Resistance to antimicrobial agents used for animal therapy in pathogenic-, zoonotic- and indicator bacteria isolated from different food animals in Denmark: a baseline study for the Danish Integrated Antimicrobial Resistance Monitoring Programme (DANMAP)

Global antimicrobial resistance and use surveillance system (GLASS 2022): Investigating the relationship between antimicrobial resistance and antimicrobial consumption data across the participating countries

For the first time since 2015, the World Health Organization's (WHO) global Antimicrobial Resistance and Use Surveillance (GLASS) featured both global reports for antimicrobial resistance (AMR) and antimicrobial consumption (AMC) data in its annual reports. In this study we investigated the relationship of AMR with AMC within participating countries reported in the GLASS 2022 report. Our analysis found a statistically significant correlation between beta-lactam/cephalosporin and fluoroquinolones consumption and AMR to these antimicrobials associated with bloodstream E. coli and Klebsiella pneumoniae among the participating countries (P<0.05). We observed that for every 1 unit increase in defined daily dose DDD of beta-lactam/cephalosporins and quinolone consumptions among the countries, increased the recoveries of bloodstream-associated beta-lactam/cephalosporins-resistant E. coli/Klebsiella spp. by 11-22% and quinolone-resistant E. coli/Klebsiella spp. by 31-40%. When we compared the antimicrobial consumptions between the antimicrobial ATC (Alphanumeric codes developed by WHO) groups and countries, we observed a statistically significant higher daily consumption of beta-lactam-penicillins (J01C, DDD difference range: 5.23-8.13) and cephalosporins (J01D, DDD difference range: 2.57-5.13) compared to other antimicrobial groups among the countries (adjusted for multiple comparisons using Tukey's method). Between the participating countries, we observed a statistically significant higher daily consumption of antimicrobial groups in Iran (DDD difference range: 3.63-4.84) and Uganda (DDD difference range: 3.79-5.01) compared to other participating countries (adjusted for multiple comparisons using Tukey's method). Understanding AMC and how it relates to AMR at the global scale is critical in the global AMR policy development and implementation of global antimicrobial stewardship.

Antibacterial potentials of carbon dots immobilized on chitosan and glass surfaces

Due to their antibacterial activity, chitosan‑carbon dot composites possess great potential for pharmaceuticals, medicine, and food preservation. Conducting a comprehensive study of the interactions between chitosan, carbon dots, and bacteria is crucial to understanding the processes behind applying these composites. This study aimed to immobilize carbon dots (C-dots) synthesized from Elaeagnus angustifolia fruits on chitosan and glass microbeads' surfaces, to characterize the test materials obtained after synthesis and immobilization, and to investigate their antibacterial potentials. C-dot synthesis was carried out from water extract in an acidic medium with the help of microwave irradiation, and their structural and optical properties were characterized by TEM, XRD, FT-IR, UV-vis, Zeta potential, and fluorescence methods. The surface of the glass microbeads was first activated and functionalized with surface amine groups with a silaning agent. C-dots were immobilized on both glass and chitosan microbeads using a crosslinking agent. Antibacterial potentials of nine different test materials, obtained before or after immobilization, were evaluated both qualitatively (MIC and MBC) and quantitatively (GI50) on E. coli, S. typhimurium, B. subtilis, and S. aureus, with the standard broth microdilution method. FT-IR and SEM-EDX analyses showed that C-dots were immobilized on chitosan (˂1 mm) and glass (˂100 μm) microbead surfaces. C-dots reduced the cell viability by ~25 % on S. typhimurium and B. subtilis (MIC = 25 mg/mL). It was also found that the highest antibacterial effect was recorded for C-dots-glass microbeads, which had a toxic effect of 43 % on S. aureus. In addition, binding C-dots to glass microbeads increased the antibacterial effect selectively in Gram-positive bacteria, while binding to chitosan microbeads was effective in all bacteria. The study showed that the antibacterial potential of C-dots-chitosan microbeads is more effective than C-dots-glass microbeads. C-dots could be used as carbon-based nanomaterials in antibacterial surface preparation once immobilized.

