020, from the kennel of the Zoonosis Control Center, located in Belém, a city in the North of Brazil. The extracted genetic material was subjected to reverse transcription followed by real-time PCR (RT-qPCR); the positives were tested by RT-PCR with a specific primer for the RVA VP7 gene, after nucleotide sequencing and phylogenetic analysis. One sample was subjected to high-performance sequencing. A positivity of 7.8% (5/64) was observed for RVA, all characterized as G3, grouping in the G3-III lineage, with greater similarity to human samples. Different regions of the RVA genome fragments were found. These results emphasize the need for animal health surveillance to better understand the global strain dispersion of RVA and elucidate possible interspecies transmission events, monitoring the genetic diversity of this pathogen.

Suspect severe gastroenteritis associated with ingestion of caterpillar setae fragments in a cat.

A 6-month-old male neutered Domestic Shorthair cat was assessed for a 24-h history of anorexia, lethargy, depressed mentation, mild abdominal pain and persistent bradycardia. Abdominal ultrasound revealed marked thickening of the gastric wall, gastric distension, free abdominal fluid, distension and corrugation of the small intestine. Full-thickness histopathological biopsy of the gastric wall demonstrated intralesional chitinous structures whose morphology (size and presence of obvious barbs) supports these structures being urticating hairs (setae). A processionary caterpillar is considered most likely as these are the most common urticating caterpillars in Australia. This is the first case of suspected severe gastroenteritis associated with the ingestion of caterpillar setae fragments in a cat.

Molecular characterization of norovirus and sapovirus detected in animals and humans in Costa Rica: Zoo-anthropozoonotic potential of human norovirus GII.4.

Background: Noroviruses (NoV) and sapoviruses (SaV) are major causes of acute viral gastroenteritis in humans worldwide, as well as gastrointestinal infections in animals. However, it has not been determined whether these viruses are zoonotic pathogens. Aim: In this study, we investigated the presence of NoV and SaV in stool samples from dogs, pigs, cows, and humans to determine some aspects of the molecular epidemiology and the genetic relationship of several strains present in these species. Methods: Polymerase chain reaction and sequencing of NoV and SaV strains present in stool samples from humans and dogs with diarrhea, pigs, and cattle with and without diarrhea were carried out during fragmented periods from 2002 to 2012. Results: Of all samples analyzed, 11.6% (123/1,061) of the samples were positive for NoV and 0.88% (9/1,023) were positive for SaV. The phylogenetic analysis confirmed 16 human strains of NoV (HuNoV) belonging to HuNoV G?/GII.P2 (1), GII.4/GII.P4 (5), G?/GII.P4 (9), and GII.6/GII.P6 (1) and allowed us to verify and assign three strains of human SaV to genotypes GI.2 (1) and GII.5 (2). In dogs, eight strains of NoV [HuNoV G?/GII.P4 (4) and canine G?/GVI.P1 (4)] and two strains of canine SaV were determined. In pigs, six strains were assigned to HuNoV G?/GII.P4 and four strains to porcine SaV were assigned to genogroup GIII (2), GVIII (1), and GXI (1). In bovines, five strains were characterized as HuNoV G?/GII.P4. Conclusions: This study showed that NoV and SaV prototype strains have been present in humans and dogs in Costa Rica. Additionally, it revealed that the zoonotic potential of SaV is very limited, while the zoonotic implications for HuNoV GII.4 are stronger due to the simultaneous circulation of strains related to HuNoV GII.4 in four species, which suggests a zoo-anthropozoonosis.

A comprehensive molecular survey of viral pathogens associated with canine gastroenteritis.

Viral pathogens are the primary cause of canine gastroenteritis. However, few structured comprehensive studies on the viral etiology of canine gastroenteritis have been conducted. In this study, 475 rectal swabs collected over three years (2018-2021) from clinical canine gastroenteritis cases were screened for the presence of six major enteric viruses - canine parvovirus 2 (CPV-2), canine distemper virus (CDV), canine adenovirus 2 (CAdV-2), canine coronavirus (CCoV), canine astrovirus (CaAstV), and canine rotavirus (CRV) - by real-time PCR. The most frequently detected virus was CPV-2, which was present in 64.8% of the samples (subtype 2a, 21.1%; 2b, 77.4%; 2c, 1.5%), followed by CDV (8%), CaAstV (7.2%), CCoV (5.9%), and CAdV-2 (4.6%). Two to four of these viruses in different combinations were found in 16.8% of the samples, and CRV was not detected. The complete genome sequences of Indian isolates of CDV, CCoV, and CaAstV were determined for the first time, and phylogenetic analysis was performed. This study highlights the need for routine prophylactic vaccination with the appropriate vaccines. Notably, 70.3% of animals vaccinated with DHPPiL were found to be positive for at least one virus. Hence, regular molecular analysis of the prevalent viruses is crucial for addressing vaccination failures.

