Effect of Tetracycline Dose and Treatment Mode on Selection of Resistant Coliform Bacteria in Nursery Pigs

Occurrence of multidrug resistance associated with extended-spectrum β‑lactamase and the biofilm forming ability of Escherichia coli in environmental swine husbandry

Extended-spectrum beta-lactamase (ESBL) production and biofilm formation are mechanisms employed by Escherichia coli to resist beta-lactam antibiotics. Thus, we aimed to examine antibiotic resistance associated with ESBL production and biofilm formation in E. coli isolates from swine farms in Southern Thailand. In total, 159 E. coli isolates were obtained, with 44 isolates identified as ESBL producers, originating from feces (18.87 %) and wastewater (8.80 %) samples. All ESBL-producing strains exhibited resistance to ampicillin (100 %), followed by the cephalosporin group (97.73 %) and tetracycline (84.09 %). Multidrug resistance was observed in 17 isolates (38.63 %). Among the isolates from feces samples, the blaGES gene was the most prevalent, detected in 90 % of the samples, followed by blaCTX-M9 (86.67 %) and blaCTX-M1 (66.67 %), respectively. In the bacteria isolated from wastewater, both blaGES and blaCTX-M9 genes were the predominant resistance genes, detected in 100 % of the isolates, followed by blaCTX-M1 (64.29 %) and blaTEM (50 %), respectively. Strong biofilm formation was observed in 11 isolates (36.67 %) from feces and 4 isolates (25.57 %) from wastewater samples. Notably, nearly 100 % of ESBL-producing strains isolated from feces tested positive for both pgaA and pgaC genes, which play a role in intracellular adhesion and biofilm production. These findings contribute to the understanding and potential control of ESBL-producing E. coli, and the dissemination of antibiotic resistance and biofilm-related genes in swine farms.

Antimicrobial Resistance in Commensal Escherichia coli of the Porcine Gastrointestinal Tract

Antimicrobial resistance (AMR) in Escherichia coli of animal origin presents a threat to human health. Although animals are not the primary source of human infections, humans may be exposed to AMR E. coli of animal origin and their AMR genes through the food chain, direct contact with animals, and via the environment. For this reason, AMR in E. coli from food producing animals is included in most national and international AMR monitoring programmes and is the subject of a large body of research. As pig farming is one of the largest livestock sectors and the one with the highest antimicrobial use, there is considerable interest in the epidemiology of AMR in E. coli of porcine origin. This literature review presents an overview and appraisal of current knowledge of AMR in commensal E. coli of the porcine gastrointestinal tract with a focus on its evolution during the pig lifecycle and the relationship with antimicrobial use. It also presents an overview of the epidemiology of resistance to extended spectrum cephalosporins, fluoroquinolones, and colistin in pig production. The review highlights the widespread nature of AMR in the porcine commensal E. coli population, especially to the most-used classes in pig farming and discusses the complex interplay between age and antimicrobial use during the pig lifecycle.

Antibiotic Resistance Patterns and Molecular Characterization of Streptococcus suis Isolates from Swine and Humans in China

Streptococcus suis is a zoonotic pathogen that causes disease in humans after exposure to infected pigs or pig-derived food products. In this study, we examined the serotype distribution, antimicrobial resistance phenotypes and genotypes, integrative and conjugative elements (ICEs), and associated genomic environments of S. suis isolates from humans and pigs in China from 2008 to 2019. We identified isolates of 13 serotypes, predominated by serotype 2 (40/96; 41.7%), serotype 3 (10/96; 10.4%), and serotype 1 (6/96; 6.3%). Whole-genome sequencing analysis revealed that these isolates possessed 36 different sequence types (STs), and ST242 and ST117 were the most prevalent. Phylogenetic analysis revealed possible animal and human clonal transmission, while antimicrobial susceptibility testing indicated high-level resistance to macrolides, tetracyclines, and aminoglycosides. These isolates carried 24 antibiotic resistance genes (ARGs) that conferred resistance to 7 antibiotic classes. The antibiotic resistance genotypes were directly correlated with the observed phenotypes. We also identified ICEs in 10 isolates, which were present in 4 different genetic environments and possessed differing ARG combinations. We also predicted and confirmed by PCR analysis the existence of a translocatable unit (TU) in which the oxazolidinone resistance gene optrA was flanked by IS1216E elements. One-half (5/10) of the ICE-carrying strains could be mobilized by conjugation. A comparison of the parental recipient with an ICE-carrying transconjugant in a mouse in vivo thigh infection model indicated that the ICE strain could not be eliminated with tetracycline treatment. S. suis therefore poses a significant challenge to global public health and requires continuous monitoring, especially for the presence of ICEs and associated ARGs that can be transferred via conjugation. IMPORTANCE S. suis is a serious zoonotic pathogen. In this study, we investigated the epidemiological and molecular characteristics of 96 S. suis isolates from 10 different provinces of China from 2008 to 2019. A subset of these isolates (10) carried ICEs that were able to be horizontally transferred among isolates of different S. suis serotypes. A mouse thigh infection model revealed that ICE-facilitated ARG transfer promoted resistance development. S. suis requires continuous monitoring, especially for the presence of ICEs and associated ARGs that can be transferred via conjugation.

Age influences the temporal dynamics of microbiome and antimicrobial resistance genes among fecal bacteria in a cohort of production pigs

BACKGROUND

The pig gastrointestinal tract hosts a diverse microbiome, which can serve to select and maintain a reservoir of antimicrobial resistance genes (ARG). Studies suggest that the types and quantities of antimicrobial resistance (AMR) in fecal bacteria change as the animal host ages, yet the temporal dynamics of AMR within communities of bacteria in pigs during a full production cycle remains largely unstudied.

