Description of a New Clade within Subtype 1 of Betaarterivirus suid 1 Causing Severe Outbreaks in Spain.

This report describes 28 genome sequences from a new clade within subtype 1 of Betaarterivirus suid 1, formerly known as porcine reproductive and respiratory syndrome virus 1. All share a potential recombinant pattern, with a highly pathogenic Italian strain as the putative major parental sequence and three other possible parents.

Outbreaks of Acute Necrotic Enteritis and Haemolytic Crisis and Renal Disease Associated with Clostridium perfringens in Captive Toucans (Ramphastos spp).

Four toco toucans (Ramphastos toco), one channel-billed toucan (Ramphastos vitellinus) and one white-throated toucan (Ramphastos tucanus) died in two disease outbreaks in the same aviary in 2011 and 2016. Post-mortem examination revealed diffuse necrotic enteritis (NE) as the cause of death of five of these six birds. Clostridium perfringens was identified by culture and real-time multiplex PCR for C. perfringens α-, ß-, ε- and ι-toxin genes in ligated intestine of one toucan from each outbreak. At another aviary, two keel-billed toucans (Ramphastos sulfuratus) died peracutely from severe haemolytic crisis with haemoglobinaemic nephrosis and cholestasis and acute tubulointerstitial nephritis. Mild NE was present in these birds and C. perfringens was demonstrated in liver by bacterial culture and real-time multiplex PCR for C. perfringens α-, ß-, ε- and ι-toxin genes. To the authors' knowledge, this is the first description of outbreaks of NE associated with C. perfringens in captive toucans. Although haemolytic crisis has been reported in humans with C. perfringens type A septicaemia and hepatic abscesses, this presentation appears not to have been described in C. perfringens infections in toucans or other avian species. The factors causing C. perfringens proliferation and disease in the toucans were not identified. PCR for C. perfringens NetB toxin and enterotoxin genes performed retrospectively on one of the C. perfringens isolates from the second outbreak and on paraffin-embedded tissues from one dead toucan from the first outbreak was negative. With the current C. perfringens toxin typing scheme, C. perfringens type A was identified in the first two outbreaks.

Antimicrobial Resistance Profiles and Characterization of Escherichia coli Strains from Cases of Neonatal Diarrhea in Spanish Pig Farms.

Escherichia coli is considered one of the most common agents associated with neonatal diarrhea in piglets. The aim of this work was to characterize the pathogenic and antimicrobial resistance (AMR) profiles of 122 E. coli strains isolated from pigs suffering diarrhea (n = 94) and pigs without diarrhea (n = 28) of 24 farms in Spain. Virulence factors, toxins and AMR (ESBL and colistin) genes and AMR phenotypes of E. coli isolates were analyzed. Low prevalence of pathogenic E. coli strains (26%) was found in both groups. However, ETEC and VTEC strains were more frequently isolated from diarrheic piglets. Irrespectively of diarrhea occurrence, 97.5% of the strains showed a multidrug-resistance (MDR) profile to aminopenicillins, sulfonamides and tetracyclines. It was found that 22% of E. coli was CTX-M+, with CTX-M-14 being the principal allelic variant. Remarkably, 81.5% of CTX-M+ strains were isolated from diarrheic animals and presented an extended MDR profile to aminopenicillins, quinolones and aminoglycosides. Finally, low frequencies of colistin resistance genes mcr-1 (4/122) and mcr-4 (1/122) were found. MDR E. coli strains are circulating in pig farms of Spain, representing a serious threat to animal and public health. More appropriate diagnostic approaches (genetic and AMR phenotypic analysis) should be implemented in animal health to optimize antibiotic treatments.

Antimicrobial resistance profile and prevalence of extended-spectrum beta-lactamases (ESBL), AmpC beta-lactamases and colistin resistance (mcr) genes in Escherichia coli from swine between 1999 and 2018.