Campylobacter jejuni infection induces dynamic expression of avian host defense peptides in vitro and in vivo.

Campylobacter jejuni is considered as the leading cause of worldwide foodborne bacterial gastroenteritis. Chicken is the main reservoir of C. jejuni. Avian innate immune responses to C. jejuni remain poorly defined. Chicken host defense peptides (HDPs) are the major components of avian innate immune system. This study aimed to characterize the chicken HDPs responses to C. jejuni in vitro and in vivo. In the HD11 macrophage cell line, the HDPs, including AvBD1-2, CATH1-3, AvBD7, AvBD4, and AvBD6, were relatively higher expressed in untreated cells, whereas the expressions were suppressed after C. jejuni infection. In contrast, C. jejuni infection significantly increased the expression of the lower expressed HDPs, such as AvBD3, AvBD5, AvBD8-14, and CATHB1, in untreated cells. In the chicken challenge experiment, the immune tissues of spleens and cecal tonsils were collected from C. jejuni-infected and uninfected chickens at 1, 3 and 15 day post inoculation (DPI). In spleens of C. jejuni-infected chickens, only AvBD14 expression was elevated at 1 DPI. The majority of avian HDPs were significantly up-regulated at 3 DPI and dramatically decreased to the levels of uninfected controls at 15 DPI. In chicken cecal tonsils, only AvBD9 and AvBD14 were significantly up-regulated at 1 DPI with C. jejuni infection. Collectively, C. jejuni infection induced dynamic expression of chicken HDPs in both macrophage HD11 and immune tissues of chickens. Suppression of chicken HDPs expression may be an evasion strategy of C. jejuni for persistent colonization in chicken intestine by circumventing the chicken immune system.

Unusual "Asian-origin" 2c to 2b point mutant canine parvovirus (Parvoviridae) and canine astrovirus (Astroviridae) co-infection detected in vaccinated dogs with an outbreak of severe haemorrhagic gastroenteritis with high mortality rate in Hungary.

In this study, the aetiological background of an outbreak of severe haemorrhagic gastroenteritis (HGE) in a colony of purebred Jack Russell Terriers vaccinated against CPV-2 in Hungary was investigated. Canine parvovirus 2 (CPV-2, Parvoviridae) and canine astrovirus (CaAstV, Astroviridae) co-infection was identified by viral metagenomics and next-generation sequencing (VM-NGS) methods from a rectal swab of an affected 7-week-old puppy. The complete coding sequence of CPV-2 strain FR1/CPV2-2021-HUN (ON733252) and the complete genome of CaAstV strain FR1/CaAstV-2021-HUN (ON733251) were determined by VM-NGS and PCR methods. Results of sequence and phylogenetic analyses showed that CPV-2 strain FR1/CPV2-2021-HUN was different from the applied vaccine strains and previously identified strains from Hungary but showed high sequence identity (> 99.8%) and close phylogenetic relationship to recently described "Asian-origin" CPV-2c strains from Italy. But, based on the single amino acid difference on position 426 of VP2 (Glu/Asp) between the study strain and the closest relatives, FR1/CPV2-2021-HUN belonged to the 2b antigenic type rather than 2c. The CaAstV strain FR1/CaAstV-2021-HUN showed close relationship with a CaAstV strain identified previously from a diarrhoeic dog in Hungary. Both viruses were continuously detectable by PCR in additional enteric samples, and the CPV-2 could also be detected in several (n = 32) tissue samples from 9 affected deceased puppies. Further comparative studies are necessary to confirm the role of the point mutation causing the change in the antigenic type of this "Asian-origin" CPV-2 and/or the role of CaAstV co-infection in the development and/or severity of (haemorrhagic) gastroenteritis among dogs vaccinated against CPV-2.

Exclusive circulation of canine parvovirus type 2c in the Guadalajara metropolitan area in western Mexico: a five-year study.

