Molecular characterization of Streptococcus uberis strains, isolated in a longitudinal study from milk of a commercial South African dairy herd.

Streptococcus uberis is a significant emerging mastitis pathogen with environmental and hostadaptive properties. Mastitis caused by Strep. uberis is increasing in South Africa, particularly in pasture-based herds irrigating with slurry. This field study aimed to identify strain types using MALDI-TOF and MLST and evaluate the Strep's behavioural patterns (host-adaptive versus environmental). uberis isolates over an extended period from a South African dairy herd with a high prevalence of Strep. uberis intramammary infection. The study involved 70 (63 retrospective and seven recent) samples, isolated from 53 cows, which were used for MLST sequencing of the seven housekeeping genes (gki, recP, ddl, tdk, arc, tpi, and yqiL). The study disclosed a herd prevalence of 7.44% Strep. uberis intramammary infection (IMI), responsible for 21.26% of clinical mastitis cases in this herd. Of the Strep. uberis positive clinical cases, 25% had repeat occurrences during the same lactation period. The consecutive repeat Strep. uberis cases were 34 (2x), 13 (3x), and 7 (4x). The study identified 41 novel Strep. uberis strain types from 64/70 isolates, attributable to novel alleles (29) or novel sequences of existing alleles of previously identified alleles. The study revealed that one existing Strep. uberis strain type (ST) 1613 (6/70) was to be identified and belonged to the clonal complex (CC) ST-86. All the other strain types of the isolates investigated in this study were novel. They were within the common CC (ST-5, ST-86, and ST-143) or not allocated (owing to the lack of data generated from whole genome sequencing). The longitudinal study 2021 (three-monthly milk samples) n=64/70 and 2024 (specific milk samples) n=7/70 from cows identified as high-interest cows, possibly showing as chronic cases on repeat collections (culture, MALDI-TOF, and Kirby Bauer). The finding was not entirely down to suspected hostadaptive strains of Strep. uberis but relatively novel strains creating new infections. The heterogeneity of the Strep. uberis isolates in this study agreed with other research identifying the environment as the primary source of strains. This study can aid farmers and veterinarians in managing Strep. uberis mastitis is more effective in the field by better classifying what is meant by repeat, non-cure, and new infections amid farming practices favouring higher pathogen loads (environment) and challenges for the cows. Contrary to what was expected, the study identified new infections with diverse Strep caused most suspected chronic intramammary infection (IMI). Uberis strains are dominated by novel environmental strains (high heterogeneity of ST and CC from all 70 isolates).