Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California

Salmonella spp. in Domestic Ruminants, Evaluation of Antimicrobial Resistance Based on the One Health Approach-A Systematic Review and Meta-Analysis

Salmonella spp. pose a global threat as a leading cause of foodborne illnesses, particularly prevalent in the European Union (EU), where it remains the second cause of foodborne outbreaks. The emergence of antimicrobial resistance (AMR) in Salmonella spp. has become a critical concern, complicating treatment strategies and escalating the risk of severe infections. The study focuses on large and small ruminants, identifying a prevalence of Salmonella spp. in slaughterhouses and revealing varied AMR rates across antimicrobial families throughout a meta-analysis. Also, comparison with AMR in human medicine was carried out by a systematic review. The results of the present meta-analysis displayed a prevalence of Salmonella spp. in large and small ruminants at slaughterhouses of 8.01% (8.31%, cattle; 7.04%, goats; 6.12%, sheep). According to the AMR of Salmonella spp., 20, 14, and 13 out of 62 antimicrobials studied were classified as low (<5%), high (>5% but <10%), and very high (>10%), respectively. Salmonella spp. did not display AMR against aztreonam, mezlocillin, ertapenem, meropenem, cefoxitin, ceftazidime, levofloxacin, tilmicosin, linezolid, fosfomycin, furazolidone, quinupristin, trimethoprim and spectinomycin. In contrast, a prevalence of 100% of AMR has been described against ofloxacin, lincomycin, and cloxacillin. In the context of the main antibiotics used in the treatment of human salmonellosis, azithromycin was shown to have the highest resistance among Salmonella spp. isolates from humans. Regarding cephalosporins, which are also used for the treatment of salmonellosis in humans, the prevalence of Salmonella spp. resistance to this class of antibiotics was similar in both human and animal samples. Concerning quinolones, despite a heightened resistance profile in Salmonella spp. isolates from ruminant samples, there appears to be no discernible compromise to the efficacy of salmonellosis treatment in humans since lower prevalences of AMR in Salmonella spp. isolated from human specimens were observed. Although the resistance of Salmonella spp. indicates some degree of concern, most antibiotics are not used in veterinary medicine. Thus, the contribution of cattle, sheep and goats to the rise of antibiotic resistance of Salmonella spp. and its potential impact on public health appears to be relatively insignificant, due to their low prevalence in carcasses and organs. Nevertheless, the observed low prevalence of Salmonella spp. in ruminants at slaughterhouse and the correspondingly low AMR rates of Salmonella spp. to key antibiotics employed in human medicine do not indicate that ruminant livestock poses a substantial public health risk concerning the transmission of AMR. Thus, the results observed in both the meta-analysis and systematic review suggests that AMR is not solely attributed to veterinary antibiotic use but is also influenced by factors such as animal health management (i.e., biosecurity measures, prophylactic schemes) and human medicine.

Frequency of isolation and phenotypic antimicrobial resistance of fecal Salmonella enterica recovered from dairy cattle in Canada

Salmonellosis is one of the leading causes of gastrointestinal infections in humans. In Canada, it is estimated that approximately 87,500 cases of salmonellosis occur every year in humans, resulting in 17 deaths. In the United States, it is estimated that 26,500 hospitalizations and 420 deaths occur every year. In dairy cattle, infections caused by nontyphoidal Salmonella enterica can cause mild to severe disease, including enteritis, pneumonia, and septicemia. Our study objectives were to determine the proportion of fecal samples positive for Salmonella in dairy cattle in Canada and determine the resistance pattern of these isolates. We used data collected through the Canadian Dairy Network for Antimicrobial Stewardship and Resistance (CaDNetASR). Pooled fecal samples from preweaning calves, postweaning heifers, lactating cows, and manure storage were cultured for Salmonella, and the isolates were identified using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Antimicrobial susceptibilities were determined using the minimum inhibitory concentration test, and resistance interpretation was made according to the Clinical and Laboratory Standards Institute. A 2-level, multivariable logistic regression model was built to determine the probability of recovering Salmonella from a sample, accounting for province, year, and sample source. The proportion of farms with at least one positive sample were 12% (17/140), 19% (28/144), and 17% (24/144) for the sampling years 2019, 2020, and 2021, respectively. Out of the 113 Salmonella isolates, 23 different serovars were identified. The occurrence of Salmonella appeared to be clustered by farms and provinces. The most common serovars identified were Infantis (14%) and Typhimurium (14%). Overall, 21% (24/113) of the Salmonella isolates were resistant to at least one antimicrobial. Resistance to tetracycline was commonly observed (17%); however, very limited resistance to category I antimicrobials (categorization according to Health Canada that includes third-generation cephalosporins, fluoroquinolones, polymyxins, and carbapenems) was observed, with one isolate resistant to amoxicillin and clavulanic acid. The proportion of Salmonella isolates resistant to 2 and 3 antimicrobial classes was 3.5% and 8.8%, respectively. Our study provided valuable information on the proportion of fecal samples positive for Salmonella, the serovars identified, and the associated resistance patterns across CaDNetASR herds, at regional and national levels.

