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1The Omicron SARS-CoV-2 variant of concern (VOC lineage B.1.1.529), which became dominant in many countries during early 2022, includes several subvariants with strikingly different genetic characteristics. Several countries, including Denmark, have observed the two Omicron subvariants: BA.1 and BA.2. In Denmark the latter has rapidly replaced the former as the dominant subvariant. Based on nationwide Danish data, we estimate the transmission dynamics of BA.1 and BA.2 following the spread of Omicron VOC within Danish households in late December 2021 and early January 2022. Among 8,541 primary household cases, of which 2,122 were BA.2, we identified a total of 5,702 secondary infections among 17,945 potential secondary cases during a 1-7 day follow-up period. The secondary attack rate (SAR) was estimated as 29% and 39% in households infected with Omicron BA.1 and BA.2, respectively. We found BA.2 to be associated with an increased susceptibility of infection for unvaccinated individuals (Odds Ratio (OR) 2.19; 95%-CI 1.58-3.04), fully vaccinated individuals (OR 2.45; 95%-CI 1.77-3.40) and booster-vaccinated individuals (OR 2.99; 95%-CI 2.11-4.24), compared to BA.1. We also found an increased transmissibility from unvaccinated primary cases in BA.2 households when compared to BA.1 households, with an OR of 2.62 (95%-CI 1.96-3.52). The pattern of increased transmissibility in BA.2 households was not observed for fully vaccinated and booster-vaccinated primary cases, where the OR of transmission was below 1 for BA.2 compared to BA.1. We conclude that Omicron BA.2 is inherently substantially more transmissible than BA.1, and that it also possesses immune-evasive properties that further reduce the protective effect of vaccination against infection, but do not increase its transmissibility from vaccinated individuals with breakthrough infections.
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INTRODUCTION: The prudent use of antibiotics in veterinary medicine necessitates the selection of antibiotic compounds with narrow-spectrums targeted against the specific pathogens involved. The same pathotype of enterotoxigenic E. coli (ETEC) was recently found both in diarrhoeic pigs and in samples from the pen floor where the pigs were housed. The first objective of this study was to compare resistance profiles from ETEC isolates and Non-ETEC isolates. The second objective was to evaluate the agreement between resistance profiles of ETEC isolated from pen floor samples and from individual rectal samples from pigs. Across three Danish pig herds, faecal samples were collected from the floors of 31 pens that had a within-pen diarrhoea prevalence of >25%, and from rectal samples of 93 diarrhoeic nursery pigs from the same pens. A total of 380 E. coli isolates were analysed by PCR and classified as ETEC when genes for adhesin factors and enterotoxins were detected. Minimum inhibitory concentrations of 13 antimicrobial agents were determined by the broth micro dilution method. Isolates were classified as resistant based on clinical breakpoints. RESULTS: Based on logistic regression models, the odds of Non-ETEC isolates (n=291) being pan-susceptible were significantly higher compared to ETEC isolates (n=89), (P<0.001, OR=20.22, CI95%=6.35-64.35). The odds of ETEC isolates having multidrug resistance were significantly higher compared to Non-ETEC isolates (p<0.001, OR: 7.21, CI95%: 2.87-18.10). The odds of an isolate being resistant were significantly higher in ETEC isolates compared to Non-ETEC isolates for ampicillin (p<0.001), apramycin (p=0.003), sulphamethoxazole (p<0.001) and trimethoprim (p<0.001). No overlap of resistance patterns between the three study herds was observed in the sampled ETEC isolates. In addition, there was generally good or excellent agreement when comparing resistance profiles from isolates from the same pen (pen floor and pig samples), and perfect agreement (Kappa=1.000, SE=0.316) was observed for ampicillin, apramycin, gentamycin, sulphamethoxazole, tetracycline and trimethoprim. CONCLUSIONS: We found that ETEC isolates were more resistant than Non-ETEC isolates. Furthermore, this study indicates that resistance testing of ETEC isolates from pen floor samples can be used as a convenient sampling method for resistance testing and in the selection of clinically relevant antimicrobial agents in the treatment of diarrhoeic pigs. The herd-level variation of resistance in ETEC isolates emphasises the importance of performing antimicrobial susceptibility testing at farm level when selecting antimicrobial agents for the treatment of E. coli-related diarrhoea.
