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

Whole-genome sequencing of multidrug-resistant Klebsiella pneumoniae with capsular serotype K2 isolates from mink in China

BACKGROUND

Klebsiella pneumoniae is a zoonotic opportunistic pathogen, and also one of the common pathogenic bacteria causing mink pneumonia. The aim of this study was to get a better understanding of the whole-genome of multi-drug resistant Klebsiella pneumoniae with K2 serotype in China. This study for the first time to analyze Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, resistance and virulence genes of Klebsiella pneumoniae in mink.

RESULTS

The isolate was Klebsiella pneumoniae with serotype K2 and ST6189 by PCR method. The string test was positive and showed high mucus phenotype. There was one plasmid with IncFIB replicons in the genome. The virulence factors including capsule, lipopolysaccharide, adhesin, iron uptake system, urease, secretory system, regulatory gene (rcsA, rcsB), determinants of pili adhesion, enolase and magnesium ion absorption related genes. The strain was multi-drug resistant. A total of 26  resistance genes, including beta-lactam, aminoglycosides, tetracycline, fluoroquinolones, sulfonamides, amide alcohols, macrolides, rifampicin, fosfomycin, vancomycin, diaminopyrimidines and polymyxin. Multidrug-resistant efflux protein AcrA, AcrB, TolC, were predicted in the strain.

CONCLUSION

It was the first to identify that serotype K2 K. pneumonia with ST6189 isolated from mink in China. The finding indicated that hypervirulent and multi-drug resistant K. pneumoniae was exist in Chinese mink. The whole-genome of K. pneumoniae isolates have importance in mink farming practice.

Aggregation-induced emission carbon dots as Al3+-mediated nanoaggregate probe for rapid and selective detection of tetracycline

Worldwide abuse of tetracycline (TC) seriously threatens environmental safety and human health. Metal-TC complexes formed by residual TC in the environment can also contribute to the spread of antibiotic resistance. Therefore, monitoring of TC residues is still required. Here, we report novel aggregation-induced emission carbon dots (AIE-Cdots) as nanoaggregate probes for the rapid and selective detection of TC residue. Riboflavin precursors with rotational functional groups led to the development of AIE-Cdots. The aggregation of AIE-Cdots was induced selectively for Al3+, amplifying the fluorescence signals owing to the restricted rotation of the side chains on the AIE-Cdot surface. The fluorescence signal of such Al3+-mediated nanoaggregates (Al3+-NAs) was further triggered by the structural fixation of TC at the Al3+ active sites, suggesting the formation of TC-coordinated Al3+-NAs. A linear correlation was observed in the TC concentration range of 0-10 μM with a detection limit of 42 nM. In addition, the strong Al3+ binding affinity of AIE-Cdots produced similar NAs and enhanced fluorescence signals in Al3+-TC mixtures. These AIE-Cdots-based nanoplatforms have a rapid response, good selectivity, and reliable accuracy for detecting TC or aluminum complexes, meeting the requirements for hazardous substance monitoring and removal in environmental applications.

Effect of feeding dairy calves with milk fermented with selected probiotic strains on occurrence of diarrhoea, carriage of pathogenic and zoonotic microorganisms and growth performance

Calf-diarrhoea is a major health problem in dairy calves and a primary reason for use of antimicrobials. We aimed to investigate the effect of feeding milk fermented with a combination of four probiotic bacterial strains to young-calves on; occurrence of diarrhoea and associated-pathogens (bacteria, virus and parasites), shedding of Salmonella Dublin and Campylobacter, occurrence of virulence genes linked to Clostridium perfringens, Enterotoxigenic Escherichia coli and shiga-toxin producing E. coli (STEC), as well as growth performance. For this, 143 new-born calves from three Danish dairy-farms were allocated into Treatment- (fed the fermented milk for the first 8-weeks-of-life) and Control-groups (fed regular farm-milk). Diarrhoea was observed in 18.6 % (Farm 1), 22.4 % (Farm 2) and 15.7 % (Farm 3) of the total registrations mainly within the first 3-weeks-of-life. C. perfringens was the most frequently detected pathogen. The treatment did not affect the occurrence of virulence genes linked to STEC and C. perfringens and, overall, their detection levels were very low/undetected. The statistical model applied found no significant effect of the treatment on prevalence of early-diarrhoea (≤ 3 weeks), late-diarrhoea (>3 weeks), occurrence of C. perfringens and Cryptosporidium parvum or levels of Campylobacter spp. Limited detection of the other pathogens and associated virulence-genes under study, did not allow for assessment of the impact of the treatment on their occurrence. Notably, the feeding-approach showed a significant detrimental effect on daily-weight-gain. The inefficacy of the treatment may be associated with the complexity of influencing factors under field conditions including management practices.