Antimicrobial resistance profiles of Escherichia coli derived from an integrated agroforestry-livestock system in Deli Serdang Regency, Indonesia

Background and Aim

Antimicrobial resistance (AMR) has become a significant global concern. Epidemiological data do not provide a robust description of the potential risks associated with AMR in the integrated agroforestry-livestock systems in Indonesia. Thus, the present study investigated the phenotypic and multidrug resistance (MDR) profiles of Escherichia coli strains isolated from the feces of livestock raised in the agro-silvopastoral system in Deli Serdang Regency, North Sumatra Province.

Materials and Methods

A standard microbiological culture procedure was followed to isolate the organism and test antibiotic susceptibility using the Kirby-Bauer disk diffusion protocol. Furthermore, the multiple antibiotic resistance index was determined. Univariate analysis was conducted to identify the risk factors associated with AMR.

Results

The vast majority (77.5%) of livestock farmers were aged >30 years. All farmers were men and had no higher education (100% of them). The majority of the animal species managed were cattle and goats (37.5% each) and the livestock grazing pasture system (67.5%). In addition, the majority of farmers reported high antimicrobial use on their farms (87.5%). Of the samples (n = 142) analyzed, n = 70 were positive, with an overall prevalence of 44.4%. The species-specific prevalences of E. coli were 32.5%, 47.8%, and 50% in buffalo, goat, and cattle, respectively. Ampicillin and tetracyclines exhibited high resistance levels among the studied animal species. A relatively lower MDR for E. coli was associated with grazing on the pasture.

Conclusion

The findings from the current study provide baseline epidemiological information for future robust studies aimed at elucidating the drivers and patterns of AMR in agro-silvopastoral systems in the study area or elsewhere.

Prevalence and antimicrobial resistance of Salmonella and ESBL E. coli isolated from dairy cattle in Henan Province, China

Salmonella and ESBL-producing E. coli pose a threat to public health through the food chain. A cross-sectional study was conducted to determine the prevalence and antimicrobial resistance of Salmonella and ESBL E. coli in apparently healthy lactating dairy cattle in Henan Province. Thirty-five lactating cows per farm were sampled by fecal swabbing from 38 farms, with samples being pooled to a total of 7 pooled samples per herd. Eight of the 266 pooled fecal samples (3.0%) were positive for Salmonella (95% confidence intervals (CI): 1.3, 5.8) with a herd-level Salmonella prevalence of 13.2% (95% CI: 4.4, 28.1). The within-herd prevalence for pooled samples for Salmonella ranged from 0.0% to 28.6%. A high proportion of resistance to tetracycline (6/8) and florfenicol (6/8) was obtained in the cultured Salmonella. Multi-drug resistant isolates were observed on 4/5 Salmonella-positive farms. ESBL E. coli were identified on all farms (100% - 34/34, 95% CI: 89.7, 100). All ESBL E. coli isolates (n = 216) contained the bla_CTX-M gene and two isolates also contained the bla_TEM gene. Our study reports the prevalence and antimicrobial resistance of Salmonella and ESBL E. coli in apparently healthy lactating dairy cows from Henan Province.

Prevalence and antimicrobial resistance of Salmonella and the enumeration of ESBL E. coli in dairy farms in Hubei Province, China

Dairy cattle and their products have been linked to human outbreaks of Salmonella and Escherichia coli (E. coli). The objective of this study was to estimate the prevalence and antimicrobial resistance of Salmonella and to enumerate Extended-spectrum β-lactamase (ESBL)-producing E. coli in apparently healthy lactating dairy cows in Hubei Province, China. In a cross-sectional study, a total of 291 adult lactating dairy cows from 10 dairy farms were sampled for the detection of Salmonella and ESBL E. coli. Overall, Salmonella was cultured from 15 out of 291 sampled animals (5.2 %; 95 % confidence intervals (CI): 2.9, 8.4), all from two herds with a herd prevalence of 20.0 % (95 % CI: 2.5, 55.6) and the main serotype being S. Dublin. The within-herd prevalence ranged between 0.0 % and 33.3 %. ESBL E. coli was detected by culture in all farms with an animal level prevalence of 59.1 % (95 % CI: 53.2, 64.8) and 116 samples (39.9 %, 95 % CI: 34.2, 45.7) contained ESBL E. coli with a number exceeding 10⁴ CFU/g feces. Sixty percent (9/15) of Salmonella isolates were resistant to ampicillin, however all isolates were sensitive to the other 8 antimicrobials tested. Ninety percent (95 % CI: 84.6, 94.1) of ESBL E. coli contained the resistance gene bla_CTX-M, but no ESBL Salmonella was found. Our findings contribute to the understanding of the prevalence and antimicrobial resistance of Salmonella and the enumeration of ESBL E. coli and will assist in the decision-making for the control of Salmonella in Hubei Province.