RESULTS

A longitudinal study was performed to evaluate the dynamics of fecal microbiome and AMR in a cohort of pigs during a production cycle; from birth to market age. Our data showed that piglet fecal microbial communities assemble rapidly after birth and become more diverse with age. Individual piglet fecal microbiomes progressed along similar trajectories with age-specific community types/enterotypes and showed a clear shift from E. coli/Shigella-, Fusobacteria-, Bacteroides-dominant enterotypes to Prevotella-, Megaspheara-, and Lactobacillus-dominated enterotypes with aging. Even when the fecal microbiome was the least diverse, the richness of ARGs, quantities of AMR gene copies, and counts of AMR fecal bacteria were highest in piglets at 2 days of age; subsequently, these declined over time, likely due to age-related competitive changes in the underlying microbiome. ARGs conferring resistance to metals and multi-compound/biocides were detected predominately at the earliest sampled ages.

CONCLUSIONS

The fecal microbiome and resistome-along with evaluated descriptors of phenotypic antimicrobial susceptibility of fecal bacteria-among a cohort of pigs, demonstrated opposing trajectories in diversity primarily driven by the aging of pigs.

Distribution Patterns of Antibiotic Resistance Genes and Their Bacterial Hosts in a Manure Lagoon of a Large-Scale Swine Finishing Facility

The spread of antibiotic resistance genes (ARGs) that are present in livestock manures, which are discharged into the environment, is a severe threat to human and animal health. Here, we used 16S rRNA gene profiling and metagenomic analysis to characterize microbial community composition and antibiotic resistance in a manure storage lagoon from a large-scale swine finishing facility. Manure samples were collected at intervals of two years. Both the prokaryotic community and the resistome were dominated by the Firmicutes, Proteobacteria and Bacteroidota. Metagenomic analysis of two samples revealed 726 and 641 ARGs classified into 59 and 46 AMR gene families. Besides multidrug efflux pumps, the predominating ARGs potentially encoded resistance to tetracyclines, macrolide-lincosamide-streptogramin, aminoglycosides, peptide antibiotics, rifamycin, chloramphenicol, and beta-lactams. Genes from all predominant AMR gene families were found in both samples indicating overall long-term stability of the resistome. Antibiotic efflux pumps were the primary type of ARGs in the Proteobacteria, while antibiotic target alteration or protection was the main mechanism of resistance in the Firmicutes, Actinobacteriota and Bacteroidota. Metagenome-assembled genomes (MAG) of four multidrug-resistant strains were assembled. The first MAG, assigned to Escherichia flexneri, contained 46 ARGs, including multidrug efflux pumps, modified porins, beta-lactamases, and genes conferring resistance to peptide antibiotics. The second MAG, assigned to the family Alcaligenaceae, contained 18 ARGs encoding resistance to macrolide-lincosamide-streptogramin, tetracyclines, aminoglycosides and diaminopyrimidins. Two other MAGs representing the genera Atopostipes and Prevotella, contained four and seven ARGs, respectively. All these MAGs represented minor community members and accounted for less than 0.3% of the whole metagenome. Overall, a few lineages originated from the gut but relatively rare in the manure storage lagoon, are the main source of ARGs and some of them carry multiple resistance determinants.

Efficacy of neomycin dosing regimens for treating enterotoxigenic Escherichia coli-related post-weaning diarrhoea in a Danish nursery pig herd not using medicinal zinc oxide

Neomycin is a concentration-dependant aminoglycoside antimicrobial used to treat enterotoxigenic Escherichia coli (ETEC)-related post-weaning diarrhoea (PWD) in pigs. The objective was to compare the efficacy of neomycin administered in a single high dose (50,000 IU/kg) and a standard dose and frequency (25,000 IU/kg daily for 3 consecutive days) in reducing the number of pigs with clinical PWD. We also aimed to evaluate the development of antimicrobial resistance in E. coli following neomycin treatment. The study was performed in a Danish herd not using medicinal zinc oxide and experiencing outbreaks of PWD caused by ETEC in the first week after weaning. Pigs from six batches with perianal faecal staining on days 4–6 after weaning and a faecal score of 3–4 were ear tagged and treated with neomycin. Pens were randomly assigned to a treatment group before inclusion. A total of 772 pigs (471 in the control group and 301 in the experimental group) were included and treated orally. The apparent prevalence of diarrhoea on the first day of inclusion across six batches (n = 1,875) was 27%. The efficacy of the neomycin treatment strategy was 86% for the control group and 91% for the single high-dose group (p = 0.043), and the mean percentage (standard deviation (sd)) of haemolytic E. coli-like colonies was 12% (26) and 26% (37) (p < 0.001), respectively. Neomycin resistance did not differ between groups. Before treatment, all analysed isolates were identified as ETEC (n = 142), while after treatment, 91% were identified as ETEC (n = 69) and 9% (n = 7) as non-ETEC E. coli (without fimbria or toxins). A higher cure rate in the single high-dose group suggests that ETEC-related PWD can be treated with a single high dose of 50,000 IU/kg of neomycin, thereby reducing antimicrobial use by 33% compared to the standard treatment of 25,000 IU/kg for 3 consecutive days. The study indicated a higher number of haemolytic E. coli in the single high-dose group after treatment, but no evidence of increased neomycin resistance in coliforms was observed compared to the standard treatment.

