Association between Antibiotic Consumption and Resistance in Mink Production.

Antibiotic consumption is considered to be a main driver of antibiotic resistant bacteria. Mink breeding follows a distinctive seasonal reproduction cycle, and all of the mink produced in the northern hemisphere are bred, born, and pelted around the same time of year. Some of the diseases are age-related, which is reflected in the seasonal variation of antibiotic consumption. The seasonality makes mink a good model for the investigation of the association between antibiotic consumption and resistance. The objectives of this study were (1) to monitor the farm level of antibiotic resistance during one production cycle and (2) to assess the potential associations between antibiotic consumption and resistance. Twenty-four farms were included in this study (Denmark n = 20, Iceland n = 2, and The Netherlands n = 2), following a cohort of animals born in 2018. Staphylococcus delphini and Escherichia coli were isolated from samples of the carcasses and faeces and were collected randomly. The isolates were susceptibility tested and subsequently divided into the sensitive wildtype (WT) and the resistant non-wildtype (NWT) populations. The antibiotic consumption relative to the sampling periods was assessed as having a short-term or a long-term impact, i.e., in two explanatory factors. For both S. delphini and E. coli, a large between-farm variation of NWT profiles was detected. In the final multivariable, generalized linear mixed models, significant associations between NWT isolates and the consumption of specific antibiotics were found: the short-term use of tetracyclines in the growth period was associated with the occurrence of tetracycline NWT E. coli in the growth period (OR: 11.94 [1.78; 89.28]), and the long-term use of macrolide and tetracyclines was associated with the occurrence of erythromycin NWT S. delphini in the weaning period (OR: 18.2 [2.26; 321.36]) and tetracycline NWT S. delphini in the growth period (OR: 8.2 [1.27; 63.31]), respectively. Farms with zero consumption in the study years prior to sampling also had a substantial proportion of NWT isolates, indicating that NWT isolates are persistent and/or widely spread in the environment. Generally, a high occurrence of tetracycline NWTs was observed. NWT isolates with resistance against the most commonly used antibiotics were found on all the farms, stressing the need for routine surveillance and the prudent use of antibiotics. The results offer a preview of the complex relationship between consumption and resistance, demonstrating some significant associations between use and resistance. Moreover, antibiotic-resistant bacteria are present even on farms with no antibiotic consumption over extended periods, and theoretical explanations supported by the data are offered.

First finding of Streptococcus phocae infections in mink (Neovison vison).

Streptococcus phocae infection has been described in salmon, sea otters, and several families of pinnipeds. The pathology of the infected animals has mainly been located in the respiratory tract and reproductive system, and with indications of septicemia. In this study, we report the finding of S. phocae in diagnostic material from three unrelated cases of farmed mink. Since S. phocae initially has been described in pinnipeds, two isolates from wild harbor seals were included. All isolates originated from Denmark. To our knowledge, this is the first report of S. phocae infection in mink. The animals (three mink, two seals) were necropsied, and samples were collected for bacteriology, virology, and histopathology. Additionally, the S. phocae isolates were whole genome sequenced and compared to sequences of previously reported isolates from other host species. S. phocae was isolated from the lungs of one mink and one seal with bacteremia, and from one seal with pneumonia. The two remaining mink had dermal infections on the paws and S. phocae was isolated from the lesions. The analysis of the sequence data showed that the three mink isolates and one seal isolate were closely related. Further investigation is needed to conclude whether S. phocae is establishing as commensal in farmed mink and to uncover the infection related pathology in mink. Streptococcus phocae has been described as an emerging pathogen in other species, therefore future awareness and surveillance of this pathogen is crucial.

Livestock-associated MRSA survival on house flies (Musca domestica) and stable flies (Stomoxys calcitrans) after removal from a Danish pig farm.

We caught stable- and house flies on a Danish LA-MRSA positive pig farm. Stable- and house flies were housed together and culled over time to test for the presence of live LA-MRSA bacteria at 24 h intervals to establish the length of time for which LA-MRSA can persist on flies. On average, 7% of stable flies and 27% of house flies tested positive for LA-MRSA immediately upon removal from the farm. LA-MRSA prevalence decreased over time and estimates based on a Kaplan-Meier time-to-event analysis indicated that the probability of a stable- or house fly testing positive for LA-MRSA was 5.4% and 7.8% after 24 h, 3.5% and 4.3% after 48 h, 3.1% and 2.2% after 72 h and 0.4% and 0% after 96 h of removal from the pig farm, respectively. Simultaneously, we found that caged cultivated house flies became carriers of LA-MRSA, without direct contact with pigs, in the same proportions as wild flies inside the farm. We provide distance distributions of Danish pig farms and residential addresses as well as the calculated maximum dispersal potentials of stable- and house flies, which suggest that there is a potential for stable- and house flies dispersing live LA-MRSA bacteria into the surrounding environment of a pig farm. This potential should therefore be considered when modelling the spread between farms or the risk posed to humans living in close proximity to LA-MRSA pig farm sources.

