Intramammary infections in lactating Jersey cows: Prevalence of microbial organisms and association with milk somatic cell count and persistence of infection.

There is limited data available regarding pathogens causing intramammary infections (IMI) in Jersey cows. The objectives of this study were to characterize the prevalence of IMI caused by different microorganisms in lactating Jersey cattle and evaluate the associations among microbes and somatic cell count (SCC) and persistence of IMI. This prospective, observational, longitudinal study included lactating Jersey cows (n = 753) from 4 farms within a 250-mile radius of Columbia, Missouri. Quarter foremilk samples were aseptically collected monthly for 3 consecutive months. Microorganisms were identified using aerobic milk culture and MALDI-TOF mass spectrometry. A commercial laboratory measured SCC using flow cytometry. Milk culture results were used to classify single microorganism infections as persistent (same microorganism species identified at first sampling and one other sampling) or non-persistent infection. Mixed models were built to evaluate the associations between IMI status and lnSCC as well as persistence and lnSCC. Overall, staphylococci were the most commonly isolated microorganisms among the 7,370 quarter-level milk samples collected. Median prevalence (using all 3 samplings) of specific microbes varied among farms; however, Staphylococcus chromogenes was a common species found at all farms. The most common microbial species that persisted were Staph. chromogenes, Staphylococcus aureus, Staphylococcus simulans, and Streptococcus uberis. Streptococcus dysgalactiae and Staph. aureus were the IMI associated with the most inflammation based on lnSCC. The small number of herds included in this study with the large variation in herd type limits the generalizability of the data. However, results of this study seem to be similar to those of previous studies in other breeds, suggesting management factors are more important than breed-specific differences when evaluating causes of IMI and associated subclinical mastitis

Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

SARS-CoV-2 infections were rising during early summer 2021 in many countries associated with the Delta variant. We assessed RT-PCR swab-positivity in the REal-time Assessment of Community Transmission-1 (REACT-1) study in England. We observed sustained exponential growth with average doubling time (June-July 2021) of 25 days driven by complete replacement of Alpha variant by Delta, and by high prevalence at younger less-vaccinated ages. Unvaccinated people were three times more likely than double-vaccinated people to test positive. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination

SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

Abstract Background Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape. Methods We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September–27 September 2021) and 15 (19 October–5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month. Results We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8–23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England. Conclusions As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals. </jats:sec