Antimicrobial resistance in Escherichia coli isolated from pigs and associations with aggregated antimicrobial usage in Ireland: A herd-level exploration

AIMS

Antimicrobial resistance (AMR) is of significant global concern and is a major One Health issue. There is evidence to suggest that increased antimicrobial usage (AMU) can be associated with AMR patterns, and therefore, there have been efforts to reduce AMU in anticipation of reducing AMR emergence risk. The aim of this study was to investigate whether there were any associations between AMU and AMR patterns of commensal Escherichia coli isolated from pig herds in Ireland.

METHODS AND RESULTS

Data on AMR from a panel of antimicrobials (AMDs) were gathered as part of national surveillance activities. These data were associated with reported usage of AMDs, on a year-quarter basis, measured in mg/kg at a herd-level using generalized estimating equation regression analysis. Associations were tested with AMR presence or multi-drug resistance (MDR; ≥3 classes) profiles and total AMU during the contemporaneous quarter and previous quarter, respectively. Furthermore, individual and AMD class-based associations were tested. The final dataset contained 218 observations (herd-quarter usage and AMR resistance profile) from 122 herds during 2019-2021. Apparent resistance prevalence varied according to AMD type, with the highest mean prevalence found with tetracycline at 51.57% (95% CI: 45.06%-58.09%). There were significant associations between a herd obtaining a positive AMR result for any AMDs and the overall levels of AMU during the year-quarter. Furthermore, there were significant positive associations between MDR and total AMU. At the compound level, chloramphenicol resistance was significantly associated with increased usage of trimethoprim/sulfadiazine and chlortetracycline, respectively (p < 0.010). Tetracycline resistance was associated with increased use of chlortetracycline (p = 0.008). At the antimicrobial class level, there was a significant positive relationship between the usage of phenicol and the probability of a resistance for chloramphenicol (p = 0.026) and between the usage of tetracycline and tetracycline resistance probability (p = 0.018).

CONCLUSIONS

Our data provide evidence of associations between overall AMU and AMR or MDR risk at the herd-quarter level. There was also evidence of associations between specific AMDs and patterns of resistance. Associations varied depending on whether time lags in usage were modelled or how usage was modelled (e.g. dichotomized or continuous). Associations with rarely used AMDs (e.g. critically important AMDs) were precluded due to a lack of statistical power. Continued monitoring of both AMU and AMR is crucial to assess the impacts of policy changes aimed at reducing AMU.

Modelling the effectiveness of surveillance based on metagenomics in detecting, monitoring, and forecasting antimicrobial resistance in livestock production under economic constraints

Current surveillance of antimicrobial resistance (AMR) is mostly based on testing indicator bacteria using minimum inhibitory concentration (MIC) panels. Metagenomics has the potential to identify all known antimicrobial resistant genes (ARGs) in complex samples and thereby detect changes in the occurrence earlier. Here, we simulate the results of an AMR surveillance program based on metagenomics in the Danish pig population. We modelled both an increase in the occurrence of ARGs and an introduction of a new ARG in a few farms and the subsequent spread to the entire population. To make the simulation realistic, the total cost of the surveillance was constrained, and the sampling schedule was set at one pool per month with 5, 20, 50, or 100 samples. Our simulations demonstrate that a pool of 20-50 samples and a sequencing depth of 250 million fragments resulted in the shortest time to detection in both scenarios, with a time delay to detection of change of [Formula: see text]15 months in all scenarios. Compared with culture-based surveillance, our simulation indicates that there are neither significant reductions nor increases in time to detect a change using metagenomics. The benefit of metagenomics is that it is possible to monitor all known resistance in one sampling and laboratory procedure in contrast to the current monitoring that is based on the phenotypic characterisation of selected indicator bacterial species. Therefore, overall changes in AMR in a population will be detected earlier using metagenomics due to the fact that the resistance gene does not have to be transferred to and expressed by an indicator bacteria before it is possible to detect.

Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China

China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Temperature and humidity in the barns were also correlated with ARG presence. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.

Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018

BackgroundIn Denmark, antimicrobial resistance (AMR) in pigs has been monitored since 1995 by phenotypic approaches using the same indicator bacteria. Emerging methodologies, such as metagenomics, may allow novel surveillance ways.AimThis study aimed to assess the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics.MethodsWe collated existing data on AMR and antimicrobial use (AMU) from the Danish surveillance programme and performed metagenomics sequencing on caecal samples that had been collected/stored through the programme during 1999-2004 and 2015-2018. We compared phenotypic and metagenomics results regarding AMR, and the correlation of both with AMU.ResultsVia the relative abundance of AMR genes, metagenomics allowed to rank these genes as well as the AMRs they contributed to, by their level of occurrence. Across the two study periods, resistance to aminoglycosides, macrolides, tetracycline, and beta-lactams appeared prominent, while resistance to fosfomycin and quinolones appeared low. In 2015-2018 sulfonamide resistance shifted from a low occurrence category to an intermediate one. Resistance to glycopeptides consistently decreased during the entire study period. Outcomes of both phenotypic and metagenomics approaches appeared to positively correlate with AMU. Metagenomics further allowed to identify multiple time-lagged correlations between AMU and AMR, the most evident being that increased macrolide use in sow/piglets or fatteners led to increased macrolide resistance with a lag of 3-6 months.ConclusionWe validated the long-term usefulness of indicator bacteria and showed that metagenomics is a promising approach for AMR surveillance.

One Health Surveillance of Antimicrobial Use and Resistance: Challenges and Successes of Implementing Surveillance Programs in Sri Lanka

Background: Sri Lanka is a low-income country, as defined by the World Bank. The country suffered further economic downturn during the COVID-19 pandemic. This situation adversely affected the prioritization of policies and programs around healthcare and public health. In particular, inflation, fuel prices, and shortage of food supplies increased struggles to implement antimicrobial resistance (AMR) programs. However, in the long run, it is crucial to gather data and evidence to plan AMR policies and track interventions. (1) Aim: To establish and reiterate the importance of prioritizing AMR programs in the One Health framework, the Fleming Fellows collected and studied antimicrobial use/consumption (AMU/AMC) and resistance (AMR) in humans, food-producing animals, and the environment. (2) Methods: A systematic and cross-sectional study was conducted between 2019 and 2021. By way of coordinating an AMU/AMC and AMR prevalence study across six agencies from human health and food-producing animal sectors, the authors established a field epidemiology study, laboratory testing, and data processing at their institutions. AMU/AMC patterns were surveyed using questionnaires and interviews, while AMR samples were collected for antibiotic susceptibility tests and genomic tests. Samples were tested for phenotypic and genotypic resistance. (3) Results: In human samples, resistance was highest to beta-lactam antibiotics. In non-human samples, resistance was highest to erythromycin, a highest-priority, critically important antibiotic defined by the World Health Organization. From government records, tylosin was sold the most in the food-producing animal sector. (4) Conclusions: Sri Lanka AMU and AMR trends in human and non-human sectors can be ascertained by a One Health framework. Further coordinated, consistent, and sustainable planning is feasible, and can help implement an AMU/AMR surveillance system in Sri Lanka.

Antimicrobial Usage by Small-Scale Commercial Poultry Farmers in Mid-Western District of Masindi Uganda: Patterns, Public Health Implications, and Antimicrobial Resistance of E. coli

Background

Poultry production in Uganda is growing at a fast rate due to increasing demand, notwithstanding, poor husbandry practices, and diseases, prompting farmers to rear healthy productive flocks with antimicrobials. The study evaluated the knowledge and practices as regards the use of antibiotics among poultry farmers in Masindi district and determined the antibiotic susceptibility profiles of E. coli strains from chickens.

