Changes in tetracycline susceptibility of enteric bacteria following switching to nonmedicated milk replacer for dairy calves

Invited Review: Antimicrobial Use and Antimicrobial Resistance in Pathogens Associated with Diarrhea and Pneumonia in Dairy Calves

Antimicrobial use (AMU) is the major driver of antimicrobial resistance (AMR) among bacteria in dairy herds. There have been numerous studies on AMU and AMR in dairy cows; however, studies on AMU and AMR in dairy calves are limited. A comprehensive overview of the current state of knowledge of AMU and AMR among pathogens in dairy calves is important for the development of scientifically supported and applicable measures to curb antimicrobial use and the increasing risk of AMR. Therefore, we performed a systematic review of research on AMU and AMR in dairy calves. A total of 75 publications were included, of which 19 studies reported AMU data for dairy calves and 68 described AMR profiles of the four most prevalent bacteria that are associated with calf diarrhea and calf pneumonia. Large variation in AMU was found among herds across different regions. There seems to be a positive association between exposure to antimicrobials and occurrence of resistance. Most AMU was accounted for by treatment of diseases, while a small proportion of AMU was prophylactic. AMU was more common in treating calf diarrhea than in treating pneumonia, and the resistance rates in bacteria associated with diarrhea were higher than those in pathogens related to pneumonia. Organic farms used significantly fewer antimicrobials to treat calf disease; however, the antimicrobial resistance rates of bacteria associated with calf diarrhea and pneumonia on both types of farms were comparable. Feeding waste or pasteurized milk was associated with a higher risk of AMR in pathogens. Altogether, this review summarizes AMU and AMR data for dairy calves and suggests areas for future research, providing evidence for the design of antimicrobial use stewardship programs in dairy calf farming.

Antimicrobial Resistance of Escherichia coli in Dairy Calves: A 15-Year Retrospective Analysis and Comparison of Treated and Untreated Animals

Simple Summary

In dairy production, antimicrobial resistance (AMR) is both a health and economic issue that may lead to treatment failures and the spread of multidrug-resistant pathogens. Epidemiological and farm data on AMR are instrumental for selecting the appropriate therapy. However, such data are not always available. We investigated the AMR profile of 2612 Escherichia coli strains isolated from cases of calf diarrhea over a 15-year period (2002–2016). Furthermore, the AMR profiles and major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves were examined, with a comparison made between those treated with antimicrobials (n = 406) and not treated (n = 99) as well as between the two age groups to evaluate the potential effects of treatments on AMR and pathogenicity. Resistance to tetracycline was the most common, followed by resistance to sulfamethoxazole/trimethoprim and flumequine. Treated calves showed a higher rate of AMR and virulence genes. These results highlight the risk of the frequent use of antimicrobials on calf microflora in leading to potentially ineffective treatments. A higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol was found in 1-week-old calves, suggesting the environment as a possible AMR source. In conclusion, measures such as improved hygiene in the calving pen, antimicrobial stewardship, and monitoring for resistant pathogens in manure should be promoted to prevent the spread of AMR.

Abstract

The health problem of antimicrobial resistance (AMR) involves several species. AMR surveillance is essential to identify its development and design control strategies; however, available data are still limited in some contexts. The AMR profiles of 2612 E. coli strains isolated over a period of 15 years (2002–2016) from calf enteric cases were analyzed to determine the presence of resistance and their temporal dynamics. Furthermore, the AMR profiles and the presence of the major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves, 406 treated with antimicrobials and 99 untreated, were analyzed and compared to investigate the potential effects of treatment on AMR and strain pathogenicity. Resistance to tetracycline (90.70%) was the most common, followed by resistance to sulfamethoxazole/trimethoprim (77.70%) and flumequine (72.10%). The significantly higher percentage of AMR and virulence gene expression recorded in treated calves, combined with the statistically higher resistance to sulfamethoxazole/trimethoprim in E. coli with K99, corroborates the notion of resistance being induced by the frequent use of antimicrobials, leading to treatments potentially becoming ineffective. The significantly higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol in isolates from 1-week-old calves suggests the role of the environment as a source of contamination that should be investigated further.

