Whole-genome sequencing-based antimicrobial resistance and shedding dynamics of Escherichia coli isolated from calves before and after antimicrobial group treatments.

The fattening of calves is often associated with high antimicrobial use and the selection of antimicrobial resistance (AMR). The objective of this observational longitudinal study was to describe the AMR and strain dynamics, using whole-genome sequencing (WGS), of fecal Escherichia coli in a cohort of 22 calves. All calves received antimicrobial group treatments on Day (D) 1 (oxytetracycline, intramuscularly) and on D4 through D12 (doxycycline, in-feed). Additionally, eight calves received individual parenteral treatments between D7 and D59, including florfenicol, amoxicillin, marbofloxacin, and gamithromycin. Rectal swabs were collected from all calves on D1 (prior to treatment), D2, D9, and D82. The swabs were spread onto Enterobacterales-selective agar, and three E. coli colonies per plate were subjected to WGS. Out of 264 isolates across all calves and sampling times, 80 unique strains were identified, a majority of which harbored genes conferring resistance to tetracyclines, streptomycin, and sulfonamides. The diversity of strains decreased during the in-feed antimicrobial group treatment of the calves. On D82, 90% of isolates were strains that were not isolated at previous sampling times, and the median number per strain of AMR determinants to tetracyclines, florfenicol, ß-lactams, quinolones, or macrolides decreased compared to D9. Additionally, clonal dissemination of some strains represented the main transmission route of AMR determinants. In this study, WGS revealed important variations in strain diversity and genotypic AMR of fecal E. coli over time in calves subjected to group antimicrobial treatments. IMPORTANCE: The continued emergence and spread of antimicrobial resistance (AMR) determinants are serious global concerns. The dynamics of AMR spread and persistence in bacterial and animal host populations are complex and not solely driven by antimicrobial selection pressure. In calf fattening, both antimicrobial use and carriage prevalence of antimicrobial-resistant bacteria are generally recognized as high. This study provides new insights into the short-term, within-farm dynamics and transmission of AMR determinants in Escherichia coli from the dominant fecal flora of calves subjected to antimicrobial group treatments during the rearing period. The diversity of E. coli strains decreased over time, although, in contrast to previous observations in extended-spectrum ß-lactamase-producing Enterobacterales, the predominance of a few clones was not observed. The spread of AMR determinants occurred through the dissemination of clonal strains among calves. The median number per strain of AMR determinants conferring resistance to selected antimicrobials decreased toward the end of the rearing period.

Swiss Dairy Farmers' Perceptions Surrounding the Disposal of Waste Milk Containing Antibiotic Residues and Antibiotic Resistance.

The feeding of waste milk containing antibiotic residues (WMA) to calves has been associated with the shedding of antibiotic-resistant bacteria by calves. However, little is known regarding farmers' intrinsic factors affecting this practice, and on which it would be relevant to intervene in order to change this practice. The objectives of this study were (1) to describe the farmers' intrinsic factors, such as perceived benefits, risks, and social norms related to the feeding of WMA to calves, antibiotic resistance, and antibiotic use, and (2) to evaluate how the feeding of WMA to calves is related to farmers' personal values and perceptions related to WMA feeding and antibiotic resistance. Answers to an online survey were collected from 233 Swiss dairy producers (38.3% response rate). The proportion of respondents who fed WMA to calves was 48.3%. In a hierarchical logistic regression model, only perception factors extracted by factor analysis were associated with the feeding of WMA to calves, namely (in decreasing order of magnitude): farm-level benefits of WMA feeding, the interaction of farm-level benefits with support from governmental authorities, and causes and threats of antibiotic resistance. The results suggest that, in order to reduce the feeding of WMA to calves, communications to dairy producers should focus on changing the perceived benefits of this practice in comparison to those of alternative WMA disposal methods carrying a lower risk of antibiotic resistance. The involvement of veterinarians and governmental authorities in these communications and in supporting producers may increase the successful adoption of alternative WMA disposal methods.

Association between species-specific staphylococcal intramammary infections and milk somatic cell score over time in dairy goats.