Methods

A cross-sectional study using a closed-end questionnaire was conducted in 140 selected small-scale commercial poultry farms in Masindi district between June and December, 2020. Analyzed qualitative data were presented as frequencies, percentages, and their 95% confidence intervals (95% CI). Fecal swabs from chickens were inoculated onto a MacConkey agar, and E. coli was confirmed by standard biochemical tests. Antimicrobial susceptibility was determined by the disk diffusion method for 7 antibiotics.

Results

Most farmers (74%) used antibiotics, mainly tetracycline (51.4%) and sulfonamides (28.6%), given to the chicks (45%), for both curative and prophylaxis purposes (80%), and via drinking water (67%). Farmers mainly used antibiotics recommended by the veterinarian (76.4%), more than relying on experience (10.7%), while 45% were involved in self-medicating the birds. On choosing the correct dosage, 45.7% read the instruction, and 42.9% consulted a veterinarian. Only 10.7% observed the drug withdrawal period, while 53.6% consumed eggs at home or sold eggs (35.7%) from birds under treatment. Of the 200 E. coli strains, 90 (45.0%) were resistant to one drug, 74 (37.0%) to two, and multidrug resistance to three classes of antibiotics was 36 (18.0%). Overall, E. coli resistance to tetracycline was (69.0%), ampicillin (37.0%), sulfonamides (36.0%), and to kanamycin (1.5%).

Conclusions

The small-scale poultry farmers frequently use antimicrobial drugs, mainly tetracycline and sulfonamides for curative and prophylaxis. Thus, enforcing measures against antibiotic use supported by a strong veterinary service sector and farmers' training on judicious use of antimicrobials are needed.

Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.

Epidemiological Cut-Off Values and Multidrug Resistance of Escherichia coli Isolated from Domesticated Poultry and Pigs Reared in Mwanza, Tanzania: A Cross-Section Study

Increasing antimicrobial resistance (AMR) colonizing domesticated animals is a global concern threatening food safety. This study aimed at determining the prevalence of multidrug resistance (MDR) and epidemiological cut-off values (ECVs) of E. coli isolated from poultry and pigs in Mwanza, Tanzania. This cross-sectional study was conducted between June and August 2021, involving 297 pigs, 191 broilers, and 203 layers. Rectal and cloacal swabs were collected and processed following standard guidelines. ECVs were determined using normalized resistance interpretation (NRI), a computer software, and descriptive analysis was performed using STATA version 13.0. The overall prevalence of MDR E.coli was 63.2%, whereas poultry (87.5% layers and 86.3% broilers) were more colonized than pigs (31.8%) (p < 0.001). Based on ECVs of antibiotics tested, E. coli from broilers, layers, and pigs exhibited different resistance patterns hence different populations. Exotic breed (p < 0.001) and recent antimicrobial use (p < 0.001) significantly predicted colonization with MDR E. coli. Veterinary officers should implement regulations that prohibit the inappropriate use of antimicrobial agents in livestock keeping.

Genetic Characterization of Antibiotic Resistant Enterobacteriaceae Isolates From Bovine Animals and the Environment in Nigeria