Differences in the Microbial Community and Resistome Structures of Feces from Preweaned Calves and Lactating Dairy Cows in Commercial Dairy Herds

Preweaned dairy calves and lactating dairy cows are known reservoirs of antibiotic-resistant bacteria. To further understand the differences in the resistomes and microbial communities between the two, we sequenced the metagenomes of fecal composite samples from preweaned dairy calves and lactating dairy cows on 17 commercial dairy farms (n = 34 samples). Results indicated significant differences in the structures of the microbial communities (analysis of similarities [ANOSIM] R = 0.81, p = 0.001) and resistomes (ANOSIM R = 0.93 to 0.96, p = 0.001) between the two age groups. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the predominant members of the communities, but when the groups were compared, Bacteroidetes and Verrumicrobia were significantly more abundant in calf fecal composite samples, whereas Firmicutes, Spirochaetes, Deinococcus-Thermus, Lentisphaerae, Planctomycetes, Chlorofexi, and Saccharibacteria-(TM7) were more abundant in lactating cow samples. Diverse suites of antibiotic resistance genes (ARGs) were identified in all samples, with the most frequently detected being assigned to tetracycline and aminoglycoside resistance. When the two groups were compared, ARGs were significantly more abundant in composite fecal samples from calves than those from lactating cows (calf median ARG abundance = 1.8 × 10⁰ ARG/16S ribosomal RNA [rRNA], cow median ARG abundance = 1.7 × 10^-1 ARG/16S rRNA) and at the antibiotic resistance class level, the relative abundance of tetracycline, trimethoprim, aminoglycoside, macrolide-lincosamide-streptogramin B, β-lactam, and phenicol resistance genes was significantly higher in calf samples than in cow samples. Results of this study indicate that composite feces from preweaned calves harbor different bacterial communities and resistomes than composite feces from lactating cows, with a greater abundance of resistance genes detected in preweaned calf feces.

Influence of early use of antimicrobial on the health and performance of Holstein calves in the first month of life

ABSTRACT: The early use of antimicrobial therapy has been introduced in many farms to prevent diarrhea and respiratory disease in young calves; however, there is controversy about whether this practice has a beneficial effect on the health of these animals. This study evaluated the influence of the early use of antimicrobials on the health and performance of neonatal Holstein calves. Twenty-six Holstein calves were screened and divided into two groups, according to the administration (ATB+), or not (ATB-) of tulathromycin (2.5mg/kg, subcutaneously) within the first 12 hours of life. Calves were evaluated by general clinical examination, fecal score, respiratory score, and external palpation of the umbilical region, besides fecal output of dry matter. Anemia was determined by using an automatic system and, also, using a commercial kit for iron dosage. Diarrhea was diagnosed by a centrifuge-flotation technique using a sugar solution (Cryptosporidium) and multiplex semi-nested RT-PCR (rotavirus/coronavirus). The performance of the calves was estimated by Daily Weight Gain (DWG). The young dairy calves were evaluated within 12 hours of birth (≤12h) and at 3-5th (D3-5), 7-9th (D7-9), 13-15th (D13-15), 20-23rd (D20-23), and 27-30th (D27-30) days of life. No difference was noted between the ATB+ and ATB- groups concerning heart rate, respiratory frequency, and rectal temperature. Erythrogram showed a higher frequency of anemia in ATB- group (P=0.016) at the D3-5 check-up; lower values of serum iron were also observed simultaneously (P=0.051). Thirteen cases of respiratory disease were detected during this study; however, no significant difference was observed between the groups in this regard. The frequency of diarrhea (fecal score 2-3) was high in both groups, peaking at D13-D15. No differences were noted between the groups regarding the frequency of diarrhea when considering the dry fecal matter. The predominant etiological agent for diarrhea was Cryptosporidium spp.. The DWG was similar between groups, with maximum weight reduction on D13-15. The administration of tulathromycin in prophylactic dose (2.5mg/kg) at birth decreased the frequency of anemia but did not influence weight gain or the prevalence of diarrhea.