The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs

BACKGROUND

Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory syndrome (PRRS), which is caused by a virus that predisposes infected animals to secondary bacterial infections. Numerous antimicrobial protocols are used to treat PRRS, but we have little insight into how these treatment schemes impact antimicrobial resistance (AMR) dynamics within the fecal microbiome of commercial swine. The aim of this study was to determine whether different PRRS-relevant antimicrobial treatment protocols were associated with differences in the fecal microbiome and resistome of growing pigs. To accomplish this, we used a metagenomics approach to characterize and compare the longitudinal wean-to-market resistome and microbiome of pigs challenged with PRRS virus and then exposed to different antimicrobial treatments, and a group of control pigs not challenged with PRRS virus and having minimal antimicrobial exposure. Genomic DNA was extracted from pen-level composite fecal samples from each treatment group and subjected to metagenomic sequencing and microbiome-resistome bioinformatic and statistical analysis. Microbiome-resistome profiles were compared over time and between treatment groups.

RESULTS

Fecal microbiome and resistome compositions both changed significantly over time, with a dramatic and stereotypic shift between weaning and 9 days post-weaning (dpw). Antimicrobial resistance gene (ARG) richness and diversity were significantly higher at earlier time points, while microbiome richness and diversity were significantly lower. The post-weaning shift was characterized by transition from a Bacteroides-dominated enterotype to Lactobacillus- and Streptococcus-dominated enterotypes. Both the microbiome and resistome stabilized by 44 dpw, at which point the trajectory of microbiome-resistome maturation began to diverge slightly between the treatment groups, potentially due to physical clustering of the pigs. Challenge with PRRS virus seemed to correspond to the re-appearance of many very rare and low-abundance ARGs within the feces of challenged pigs. Despite very different antimicrobial exposures after challenge with PRRS virus, resistome composition remained largely similar between the treatment groups. Differences in ARG abundance between the groups were mostly driven by temporal changes in abundance that occurred prior to antimicrobial exposures, with the exception of ermG, which increased in the feces of treated pigs, and was significantly more abundant in the feces of these pigs compared to the pigs that did not receive post-PRRS antimicrobials.

CONCLUSIONS

The fecal microbiome-resistome of growing pigs exhibited a stereotypic trajectory driven largely by weaning and physiologic aging of the pigs. Events such as viral illness, antimicrobial exposures, and physical grouping of the pigs exerted significant yet relatively minor influence over this trajectory. Therefore, the AMR profile of market-age pigs is the culmination of the life history of the individual pigs and the populations to which they belong. Disease status alone may be a significant driver of AMR in market-age pigs, and understanding the interaction between disease processes and antimicrobial exposures on the swine microbiome-resistome is crucial to developing effective, robust, and reproducible interventions to control AMR. Video Abstract.

Effect of Intramuscularly Administered Oxytetracycline or Enrofloxacin on Vancomycin-Resistant Enterococci, Extended Spectrum Beta-Lactamase- and Carbapenemase-Producing Enterobacteriaceae in Pigs

Simple Summary

Nowadays, there is great concern about the prevalence of multidrug resistant bacteria in food-producing animals since they are potential sources of transmission to humans. The aim of this work was to evaluate the effect of two antibiotics (oxytetracycline and enrofloxacin) treatments in pigs on resistant bacteria that are considered a threat to public health. This study highlights that the use of oxytetracycline or enrofloxacin in food-producing animals could select resistant bacteria in pig faeces. Special care should be taken to avoid faecal contamination of carcasses during slaughter.

Abstract

Nowadays, there is a great concern about the prevalence of multidrug resistant Enterococcus spp. and Enterobacteriaceae in food-producing animals. The aim of this work was to evaluate the effect of oxytetracycline or enrofloxacin treatment on vancomycin-resistant enterococci (VRE), extended spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacteriaceae in pigs. A total of 26 piglets were received and distributed in three groups. Group 1 was treated with enrofloxacin (N = 12), group 2 with oxytetracycline (N = 10) and group 3 did not receive any treatment (control group) (N = 4). A higher number of vancomycin-resistant E. faecium were recovered compared to E. faecalis. In the pigs treated with enrofloxacin, vancomycin resistant E. faecium was found in a higher percentage of animals than in the control group. ESBL-producing E. coli was not detected in rectal samples from control animals. However, it was detected in 17–20% of animals treated with oxytetracycline on days 6 to 17 and in 17–50% of the animals treated with enrofloxacin. Carbapenemase-producing E. coli was isolated in animals treated with oxytetracycline, but not in animals treated with enrofloxacin or in the control group. This study highlights that the use of oxytetracycline or enrofloxacin in food-producing animals could select ESBL and carbapenemase-producing E. coli. Further studies shall be needed to validate the results obtained, considering a more robust and extended experimental design.

Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

This study aimed to compare the fecal microbiome and antimicrobial resistance between captive and free-range sika deer with the same exposure to antibiotic anthelmintics. The taxonomic differences mainly involved significant changes in the dominant phyla, genera, and species. Linear discriminant analysis effect size (LEfSe) analysis revealed that 22 taxa were significantly different between the two groups. The KEGG analysis showed that the fecal microbiome metabolic function, and all level 2 categories in metabolism had higher abundance in the free-range deer. Based on the carbohydrate-active enzyme (CAZy) database analysis, glycoside hydrolases and carbohydrate-binding modules showed remarkable differences between the two groups. Regarding antibiotic resistance, tetQ and lnuC dominated the antibiotic resistance ontology (ARO) terms, and tetracycline and lincosamide resistance dominated the antimicrobial resistance patterns. Furthermore, the lnuC, ErmF, and tetW/N/W AROs and lincosamide resistance showed higher abundance in the captive deer, suggesting that captivity may yield more serious resistance issues because of the differences in greenfeed diet, breeding density, and/or housing environment. The results also revealed important associations between the phylum Proteobacteria, genus Prevotella, and major antibiotic resistance genes. Although the present study was a pilot study with a limited sample size that was insufficient control for some potential factors, it serves as the metagenomic study on the microbial communities and antimicrobial resistance in sika deer.