Employing MIC Data for Mink Pathogens to Propose Tentative Epidemiological Cut-Off Values: A Step Toward Rationalizing Antimicrobial Use in Mink.

Optimizing antimicrobial dosage regimens and development of breakpoints for antimicrobial susceptibility testing are important prerequisites for rational antimicrobial use. The objectives of the study were (1) to produce MIC data for four mink pathogens and (2) to employ these MIC data to support the development of tentative epidemiological cut-off values (TECOFFs), which may be used for future development of mink-specific antimicrobial dosages and breakpoints. Broth microdilution was used to establish MIC distributions for 322 mink bacterial isolates of clinical origin from six European mink-producing countries. The included species were E. coli (n = 162), S. delphini (n = 63), S. canis (n = 42), and P. aeruginosa (n = 55). Sixty-four E. coli isolates and 34 S. delphini isolates were whole-genome sequenced and analyzed for antimicrobial resistance genes. No EUCAST MIC data are available on S. delphini and S. canis, hence tentative ECOFFs were suggested for the majority of the tested antimicrobials. For E. coli and P. aeruginosa, the wildtype distributions were in accordance with EUCAST data. Overall, the genotypes of the sequenced isolates were in concordance with the phenotypes. These data constitute an important piece in the puzzle of developing antimicrobial dosages and clinical breakpoints for mink. Until pharmacokinetic and clinical data become available, the (tentative) ECOFFs can be used for monitoring resistance development and as surrogates for clinical breakpoints.

Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis.

BACKGROUND: The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including antimicrobial resistance genes encoded by mobile genetic elements (MGEs). Here, we investigate this mobilome in successful hospital associated genetic lineages, E. faecium sequence type (ST)17 (n=10) and ST78 (n=10), E. faecalis ST6 (n=10) and ST40 (n=10) by DNA microarray analyses. RESULTS: The hybridization patterns of 272 representative targets including plasmid backbones (n=85), transposable elements (n=85), resistance determinants (n=67), prophages (n=29) and clustered regularly interspaced short palindromic repeats (CRISPR)-cas sequences (n=6) separated the strains according to species, and for E. faecalis also according to STs. RCR-, Rep_3-, RepA_N- and Inc18-family plasmids were highly prevalent and with the exception of Rep_3, evenly distributed between the species. There was a considerable difference in the replicon profile, with rep 17/pRUM , rep 2/pRE25 , rep 14/EFNP1 and rep 20/pLG1 dominating in E. faecium and rep 9/pCF10 , rep 2/pRE25 and rep 7 in E. faecalis strains. We observed an overall high correlation between the presence and absence of genes coding for resistance towards antibiotics, metals, biocides and their corresponding MGEs as well as their phenotypic antimicrobial susceptibility pattern. Although most IS families were represented in both E. faecalis and E. faecium, specific IS elements within these families were distributed in only one species. The prevalence of IS256-, IS3-, ISL3-, IS200/IS605-, IS110-, IS982- and IS4-transposases was significantly higher in E. faecium than E. faecalis, and that of IS110-, IS982- and IS1182-transposases in E. faecalis ST6 compared to ST40. Notably, the transposases of IS981, ISEfm1 and IS1678 that have only been reported in few enterococcal isolates were well represented in the E. faecium strains. E. faecalis ST40 strains harboured possible functional CRISPR-Cas systems, and still resistance and prophage sequences were generally well represented. CONCLUSIONS: The targeted MGEs were highly prevalent among the selected STs, underlining their potential importance in the evolution of hospital-adapted lineages of enterococci. Although the propensity of inter-species horizontal gene transfer (HGT) must be emphasized, the considerable species-specificity of these MGEs indicates a separate vertical evolution of MGEs within each species, and for E. faecalis within each ST.

Presence of glycopeptide-encoding plasmids in enterococcal isolates from food and humans in Denmark.