Antimicrobial Resistance in Fecal Escherichia coli and Salmonella enterica from Dairy Calves: A Systematic Review

The discovery of antibiotics brought with it many advances in the health and well-being of humans and animals; however, in recent years development of antimicrobial resistance (AMR) has increasingly become a concern. Much of the antibiotic use on dairy farms is for disease management in mature cattle, and AMR in fecal organisms is relatively rare in this group. However, young dairy calves often carry high levels of AMR in their fecal Escherichia coli and Salmonella enterica, which could provide a potential reservoir of AMR genes on dairy farms. To develop practical and effective antibiotic stewardship policies for dairy calf rearing, it is vital to have a solid understanding of the current state of knowledge regarding AMR in these animals. A systematic review process was used to summarize the current scientific literature regarding AMR in fecal S. enterica and E. coli and associations between management practices and AMR prevalence in dairy calves in the United States and Canada. Seven online databases were searched for literature published from 1997 to 2018. Multiple studies indicated an association between preweaned calves and increased risk of fecal shedding of resistant bacteria, compared to other animal groups on dairy farms. There also was evidence, although less consistent, of an impact of antibiotic treatment, antibiotic-containing milk replacer feeding, and feeding nonsalable or waste milk (WM) on the presence of AMR bacteria. Overall, the research summarized in this systematic review highlights the need for continued research on the impact of management practices, including antibiotic use, WM feeding, and disease prevention practices in reducing AMR in E. coli and S. enterica in dairy calves. In addition, few data were available on physiological and microbiological factors that may contribute to the high relative populations of resistant bacteria in young calves, suggesting another valuable area of future research.

Effects of feeding pasteurized waste milk to dairy calves on phenotypes and genotypes of antimicrobial resistance in fecal Escherichia coli isolates before and after weaning

The aim of this study was to evaluate the effects of feeding pasteurized waste milk (pWM) to calves on antimicrobial resistance of fecal Escherichia coli at both phenotypic and genotypic levels. Fifty-two Holstein female calves (3 ± 1.3 d of age) were fed 1 of the 2 different types of milk: milk replacer (MR) without antimicrobials or pWM with β-lactam residues until weaning at 49 d of age. Fecal swabs of all calves were obtained on d 0, 35, and 56 of the study and 3 E. coli isolates per sample were studied. Phenotypic resistance was tested by the disk diffusion method against a panel of 12 antimicrobials. A total of 13 resistance genes consisting of β-lactam, sulfonamide, tetracycline, and aminoglycoside families were examined by PCR. Feeding pWM to calves increased the presence of phenotypic resistance to ampicillin, cephalotin, ceftiofur, and florfenicol in fecal E. coli compared with MR-fed calves. However, the presence of resistance to sulfonamides, tetracyclines, and aminoglycosides was common in dairy calves independent of their milk-feeding source, suggesting other factors apart from the feeding source are involved in the emergence of antimicrobial resistance.

Acquisition and persistence of antimicrobial-resistant bacteria isolated from dogs and cats admitted to a veterinary teaching hospital

OBJECTIVE

To assess antimicrobial resistance among bacteria isolated from dogs and cats admitted to a veterinary teaching hospital (VTH), determine the incidence of acquisition of and frequency of persistent colonization by antimicrobial-resistant organisms among these animals, and identify risk factors associated with these variables.

DESIGN

Prospective longitudinal study.

ANIMALS

622 dogs and 92 cats admitted to a VTH and expected to stay ≥ 48 hours.

PROCEDURES

Samples were collected with rectal and nasal or oropharyngeal swabs at admission and discharge. Isolates of enterococci, staphylococci, and Escherichia coli were tested for antimicrobial resistance via microbroth dilution methods. A subset of isolates was analyzed with pulsed-field gel electrophoresis and multilocus sequence typing. Significant trends in proportions of organisms with antimicrobial resistance over the 3-year study period were assessed.