Molecular Characterisation of Antimicrobial Resistance in E. coli Isolates from Piglets in the West Region of Romania

Antibiotics are widely used for prophylaxis and therapy, reducing morbidity and mortality produced by bacterial pathogensin pigs, including infections caused by Escherichia coli. The aim of this study was to characterise antibiotic resistance phenotypes and genotypes in E. coli isolates in pigs in West Romanian grower farms. Differential phenotypic susceptibility profiles and the contribution of resistance genes to phenotypic expression of susceptibility or resistance were evaluated. A total of 76 E. coli isolates were identified and confirmed by the MicroScan Walk Away System. The occurrence of four resistance genes, ampC, blaZ, blaTEM and tetK in strains resistant to 13 antibiotics was assessed. Of the E. coli isolates, 0% showed resistance to meropenem, 3.9% to tigecycline and 10.5% to piperacillin/tazobactam, whereas, in contrast, 100% were resistant to ampicillin and mezlocillin, 76.31% to piperacillin and 59.3% to tetracycline. The prevalence of resistance genes in resistant isolates detected by q-PCR analysis was 97.0% for ampC, 96% for blaZ, 32.9% for blaTEM and 58.8% for tetK. Penetrance (the proportion of individuals carrying a particular variant of a gene that also expresses an associated trait) was 50% for ampC (32% for amoxicillin/clavulanate, 62% for cefazolin, 32% for cefepime, 100% for cefotaxime, 56% for cefuroxime and 99% for ampicillin), 65% for blaZ (32% for amoxicillin/clavulanate and 99% for ampicillin), 51% for blaTEM (81% for piperacillin) and 44% for the tetK gene (83% for tetracycline). The result of phenotypic antibiotic resistance testing may indicate the presence of plasmid-borne resistance, with a diagnostic odds ratio of a positive phenotypic resistance for tetK being 4.52. As a management decision, the maximum penetrance admitted for using a specific antibiotic for E. coli infections in pigs is recommended to be less than 20%.

The effects of antibiotic use on the dynamics of the microbiome and resistome in pigs

Antibiotics are widely used in pig farming across the world which has led to concerns about the potential impact on human health through the selection of antibiotic resistant pathogenic bacteria. This worry has resulted in the development of a production scheme known as pigs Raised Without Antibiotics (RWA), in which pigs are produced in commercial farms, but are ear-tagged as RWA until slaughter unless they receive treatment, thus allowing the farmer to sell the pigs either as premium priced RWA or as conventional meat. Development of antibiotic resistance in pig farming has been studied in national surveys of antibiotic usage and resistance, as well as in experimental studies of groups of pigs, but not in individual pigs followed longitudinally in a commercial pig farm. In this study, a cohort of RWA designated pigs were sampled at 10 time points from birth until slaughter along with pen-mates treated with antibiotics at the same farm. From these samples, the microbiome, determined using 16S sequencing, and the resistome, as determined using qPCR for 82 resistance genes, was investigated, allowing us to examine the difference between RWA pigs and antibiotic treated pigs. We furthermore included 176 additional pigs from six different RWA farms which were sampled at the slaughterhouse as an endpoint to substantiate the cohort as well as for evaluation of intra-farm variability. The results showed a clear effect of age in both the microbiome and resistome composition from early life up until slaughter. As a function of antibiotic treatment, however, we observed a small but significant divergence between treated and untreated animals in their microbiome composition immediately following treatment, which disappeared before 8 weeks of age. The effect on the resistome was evident and an effect of treatment could still be detected at week 8. In animals sampled at the slaughterhouse, we observed no difference in the microbiome or the resistome as a result of treatment status but did see a strong effect of farm origin. Network analysis of co-occurrence of microbiome and resistome data suggested that some resistance genes may be transferred through mobile genetic elements, so we used Hi-C metagenomics on a subset of samples to investigate this. We conclude that antibiotic treatment has a differential effect on the microbiome vs. the resistome and that although resistance gene load is increased by antibiotic treatment load, this effect disappears before slaughter. More studies are needed to elucidate the optimal way to rear pigs without antibiotics.