IMPORTANCE We used a metagenomic approach to investigate whether and how captive and free-range impact the microbial communities and antimicrobial resistance in sika deer. The results provide solid evidence of the significant impacts on the microbial composition and function in captive and free-range sika deer. Interestingly, although the sika deer had the same exposure to antibiotic anthelmintics, the antimicrobial resistances were affected by the breeding environment.

Antibiotic Resistance: From Pig to Meat

Pork meat is in high demand worldwide and this is expected to increase. Pork is often raised in intensive conditions, which is conducive to the spread of infectious diseases. Vaccines, antibiotics, and other biosafety measures help mitigate the impact of infectious diseases. However, bacterial strains resistant to antibiotics are more and more frequently found in pig farms, animals, and the environment. It is now recognized that a holistic perspective is needed to sustainably fight antibiotic resistance, and that an integrated One Health approach is essential. With this in mind, this review tackles antibiotic resistance throughout the pork raising process, including their microbiome; many factors of their environment (agricultural workers, farms, rivers, etc.); and an overview of the impact of antibiotic resistance on pork meat, which is the end product available to consumers. Antibiotic resistance, while a natural process, is a public health concern. If we react, and act, collectively, it is expected to be, at least partially, reversible with judicious antibiotic usage and the development of innovative strategies and tools to foster animal health.

Prediction of Minocycline Activity in the Gut From a Pig Preclinical Model Using a Pharmacokinetic -Pharmacodynamic Approach

The increase of multidrug-resistant (MDR) bacteria has renewed interest in old antibiotics, such as minocycline, that can be active against various MDR Gram-negative pathogens. The elimination of minocycline by both kidneys and liver makes it suitable for impaired renal function patients. However, the drawback is the possible elimination of a high amount of drug in the intestines, with potential impact on the digestive microbiota during treatment. This study aimed to predict the potential activity of minocycline against Enterobacterales in the gut after parenteral administration, by combining in vivo and in vitro studies. Total minocycline concentrations were determined by UPLC-UV in the plasma and intestinal content of piglets following intravenous administration. In parallel, the in vitro activity of minocycline was assessed against two Escherichia coli strains in sterilized intestinal contents, and compared to activity in a standard broth. We found that minocycline concentrations were 6–39 times higher in intestinal contents than plasma. Furthermore, minocycline was 5- to 245-fold less active in large intestine content than in a standard broth. Using this PK-PD approach, we propose a preclinical pig model describing the link between systemic and gut exposure to minocycline, and exploring its activity against intestinal Enterobacterales by taking into account the impact of intestinal contents.

Association between antimicrobial usage and resistance in Salmonella from poultry farms in Nigeria

BACKGROUND

Antimicrobial resistance (AMR) is a global health threat affecting treatment outcome in animals and humans. A pre-requisite for development of AMR reduction strategies is knowledge of antimicrobial use patterns, and how these affect resistance development. The aim of this study was to determine antimicrobial usage (AMU) and whether such usage was associated with AMR in Salmonella from poultry farms in Northwest Nigeria.

RESULTS

Fifteen (37%) of antimicrobial products observed contained compounds that are of highest priority and critically important for human medicine. Broilers chicken consumed higher (28 ± 14 mg/kg active ingredients) amounts of antimicrobials compared to layers (13 ± 8 mg/kg) per week (p = 0.0009). Surprisingly, chickens raised under backyard system consumed higher amounts of antimicrobials (34 ± 7 mg/kg) than poultry in other systems (p = 0.02). High levels of resistance to tetracycline (58%), sulphonamides (65%), ciprofloxacin (46%) and gentamicin (42%) correlated with high farm level usage of these antimicrobials, and there was a strong correlation (r = 0.9) between farm usage and resistance of isolates to the same antimicrobials (p = 0.03).

CONCLUSION

High AMU, including use of highest priority critically important antimicrobials was observed at poultry farms in Northwest Nigeria. AMU correlated with high levels of resistance. Communication of prudent use of antimicrobials to farmers and regulation to obtain reduction in AMU should be a priority.

Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces

While it is well recognized that the environmental resistome is global, diverse, and augmented by human activities, it has been difficult to assess risk because of the inability to culture many environmental organisms, and it is difficult to evaluate risk from current sequence-based environmental methods. The four most important criteria to determine risk are whether the antibiotic-resistance genes (ARGs) are a complete, potentially functional complement; if they are linked with other resistances; whether they are mobile; and the identity of their host. Long-read sequencing fills this important gap between culture and short sequence-based methods. To address these criteria, we collected feces from a ceftiofur-treated cow, enriched the samples in the presence of antibiotics to favor ARG functionality, and sequenced long reads using Nanopore and PacBio technologies. Multidrug-resistance genes comprised 58% of resistome abundance, but only 0.8% of them were plasmid associated; fluroquinolone-, aminoglycoside-, macrolide-lincosamide-streptogramin (MLS)-, and β-lactam-resistance genes accounted for 2.7 to 12.3% of resistome abundance but with 19 to 78% located on plasmids. A variety of plasmid types were assembled, some of which share low similarity to plasmids in current databases. Enterobacteriaceae were dominant hosts of antibiotic-resistant plasmids; physical linkage of extended-spectrum β-lactamase genes (CTX-M, TEM, CMY, and CARB) was largely found with aminoglycoside-, MLS-, tetracycline-, trimethoprim-, phenicol-, sulfonamide-, and mercury-resistance genes. A draft circular chromosome of Vagococcus lutrae was assembled; it carries MLS-, tetracycline- (including tetM and tetL on an integrative conjugative element), and trimethoprim-resistance genes flanked by many transposase genes and insertion sequences, implying that they remain transferrable.