Enterococci and especially glycopeptides-resistant enterococci (GRE) are a growing concern due to their ability to cause infections in hospitals. Transmission of antimicrobial resistance between reservoirs such as animals, meat, and humans are in most cases linked to transmission of mobile genetic elements (MGE) such as plasmids and transposons. Presence of MGE was tested in all GRE isolated from food in Denmark in 2005-2007 including the first vanA mediated Enterococcus faecalis isolated from food. The ability of these plasmids to transfer and persist among enterococci was investigated using newly developed techniques for classification of plasmids. Replicons associated with sex pheromone-inducible plasmids were detected in all GR E. faecalis, whereas GR Enterococcus faecium contained plasmids known to be widely distributed among enterococci. vanA resistance is common in E. faecium isolates from meat and animals in Europe and is rarely found in E. faecalis. This article describes the first characterization of MGE from vanA mediated E. faecalis, thus linking this resistance genotype to pheromone responding plasmids.

Evaluation of Petrifilm Select E. coli Count Plate medium to discriminate antimicrobial resistant Escherichia coli.

BACKGROUND: Screening and enumeration of antimicrobial resistant Escherichia coli directly from samples is needed to identify emerging resistant clones and obtain quantitative data for risk assessment. Aim of this study was to evaluate the performance of 3M Petrifilm Select E. coli Count Plate (SEC plate) supplemented with antimicrobials to discriminate antimicrobial-resistant and non-resistant E. coli. METHOD: A range of E. coli isolates were tested by agar dilution method comparing the Minimal Inhibitory Concentration (MIC) for eight antimicrobials obtained by Mueller-Hinton II agar, MacConkey agar and SEC plates. Kappa statistics was used to assess the levels of agreement when classifying strains as resistant, intermediate or susceptible. RESULTS: SEC plate showed that 74% of all strains agreed within +/- 1 log2 dilution when comparing MICs with Mueller-Hinton II media. High agreement levels were found for gentamicin, ampicillin, chloramphenicol and cefotaxime, resulting in a kappa value of 0.9 and 100% agreement within +/- 1 log2 dilution. Significant variances were observed for oxytetracycline and sulphamethoxazole. Further tests showed that the observed discrepancy in classification of susceptibility to oxytetracycline by the two media could be overcome when a plate-dependent breakpoint of 64 mg/L was used for SEC plates. For sulphamethoxazole, SEC plates provided unacceptably high MICs. CONCLUSION: SEC plates showed good agreement with Mueller-Hinton II agar in MIC studies and can be used to screen and discriminate resistant E. coli for ampicillin, cephalothin, streptomycin, chloramphenicol, cefotaxime and gentamicin using CLSI standardized breakpoints, but not for sulphamethoxazole. SEC plates can also be used to discriminate oxytetracycline-resistant E. coli if a plate-dependent breakpoint value of 64 mg/L is used.

Relevance of hot spots in the evolution and transmission of Tn1546 in glycopeptide-resistant Enterococcus faecium (GREF) from broiler origin.

OBJECTIVES: Glycopeptide-resistant enterococci are still present within the broiler sector, despite the EU ban of avoparcin more than a decade ago. In the present study, we have developed a rapid method for screening the flanking regions at the integration point of Tn1546 in glycopeptide-resistant Enterococcus faecium isolated from broiler farms. METHODS: Total DNA was digested, ligated and amplified using primers from inside Tn1546. The resulting amplicons were purified and sequenced. Two new primers were designed based on obtained sequences. RESULTS: Two main insertion points have been repeatedly found in isolates from the UK (n = 150). The first insertion point revealed that 25 isolates harboured Tn1546 positioned in a sequence with 96% homology to a streptomycin adenyltransferase gene (AY604739) from a Staphylococcus intermedius plasmid. At this insertion point, a direct repeat (GTCCT) was duplicated as previously described, indicating transposition at the target site. Furthermore, this 'hot spot' was also detected in isolates from Norway (2/8) and Denmark (17/20). The second insertion point detected in 45 isolates from the UK revealed integration into an Inc18-like plasmid, most likely by a process of target site recombination. CONCLUSIONS: The presence of a common insertion point for isolates from different geographical areas could suggest the insertion of Tn1546 by transposition in a plasmid-specific site, followed by genetic rearrangement both inside the transposon and in the flanking regions.

Type 3 fimbriae, encoded by the conjugative plasmid pOLA52, enhance biofilm formation and transfer frequencies in Enterobacteriaceae strains.