Epidemiology, Environmental Risks, Virulence, and Resistance Determinants of Klebsiella pneumoniae From Dairy Cows in Hubei, China

Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen, which causes serious infections in humans and animals. To investigate the antimicrobial resistance pattern and virulence profile of K. pneumoniae, a total of 887 samples were collected from both the healthy and mastitis cows and the bedding, feed, feces, air, drinking water, spraying water, washing water, and milk cup swabs from five dairy farms in Hubei, China, during 2019 and 2020. K. pneumoniae was isolated and identified using PCR of the khe and 16S rDNA sequencing. A genotypic characterization was performed for K. pneumoniae isolates using wzi typing and multilocus sequence typing (MLST). Antimicrobial resistances were confirmed using broth microdilution against 17 antimicrobial agents and resistance and virulence genes were determined by PCR. The prevalence of K. pneumoniae was 26.94% (239/887) distributed in 101 wzi allele types (199/239, 83.26%) and 100 sequence types (STs) (209/239, 87.45%), including 5 new wzi allele type and 25 new STs. Phylogenetic analysis showed that K. pneumoniae isolated from milk, nipple swab, feed, and feces is classified in the same clone complex. By comparing with the PubMLST database, at least 67 STs have the risk of spreading in different species and regions. Interestingly, 60 STs have been isolated from humans. The isolates were highly sensitive to meropenem and colistin, but resistant to ampicillin (100%), sulfisoxazole (94.56%), cephalothin (47.28%), streptomycin (30.13%), and so on. Noteworthy, multidrug-resistant (MDR) rate was found to be 43.93% in this study. By PCR, 30 of 68 antimicrobial resistance (AMR) genes were identified; the prevalence rate of blaTEM, blaSHV, strA, strB, aadA1, and aac(6′)-Ib-cr was more than 50%. Eleven CTX-M-producing K. pneumoniae were found. The detection rate of fimH, mrkD, uge, wabG, entB, iutA, iroN, and ureA was over 85%. This study reinforces the epidemiological importance of K. pneumoniae in food-producing animals in Hubei. The emergence and spread of environmental MDR K. pneumoniae may pose a potential threat to food safety and public health.

Evaluation of the Impact of Antimicrobial Use Protocols in Porcine Reproductive and Respiratory Syndrome Virus-Infected Swine on Phenotypic Antimicrobial Resistance Patterns

