5 research outputs found
Detection and genetic characterization of enteric viruses in diarrhoea outbreaks from swine farms in Spain
Background The aim of this work was to study the prevalence and distribution of Porcine astrovirus (PAstV), Porcine
kobuvirus (PKoV), Porcine torovirus (PToV), Mammalian orthoreovirus (MRV) and Porcine mastadenovirus (PAdV) as well
as their association with widely recognized virus that cause diarrhoea in swine such as coronavirus (CoVs) and rotaviâ
rus (RVs) in diarrhoea outbreaks from Spanish swine farms. Furthermore, a selection of the viral strains was genetically
characterized.
Results PAstV, PKoV, PToV, MRV and PAdV were frequently detected. Particularly, PAstV and PKoV were detected in
almost 50% and 30% of the investigated farms, respectively, with an age-dependent distribution; PAstV was mainly
detected in postweaning and fattening pigs, while PKoV was more frequent in sucking piglets. Viral co-infections
were detected in almost half of the outbreaks, combining CoVs, RVs and the viruses studied, with a maximum of 5 difâ
ferent viral species reported in three investigated farms. Using a next generation sequencing approach, we obtained
a total of 24 ARN viral genomes (>90% genome sequence), characterizing for frst time the full genome of circulating
strains of PAstV2, PAstV4, PAstV5 and PToV on Spanish farms. Phylogenetic analyses showed that PAstV, PKoV and PToV
from Spanish swine farms clustered together with isolates of the same viral species from neighboring pig producing
countries.
Conclusions Although further studies to evaluate the role of these enteric viruses in diarrhoea outbreaks are
required, their wide distribution and frequent association in co-infections cannot be disregard. Hence, their inclusion
into routine diagnostic panels for diarrhoea in swine should be considered.
Keywords Swine, Multiplex RT-PCR, Phylogenetic analysis, Porcine astrovirus, Porcine kobuvirus, Porcine torovirus,
Mammalian orthoreovirus, Porcine mastadenovirusThis work was supported by the program of the National Institute of Agricultural and Food Research and Technology (INIA project E-RTA2015-0003-C02-01 and E-RTA2015-0003-C02-02) of Spanish Government. H. Puente, O. MencĂa-Ares, L. PĂ©rez-PĂ©rez, M. Cortey and H. ArgĂŒello were supported by Spanish Government (FPU17/00466, FPU16/03485, PRE2020-093762, RYC-2015-1715-4 and BEAGAL- 18-106, respectively) and M. GĂłmez-GarcĂa by Junta de Castilla & LeĂłn (LE131-18)info:eu-repo/semantics/publishedVersio
Antimicrobial resistance in commensal Escherichia coli and Enterococcus spp. is influenced by production system, antimicrobial use, and biosecurity measures on Spanish pig farms
peer-reviewedBackground
Antimicrobial resistance (AMR) is a global public health threat consequence of antimicrobial use (AMU) in human and animal medicine. In food-producing animals factors such as management, husbandry or biosecurity may impact AMU. Organic and extensive Iberian swine productions are based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the AMR in indicator bacteria. Here, we evaluate the usefulness of commensal Escherichia coli and Enterococcus spp. isolates as AMR bioindicators when comparing 37 Spanish pig farms from both intensive and organic-extensive production systems, considering the effect of AMU and biosecurity measures, the last only on intensive farms.
Results
The production system was the main factor contributing to explain the AMR differences in E. coli and Enterococcus spp. In both bacteria, the pansusceptible phenotype was more common (pâ<â0.001) on organic-extensive farms when compared to intensive herds. The microbiological resistance in commensal E. coli was, for most of the antimicrobials evaluated, significantly higher (pâ<â0.05) on intensive farms. In enterococci, the lincosamides usage revealed the association between AMR and AMU, with an increase in the AMR for erythromycin (pâ<â0.01), quinupristin-dalfopristin (pâ<Â 0.01) and the multidrug-resistant (MDR) phenotype (pâ<â0.05). The biosecurity measures implemented on intensive farms influenced the AMR of these bioindicators, with a slightly lower resistance to sulfamethoxazole (pâ<â0.01) and the MDR phenotype (pâ<â0.05) in E. coli isolated from farms with better cleaning and disinfection protocols. On these intensive farms, we also observed that larger herds had a higher biosecurity when compared to smaller farms (pâ<â0.01), with no significant associations between AMU and the biosecurity scores.