Parasitic Intestinal Protists of Zoonotic Relevance Detected in Pigs by Metabarcoding and Real-Time PCR

Several parasite species are shared between humans and pigs. We explored the application of next-generation sequencing-based metabarcoding supplemented with real-time PCR to fecal DNAs from 259 samples from 116 pigs in Denmark to detect and differentiate single-celled intestinal parasites of zoonotic relevance. Enterocytozoon bieneusi, Balantioides coli, and Giardia duodenalis were observed in 34/37 (92%), 148/259 (57%), and 86/259 (33%) samples, respectively. Entamoeba polecki ST1, E. polecki ST3, and Entamoeba hartmanni were detected in 104/259 (40%), 161/259 (62%), and 8/259 (3%) samples, respectively. Metabarcoding and real-time PCR detected Cryptosporidium in 90/259 (35%) and 239/259 (92%) of the samples, respectively, with Cryptosporidium suis and Cryptosporidium scrofarum observed in nearly equal proportions. Blastocystis subtypes 1, 3, 5, and 15 were found in 72 (28%), 6 (2%), 176 (68%), and 36 (14%) of 259 samples, respectively. Iodamoeba was identified in 1/259 samples (<1%), while none of 37 tested samples was positive for Dientamoeba fragilis. Our results illustrate how metabarcoding exemplifies a 'one-fits-many' approach to detecting intestinal single-celled parasites in feces supplemented with real-time PCR for selected parasites. Using metabarcoding with pathogen-specific assays may help detect emerging and previously underdetected pathogens and further elucidate the role of micro-eukaryotic parasites in human and animal health and disease.

The Effect of Colistin Treatment on the Selection of Colistin-Resistant Escherichia coli in Weaner Pigs

The treatment of diarrhea in the postweaning period is a common reason for the use of antimicrobials in pig production, and Escherichia coli is the single most important causative agent for this condition. Colistin has recently been classified as a critically important antimicrobial for human health, as it is a last-resort drug against certain multi-drug-resistant Gram-negative bacteria. Therefore, the use of colistin has been significantly reduced in some countries, including Denmark. Despite this, the drug is still commonly used to treat diarrhea in pigs in many countries, and there is a need to understand the risks associated with this practice. We performed a prospective cohort study to investigate the effect of colistin treatment on the changes in the average minimum inhibitory concentration (MIC) in commensal E. coli in a pig herd where no colistin-resistant bacteria were detectable before treatment. One group of pigs was batch treated with colistin after the clinical observation of diarrhea, one group was batch treated with colistin approximately 10 days before the expected onset of diarrhea, and a control group was not treated with colistin but provided with nonantimicrobial antidiarrheal feed supplement. Treatment with colistin in the dose and time combinations used did not result in a significant increase in the average colistin MIC values in E. coli. Moreover, no E. coli strains showed a MIC above the breakpoint of >2 mg/L against colistin. Co-selection of resistance to other antimicrobials was not observed.

Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics

This study aimed to detect the cecal microbiome, antimicrobial resistance (AMR) and heavy metal resistance genes (MRGs) in fattening pigs raised under antibiotic-free (ABF) conditions compared with ordinary industrial pigs (control, C) using whole-genome shotgun sequencing. ABF pigs showed the enrichment of Prevotella (33%) and Lactobacillus (13%), whereas Escherichia coli (40%), Fusobacterium and Bacteroides (each at 4%) were notably observed in the C group. Distinct clusters of cecal microbiota of ABF and C pigs were revealed; however, microbiota of some C pigs (C1) appeared in the same cluster as ABF and were totally separated from the remaining C pigs (C2). For AMR genes, the highest abundance tet(Q) (35.7%) and mef(A) (12.7%) were markedly observed in the ABF group whereas tet(Q) (26.2%) and tet(W) (10.4%) were shown in the C group. tet(Q) was positively correlated to Prevotella in ABF and C1 samples. In the C2 group, the prominent tet(W) was positively correlated to Fusobacterium and Bacteroides Pigs have never received tetracycline but pregnant sows used chlortetracycline once 7 d before parturition. Chromosomal Cu and Zn resistance genes were also shown in both groups regardless the received Cu and Zn feed additives. A higher abundance of multi-metal resistance genes was observed in the C group (44%) compared with the ABF group (41%). In conclusion, the microbiome clusters in some C pigs were similar to that in ABF pigs. High abundant tetracycline resistance genes interrelated to major bacteria were observed in both ABF and C pigs. MRGs were also observed.IMPORTANCE: Owing to the increased problem of AMR in farm animals, raising farm animals without antibiotics is one method that could solve this problem. Our study showed that only some tetracycline and macrolide resistance genes, tet(Q), tet(W) and mef(A), were markedly abundant in ABF and C groups. The tet(Q) and tet(W) genes interrelated to different predominant bacteria in each group, showing the potential role of major bacteria as reservoirs of AMR genes. In addition, chromosomal Cu and Zn resistance genes were also observed in both pig groups, not depending on the use of Cu and Zn additives in both farms. The association of MRGs and AMR genotypes and phenotypes together with the method to re-sensitize bacteria to antibiotics should be studied further to unveil the cause of high resistance genes and solve the problems.