Numerous factors affect milk somatic cell score (SCS) in dairy goats including physiologic factors such as stage of lactation, and pathological factors such as bacterial intramammary infection (IMI), e.g. staphylococcal IMI. The association between IMI and udder inflammation and especially differences in the inflammatory response between the different staphylococcal species are yet to be identified. The objectives of this study were to use data from a recently published longitudinal study that characterized IMI status over time to evaluate the species-specific effect of staphylococcal IMI on udder half-level milk SCS, and to evaluate the effect of time since IMI diagnosis on this relationship. Half-level milk samples for culture and determination of SCS were collected from 171 goats starting within 10 days in milk (DIM), and then at various intervals until ≥ 120 DIM. A mixed linear model was used to assess the effect of species-specific staphylococcal IMI on SCS, accounting for confounding by lentivirus infection, parity, DIM, and the contralateral half IMI status, and for repeated measurements within udder half and for clustering of halves within goat. A second model was used to evaluate the effect of time since first IMI diagnosis and its interaction with staphylococcal IMI status on the relationship between staphylococcal IMI status and SCS. Lentivirus seropositivity and contralateral half IMI status were associated with SCS. Staphylococcal IMI status was associated with SCS, with differences between species. Staphyloccocus caprae, Staphylococcus epidermidis, Staphylococcus simulans, and Staphylococcus xylosus were associated with higher SCS than a number of other species. Time since first diagnosis did not modify the relationship between IMI status and SCS.

Persistence of coagulase negative staphylococcal intramammary infections in dairy goats.

The objectives of the research described here were to describe the persistence of intramammary infections (IMI) caused by coagulase negative staphylococci (CNS) in goats using strain-typing, and to evaluate the relationship between species-specific CNS IMI and somatic cell score (SCS) at the udder-half level. Udder-half milk samples were collected from all 909 lactating goats (1817 halves; 1 blind half) in a single herd. Milk samples were cultured on Columbia blood agar, and 220 goats with at least one half yielding a single colony type CNS were enrolled for two additional half-level samplings at approximately 1-month intervals. Isolates were identified to the species level by matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry or PCR amplification and partial sequencing of tuf or rpoB. An IMI was defined as persistent when ≥1 follow-up sample yielded the same species and strain as on Day 0 based on pulsed-field gel electrophoresis. A generalised mixed linear model was used to evaluate the odds of persistence as a function of CNS species. A mixed linear model was used to evaluate the relationship between IMI status on a given day and SCS. Among 192 IMI, 69.8% were persistent based on species and strain-type. Staphylococcus simulans IMI had higher odds of persistence than Staphylococcus arlettae IMI. In primiparous goats, Staphylococcus epidermidis IMI was associated with higher SCS than S. arlettae, Staphylococcus xylosus and 'other CNS' IMI. The differences detected in the present study between CNS species, with regard to persistence of IMI and association with SCS, highlight the need to study CNS at the species and strain level to understand the pathogenicity and epidemiology of CNS in goats.

Longitudinal microbiological evaluation of subclinical non-aureus staphylococcal intramammary infections in a lentivirus-infected dairy goat herd.

The objectives of this study were to 1) correlate pre-partum teat skin colonization with non-aureus staphylococcal (NAS) intramammary infection (IMI) in early lactation, and 2) evaluate infection dynamics of subclinical NAS IMI in goats during lactation in a small ruminant lentivirus-infected herd. Pre-partum teat skin swabs (41 goats, 82 halves) and post-partum half-level milk samples (106 goats, 203 halves) were collected at various intervals starting at ≤10 days in milk (DIM) until ≥120 DIM. Teat skin colonization and IMI were defined by culture and strain-typing. The association between the pre-kidding udder-half teat skin sample status and early lactation IMI status for a given species was investigated using McNemar's exact test or logistic regression. Time to IMI elimination and time to new IMI were evaluated by discrete-time survival analysis. Halves with S. caprae isolated from teat skin prior to kidding had increased odds of S. caprae IMI ≤ 10 DIM. Time to IMI elimination varied as a function of NAS species. Intramammary infections detected >10 DIM had a higher hazard of elimination (hazard ratio [HR] 5.6, 95% CI 2.8-11.2) than IMI detected ≤10 DIM. The presence of an IMI in the contralateral half was associated with a higher hazard of new IMI (HR 2.1, 95% CI 1.3-3.4) in an uninfected half. Further studies on interventional strategies targeting early IMI and IMI caused by persistent species are warranted.