The conjugative plasmid pOLA52, which confers resistance to olaquindox and other antimicrobial agents through a multidrug efflux pump, was investigated for its ability to promote biofilm formation in Escherichia coli. Screening of a transposon-mutagenized pOLA52 clone library revealed several biofilm-deficient mutants, which all mapped within a putative operon with high homology to the mrkABCDF operon of Klebsiella pneumoniae, where these genes are responsible for type 3 fimbriae expression, attachment to surfaces and biofilm formation. Biofilm formation in microtitre plates and in urinary catheters of clones containing pOLA52 with a disrupted putative mrk operon was reduced by more than 100-fold and 2-fold, respectively, compared to mutants with an intact mrk operon. The conjugative transfer rate of pOLA52 was also significantly lower when the mrk operon was disrupted. Through reverse transcriptase analysis, it was demonstrated that the genes contained in the putative mrk operon were linked and likely to be expressed as a single operon. Immunoblotting with type 3 fimbriae (MrkA)-specific antibodies further verified expression of type 3 fimbriae. When transferred to other, potentially pathogenic, members of the family Enterobacteriaceae, including Klebsiella pneumoniae, Salmonella Typhimurium, Kluyvera sp. and Enterobacter aerogenes, pOLA52 facilitated increased biofilm formation. pOLA52 is believed to represent the first example of a conjugative plasmid encoding type 3 fimbriae, resulting in enhanced conjugation frequencies and biofilm formation of the plasmid-harbouring strain.

A longitudinal study to assess the persistence of vancomycin-resistant Enterococcus faecium (VREF) on an intensive broiler farm in the United Kingdom.

Seven years after the ban of avoparcin, VREF could still be isolated within sectors of the UK broiler industry. The aim of this study was to assess whether there is a carryover of VREF between consecutive flocks of birds, to conduct a preliminary investigation of possible routes of entry of VREF into broiler houses and to follow the dynamics of VREF shed by growing birds. A series of nine visits were made to two of six houses on a conventional broiler farm. A total of 343 vanA VREF were recovered from environmental (95/843) and faecal (248/416) samples. Significant differences were observed in the carryover of VREF between pre- and postcohort postcleaning and disinfection visits (RR 0.57, P=0.006). Ninety-nine percent of the VREF isolates were resistant to more than five antimicrobials, with 42 isolates (n=49) positive for erm(B) and 32 (n=40) for vat(E). Pulsed field gel electrophoresis (PFGE) typing identified 50 PFGE types within 15 different PFGE clusters of 90% similarity, demonstrating a high level of genetic diversity within VREF populations from epidemiologically related broiler flocks and broiler houses. Further characterization of Tn1546 from different clones showed a low diversity of Tn-types, suggesting horizontal transfer of resistance determinants between different genetic clones. Thus, this study does not only show the persistence of VREF but also of multi-drug resistant lineages of VREF.

Transposon characterization of vancomycin-resistant Enterococcus faecium (VREF) and dissemination of resistance associated with transferable plasmids.

OBJECTIVES: VanA glycopeptide resistance has persisted on broiler farms in the UK despite the absence of the antimicrobial selective pressure, avoparcin. This study aimed to investigate the contribution of horizontal gene transfer of Tn1546 versus clonal spread in the dissemination of the resistance. METHODS AND RESULTS: One hundred and one vancomycin-resistant Enterococcus faecium isolated from 19 unrelated farms have been investigated. Tn1546 characterization by long PCR and ClaI-digestions of amplicons showed a very low diversity of Tn types (n=4) in comparison to the high genotypic diversity demonstrated by PFGE (n=62). Conjugation experiments were carried out to assess the transfer of vancomycin resistance. Co-transfer of vanA together with erm(B) positioned on the same conjugative plasmid containing a replicon similar to pRE25 was demonstrated and also the presence of different plasmid replicons, associated with antimicrobial resistance on several unrelated farms. CONCLUSIONS: Horizontal transfer of vancomycin resistance may play a more important role in the persistence of antimicrobial resistance than clonal spread. The presence of different plasmid replicons, associated with antimicrobial resistance on several unrelated farms, illustrates the ability of these enterococci to acquire and disseminate mobile genetic elements within integrated livestock systems.

Substrate specificity of the OqxAB multidrug resistance pump in Escherichia coli and selected enteric bacteria.

OBJECTIVES: A plasmid-encoded multidrug efflux pump, OqxAB, identified in Escherichia coli of porcine origin, was tested for substrate specificity against selected antibiotics, detergents and disinfectants. The ability of horizontal transfer to food-borne pathogens of the Enterobacteriaceae family was also investigated. METHODS: The MICs of selected substrates were determined with a broth dilution assay using two isogenic E. coli strains, except for the presence of the oqxAB operon. A derivative of the plasmid encoding OqxAB (pOLA52) was constructed and horizontal transfer to Salmonella Typhimurium, Klebsiella pneumoniae, Kluyvera sp. and Enterobacter aerogenes was investigated. The effect of the presence of the OqxAB pump on susceptibility for selected compounds was investigated using broth dilution assays. RESULTS: The OqxAB pump conferred antimicrobial resistance or reduced susceptibility towards a variety of substrates in E. coli. These included animal growth promoters, antimicrobials, disinfectants and detergents. pOLA52 could readily be transferred to enterobacterial pathogens. Transconjugants showed reduced susceptibility towards chloramphenicol, ciprofloxacin and olaquindox. CONCLUSIONS: The plasmid-encoded OqxAB pump has a wide substrate specificity and can be transferred between Enterobacteriaceae conferring reduced susceptibility to a multitude of substrates. These results could indicate some dependence on the outer membrane proteins present in the different species.