First Report on Abortion Caused by Salmonella enterica subsp. enterica Serovar Enteritidis in Water Buffalo (Bubalus bubalis)

Salmonella enterica subsp. enterica Serovar Enteritidis is one of the major pathogens associated with enteric diseases in animals and humans. Thus, due to the importance of Salmonella spp. infections for animal production and public health, the aim of the present study was to describe the first detection of S. enteritidis in an aborted water buffalo fetus in southern Italy by characterizing the phylogroup profile and the antimicrobial susceptibility of the isolated pathogenic strains. The different clinical manifestations of salmonellosis in animals include diarrhea, abortion, pneumonia, septic arthritis, meningitis, and others, depending on the virulence of the serovars, infectious dose, and host immunity. This study reports the first case of abortion caused by Salmonella enterica subsp enterica serovar Enteritidis in water buffalo (Bubalus bubalis) in the Campania region, southern Italy. Complete necropsy was performed on the aborted water buffalo fetus under study, and samples and swabs from different organs were collected. Samples were processed by microbiological and molecular analyses to detect bacterial, viral, and protozoarian pathogens possibly responsible for abortion. Whole genome sequencing (WGS) was carried out to further characterize the isolated S. Enteritidis strain. Our findings highlight the crucial role of S. Enteritidis as a potential abortive agent in water buffalo and its presence should therefore be investigated in cases of bubaline abortion.

Observational study on antimicrobial resistance in Escherichia coli and Salmonella isolates from Ontario calf samples submitted to a diagnostic laboratory from 2007 to 2020

The objectives of this study were to i) describe Escherichia coli and Salmonella isolates; ii) investigate the temporal trends in antimicrobial resistance (AMR) profiles; and iii) evaluate the impact of season and age on these AMR profiles from diagnostic and post-mortem samples in Ontario calves ≤ 2-months-old submitted from 2007 to 2020 to the Animal Health Laboratory in Guelph, Ontario, Canada. Antimicrobial susceptibility testing results were measured by the Kirby-Bauer disk diffusion method. A total of 1291 isolates with AMR profiles were obtained from calves, with E. coli (n = 434) and Salmonella (n = 378) being the most common bacteria characterized for AMR. For E. coli, 79% of isolates tested showed a positive result in F5/K99, whereas for Salmonella isolates, S. Typhimurium (33%) and S. Dublin (22%) were the 2 most common serotypes identified. Multivariable logistic regression models were built to evaluate AMR profiles for E. coli (n = 414) and Salmonella (n = 357) to each antimicrobial tested. Most E. coli isolates (91%) and Salmonella isolates (97%) were resistant to at least one of the antimicrobials tested. In general, E. coli and Salmonella had higher odds of resistance in calves aged ≥ 2 wk compared to 1-week-old calves, and little difference was seen in the level of resistance over the years observed or between seasons in most of the antimicrobials tested. Prospective research should investigate potential risk factors for the development of AMR in calves examples being antimicrobial use and farm management practices.

Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing

Livestock represent a possible reservoir for facilitating the transmission of the zoonotic foodborne pathogen Salmonella enterica to humans; there is also concern that strains can acquire resistance to antimicrobials in the farm environment. Here, whole-genome sequencing (WGS) was used to characterize Salmonella strains (n = 128) isolated from healthy dairy cattle and their associated environments on 13 New York State farms to assess the diversity and microevolution of this important pathogen at the level of the individual herd. Additionally, the accuracy and concordance of multiple in silico tools are assessed, including: (i) two in silico serotyping tools, (ii) combinations of five antimicrobial resistance (AMR) determinant detection tools and one to five AMR determinant databases, and (iii) one antimicrobial minimum inhibitory concentration (MIC) prediction tool. For the isolates sequenced here, in silico serotyping methods outperformed traditional serotyping and resolved all un-typable and/or ambiguous serotype assignments. Serotypes assigned in silico showed greater congruency with the Salmonella whole-genome phylogeny than traditional serotype assignments, and in silico methods showed high concordance (99% agreement). In silico AMR determinant detection methods additionally showed a high degree of concordance, regardless of the pipeline or database used (≥98% agreement among susceptible/resistant assignments for all pipeline/database combinations). For AMR detection methods that relied exclusively on nucleotide BLAST, accuracy could be maximized by using a range of minimum nucleotide identity and coverage thresholds, with thresholds of 75% nucleotide identity and 50-60% coverage adequate for most pipeline/database combinations. In silico characterization of the microevolution and AMR dynamics of each of six serotype groups (S. Anatum, Cerro, Kentucky, Meleagridis, Newport, Typhimurium/Typhimurium variant Copenhagen) revealed that some lineages were strongly associated with individual farms, while others were distributed across multiple farms. Numerous AMR determinant acquisition and loss events were identified, including the recent acquisition of cephalosporin resistance-conferring bla CMY- and bla CTX-M-type beta-lactamases. The results presented here provide high-resolution insight into the temporal dynamics of AMR Salmonella at the scale of the individual farm and highlight both the strengths and limitations of WGS in tracking zoonotic pathogens and their associated AMR determinants at the livestock-human interface.

Dairy management practices associated with multi-drug resistant fecal commensals and Salmonella in cull cows: a machine learning approach

Background

Understanding the effects of herd management practices on the prevalence of multidrug-resistant pathogenic Salmonella and commensals Enterococcus spp. and Escherichia coli in dairy cattle is key in reducing antibacterial resistant infections in humans originating from food animals. Our objective was to explore the herd and cow level features associated with the multi-drug resistant, and resistance phenotypes shared between Salmonella, E. coli and Enterococcus spp. using machine learning algorithms.

Methods

Randomly collected fecal samples from cull dairy cows from six dairy farms in central California were tested for multi-drug resistance phenotypes of Salmonella, E. coli and Enterococcus spp. Using data on herd management practices collected from a questionnaire, we built three machine learning algorithms (decision tree classifier, random forest, and gradient boosting decision trees) to predict the cows shedding multidrug-resistant Salmonella and commensal bacteria.

Results

The decision tree classifier identified rolling herd average milk production as an important feature for predicting fecal shedding of multi-drug resistance in Salmonella or commensal bacteria. The number of culled animals, monthly culling frequency and percentage, herd size, and proportion of Holstein cows in the herd were found to be influential herd characteristics predicting fecal shedding of multidrug-resistant phenotypes based on random forest models for Salmonella and commensal bacteria. Gradient boosting models showed that higher culling frequency and monthly culling percentages were associated with fecal shedding of multidrug resistant Salmonella or commensal bacteria. In contrast, an overall increase in the number of culled animals on a culling day showed a negative trend with classifying a cow as shedding multidrug-resistant bacteria. Increasing rolling herd average milk production and spring season were positively associated with fecal shedding of multidrug- resistant Salmonella. Only six individual cows were detected sharing tetracycline resistance phenotypes between Salmonella and either of the commensal bacteria.

Discussion

Percent culled and culling rate reflect the increase in culling over time adjusting for herd size and were associated with shedding multidrug resistant bacteria. In contrast, number culled was negatively associated with shedding multidrug resistant bacteria which may reflect producer decisions to prioritize the culling of otherwise healthy but low-producing cows based on milk or beef prices (with respect to dairy beef), amongst other factors. Using a data-driven suite of machine learning algorithms we identified generalizable and distant associations between antimicrobial resistance in Salmonella and fecal commensal bacteria, that can help develop a producer-friendly and data-informed risk assessment tool to reduce shedding of multidrug-resistant bacteria in cull dairy cows.

Effect of Antimicrobial Treatment on the Dynamics of Ceftiofur Resistance in Enterobacteriaceae from Adult California Dairy Cows