Canine parvovirus type 2 (CPV-2) infection in dogs is associated with severe gastroenteritis, bloody diarrhea, and vomiting, resulting in high rates of death, especially in unvaccinated puppies within the first months of age. There are three variants, called CPV-2a, CPV-2b, and CPV-2c, co-circulating worldwide. Our group previously reported that the only circulating CPV-2 variant in the Guadalajara metropolitan area in western Mexico was type 2c. Now, a five-year study was performed in order to investigate the possible dominance of CPV-2c in our region. Rectal swabs were collected from 146 dogs with clinical gastroenteritis from May 2014 to August 2019 at the Veterinary Hospital of the University of Guadalajara. Of these, 90 dogs tested positive for canine parvovirus by PCR. Most of the infected dogs with CPV-2 had a partial or incomplete vaccination status (n = 88, 97.8%). Approximately 65% (n = 59) of them were mixed-breed dogs, 77.8% (n = 70) were under 6 months of age, and 37.8% (n = 34) of them died from clinical complications. RFLP analysis of amplicons derived from the vp2 gene showed that all 90 DNA samples corresponded to CPV-2c, with no evidence of the presence of CPV-2a or CPV-2b variants. Twenty-nine of the 90 DNA samples were selected for amplification of a portion of the vp2 gene, and sequencing of these amplicons showed that all of them had the sequence GAA at codon 426, encoding the amino acid glutamic acid, which is characteristic of CPV-2c. Phylogenetic analysis showed that the CPV-2c sequences were related to those of viruses from Europe and South America. The present study indicates that CPV-2c is still the only variant circulating in the dog population of the Guadalajara metropolitan area.

Case of necrotic enteritis associated with campylobacteriosis and coccidiosis in an adult Indian peacock (Pavo cristatus).

BACKGROUND: To date, Campylobacter jejuni has not been found to be pathogenic to peafowl. The available publications show that out of a total of 44 samples tested from peafowl, this bacterium was isolated only in two cases. Eimeria pavonina infestations in the peafowl have been described, but no fatal cases have been reported yet. CASE PRESENTATION: The four-year-old peacock was presented with chronic diarrhea, emaciation and weakness. Post mortem examination revealed enlarged and pale kidneys, small intestinal mucosal necrosis and thickening of intestinal wall, and pericardial effusion. The histopathological examination revealed necrotic enteritis with marked mononuclear cells infiltration associated with the presence of coccidia, additionally there was histological evidence of septicemia in liver and kidneys. Bacteria identification was based on light microscopy of the small intestine sample, culture, and biochemical tests. Further identification was based on PCR. Antimicrobial susceptibility profile was created by determination of minimal inhibitory concentration (MIC) values for 6 antimicrobial agents from 5 different classes. PCR assays were performed to detect virulence factors genes responsible for motility, cytolethal distending toxin production, adhesion and internalization. Bacteriology of the small intestine sample showed abundant growth almost exclusively of Campylobacter jejuni, resistant to ciprofloxacin, gentamycin and ampicillin. Bacteria was sensitive to Amoxicillin + clavulanic acid, tetracycline, and erythromycin. All tested virulence factors genes have been detected. The parasitological examination was performed by microscopic examination of fresh faeces and intestinal content, and revealed the moderate number of Eimeria pavonina, Histomonas meleagridis, single Capillaria spp. eggs as well Heterakis spp. like parasites. CONCLUSION: The above case shows that a virulent isolate of Campylobacter jejuni in combination with a parasitic invasion may cause chronic enteritis in peafowl, which most likely led to extreme exhaustion of the host organism and death.

First report of canine Astrovirus and Sapovirus in Greece, hosting both asymptomatic and gastroenteritis symptomatic dogs.