RESULTS

The proportion of staphylococci with antimicrobial resistance increased, whereas the proportion of E coli with resistance decreased, over time; resistance among enterococci was more variable. For 506 dogs with paired admission and discharge samples, multidrug-resistant (MDR) E coli was acquired by 40 (8%) and methicillin-resistant Staphylococcus aureus (MRSA) was acquired by 7 (1.4%); hospitalization for > 3 days was significantly associated with both variables. Most (5/7 isolates) acquired MRSA was of sequence type (ST) 5.

CONCLUSIONS AND CLINICAL RELEVANCE

Extended hospitalization was associated with increased risk of acquiring MDR E coli or MRSA, although few animals acquired MRSA. It is unclear whether associations were confounded by illness severity or use of infection control measures. Additionally, MRSA of ST5, which has been associated with small animal medicine, was the most commonly acquired MRSA in this study.

Hypovitaminosis A coupled to secondary bacterial infection in beef cattle

Background

Vitamin A is essential for normal growth, development, reproduction, cell proliferation, cell differentiation, immune function and vision. Hypovitaminosis A can lead to a series of pathological damage in animals. This report describes the case of hypovitaminosis A associated with secondary complications in calves.

Case presentation

From February to March in 2011, 2-and 3-month old beef calves presented with decreased eyesight, apparent blindness and persistent diarrhea occurred in a cattle farm of Hubei province, China. Based on history inspection and clinical observation, we made a tentative diagnosis of hypovitaminosis A. The disease was confirmed as a congenital vitamin A deficiency by determination of the concentrations of vitamin A in serum and feed samples. Furthermore, pathological and microbiological examination showed that the disease was associated with pathogenic Escherichia coli (E. coli) infection and mucosal barriers damage in intestines. The corresponding treatments were taken immediately, and the disease was finally under control for a month.

Conclusions

To our knowledge, this is the first report of hypovitaminosis A coupled to secondary infection of E. coli in beef cattle, advancing our knowledge of how vitamin A affects infection and immunity in animals. This study could also be contributed to scientific diagnosis and treatments of complex hypovitaminosis A in cattle.

Scientific Opinion on the welfare of cattle kept for beef production and the welfare in intensive calf farming systems

Information given in previous Opinions "Welfare of cattle kept for beef production" (SCAHAW, 2001) and "The risks of poor welfare in intensive calf farming systems" (EFSA, 2006) is updated and recent scientific evidence on the topics reviewed. Risks of poor welfare are identified using a structured analysis, and issues not identified in the SCAHAW (2001) beef Opinion, especially effects of housing and management on enteric and respiratory diseases are reviewed. The Opinion covers all systems of beef production, although the welfare of suckler cows or breeding bulls is not considered. The Chapter on beef cattle presents new evidence and recommendations in relation to heat and cold stress, mutilations and pain management, digestive disorders linked to high concentrate feeds and respiratory disorders linked to overstocking, inadequate ventilation, mixing of animals and failure of early diagnosis and treatment. Major welfare problems in cattle kept for beef production, as identified by risk assessment, were respiratory diseases linked to overstocking, inadequate ventilation, mixing of animals and failure of early diagnosis and treatment, digestive disorders linked to intensive concentrate feeding, lack of physically effective fibre in the diet, and behavioural disorders linked to inadequate floor space, and co-mingling in the feedlot. Major hazards for white veal calves were considered to be iron-deficiency anaemia, a direct consequence of dietary iron restriction, enteric diseases linked to high intakes of liquid feed and inadequate intake of physically effective fibre, discomfort and behavioural disorders linked to inadequate floors and floor space.