Dairy farm use of antimicrobial drugs (AMD) is a risk for the selection of antimicrobial resistance (AMR); however, these resistance dynamics are not fully understood. A cohort study on two dairy farms enrolled 96 cows with their fecal samples collected three times weekly, for the first 60 days in milk. Enterobacteriaceae were enumerated by spiral plating samples onto MacConkey agar impregnated with 0, 1, 8, 16 and 30 µg/mL ceftiofur. Negative binomial regression analyzed AMR over time. The continuum of ceftiofur concentrations permitted estimation of the minimum inhibitory concentration (MIC) and analysis using interval regression. The most common systemic AMD was ceftiofur, administered in 94% of treatments (15/16 cows). Enterobacteriaceae did not grow in 88% of samples collected from non-AMD treated cows at 8 µg/mL ceftiofur. Samples from AMD treated cows had peak counts of resistant Enterobacteriaceae during AMD treatment and returned to baseline counts by 3-4 days post-treatment at 8 µg/mL. Sensitive Enterobacteriaceae (0-1 µg/mL ceftiofur) were reduced below pre-treated levels for 29-35 days post-AMD treatment. Population MIC peaked during AMD treatment and returned to baseline levels by 7-8 days. We conclude that the effect of systemic ceftiofur on the resistance of Enterobacteriaceae in early lactation dairy cows was limited in duration.

An Abattoir-Based Study on the Prevalence of Salmonella Fecal Carriage and ESBL Related Antimicrobial Resistance from Culled Adult Dairy Cows in Wuhan, China

The objective of this study was to estimate the fecal carriage of Salmonella spp. among culled adult dairy cows presented to an abattoir in Wuhan, China and to evaluate their antimicrobial resistance profiles. Rectal swabs from 138 culled cows were cultured. Laboratory analysis involved the identification of Salmonella, the susceptibility assessment and the presence of Extended Spectrum β-lactamases and mcr genes in the isolates. An overall prevalence of Salmonella of 29.0% was recorded with 63.4% (26/41) and 2.4% (1/41) of the isolates identified as S. Typhimurium and S. Dublin, respectively. The occurrence of Salmonella was higher (odd ratios: 3.3) in culled cows originating from the northeast zone of China than cows originating from the central and north zones. Twenty multi-drug resistant strains (resistant to three or more antimicrobial agents) were detected (48.8%) and overall, a high resistance to ampicillin (36/41) and tetracycline (15/41) was observed. Extended Spectrum β-lactamases phenotypes were found in 7/41 isolates, of which all contained the bla_CTX-M resistance gene, and no mcr genes were found by polymerase chain reaction. The high prevalence of Salmonella fecal carriage and antimicrobial resistance may contribute to an increased risk of Salmonella transmission to food.

Analysis of puerperal metritis treatment records in a grazing dairy farm in Argentina

OBJECTIVE

To assess the efficacy of antibiotic usage for the treatment of puerperal metritis (PM) and its association with reproductive performance, a retrospective cohort study including a total of 9168 records of cows from a dairy farm in Argentina was run.

MATERIAL AND METHODS

Cows having a PM3 (metricheck, scale 0-3) and treated with ceftiofur (ceftiofur crystalline free acid, 6.6 mg/kg) at 0-21 days postpartum (p. p.) (n = 2688), and cows having a PM 1-2 and not treated with an antibiotic at 0-21 days p. p. (n = 6480) were included in the study. All cows were reexamined with metricheck to assess the clinical cure (vaginal discharge [VD] score 0), partial cure (VD score similar or lower than previous), no cure (VD score higher than previous). Cows with a metricheck VD1-3 after 0-21 days p. p. were diagnosed as clinical endometritis (CE) 1-3. The occurrence of PM1-3, cure rate, calving to conception interval, the hazard of pregnancy, odds for non-pregnancy, and odds for CE were analyzed using SAS software.

RESULTS

A total of 8876 PM1-3 records were included, 2435 records of PM3 treatments with ceftiofur (27.43 %), and 6441 records of PM1-2 (72.57 %) with no treatment. Cows having PM1 and PM2 became pregnant 14 and 12 days earlier than cows with PM3 (p < 0.001). The PM3 ceftiofur treated cows had a clinical cure of 24.85 % (PM0); 53.63 % had a partially cure; and 18.52 % no cure. Conversely, cows with PM1-2 had a 51.96 %, 20.70 %, and 24.53 % cure rate, respectively (p < 0.001). Cows having complete cure became pregnant 13 and 11 days earlier than cows having partial cure and no cure (p < 0.001). Cows that had PM3 during the first 21 days p. p. had twice the chances of developing CE compared to cows having PM1-2 (41.28 % vs. 24.14 %, p < 0.001). After 21 days p. p., less than 1 % of cows with clinical cure developed CE compared to 63.32 % that developed CE with partial cure, and 38.21 % with no cure (p < 0.001).

CONCLUSION AND CLINICAL RELEVANCE

After ceftiofur treatment, 78 % of cows were cured when measured by disappearance of fetid VD but only 25 % of cows had clinical cure when measured by appearance of a clear VD. The cows that remained with clinical metritis had more chances of having CE after 21 days p. p. and had more days open than cows with clear normal VD.