BACKGROUND: Astrovirus, Norovirus and Sapovirus are widely distributed viruses in humans and animals worldwide. They have frequently been associated with disease, mainly of gastroenteric nature. In dogs, these viruses have been detected both in symptomatic and asymptomatic animals, mainly of young age. METHODS: In the present epidemiologic study, we investigated the presence of canine Astrovirus (CAstV), canine Norovirus (canine NoV) and canine Sapovirus (Canine SaV) in saliva and stools of 201 domestic dogs originating from throughout Greece, based on two different molecular methods, i.e. conventional and SYBR-Green Real-time RT-PCR. The samples derived from young and adult asymptomatic and symptomatic animals. CAstV was detected in 15/201 (7.5%) and 29/201 (15%) of the examined dogs using conventional RT-PCR and SYBR-Green Real time RT-PCR, respectively. RESULTS: The prevalence of the virus was higher at healthy dogs, with a slight discrepancy of the two methods on the aspect of age (67% young dogs with the method of conventional RT-PCR, versus 52% adult positive dogs with the method of SYBR-Green Real-time RT-PCR). Canine SaV was detected in 52/201 (23%) of the dogs (mainly young and asymptomatic), with the method of SYBR-Green Real-time RT-PCR only, while canine NoV was not detected in any sample with either of the two methods applied. Sequencing of the CAstV positive samples resulted in the acquisition of one CAstV sequence. Phylogenetic analysis confirmed the results, clustering the CAstV sequence with homologous canine hosting sequences from other countries. CONCLUSIONS: CAstV and Canine SaV were proved to circulate in Greek dogs. SYBR-Green Real time RT-PCR showed greater sensitivity in the detection of these viruses. Additionally, we were able to specify the CAstV strain that circulates in Greece, through phylogenetic analysis. To our knowledge, this is the first epidemiological study of CAstV and canine SaV in dogs in Greece, as well as the first time detected in dogs from Greece.

The prevalence, counts, and MLST genotypes of Campylobacter in poultry meat and genomic comparison with clinical isolates.

Since 2005 campylobacteriosis has been the most commonly reported gastrointestinal infection in humans in the European Union with more than 200,000 cases annually. Also Campylobacter is one of the most frequent cause of food-borne outbreaks with 319 outbreaks reported to EFSA, involving 1,254 cases of disease and 125 hospitalizations in EU in 2019. Importantly poultry meat is one of the most common source for the sporadic Campylobacter infections and for strong-evidence campylobacteriosis food-borne outbreaks in EU. In present study, 429 fresh broiler chicken meat samples of Estonian, Latvian, and Lithuanian origin were collected from Estonian retail level and analyzed on a monthly basis between September 2018 and October 2019. Campylobacter spp. were isolated in 141 (32.9%) of 429 broiler chicken meat samples. Altogether 3 (1.8%), 49 (36.8%), and 89 (66.9%) of Estonian, Latvian, and Lithuanian origin broiler chicken meat samples were positive for Campylobacter spp. Among Campylobacter-positive samples, 62 (14.5%) contained Campylobacter spp. below 100 CFU/g and in 28 (6.5%) samples the count of Campylobacter spp. exceeded 1,000 CFU/g. A high prevalence of Campylobacter spp. in fresh broiler chicken meat of Lithuanian and Latvian origin in Estonian retail was observed. Additionally, 22 different multilocus sequence types were identified among 55 genotyped isolates of broiler chicken meat and human origin, of which 45 were Campylobacter jejuni (C. jejuni) and 10 were Campylobacter coli (C. coli). The most prevalent multilocus sequence types among C. jejuni was ST2229 and among C. coli ST832, ST872. C. jejuni genotypes found in both broiler chicken meat and human origin samples were ST122, ST464, ST7355, and ST9882, which indicates that imported fresh broiler chicken meat is likely the cause of human campylobacteriosis in Estonia.

A pilot study revealing host-associated genetic signatures for source attribution of sporadic Campylobacter jejuni infection in Egypt.

Campylobacter jejuni (C. jejuni), is considered among the most common bacterial causes of human bacterial gastroenteritis worldwide. The epidemiology and the transmission dynamics of campylobacteriosis in Egypt remain poorly defined due to the limited use of high-resolution typing methods. In this pilot study, we evaluated the discriminatory power of multiple typing 'gene-by-gene based' techniques to characterize C. jejuni obtained from different sources and estimate the relative contribution of different potential sources of C. jejuni infection in Egypt. Whole genome sequencing (WGS) was performed on 90 C. jejuni isolates recovered from clinical samples, retail chicken, and dairy products in Egypt from 2017 to 2018. Comparative genomic analysis was performed using conventional seven-locus multilocus sequence typing (MLST), ribosomal MLST (rMLST), core genome MLST (cgMLST), allelic variation in 15 host-segregating (HS) markers, and comparative genomic fingerprinting (CGF40). The probabilistic source attribution was performed via STRUCTURE software using MLST, CGF40, cgMLST and allelic variation in HS markers. Comparison of the discriminatory power of the aforementioned genotyping methods revealed cgMLST to be the most discriminative method, followed by HS markers. The source attribution analysis showed the role of retail chicken as a source of infection among clinical cases in Egypt when HS and cgMLST were used (64.2% and 52.3% of clinical isolates were assigned to this source, respectively). Interestingly, the cattle reservoir was also identified as a contributor to C. jejuni infection in Egypt; 35.8% and 47.7% of clinical isolates were assigned to this source by HS and cgMLST, respectively. Here, we provided evidence of the importance of using WGS typing methods to facilitate source tracking of C. jejuni. Our findings suggest the importance of non-poultry sources, together with the previously reported role of retail chicken in human campylobacteriosis in Egypt that can provide insights to inform national control measures.