Effect of ampicillin, cephalexin, ceftiofur and tetracycline treatment on selection of resistant coliforms in a swine faecal microcosmos

AIMS

To analyse and compare the effect of selection power for antimicrobial resistance (AMR) in coliforms of two kinds of β-lactams-aminopenicillins; ampicillin (Amp) and cephalosporins; cephalexin (Cpn) and ceftiofur (Cef)-and tetracycline (Tet) using an approach based on a swine faecal microcosmos.

METHODS AND RESULTS

Sixteen faecal samples from 32 pigs (mixed two by two) were treated with Amp, Cpn, Cef and Tet for 6 h (T6h) at concentrations expected to reach the animals gut when using in vivo standard doses. Controls (no drug added) were also tested. Next, samples were 1 : 100 diluted and left under the same conditions (no antimicrobial added) for further 20 h (T20h). The proportion of resistant coliform bacteria (R coliforms) to each antimicrobial was analysed just before starting the treatment (T0), at T6h and at T20h. Coselection was also studied by replica plating. Treatment for 6 h yielded significant increase in proportion of R coliforms, regardless of the drug and lack of selection pressure showed different effects at T20h depending on the antimicrobial used. Selective pressure was associated with the type of the β-lactam with Amp selecting for significantly higher numbers of R coliforms than cephalosporins.

CONCLUSIONS

AMR development was observed following short treatment, and for Amp and Tet treatment, resistance persisted 20 h beyond the interruption of treatment. An association between kind of β-lactam and power of selection was found.

SIGNIFICANCE AND IMPACT OF THE STUDY

AMR represents a threat to human health globally and antimicrobial treatment of livestock has a direct impact on this problem. Through our approach based on a swine faecal microcosmos, we demonstrated the effect on AMR development of several drugs commonly used in livestock. Cephalosporins, representing last-line antimicrobials in human medicine, exerted lower selective pressure than Amp under the conditions used and yielded higher proportion of multidrug-R strains.

Quantitative and qualitative analysis of antimicrobial usage patterns in 180 selected farrow-to-finish pig farms from nine European countries based on single batch and purchase data

OBJECTIVES

Farm-level quantification of antimicrobial usage (AMU) in pig farms.

METHODS

In a cross-sectional study, AMU data on group treatments administered to a single batch of fattening pigs from birth to slaughter (group treatment data) and antimicrobials purchased during 1 year (purchase data) were collected at 180 pig farms in nine European countries. AMU was quantified using treatment incidence (TI) based on defined (DDDvet) and used (UDDvet) daily doses and defined (DCDvet) and used (UCDvet) course doses.

RESULTS

The majority of antimicrobial group treatments were administered to weaners (69.5% of total TIDDDvet) followed by sucklers (22.5% of total TIDDDvet). AMU varied considerably between farms with a median TIDDDvet of 9.2 and 7.1 for a standardized rearing period of 200 days based on group treatment and purchase data, respectively. In general, UDDvet and UCDvet were higher than DDDvet and DCDvet, respectively, suggesting that either the defined doses were set too low or that group treatments were often dosed too high and/or administered for too long. Extended-spectrum penicillins (31.2%) and polymyxins (24.7%) were the active substances most often used in group treatments, with the majority administered through feed or water (82%). Higher AMU at a young age was associated with higher use in older pigs.

CONCLUSIONS

Collecting farm-level AMU data of good quality is challenging and results differ based on how data are collected (group treatment data versus purchase data) and reported (defined versus used daily and course doses).

Phenotypic antimicrobial resistance in Escherichia coli strains isolated from swine husbandries in North Western Germany - temporal patterns in samples from laboratory practice from 2006 to 2017

Background

Since 2011, antibiotic usage has decreased continuously in livestock in Germany. Whether this is accompanied by a reduction in bacterial antimicrobial resistance has not been proven so far. In this study 3054 Escherichia coli (E. coli) isolates from pigs which had suffered from disease on 2161 farms in North Western Germany were evaluated retrospectively from 2006 to 2017 for trends in their antimicrobial resistance pattern. Data were substantially related to the “pre-reduction period” and were therefore suggested as a basis for this task.

Minimal inhibitory concentrations for selected antimicrobial substances were evaluated for E. coli strains isolated from different organs of diseased swine sampled for routine diagnostic. In total, 81% of E. coli were isolated from faeces or the gastrointestinal tract, 11% from the genito-urinary tract and 8% from other organs. Susceptibility testing and classification of isolates in accordance with clinical cut-offs followed the Clinical and Laboratory Standards Institute (CLSI). If no clinical cut-offs were available for the respective combination of species, substance and organ, other published clinical cut-offs were used.

Results

Differences in susceptibility patterns between isolates from the gastrointestinal and genito-urinary tract were found for most substances. Isolates from the genito-urinary tract were less frequently resistant to ampicillin, apramycin, colistin, neomycin, spectinomycin and tetracycline and more frequently resistant to enrofloxacin and florfenicol.

A multifactorial logistic regression model revealed time-dependent decreases in frequency of resistant isolates for neomycin, spectinomycin and tetracycline. For colistin, the highest percentage of resistant isolates with 16.0% was found in 2015 followed by a decrease to the level of 2009–2010 in 2017. A decrease in frequencies of ampicillin-resistant isolates was dependent on the age-group and time period. Irrespective of the year, less than 15% E. coli isolates were resistant to apramycin, cephalosporins, colistin, enrofloxacin, florfenicol, gentamicin and neomycin.