Staphylococcal intramammary infection dynamics and the relationship with milk quality parameters in dairy goats over the dry period.

The objectives of this study were (1) to report the rates of new intramammary infection (IMI) and spontaneous IMI cure over the dry period in 3 dairy goat herds; (2) to evaluate the factors predicting infection dynamics over the dry period; and (3) to define milk quality parameter thresholds that predict infection dynamics over the dry period. Two consecutive udder-half milk samples were collected 10 to 14 d apart before dry-off from 288 goats in 3 herds, and 2 consecutive udder-half samples were collected 7 to 14 d apart in the following lactation, with the first sample being collected ≤10 d in milk, from 200 of the same goats. In 2 of the herds, udder-half milk samples were also collected at the same time points (n = 312 halves; 157 goats) for measurement of milk quality parameters. Standard aerobic culture of milk samples was performed for the detection of mastitis pathogens. To rule out the presence of Mycoplasma spp. IMI, milk samples were also cultured on modified Hayflick medium. Non-Mycoplasma isolates were speciated using MALDI-TOF mass spectrometry. Staphylococcal isolates, when not identified by MALDI-TOF, were speciated using partial gene sequence analysis of rpoB or tuf. When >1 sample from an udder half yielded the same species, available isolates from the first and last positive samples for that species were strain-typed using pulsed-field gel electrophoresis. Incidence of new IMI and cure rate were computed. Generalized linear mixed regression models were built to evaluate the associations between new IMI and pre-dry somatic cell score (SCS), between IMI persistence and half-level SCS, and between IMI persistence and pre-dry IMI species. Thresholds for pre-dry SCS and lactose concentration were computed to predict IMI persistence. Overall, 12.6% (48/380) of halves had a persistent IMI. Cumulative incidence of new IMI over the dry period was 13.2%, and cure rate was 52.0%. Pre-dry SCS was not associated with odds of new IMI or IMI persistence. Pre-dry IMI species was not associated with odds of persistence. Lactose concentration was not associated with odds of persistence. Regardless of culture data, the optimal pre-dry SCS threshold to detect IMI that would persist into the next lactation was 8.7, with sensitivity and specificity of 50 and 73.8%, respectively. Further studies on the effect of control measures on species-specific incidence and cure rates during the dry period are warranted.

Use of ultrasonographic fetometry for the estimation of days to kidding in dairy does.

The objective of this study was to predict the number of days to kidding in dairy goats by ultrasonographic measurement of three consecutive ribs and intercostal spaces or trunk diameter of fetuses. Two groups of primiparous and multiparous goats were examined by transabdominal ultrasonography. Actual kidding date was used to compute the true number of days to kidding relative to the ultrasound examination day. Linear regression models were built to predict days to kidding based on fetal measurements, parity, and number of kids. The model using the width of three consecutive ribs and intercostal spaces (n = 29 goats) showed a curvilinear relationship between days to kidding and rib distance (R2 = 0.60; P < 0.01). The trunk diameter model (n = 135 goats) showed a curvilinear relationship between days to kidding and trunk diameter with an effect of parity (R2 = 0.81; P < 0.01).

Immune complex glomerulonephritis of suspected iatrogenic origin in five Japanese Black calves.