Susceptibility of bacteria isolated from pigs to tiamulin and enrofloxacin metabolites.

Susceptibilities to metabolites of tiamulin (TIA) and enrofloxacin (ENR) were tested using selected bacteria with previously defined minimal inhibitory concentrations (MIC). The TIA metabolites tested were: N-deethyl-tiamulin (DTIA), 2beta-hydroxy-tiamulin (2beta-HTIA) and 8alpha-hydroxy-tiamulin (8alpha-HTIA), and the ENR metabolites were: ciprofloxacin (CIP) and enrofloxacin N-oxide (ENR-N). Bacteria, all of porcine origin, were selected as representatives of bacterial infections (Staphylococcus hyicus and Actinobacillus pleuropneumoniae), zoonotic bacteria (Campylobacter coli) and indicator bacteria (Escherichia coli and enterococci). Furthermore the effects of these compounds were tested on the microbial community of active sludge to test any negative effect on colony forming units (CFU). DTIA had a potency of 12.5-50% of the potency of TIA. 2beta-HTIA and 8alpha-HTIA had potencies less than 1% of the potency of TIA. ENR-N had a potency of 0.75-1.5% of the potency of ENR, while CIP and ENR had similar potencies. Results obtained here indicate that CIP and DTIA could contribute to the selective pressure for upholding antimicrobial resistant bacteria in animals under ENR or TIA treatment. The most potent metabolites CIP and DTIA showed considerable potencies against activated sludge bacteria compared to the parent compounds. EC(50) (microg/ml) for ENR, CIP, TIA and DTIA were 0.018 [95% CI: 0.028-0.149], 0.064 [95% CI: 0.007-0.046], 6.0 [95% CI: 3.6-9.8], and 9.7 [95% CI: 5.8-16.3], respectively. This indicates that the compounds can change the bacterial population in the sludge, and hereby alter the properties of the sludge.

Effect of tetracycline residues in pig manure slurry on tetracycline-resistant bacteria and resistance gene tet(M) in soil microcosms.

Effects of tetracycline residues from pig manure slurry on the prevalence of tetracycline-resistant bacteria and the tetracycline resistance gene, tet(M), were studied in soil microcosms. Four types of soil microcosms were established for a period of 152 days, supplemented with combinations of pig manure slurry and a tetracycline-resistant Enterococcus faecalis, CG110, containing the tetracycline resistance gene tet(M) (on the conjugative transposon, Tn916). The prevalence of both tetracycline-resistant aerobic bacteria and tetracycline-resistant enterococci declined rapidly until day 45 where no significant differences in the levels of tetracycline-resistant bacteria in any of the four types of microcosms could be detected. tet(M) could be detected in microcosms supplemented with either pig manure slurry and/or E. faecalis CG110 (tet(M)) for the whole period (152 days). tet(M) could be detected longer than tetracycline-resistant enterococci could be isolated (limit of detection 100 CFU/g soil) probably due to viable but not culturable (VBNC) bacteria with tet(M), horizontal gene transfer of tet(M) to indigenous soil bacteria or presence of "free" DNA. The concentration of chlortetracycline and oxytetracycline were almost stable through out the experimental period, but the tetracycline concentrations had no effect on prevalence of tetracycline-resistant bacteria. The presented microcosm approach simulated natural farmland conditions well and supported results from previous field studies.

Analysis of gyrA and parC mutations in enterococci from environmental samples with reduced susceptibility to ciprofloxacin.

The quinolone resistance determining regions of gyrA and parC in four species of enterococci from environmental samples with reduced susceptibility to ciprofloxacin were sequenced. The nucleotide sequence variations of parC could be related to the different enterococcal species. Mutations in Enterococcus faecalis and Enterococcus faecium related to reduced susceptibility were identical to mutations detected in E. faecalis and E. faecium of clinical origin. A minimal inhibitory concentration of 8 microg ml(-1) to ciprofloxacin was not associated with any mutations in the gyrA and parC gene of Enterococcus casseliflavus and Enterococcus gallinarum. These two species may be intrinsically less susceptible to ciprofloxacin.