Conclusion

An overall time-dependent decrease in the percentage of resistant E. coli isolates was found for some substances. These data from diseased animals indicate an impact of a general reduction in antibiotic usage on development of bacterial antimicrobial resistance in the field and can support the decision-making of swine practitioners for treatment options in swine.

Effect of tetracycline treatment regimens on antibiotic resistance gene selection over time in nursery pigs

Background

The majority of antimicrobials given during the production of pigs are given to nursery pigs. The influence of antimicrobial use on the levels of antimicrobial resistant (AMR) genes is important to quantify to be able to assess the impact of resistance on the food chain and risk to human and animal health.

Results

This study investigated the response on the levels of nine AMR genes to five different treatment strategies with oxytetracycline, and the dynamics of gene abundance over time by following 1167 pigs from five different farms in Denmark.

The results showed no significant difference between treatments and an increase in abundance for the efflux pump encoding tet(A) gene and the genes encoding the ribosomal protection proteins tet(O) and tet(W) tetracycline resistant genes following treatment, while tet(M) showed no response to treatment. However, it was also observed that the levels of tet(O), tet(W), and ermB in some farms would drift more over time compared to a single treatment-course with antibiotic.

Conclusion

This study underlines the large variation in AMR levels under natural conditions and the need for increased investigation of the complex interactions of antimicrobial treatment and other environmental and managerial practices in swine production on AMR gene abundance.

Antibiotic resistance in Escherichia coli from pigs from birth to slaughter and its association with antibiotic treatment

The purpose of this longitudinal study was to describe the occurrence of antibiotic resistance in faecal Escherichia coli isolated from pigs between birth and slaughter and its association with antibiotic treatment. Four objectives were addressed: comparison of antibiotic resistance in isolates from a) treated vs. non-treated pigs, b) follow-up vs. initial samples of treated and non-treated pigs, c) pigs receiving treatments via different administration routes and d) sows and their piglets. Each comparison addressed the following antibiotic groups used for treatment: beta-lactams, tetracyclines, polymyxins and macrolides, and the susceptibility of E. coli isolates to the respective agents: ampicillin, tetracycline, colistin and azithromycin. Between 2014 and 2016, 406 focal animals from 29 commercial breeding herds were followed from birth to the end of the relevant fattening periods. All antibiotic treatments in these pigs were documented. Faecal samples were collected from the focal pigs once while suckling, once after weaning and three times during fattening, and from their dams once around farrowing. Escherichia coli isolated from these samples was tested for antibiotic susceptibility. In total, 264 animals from 19 breeding herds were treated with an antibiotic at least once during their lifetime. Beta-lactams, tetracyclines and colistin were used most frequently. Piglets were treated individually by injection (n = 108 treatments) or via drench (9); weaners via feed (192) or water (56) and fatteners via feed (30) or injection (15). Resistance to ampicillin and tetracycline in E. coli was already common prior to antibiotic treatment. Resistance proportions were higher for beta-lactam-, tetracycline-, colistin- and macrolide-treated pigs compared to untreated pigs at different sampling periods (p < 0.05; Fisher's exact test). In the logistic analysis, the difference was confirmed for beta-lactam-treated vs. untreated pigs. In E. coli from macrolide-untreated pigs, resistance to azithromycin was more frequent compared to pre-treatment values. Route of application did not affect rates of antibiotic resistance in the logistic analysis even though Fisher's exact test indicated associations for beta-lactams (feed/water vs. injection), tetracyclines (feed/water vs. non-treatment) and macrolides (tulathromycin-injection vs. tylosin in feed). Piglets were more likely to carry an E. coli resistant to ampicillin or azithromycin if their dams did so as well. Our results suggest further research on resistance effects by administration routes is required. Reducing antibiotic resistance in sows might lead to a lower level of beta-lactam or macrolide-resistant E. coli among their progeny. To preserve treatment options for bacterial infections, antibiotic use should be restricted to necessary cases.

Occurrence and Antimicrobial Profile of Bacterial Pathogens in Former Foodstuff Meat Products Used for Pet Diets

European legislation stipulates that food no longer intended for human consumption, due to commercial reasons, manufacturing problems, or some defect, can be used in pet feed. However, the presence of former foodstuffs in pet diets could constitute a public health issue because pets can act as reservoirs of antimicrobial resistance genes. In this study, for the first time, biological hazards due to the presence of Escherichia coli and Salmonella in former foodstuff meat products were evaluated. Among the 112 samples of packaged fresh meat (poultry, pork, and beef) collected from cold storage warehouses of a mass market retailer, the overall prevalence of E. coli and Salmonella, the prevalence of strains with multidrug resistance, the phenotypic and genotypic characteristics of strains that produce extended-spectrum β-lactamase, and the presence of biofilm producers were assessed. A high prevalence of E. coli was observed in former foodstuffs of poultry (100%), pork (100%), and beef (93.3%). Salmonella Derby and Salmonella Typhimurium were found in 11.5% of the poultry samples, and Salmonella Typhimurium was found in 13.3% of the pork samples. Salmonella was not recovered from the beef samples. Multidrug resistance was found in E. coli and Salmonella isolates from poultry, pork, and beef. Overall, 18.2% of E. coli isolates and 20% of Salmonella isolates were resistant to various types of antibiotics with various mechanisms of action. Salmonella isolates from pork are an important source of extended-spectrum β-lactamase production. Both E. coli and Salmonella were carriers of antibiotic resistance marker genes ( bla_TEM, bla_SHV, and bla_CTX-M) associated with β-lactamase production in poultry and pork. Approximately 30% of the E. coli isolates from the various types of meat were phenotypically biofilm producers, and all carried the fimH gene. These findings indicate that the use of former foodstuff meat products in pet diets can represent a risk for public health.