Conclusions
Overall, this study evidences that the production system and, to a lesser extent, the biosecurity measures, contribute to the AMR development in commensal E. coli and Enterococcus spp., with antimicrobial usage as the main differential factor, and demonstrates the potential value of these bacteria as bioindicators on pig farms in AMR surveillance programs
Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms
P. 1-17Background: The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by
antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a
more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how
sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment.
Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared
to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from
38 farms.
Results: Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive
farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome
across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those
from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were
defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences
between intensive and extensive farms could be linked to differences in the abundance of mobile genetic
elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs
between intensive and extensive herds, a significantly higher abundance of integrons in the environment and
plasmids, regardless of the sample type, was detected on intensive farms.
Conclusions: Overall, this study shows how AMU, production system, and sample type influence, mainly through
MGEs, the profile and dispersion of ARGs in pig production.S
Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity
ArtĂculo versiĂłn publicadaBackground: The microorganisms that inhabit food processing environments (FPE) can strongly influence the
associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant
microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat
processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a
detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.
Results: We identified a relatively restricted principal microbiota dominated by Pseudomonas during the first 2
months, while a higher taxonomic diversity, an increased representation of other taxa (e.g., Acinetobacter,
Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An
increase in total abundance, alpha diversity, and ÎČ-dispersion of ARGs, which were predominantly assigned to
Acinetobacter and associated with resistance to certain antimicrobials frequently used on pig farms of the region,
was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum ÎČ-lactamase-
producing Enterobacteriaceae and vancomycin-resistant Enterococcaceae was observed when cutting activities
started. ARGs associated with resistance to ÎČ-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently
co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly
detected at the later sampling times in drains.
Conclusions: The observations made suggest that pig carcasses were a source of resistant bacteria that then
colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces,
represented a reservoir for the spread of ARGs in the meat processing facility.S
Detection and genetic characterization of enteric viruses in diarrhoea outbreaks from swine farms in Spain
Abstract Background The aim of this work was to study the prevalence and distribution of Porcine astrovirus (PAstV), Porcine kobuvirus (PKoV), Porcine torovirus (PToV), Mammalian orthoreovirus (MRV) and Porcine mastadenovirus (PAdV) as well as their association with widely recognized virus that cause diarrhoea in swine such as coronavirus (CoVs) and rotavirus (RVs) in diarrhoea outbreaks from Spanish swine farms. Furthermore, a selection of the viral strains was genetically characterized. Results PAstV, PKoV, PToV, MRV and PAdV were frequently detected. Particularly, PAstV and PKoV were detected in almost 50% and 30% of the investigated farms, respectively, with an age-dependent distribution; PAstV was mainly detected in postweaning and fattening pigs, while PKoV was more frequent in sucking piglets. Viral co-infections were detected in almost half of the outbreaks, combining CoVs, RVs and the viruses studied, with a maximum of 5 different viral species reported in three investigated farms. Using a next generation sequencing approach, we obtained a total of 24 ARN viral genomes (>â90% genome sequence), characterizing for first time the full genome of circulating strains of PAstV2, PAstV4, PAstV5 and PToV on Spanish farms. Phylogenetic analyses showed that PAstV, PKoV and PToV from Spanish swine farms clustered together with isolates of the same viral species from neighboring pig producing countries. Conclusions Although further studies to evaluate the role of these enteric viruses in diarrhoea outbreaks are required, their wide distribution and frequent association in co-infections cannot be disregard. Hence, their inclusion into routine diagnostic panels for diarrhoea in swine should be considered