Excretion of antibiotic resistance genes by dairy calves fed milk replacers with varying doses of antibiotics

Elevated levels of antibiotic resistance genes (ARGs) in soil and water have been linked to livestock farms and in some cases feed antibiotics may select for antibiotic resistant gut microbiota. The purpose of this study was to examine the establishment of ARGs in the feces of calves receiving milk replacer containing no antibiotics versus subtherapeutic or therapeutic doses of tetracycline and neomycin. The effect of antibiotics on calf health was also of interest. Twenty-eight male and female dairy calves were assigned to one of the three antibiotic treatment groups at birth and fecal samples were collected at weeks 6, 7 (prior to weaning), and 12 (5 weeks after weaning). ARGs corresponding to the tetracycline (tetC, tetG, tetO, tetW, and tetX), macrolide (ermB, ermF), and sulfonamide (sul1, sul2) classes of antibiotics along with the class I integron gene, intI1, were monitored by quantitative polymerase chain reaction as potential indicators of direct selection, co-selection, or horizontal gene transfer of ARGs. Surprisingly, there was no significant effect of antibiotic treatment on the absolute abundance (gene copies per gram wet manure) of any of the ARGs except ermF, which was lower in the antibiotic-treated calf manure, presumably because a significant portion of host bacterial cells carrying ermF were not resistant to tetracycline or neomycin. However, relative abundance (gene copies normalized to 16S rRNA genes) of tetO was higher in calves fed the highest dose of antibiotic than in the other treatments. All genes, except tetC and intI1, were detectable in feces from 6 weeks onward, and tetW and tetG significantly increased (P < 0.10), even in control calves. Overall, the results provide new insight into the colonization of calf gut flora with ARGs in the early weeks. Although feed antibiotics exerted little effect on the ARGs monitored in this study, the fact that they also provided no health benefit suggests that the greater than conventional nutritional intake applied in this study overrides previously reported health benefits of antibiotics. The results suggest potential benefit of broader management strategies, and that cost and risk may be avoided by minimizing incorporation of antibiotics in milk replacer.

Longer-duration uses of tetracyclines and penicillins in U.S. food-producing animals: Indications and microbiologic effects

We review and analyze regulatory categories for longer duration of use (defined as ≥ 7 day) tetracyclines (TCs) and penicillins (PNs) approved for U.S. livestock and poultry, together with scientific studies, surveillance programs and risk assessments pertaining to antimicrobial resistance. Indications listed on a government database were grouped into three broad categories according to the terminology used to describe their use: disease control (C), treatment (T) and growth improvement (G). Consistent with mostly therapeutic uses, the majority (86%) of listed indications had C and/or T terms. Several studies showed interruption of early disease stages in animals and modulation of intestinal microflora. Longer-duration exposures are consistent with bacteriostatic modes of action, where adequate exposure time as well as concentration is needed for sufficient antimicrobial activity. Other effects identified included reduced animal pathogen prevalence, toxin formation, inflammation, environmental impacts, improved animal health, reproductive measures, nutrient utilization, and others. Several animal studies have shown a limited, dose-proportionate, selective increase in resistance prevalence among commensal animal bacteria following longer-duration exposures. Pathogen surveillance programs showed overall stable or declining resistance trends among sentinel bacteria. Quantitative, microbiologically detailed resistance risk assessments indicate small probabilities of human treatment failure due to resistance under current conditions. Evaluations of longer-duration uses of TCs, PNs, and other antimicrobial classes used in food-producing animals should consider mechanisms of activity, known individual- and population-level health and waste reduction effects in addition to resistance risks.

Comparison of phenotypic and genotypic antimicrobial profiles in Escherichia coli and Salmonella enterica from the same dairy cattle farms

Transmission of antimicrobial drug resistance from resistant bacteria to non-resistant strains is an important public health issue. In this study, we have examined the possibility of multiple resistance gene transfer between Escherichia coli and Salmonella in the natural setting. Bacteria isolated from calves concurrently shedding E. coli and Salmonella showed similar antimicrobial drug resistance patterns as measured by a broth dilution method. However, microarray analysis of the antibiotic resistance at the gene level revealed several differences in resistance gene profile. Resistance profiles of E. coli isolated from different farms were closer than the profile of E. coli and Salmonella isolated from the same farm. This shows that the chance of multiple resistance gene transfers between these species is unlikely.