A longitudinal study was conducted to assess the impact of different antimicrobial exposures of nursery-phase pigs on patterns of phenotypic antimicrobial resistance (AMR) in fecal indicator organisms throughout the growing phase. Based on practical approaches used to treat moderate to severe porcine reproductive and respiratory syndrome virus (PRRSV)-associated secondary bacterial infections, two antimicrobial protocols of differing intensities of exposure [44.1 and 181.5 animal-treatment days per 1000 animal days at risk (ATD)] were compared with a control group with minimal antimicrobial exposure (2.1 ATD). Litter-matched pigs (n = 108) with no prior antimicrobial exposure were assigned randomly to the treatment groups. Pen fecal samples were collected nine times during the wean-to-finish period and cultured for Escherichia coli and Enterococcus spp. Antimicrobial-susceptibility testing was conducted using NARMS Gram-negative and Gram-positive antibiotic panels. Despite up to 65-fold difference in ATD, few and modest differences were observed between groups and over time. Resistance patterns at marketing overall remained similar to those observed at weaning, prior to any antimicrobial exposures. Those differences observed could not readily be reconciled with the patterns of antimicrobial exposure. Resistance of E. coli to streptomycin was higher in the group exposed to 44.1 ATD, but no aminoglycosides were used. In all instances where resistances differed between time points, the higher resistance occurred early in the trial prior to any antimicrobial exposures. These minimal impacts on AMR despite substantially different antimicrobial exposures point to the lack of understanding of the drivers of AMR at the population level and the likely importance of factors other than antimicrobial exposure. IMPORTANCE Despite a recognized need for more longitudinal studies to assess the effects of antimicrobial use on resistance in food animals, they remain sparse in the literature, and most longitudinal studies of pigs have been observational. The current experimental study had the advantages of greater control of potential confounding, precise measurement of antimicrobial exposures which differed markedly between groups and tracking of pigs until market age. Overall, resistance patterns were remarkably stable between the treatment groups over time, and the differences observed could not be readily reconciled with the antimicrobial exposures, indicating the likely importance of other determinants of AMR at the population level.

Controlled Synthesis of CuS and Cu9S5 and Their Application in the Photocatalytic Mineralization of Tetracycline

Pure-phase Cu2−xS (x = 1, 0.2) nanoparticles have been synthesized by the thermal decomposition of copper(II) dithiocarbamate as a single-source precursor in oleylamine as a capping agent. The compositions of the Cu2−xS nanocrystals varied from CuS (covellite) through the mixture of phases (CuS and Cu7.2S4) to Cu9S5 (digenite) by simply varying the temperature of synthesis. The crystallinity and morphology of the copper sulfides were studied using X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM), which showed pure phases at low (120 °C) and high (220 °C) temperatures and a mixture of phases at intermediate temperatures (150 and 180 °C). Covellite was of a spherical morphology, while digenite was rod shaped. The optical properties of these nanocrystals were characterized by UV−vis–NIR and photoluminescence spectroscopies. Both samples had very similar absorption spectra but distinguishable fluorescence properties and exhibited a blue shift in their band gap energies compared to bulk Cu2−xS. The pure phases were used as catalysts for the photocatalytic degradation of tetracycline (TC) under visible-light irradiation. The results demonstrated that the photocatalytic activity of the digenite phase exhibited higher catalytic degradation of 98.5% compared to the covellite phase, which showed 88% degradation within the 120 min reaction time using 80 mg of the catalysts. The higher degradation efficiency achieved with the digenite phase was attributed to its higher absorption of the visible light compared to covellite.

Replacement of Metaphylactic Antimicrobial Therapy by Oral Administration of Ligilactobacillus salivarius MP100 in a Pig Farm

Antibiotic use in swine production contributes to the emergence and spread of resistant bacteria, which poses a threat on human health. Therefore, alternative approaches must be developed. The objective of this work was the characterization of the probiotic properties of a Ligilactobacillus salivarius strain isolated from sow's milk and its application as an inoculated fermented feed to pregnant sows and piglets. The study was carried in a farm in which metaphylactic use of antimicrobials (including zinc oxide) was eliminated at the time of starting the probiotic intervention, which lasted for 2 years. Feces from 8-week-old piglets were collected before and after the treatment and microbiological and biochemical analyses were performed. The procedure led to an increase in the concentrations of clostridia and lactobacilli-related bacteria. Parallel, an increase in the concentration of butyrate, propionate and acetate was observed and a notable reduction in the presence of antibiotic resistant lactobacilli became apparent. In conclusion, replacement of antimicrobials by a microbiota-friendly approach was feasible and led to positive microbiological and biochemical changes in the enteric environment.

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.

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.