The frequent usage of antibiotics in livestock has led to the spread of resistant bacteria within animals and their products, with a global warning in public health and veterinarians to monitor such resistances. This study aimed to determine antibiotic resistance patterns and genes in pig farms from Spain during the last twenty years. Susceptibility to six antibiotics commonly used in pig production was tested by qualitative (disk diffusion) and quantitative (minimum inhibitory concentration, MIC) methods in 200 strains of Escherichia coli which had been isolated between 1999 and 2018 from clinical cases of diarrhoea in neonatal and post-weaned piglets. Results showed resistance around 100% for amoxicillin and tetracycline since 1999, and a progressive increase in ceftiofur resistance throughout the studied period. For colistin, it was detected a resistance peak (17.5% of the strains) in the 2011-2014 period. Concerning gentamicin, 11 of 30 strains with intermediate susceptibility by the disk diffusion method were resistant by MIC. Besides, the most frequent antimicrobial resistance genes were the extended-spectrum beta-lactamase (ESBL) bla CTX-M (13.5% of strains, being CTX-M-14, CTX-M-1 and CTX-M-32 the most prevalent genomes, followed by CTX-M-27, CTX-M-9 and CTX-M-3), AmpC-type beta-lactamase (AmpC) bla CMY-2 (3%) and colistin resistance genes mcr-4 (13%), mcr-1 (7%) and in less proportion mcr-5 (3%). Interestingly, these mcr genes were already detected in strains isolated in 2000, more than a decade before their first description. However, poor concordance between the genotypic mcr profile and the phenotypical testing by MIC was found in this study. These results indicate that although being a current concern, resistance genes and therefore antimicrobial resistant phenotypes were already present in pig farms at the beginning of the century.

Prevalence of enteric pathogens in diarrheic and non-diarrheic samples from pig farms with neonatal diarrhea in the North East of Spain.

Diarrhea is one of the major causes of neonatal mortality in pigs. In the present study, 31 pig farms with outbreaks of neonatal diarrhea were investigated in Catalonia (NE Spain) from February 2017 until June 2018. Two hundred and fifteen diarrheic samples from 1 to 7 days old piglets were tested for a panel of enteric pathogens. In 19 of the studied farms additional fecal samples from apparently healthy pen-mates were collected and tested for the same panel of infectious agents. Samples were bacteriologically cultured and tested by PCR for E. coli virulence factors genes, C. perfringens types A and C toxins (Cpα, Cpß, Cpß2) and C. difficile toxins (TcdA, TcdB). Moreover, Rotavirus A (RVA), Rotavirus B (RVB), Rotavirus C (RVC), porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV) were also determined by RT-qPCR. More than one pathogen could be detected in all of the outbreaks. Nevertheless, RVA was the only agent that could be statistically correlated with the outcome of diarrhea. For the other viruses and bacteria analyzed significant differences between the diseased pigs and the controls were not found. In spite of this, the individual analysis of each of the studied farms indicated that other agents such as RVB, RVC, toxigenic C. difficile or pathogenic E. coli could play a relevant role in the outbreak of diarrhea. In conclusion, the large diversity of agent combinations and disease situations detected in neonatal diarrhea outbreaks of this study stand for a more personalized diagnosis and management advice at a farm level.

A health evaluation in a colony of captive collared peccaries (Tayassu tajacu) in the Eastern Amazon.

This study pretends to determine baseline data on the health and mortality of a colony of captive collared peccaries in the Eastern Amazon (Belém, State of Pará, Brazil) during a 65-months survey. Thirty-nine out of 166 animals (23.5%) died and were examined post-mortem. Monthly mortality averaged 1.2%. The highest mortality rate was observed in newborns (74.4%). Abandonment by the mother and aggression were responsible for 24.1% and 13.8% of the total newborn deaths, respectively. Most frequent causes of non-neonatal death were food poisoning (50.0%) due to an episode of accidental bitter cassava leaves ingestion and traumatism due to aggressions between animals (10.0%). Results from serology for different infectious diseases showed that 4.9% (2/41) collared peccaries had antibodies against Brucella spp. and 9.8% (4/41) animals had antibodies to two different Leptospira spp. serovars, butembo and autumnalis. This is the first survey of morbidity and mortality in captive collared peccaries in the Amazon region.