Antimicrobial Resistance in Leptospira, Brucella, and Other Rarely Investigated Veterinary and Zoonotic Pathogens

Leptospira, Brucella, and Borrelia are major agents of zoonotic disease, causing high morbidity and, in some cases, significant mortality in humans. For all three genera, prompt diagnosis and appropriate antimicrobial therapy are required to prevent the development of chronic, debilitating illness. Leptospira spp. are intrinsically resistant to several antimicrobial classes; however, there is little evidence in the literature for development of acquired resistance to antimicrobial agents used for clinical treatment of acute leptospirosis. For Brucella infections, there are numerous reports of relapses following therapy, but it is unclear whether this is due to sequestration within infected sites (e.g., bone) or the development of acquired resistance. Brucella have maintained their susceptibility to doxycycline and rifampicin, which in combination remain the most common treatments of brucellosis in humans. In vitro induced point mutations are described as imparting resistance to rifampicin (rpoB) and fluoroquinolones (gyrA). The clinical significance of these mutations is unclear. For Borrelia burgdorferi, although acquired resistance to some antimicrobial agents has been described, resistance due to bacterial persister cells surviving in the presence of antimicrobial, with no apparent increase in the MIC of the organism, have been recently described. Of the remaining veterinary fastidious pathogens, Lawsonia intracellularis is the most interesting from an antimicrobial resistance perspective because it can only be grown in cell culture, making in vitro susceptibility testing challenging. MIC testing has been undertaken on a small number of isolates, and some differences in susceptibility to macrolides have been demonstrated between isolates obtained from different regions.

Optimization of Antimicrobial Treatment to Minimize Resistance Selection

Optimization of antimicrobial treatment is a cornerstone in the fight against antimicrobial resistance. Various national and international authorities and professional veterinary and farming associations have released generic guidelines on prudent antimicrobial use in animals. However, these generic guidelines need to be translated into a set of animal species- and disease-specific practice recommendations. This article focuses on prevention of antimicrobial resistance and its complex relationship with treatment efficacy, highlighting key situations where the current antimicrobial drug products, treatment recommendations, and practices may be insufficient to minimize antimicrobial selection. The authors address this topic using a multidisciplinary approach involving microbiology, pharmacology, clinical medicine, and animal husbandry. In the first part of the article, we define four key targets for implementing the concept of optimal antimicrobial treatment in veterinary practice: (i) reduction of overall antimicrobial consumption, (ii) improved use of diagnostic testing, (iii) prudent use of second-line, critically important antimicrobials, and (iv) optimization of dosage regimens. In the second part, we provided practice recommendations for achieving these four targets, with reference to specific conditions that account for most antimicrobial use in pigs (intestinal and respiratory disease), cattle (respiratory disease and mastitis), dogs and cats (skin, intestinal, genitourinary, and respiratory disease), and horses (upper respiratory disease, neonatal foal care, and surgical infections). Lastly, we present perspectives on the education and research needs for improving antimicrobial use in the future.

In vitro synergy of sertraline and tetracycline cannot be reproduced in pigs orally challenged with a tetracycline resistant Escherichia coli

Background

Antimicrobial helper-compounds may reverse antimicrobial resistance. Sertraline, a antidepressant drug, has been suggested as a tetracycline helper-compound. Tetracycline is the preferred antimicrobial for treatment of enteric diseases in pigs. This study is the first to evaluate the potency of sertraline as a tetracycline adjuvant in pigs.

Methods

Forty-eight nursery pigs were divided into four treatment groups: Tetracycline, sertraline, tetracycline/sertraline or un-medicated control. Fecal and ileal samples were obtained before treatment, 48 h and nine days after five days of treatment, respectively. Colony forming units (CFU) of tetracycline resistant coliforms in each sample (ileal or fecal) and CFU of an orally inoculated tetracycline-resistant strain of Escherichia coli were determined at each sampling point. The microbiome of fecal and ileal and samples was analyzed by sequencing of the 16S V3-V4 region.

Results

The results did not provide evidence that sertraline in combination with tetracycline has any impact on tetracycline resistant bacteria in either fecal or ileum samples, while in the tetracycline treated group of pigs, an increase in the prevalence of a tetracycline resistant indicator strain of Escherichia coli shortly after ended five-day treatment was observed. The ileal samples obtained shortly after ended treatment showed treatment-associated changes in the composition of the microbiota in the groups of pigs treated with tetracycline (+/−) sertraline. While tetracycline treatment increased the abundance in the reads of E. coli, sertraline/tetracycline treatment led to increased abundances of Streptococcus spp. and decreased abundances of Lactobacillus spp. However, all observed differences (on CFU counts and microbiota composition) between groups shortly after treatment had diminished in less than two weeks after last treatment day.

Conclusions

Sertraline (+/−) tetracycline treatment did not reduce the long-term level of tetracycline-resistant bacteria in the feces or small intestine contents of piglets compared to the un-medicated control group of pigs. The result of this study reflects the importance of in vivo studies for confirmation of the antimicrobial helper-compound potential of an in vitro active compound.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1383-5) contains supplementary material, which is available to authorized users.