Antimicrobial Resistance Among Escherichia coli Isolated from Veal Calf Operations in Pennsylvania

Effects of Organic Soil Amendments on Antimicrobial-Resistant Bacteria in Urban Agriculture Environments

Biological soil amendments of animal origin (BSAAOs) are widely used in urban agriculture to improve soil quality. Although BSAAO use is regulated due to risks for introducing foodborne pathogens, effects on antimicrobial-resistant (AMR) bacteria are not well established. Here, we aimed to explore the impacts of BSAAOs on levels of resident AMR bacteria in leafy vegetable production environments (i.e., kale, lettuce, chard, cabbage) across urban farms and community gardens in the greater Washington D.C. area (n = 7 sites). Leaf tissue (LT), root zone soil (RZS; amended soil in crop beds), and bulk soil (BS; site perimeter) were collected and analyzed for concentrations of total heterotrophic bacteria (THB), ampicillin (Amp) or tetracycline (Tet) resistant THB, and coliforms. As expected, amended plots harbored significantly higher concentrations of THB than bulk soil (P < 0.001). The increases in total bacteria associated with reduced fractions of Tet-resistant bacteria (P = 0.008), as well as case-specific trends for reduced fractions of Amp-resistant bacteria and coliforms. Site-to-site variation in concentrations of AMR bacteria in soil and vegetable samples reflected differences in land history and crop management, while within-site variation was associated with specific amendment sources, as well as vegetable type and cultivar. Representative isolates of the AMR bacteria and coliforms were further screened for multidrug resistance (MDR) phenotypes, and a high frequency was observed for the former. In amended soils, as the soil pH (range 6.56-7.80) positively correlated with the fraction of Tet-resistant bacteria (rho = 0.529; P < 0.001), crop management strategies targeting pH may have applications to control related risks. Overall, our findings demonstrate that soil amendments promote soil bacteria concentrations and have important implications for limiting the spread of AMR bacteria, at least in the urban landscape.

The characterisation of antimicrobial resistant Escherichia coli from dairy calves

Introduction. Dairy calves, particularly pre-weaned calves have been identified as a common source of multidrug resistant (MDR) Escherichia coli.Gap statement. E. coli strains isolated from dairy calves and the location of their resistance genes (plasmid or chromosomal) have not been well characterised.Aim. To characterise the phenotypic and genotypic features as well as the population structure of antimicrobial-resistant E. coli isolated from calves located on dairy farms that feed waste-milk to their replacement calves.Methodology. Recto-anal swab enrichments from 40 dairy calves (≤ 14 days old) located on four dairy farms were examined for tetracycline, streptomycin, ciprofloxacin, and third-generation cephalosporin resistant E. coli. Whole genome sequencing was performed using both short- and long-read technologies on selected antimicrobial resistant E. coli.Results. Fifty-eight percent (23/40) of calves harboured antimicrobial resistant E. coli: 43 % (17/40) harboured tetracycline resistant, and 23 % (9/40) harboured chromosomal mediated AmpC producing E. coli. Whole genome sequencing of 27 isolates revealed five sequence types, with ST88 being the dominant ST (17/27, 63 % of the sequenced isolates) followed by ST1308 (3/27, 11 %), along with the extraintestinal pathogenic E. coli lineages ST69 (3/27, 11 %), ST10 (2/27, 7 %), and ST58 (2/27, 7 %). Additionally, 16 isolates were MDR, harbouring additional resistance genes that were not tested phenotypically. Oxford Nanopore long-read sequencing technologies enabled the location of multiple resistant gene cassettes in IncF plasmids to be determined.Conclusion. Our study identified a high incidence of tetracycline and streptomycin-resistant E. coli in dairy calves, and highlighted the presence of multidrug-resistant strains, emphasising the need for further investigation into potential associations with farm management practices.

Antimicrobial Use and Resistance in Surplus Dairy Calf Production Systems

Surplus calves, which consist predominately of male calves born on dairy farms, are an underrecognized source of antimicrobial-resistant (AMR) pathogens. Current production systems for surplus calves have important risk factors for the dissemination of pathogens, including the high degree of commingling during auction and transportation and sometimes inadequate care early in life. These circumstances contribute to an increased risk of respiratory and other infectious diseases, resulting in higher antimicrobial use (AMU) and the development of AMR. Several studies have shown that surplus calves harbor AMR genes and pathogens that are resistant to critically important antimicrobials. This is a potential concern as the resistant pathogens and genes can be shared between animal, human and environmental microbiomes. Although knowledge of AMU and AMR has grown substantially in dairy and beef cattle systems, comparable studies in surplus calves have been mostly neglected in North America. Therefore, the overall goal of this narrative review is to summarize the existing literature regarding AMU and AMR in surplus dairy calf production, highlight the management practices contributing to the increased AMU and the resulting AMR, and discuss potential strategies and barriers for improved antimicrobial stewardship in surplus calf production systems.