Geographic, farm, and animal factors associated with multiple antimicrobial resistance in fecal Escherichia coli isolates from cattle in the western United States

OBJECTIVE

To describe geographic, farm-type, and animal-type factors associated with multiple antimicrobial resistance (MAR) in fecal Escherichia coli isolates from cattle.

DESIGN

Cross-sectional field study.

SAMPLE POPULATION

1,736 fecal samples from cattle on 38 farms in California, Oregon, and Washington.

PROCEDURES

Fecal samples were collected from preweaned calves (2 to 4 weeks old) and cows that recently calved on dairy and beef cow-calf farms, preweaned calves on calf ranches, and 1-year-old steers on feedlots. One fecal E coli isolate per sample was isolated, and antimicrobial susceptibility was tested. Escherichia coli isolates were initially clustered by antimicrobial resistance patterns and categorized by number of antimicrobial resistances. A generalized estimating equations cumulative logistic regression model was used to identify factors associated with an increase in MAR in fecal E coli isolates from cattle.

RESULTS

MAR was higher in E coli isolates from cattle in California, compared with those from cattle in Washington or Oregon. Multiple antimicrobial resistance was highest in E coli isolates from calves on calf ranches and progressively lower in isolates from feedlot steers, dairy cattle, and beef cattle. Multiple antimicrobial resistance was higher in E coli isolates from calves than from adult cattle, in E coli isolates from cattle of conventional farms than of organic farms, and in isolates from beef cattle in intensive dairy farm regions than from beef cattle distant from dairy farm regions.

CONCLUSIONS AND CLINICAL RELEVANCE

MAR in fecal E coli isolates from cattle was influenced by factors not directly associated with the use of antimicrobials, including geographic region, animal age, and purpose (beef vs dairy).

Targeting therapy to minimize antimicrobial use in preweaned calves: effects on health, growth, and treatment costs

Prophylactic and therapeutic antimicrobial use in food animals is questioned because of the potential for development of resistant bacteria and future inability to use some antimicrobials for human or animal disease. The objectives of this study were to determine the effect of raising preweaned dairy calves without antimicrobials in the milk and minimizing therapeutic antimicrobial treatment on morbidity, mortality, weight gain, and treatment costs. Newborn calves (n = 358) were allocated to 1 of 4 groups, housed outdoors in individual hutches, and monitored for 28 d. Calves in the conventional therapy (CT) group were treated as per dairy protocol with sulfamethoxazole/trimethoprim, spectinomycin, penicillin, and bismuth-pectin for diarrhea. The targeted therapy (TT) group included bismuth-pectin for diarrhea and antimicrobial treatment only in cases of fever or depressed attitude. Within CT and TT groups, calves were equally assigned to receive neomycin and tetracycline in their milk for the first 2 wk of life (AB-milk) or no antimicrobials (NoAB-milk). Daily health evaluations included fecal consistency, respiratory disease, attitude, and hydration status as well as milk and grain consumption. A negative binomial model evaluated the total number of days with diarrhea days in each group. General linear models were used to assess average daily weight gain and grain consumption. Conventionally treated calves had 70% more days with diarrhea than TT calves, and AB-milk calves had 31% more days with diarrhea compared with NoAB-milk calves. The TT calves tended to have a higher average daily gain by 28 d and consumed more grain compared with CT calves. If antimicrobials were used only for diarrhea cases with fever, inappetence, or depression and no in-milk antimicrobials were used, a $10 per calf savings could be realized. Targeting antimicrobial therapy of calf diarrhea cases is prudent not only to save the drugs for future use but also to prevent the potential for antibiotic-associated diarrhea and reduce calf-rearing costs.

Changes in multidrug resistance of enteric bacteria following an intervention to reduce antimicrobial resistance in dairy calves

An intervention study was conducted to determine whether discontinuing the feeding of milk replacer medicated with oxytetracycline and neomycin to preweaned calves reduced antimicrobial resistance in Salmonella, Campylobacter, and Escherichia coli bacteria. Results demonstrated that the intervention did reduce multidrug resistance in these bacteria but that other factors also influenced multidrug resistance.