Five Japanese Black embryo transfer calves from a single embryo flush, 30 to 45-days-old, including 4 live animals for clinical examination and 1 dead for necropsy, were presented with a history of decreased milk intake and hypoproteinemia. Consistent clinicopathological abnormalities in the 4 calves presented for clinical evaluation included hyperkalemia, hyperphosphatemia, hypoproteinemia, hypoalbuminemia, hyperbilirubinemia, increased creatine phosphokinase activity, and proteinuria. Four calves ultimately were necropsied and all had histologic evidence of immune complex glomerulonephritis. Glomerulonephritis in these calves was hypothesized to have resulted from the interaction of passively acquired antibodies at birth and active immunization at 7 and 28 days of age with a Salmonella Typhimurium core antigen vaccine.

A retrospective study of 29 cases of otitis media/interna in dairy calves.

Epidemiological data, clinical findings, laboratory data, medical imaging, and outcomes were reviewed in 29 dairy calves with otitis media/interna. Age at admission ranged from 1 to 24 wk. The majority of calves were referred during winter. Clinical signs included drooping ear, ptosis, head tilt, abnormal nystagmus, strabismus, dysphagia, regurgitation, stiff neck, opisthotonos, facial hyperesthesia, and purulent aural discharge. Intranasal endoscopic examination of 5 animals revealed nasopharyngeal collapse in 4. Cerebrospinal fluid (CSF) was abnormal in all of 7 cases. Mycoplasma bovis was cultured from all but 1 case with external ear or tympanic bullae samples (n = 12), and Mycoplasma arginini was cultured from the remaining ear sample. Radiographs of the tympanic bullae were performed in 24 calves, tomodensitometry (CT) in 3 calves and ultrasound in 4 calves. According to medical imaging techniques or necropsy, 69% of the cases were classified as chronic. Mean duration of treatment was 23.3 d. The rate of clinical recovery was 75%.Epidemiological data, clinical findings, laboratory data, medical imaging, and outcomes were reviewed in 29 dairy calves with otitis media/interna. Age at admission ranged from 1 to 24 wk. The majority of calves were referred during winter. Clinical signs included drooping ear, ptosis, head tilt, abnormal nystagmus, strabismus, dysphagia, regurgitation, stiff neck, opisthotonos, facial hyperesthesia, and purulent aural discharge. Intranasal endoscopic examination of 5 animals revealed nasopharyngeal collapse in 4. Cerebrospinal fluid (CSF) was abnormal in all of 7 cases. Mycoplasma bovis was cultured from all but 1 case with external ear or tympanic bullae samples (n = 12), and Mycoplasma arginini was cultured from the remaining ear sample. Radiographs of the tympanic bullae were performed in 24 calves, tomodensitometry (CT) in 3 calves and ultrasound in 4 calves. According to medical imaging techniques or necropsy, 69% of the cases were classified as chronic. Mean duration of treatment was 23.3 d. The rate of clinical recovery was 75%.

RésuméÉtude rétrospective de 29 cas d'otite moyenne/interne chez les veaux laitiers. Les données épidémiologiques, les signes cliniques, les résultats de laboratoire et d'imagerie médicale et l'évolution de 29 veaux atteints d'otite moyenne/interne sont présentés. L'âge à la présentation variait de 1 à 24 semaines. La majorité des veaux ont été admis en hiver. Les signes cliniques incluaient une oreille tombante, une ptose de la paupière, une tête penchée, un nystagmus pathologique, un strabisme, de la dysphagie, des régurgitations, une raideur cervicale, de l'opisthotonos, de l'hyperesthésie faciale et une écoulements purulente de l'oreille. L'endoscopie des voies respiratoires supérieures a révélé un collapse du nasopharynx dans 4 cas sur 5. L'analyse du liquide céphalo-rachidien était anormale chez 7 veaux. Mycoplasma bovis a été isolé de tous les cas à partir d'échantillons d'oreille externe ou de bulle tympanique sauf 1 (n = 12) où Mycoplasma arginini a été isolé. La radiographie des bulles tympaniques a été réalisée sur 24 cas, la tomodensitométrie sur 3 cas et l'échographie sur 4 cas. Selon les techniques d'imagerie médicale ou la nécropsie, 69 % des cas étaient chroniques. La durée moyenne du traitement était de 23,3 jours. Le pronostic était de 75 %.(Traduit par les auteurs).