Prevalence and Sources of Salmonella Lymph Node Infection in Special-Fed Veal Calves

ABSTRACT

Peripheral lymph nodes (LNs) have been implicated as potential contaminants of ground beef, yet the source and timing of Salmonella LN infection in cattle is still unclear, limiting targeted intervention. The aim of this study was to leverage the vertical integration of special-fed veal production to identify preharvest environmental exposures, specifically in livestock trailers and harvest facility holding pens where calves spend 30 min to 4 h, that result in Salmonella LN infection. Ten cohorts of 80 to 82 veal calves were followed through the harvest process, and environmental samples were collected in barns, trailers, and holding pens. Mesenteric LNs from 35 calves were collected at harvest, and 25 prefemoral LNs per cohort were pooled. Within the same cohort, for 12 samples for which the serovar of the environmental and calf LN Salmonella isolates matched, the isolates were submitted for whole genome sequencing to determine whether environmental exposure resulted in LN infection. Cohort-level Salmonella mesenteric LN prevalence ranged from 0% (0 of 35 samples) to 80% (28 of 35 samples), and pooled prefemoral LNs were positive for Salmonella in 3 of the 10 cohorts. Salmonella prevalence in samples from barns, livestock trailers, and harvest facility holding pens was 22% (13 of 60 samples), 74% (59 of 80 samples), and 93% (74 of 80 samples), respectively. Some environmental and LN isolates were multidrug resistant. Four instances of Salmonella transmission from trailers and/or holding pens to calf LNs were supported by sequence data. Salmonella serovars Agona, Give, and Muenster were identified in transmission events. One instance of transmission from the livestock trailer, two instances from holding pens, and one instance from either trailer or holding pens were observed. Further research is needed to evaluate the extent of environmental Salmonella transmission in cattle and to determine whether targeted interventions in trailers or holding pens could reduce novel Salmonella LN infection in veal calves before harvest.

HIGHLIGHTS

Shiga Toxin-Producing Escherichia coli and Milk Fat Globules

Shiga toxin-producing Escherichia coli (STEC) are zoonotic Gram-negative bacteria. While raw milk cheese consumption is healthful, contamination with pathogens such as STEC can occur due to poor hygiene practices at the farm level. STEC infections cause mild to serious symptoms in humans. The raw milk cheese-making process concentrates certain milk macromolecules such as proteins and milk fat globules (MFGs), allowing the intrinsic beneficial and pathogenic microflora to continue to thrive. MFGs are surrounded by a biological membrane, the milk fat globule membrane (MFGM), which has a globally positive health effect, including inhibition of pathogen adhesion. In this review, we provide an update on the adhesion between STEC and raw MFGs and highlight the consequences of this interaction in terms of food safety, pathogen detection, and therapeutic development.

Effect of Farm Management Practices on Morbidity and Antibiotic Usage on Calf Rearing Farms

Antimicrobial resistance has been recognized as one of the top health threats to human society. Abundant use of antibiotics in both humans and animals has led to ever-increasing antibiotic resistance in bacteria. In food production, decreasing morbidity in beef herds would be an effective way to reduce the use of antibiotics. The objective of this retrospective observational study was to determine overall morbidity on calf rearing farms and to identify associated risk factors. Data were collected by questionnaire, meat companies’ databases and the national cattle register for 28,228 calves transported to 87 calf rearing farms. All medications given to these calves were retrospectively followed for 180 days from calf arrival to the farm. In total, 34,532 parenteral antibiotic medications were administered to the 28,228 study calves (122.3%), and 17,180 calves (60.9%) were medicated with antibiotics at least once during the follow-up. Higher numbers of calves transported to the same farm and larger age variation in calves in the same arrival batch were both associated with increased morbidity. In contrast, higher arrival age of individual calves was associated with decreased morbidity. Our study identifies several factors to consider in decreasing morbidity and antibiotic usage on calf rearing farms.

A National Antimicrobial Resistance Monitoring System Survey of Antimicrobial-Resistant Foodborne Bacteria Isolated from Retail Veal in the United States

