<i>Actinobacillus suis</i> isolated from diseased pigs are phylogenetically related but harbour different number of toxin gene copies in their genomes

Kulathunga, D.G.R.S.; Fakher, Alaa Abou; Costa, Matheus de O.

doi:10.1002/vro2.45

Cited by 1 publication

(2 citation statements)

References 34 publications

(87 reference statements)

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“…The check of read quality and the pipeline to infer Ribosomal Sequence variants (RSVs) using DADA2 v1.20 was performed as described by Patel et al , 2021 (7) with slight modifications considering the following parameters: truncLen=c(220,220), trimLeft=c(17,21), maxEE=c(2,2), truncQ=c(2,2), maxN=0, rm.phix=TRUE for 16S rRNA and truncLen=c(240,200), trimLeft=c(20,22), maxEE=c(2,2), truncQ=c(2,2), maxN=0, rm.phix=TRUE for the tuf gene. In the taxonomy assignment step the bootstrap confidence threshold was mutated to 80%.…”

Section: Methodsmentioning

confidence: 99%

“…Opportunistic bacterial pathogens, including those part of the Porcine Respiratory Disease Complex (PRDC) (1, 19), such as Actinobacillus pleuropneumoniae (20), Actinobacillus suis (21), Trueperella pyogenes (22), Bordetella bronchiseptica (20), Glaesserella parasuis (11), Klebsiella pneumoniae (23), Mannheimia varigena (24), Mycoplasma hyopneumoniae (20), Mycoplasma hyorhinis (25), Pasteurella multocida (26), and Streptococcus suis (27) are often present in the porcine upper respiratory tract. In addition, potential zoonotic pathogens like LA-MRSA reside in the respiratory tract, and zoonotic spill-over of LA-MRSA occurs through occupational exposure to livestock, likely through animal contact or dust (28–30).…”

Section: Introductionmentioning

confidence: 99%

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The developing pig respiratory microbiome harbours strains antagonistic to common respiratory pathogens

Vlasblom,

Duim,

Patel

et al. 2023

Preprint

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In the global efforts to combat antimicrobial resistance and reduce antimicrobial use in pig production, there is a continuous search for methods to prevent and/or treat infections. Within this scope, we explored the relationship between the developing piglet nasal microbiome and (zoonotic) bacterial pathogens from birth until ten weeks of life. The nasal microbiome of 54 pigs was longitudinally studied over 16 time-points on nine farms in three European countries (Germany, Ireland, and the Netherlands) using amplicon sequencing targeting the V3-V4 16S rRNA region as well as thetufgene for itsStaphylococcaldiscrimination power. The piglets’ age, the farm, and the litter affected the nasal microbiome, with piglets’ age explaining 19% of the variation in microbial composition between samples. Stabilization of the microbiome occurred around two weeks post-weaning. Notably, while opportunistic pathogens were ubiquitously present, they did not cause disease. The piglet nasal microbiome often carried species associated with gut, skin, or vagina, which suggests that contact with the vaginal and faecal microbiomes shape the piglet nasal microbiome. We identified bacterial Co-Abundance Groups (CAGs) of species that were present in the nasal microbiomes in all three countries over time. Anticorrelation between these species and known bacterial pathogens identified strains that might be exploited for pathogen reduction. Further experimental evidence is required to confirm these findings. Overall, this study advances our understanding of the longitudinal development and factors influencing the piglet nasal microbiome, providing insights into its role in health and disease.ImportanceOur study on longitudinal analysis of the developing nasal microbiota of piglets in farms in three European countries showed consistent microbiome compositions and that colonization of porcine pathogens occurred in relation with anticorrelating species. These findings enhance our knowledge of co-colonizing species in the nasal cavity, and the identified microbial interactions can be explored for the development of interventions to control pathogens in porcine husbandry.

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Section: Methodsmentioning

confidence: 99%