Evolutionary history and spatiotemporal dynamic of GIII norovirus: From emergence to classification in four genotypes.

Noroviruses belong to a genetically diverse group of viruses infecting a wide range of mammalian host species, and those detected in cattle and sheep are classified within genogroup III (GIII). The current classification of norovirus in genogroups and genotypes is based on phylogenetic clustering and average distances within and between these phylogenetic clusters; however, the classification studies have been focused mainly on human norovirus, being GIII norovirus relegated. Due to the increasing number of studies on GIII norovirus, the need of an updated and extensive classification is evident. The aim of this study was to update the classification of norovirus within GIII, to describe the emergence of a circulating recombinant strain, and to reconstruct the evolutionary history of this genogroup. Two P-types (GIII.P1-2) and four genotypes (GIII.1-4) were described. For the genogroup GIII, the evolutionary rate estimated was 2.78E-3 s/s/y (95%HPD, 1.79E-3 s/s/y-3.78E-3 s/s/y), and the tMRCA was estimated around 1500 (95%HPD, 1247-1688). Despite the long history of this genogroup, the genotypes detected at present emerged in the last 100 years. Interestingly, most of the recombinant GIII.2P[1] strains detected worldwide were originated from a single recombination event and this recombinant strain was later dispersed through the world. Finally, our results indicate that a scenario of genotypes replacement through the time is highly probable.

Detection and whole genome sequencing of murine norovirus in animal facility in Italy.

Viruses belonging to the genus Norovirus (NoV) of the family Caliciviridae are the major cause of acute viral gastroenteritis worldwide. NoVs are classified into 10 genogroups (GI-GX), and those belonging to the genogroup GV are able to infect several species of rodents. To evaluate the circulation of MNV among mice housed in an Italian facility, sampling was performed over two separate periods, in 2011, and 3 years later in 2014. During the two samplings, 75 fecal samples were collected from healthy mice housed in the animal facility and subjected to RT-PCR for viral detection. After the analysis, 41/75 animals (54.6%) resulted positive for the presence of MNV in feces. Nucleotide sequencing revealed the presence of two MNV variants co-circulating in both 2011 and 2014. One MNV strain was isolated on RAW264.7 cell line, and subjected to full genome sequencing. Our study showed that the murine noroviruses are widespread in the investigated animal facility, despite guidelines for animal care and maintenance. Full genome sequence analysis of the MNV strain described in this study showed a correlation with other strains circulating in Europe. Understanding the molecular epidemiology of this virus should give insight into its natural history and evolution in mice.

Astrovirus VA1 in patients with acute gastroenteritis.

Human astroviruses (AstVs) are usually associated with acute gastroenteritis. In recent years, atypical animal-like AstVs have been identified, but their pathogenic role in humans has not been determined. Starting from 2010, there has been a growing evidence that AstVs may also be associated with encephalitis in human and animal hosts. Some human atypical AstV strains (VA1, MLB1/MLB2) display neurotropic potential, as they have been repeatedly identified in patients with AstV-related encephalitis, chiefly in immunosuppressed individuals. In this study, a VA1-like AstV was identified from a single stool sample from an outbreak of foodborne acute gastroenteritis occurred in Italy in 2018. On genome sequencing, the virus was related to the VA1-like strain UK1 (99.3% at the nucleotide level). Similar viruses were also found to circulate in paediatric patients hospitalized with AGE in the same time span, 2018, but at low prevalence (0.75%, 3/401). Gathering epidemiological data on atypical AstVs will be useful to assess the risks posed by atypical AstV infections, chiefly in medically fragile patients.