ABSTRACT

Little is known about the prevalence of antimicrobial-resistant (AMR) bacteria in veal meat in the United States. We estimated the prevalence of bacterial contamination and AMR in various veal meats collected during the 2018 U.S. National Antimicrobial Resistance Monitoring System (NARMS) survey of retail outlets in nine states and compared the prevalence with the frequency of AMR bacteria from other cattle sources sampled for NARMS. In addition, we identified genes associated with resistance to medically important antimicrobials and gleaned other genetic details about the resistant organisms. The prevalence of Campylobacter, Salmonella, Escherichia coli, and Enterococcus in veal meats collected from grocery stores in nine states was 0% (0 of 358), 0.6% (2 of 358), 21.1% (49 of 232), and 53.5% (121 of 226), respectively, with ground veal posing the highest risk for contamination. Both Salmonella isolates were resistant to at least one antimicrobial agent as were 65.3% (32 of 49) of E. coli and 73.6% (89 of 121) of Enterococcus isolates. Individual drug and multiple drug resistance levels were significantly higher (P < 0.05) in E. coli and Enterococcus from retail veal than in dairy cattle ceca and retail ground beef samples from 2018 NARMS data. Whole genome sequencing was conducted on select E. coli and Salmonella from veal. Cephalosporin resistance (blaCMY and blaCTX-M), macrolide resistance (mph), and plasmid-mediated quinolone resistance (qnr) genes and gyrA mutations were found. We also identified heavy metal resistance genes ter, ars, mer, fieF, and gol and disinfectant resistance genes qac and emrE. An stx1a-containing E. coli was also found. Sequence types were highly varied among the nine E. coli isolates that were sequenced. Several plasmid types were identified in E. coli and Salmonella, with the majority (9 of 11) of isolates containing IncF. This study illustrates that veal meat is a carrier of AMR bacteria.

HIGHLIGHTS

Genome sequences of antibiotic-resistant Escherichia coli isolated from veal calves in the USA

OBJECTIVES

The aim of this study was to describe the genome sequences of 38 antibiotic-resistant Escherichia coli isolated from veal calves.

METHODS

The isolates were recovered in 2015 from nine veal farms in the eastern USA and were screened for antibiotic susceptibility using an automated microdilution procedure. The draft genomes were sequenced on an Illumina NextSeq 500 platform and were assembled using SPAdes.

RESULTS

In total, 294 resistance genes, categorised into 42 unique genes, conferring resistance to seven different antibiotic classes were detected. Extended-spectrum β-lactamase (ESBL) genes (bla_CTX-M and bla_CMY) and the azithromycin resistance gene mph(A) were detected in multiple genomes. Furthermore, mutations in gyrA, parC and parE conferring resistance to fluoroquinolones were detected, as were mutations in the ampC promoter responsible for hyperproduction of β-lactamases. We identified 25 unique sequence types (STs), including STs that are associated with extraintestinal infections.

CONCLUSION

The results of this study indicate a high level of diversity among multidrug-resistant E. coli isolates from veal operations. The identification of multiple isolates encoding resistance to β-lactams, macrolides and fluoroquinolones as well as virulence factors responsible for human infections warrants more study on the ecology of antibiotic resistance in veal operations.

Antimicrobial Activity of Sorghum Phenolic Extract on Bovine Foodborne and Mastitis-Causing Pathogens

Antimicrobial resistance in bacterial pathogens associated with bovine mastitis and human foodborne illnesses from contaminated food and water have an impact on animal and human health. Phenolic compounds have antimicrobial properties and some specialty sorghum grains are high in phenolic compounds, and the grain extract may have the potential as a natural antimicrobial alternative. The study’s objective was to determine antimicrobial effects of sorghum phenolic extract on bacterial pathogens that cause bovine mastitis and human foodborne illnesses. Bacterial pathogens tested included Escherichia coli, Salmonella Typhimurium, Campylobacter jejuni, Campylobacter coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Klebsiella oxytoca, Staphylococcus aureus, and Enterococcus faecalis. Antibacterial activities of sorghum phenolic extracts were determined by agar-well diffusion assay. Sorghum phenolic extract was added to the wells in concentrations of 0, 100, 200, 500, 1000, or 4000 µg/mL. The control wells did not receive phenolic extract. Plates were incubated for 18–24 h, and the diameter of each zone of inhibition was measured. The results indicated that sorghum phenolic extract had inhibitory effects on Staphylococcus aureus, Enterococcus faecalis, Campylobacter jejuni, and Campylobacter coli.

The effect of neomycin inclusion in milk replacer on the health, growth, and performance of male Holstein calves during preweaning

The prophylactic use of oral antimicrobials, such as neomycin, in milk replacer (MR) or whole milk is a common practice in calf-rearing that is thought to aid in preventing disease. Heavy reliance on antimicrobials is of concern not only because of the development of antimicrobial resistance, but also because of the potentially negative effects on health. The objective of this study was to investigate the effects of neomycin on calf health and growth performance. One hundred and sixty calves (approximately 3-10 d of age), distributed across 2 experimental periods, were stratified by body weight (BW) and serum total protein, and assigned to 1 of 3 treatments: control (CON; nonmedicated MR, n = 60), short-term antibiotic (ST; neomycin mixed in MR from d 1-14, n = 50), or long-term antibiotic (LT; neomycin in ​MR from d 1-28, n = 50). Arrival BW (47.69 ± 0.87 kg) and serum total protein (5.67 ± 0.09 g/dL) were not different between treatment groups. Neomycin in ST and LT was dosed in MR at a rate of 20 mg/kg of BW and was adjusted weekly according to BW. Calf BW was measured weekly for 49 d, and health indicators (fecal score, attitude score, respiratory score, and rectal temperature), MR intake, starter intake, and the use of additional electrolytes and antimicrobials were recorded daily. Calves in the CON group experienced a higher proportion of days with diarrhea (20.32 ± 0.02%) compared with ST (14.70 ± 0.02%) or LT (13.80 ± 0.02%) calves, as well as longer bouts of diarrhea (7.45 ± 0.38 d, 5.69 ± 0.46 d, and 5.62 ± 0.45 d for CON, ST, and LT calves, respectively). Calves in the CON group also experienced higher fecal scores (score of 0.64 ± 0.04) than ST (score of 0.53 ± 0.04) or LT (score of 0.49 ± 0.04) calves, especially at d 7. However, no differences were observed in other health-related measures. The time to reach first diarrhea and first respiratory illness was not different between treatments, nor was the time to recover from respiratory illness. The time to intervention with additional electrolytes or antimicrobials was not different between treatment groups. Furthermore, growth performance, feed intake, and feed conversion ratio were not different. No differences were found when comparing ST and LT, except in the defined daily dose of total antimicrobials received. Calves in the LT group received a higher overall dose than ST calves, and both ST and LT calves received a higher dose than CON calves, which received no prophylactic antimicrobials. Given that there were no differences in performance variables and no additional health benefits aside from reduced fecal scores in calves fed neomycin, current practices involving the use of antimicrobials on dairy and veal operations need to be considered more prudently.

Metagenomic Analysis of the Microbial Communities and Resistomes of Veal Calf Feces

Antimicrobial resistance (AMR) is a major public health concern, and dairy calves, including veal calves, are known reservoirs of resistant bacteria. To investigate AMR in the fecal microbial communities of veal calves, we conducted metagenomic sequencing of feces collected from individual animals on four commercial veal operations in Pennsylvania. Fecal samples from three randomly selected calves on each farm were collected soon after the calves were brought onto the farms (n = 12), and again, just before the calves from the same cohorts were ready for slaughter (n = 12). Results indicated that the most frequently identified phyla were Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Fecal microbial communities in samples collected from the calves at the early and late stages of production were significantly different at the genus level (analysis of similarities [ANOSIM] on Bray-Curtis distances, R = 0.37, p < 0.05), but not at the phylum level. Variances among microbial communities in the feces of the younger calves were significantly higher than those from the feces of calves at the late stage of production (betadisper F = 8.25, p < 0.05). Additionally, our analyses identified a diverse set of mobile antimicrobial resistance genes (ARGs) in the veal calf feces. The fecal resistomes mostly consisted of ARGs that confer resistance to aminoglycosides, tetracyclines, and macrolide-lincosamide-streptogramin B (MLS), and these ARGs represented more than 70% of the fecal resistomes. Factors that are responsible for selection and persistence of resistant bacteria in the veal calf gut need to be identified to implement novel control points and interrupt detrimental AMR occurrence and shedding.

Prevalence of class 1 integron in Escherichia coli isolated from animal sources in Iran: a systematic review and meta-analysis

Background

Among the genetic elements, integrons may contribute to the widespread incidence and spreading of antibiotic resistance among Escherichia coli isolates. Accordingly, this review aims to investigate the prevalence of class 1 integron in E. coli isolated from animal sources in Iran.

Methods

This systematic literature search was performed from January 1, 2000 to the end of May 1, 2019.

Then, publications that met our inclusion criteria were selected for data extraction and analysis. Also, the quality of included studies was independently assessed by two researchers based on the Joanna Briggs Institute. Meta-analysis was performed by the Comprehensive Meta-Analysis (CMA) software using the random effects model, Cochran’s Q, and I² tests. Publication bias was estimated by funnel plot and Egger’s linear regression test.

Results

Based on inclusion criteria, five studies were included to meta-analysis. From those studies, the pooled prevalence of integrons was 33% (95% CI, 23.8–43.7%) ranging from 23.8 to 52.4%. There was a significant heterogeneity among the 5 studies (χ² = 11.73; p < 0.019; I² = 65.91%). Additionally, Begg’s and Egger’s tests were performed to quantitatively evaluate the publication biases. According to the results of Begg’s test (z = 1.22, p = 0.22) and Egger’s test (t = 3.03, p = 0.056), a significant publication bias was not observed.

Conclusions

Our finding revealed the relatively high prevalence of class 1 integrons among E. coli isolates. Moreover, there was a significant heterogeneity among studies and subgroup analysis also showed that there was no difference about prevalence of class 1 integrons among different sample source.