There is a link between antibiotic resistance in humans, livestock and the environment. This study was carried out to characterize antibiotic resistant bovine and environmental Enterobacteriaceae isolates from Edo state, Nigeria. A total of 109 consecutive isolates of Enterobacteriaceae were isolated from March–May 2015 from 150 fecal samples of healthy bovine animals from three farms at slaughter in Edo state Nigeria. Similarly, 43 Enterobacteriaceae isolates were also obtained from a total of 100 environmental samples from different sources. Isolates were recovered and identified from samples using standard microbiological techniques. Recovered isolates were pre-identified by the Microbact Gram-Negative identification system and confirmed with Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing (rMLST). Antibiotic susceptibility testing was carried out by Kirby-Bauer method for 14 antibiotics. Whole genome sequencing (WGS) was carried out for isolate characterization and identification of resistance determinants. Out of 109 animal and 43 environmental Enterobacteriaceae isolates, 18 (17%) and 8 (19%) isolates based on selection criteria showed antibiotic resistance and were further investigated by whole genome sequencing (WGS). Resistance genes were detected in all (100%) of the resistant bovine and environmental Enterobacteriaceae isolates. The resistance determinants included β-lactamase genes, aminoglycoside modifying enzymes, qnr genes, sulfonamide, tetracycline and trimethoprim resistance genes, respectively. Out of the 18 and 8 resistant animal and environmental isolates 3 (17%) and 2 (25%) were multidrug resistant (MDR) and had resistance determinants which included efflux genes, regulatory systems modulating antibiotic efflux and antibiotic target alteration genes. Our study shows the dissemination of antibiotic resistance especially MDR strains among Nigerian bovine and environmental Enterobacteriaceae isolates. The presence of these resistant strains in animals and the environment constitute a serious health concern indicated by the difficult treatment options of the infections caused by these organisms. To the best of our knowledge we report the first detailed genomic characterization of antibiotic resistance in bovine and environmental Enterobacteriaceae isolates for Nigeria.

Antimicrobial Use and Susceptibility of Indicator Escherichia coli in Finnish Integrated Pork Production

In pigs, antimicrobial use (AMU) practices vary at different production phases between herds and between countries. Antimicrobial resistance (AMR) development is linked to AMU but recognized as a multi-factorial issue, and thus, any information increasing knowledge of AMU and AMR relationships is valuable. We described AMU and screened the carriage of different AMR phenotypes of indicator Escherichia coli in 25 selected Finnish piglet-producing and finishing herds that formed nine birth-to-slaughter production lines. Moreover, we studied associations between AMU and AMR in both herd types and throughout the production line. Treatment records were obtained from the national Sikava register for 1year, and AMU was quantified as mg/PCU (population correction unit) and TIs (treatment incidences). For phenotypic antimicrobial susceptibility testing, ten pen-level pooled feces samples (n=250) in each herd were collected from one room representing the oldest weaned piglets or the oldest finishing pigs. Majority of the medications (96.8%) was administered parenterally, and penicillin was the predominant antimicrobial in every herd. More different antimicrobial substances were used in piglet-producing than in finishing herds (median 5 and 1, respectively, p<0.001). As mg/PCU, sows had the highest AMU and suckling piglets had the highest TIs, whereas finishing pigs were the least treated age group. The proportion of susceptible indicator E. coli isolates of all studied isolates was 59.6%. Resistance was found most commonly against tetracycline, sulfamethoxazole, trimethoprim, and ampicillin, and multi-resistant (MR) isolates (46.5% of all resistant isolates) were resistant to a maximum of four different antimicrobials. Quinolone resistance was rare, and no resistance against 3rd-generation cephalosporins, meropenem, azithromycin, colistin, gentamicin, or tigecycline was detected. The main associations between AMU and AMR were found at antimicrobial group level when use was compared with the presence of AMR phenotypes. The proportion of resistant isolates was not associated with AMU, and herd size was not associated with either AMU or AMR. We suggest that the use of narrow-spectrum beta-lactams as a primary treatment option and lack of wide application of oral group medications potentially favors a good resistance pattern in integrated pork production.

Antimicrobial resistance patterns among different Escherichia coli isolates in the Kingdom of Saudi Arabia

Antimicrobial resistance patterns among different Escherichia coli isolates in the Kingdom of Saudi Arabia. This study aimed to investigate the patterns of antimicrobial resistance in E. coli isolated from different samples, and to identify potential pathogenic isolates in Riyadh, Kingdom of Saudi Arabia (KSA). In total, 51 bacterial isolates were recovered from 113 samples of human urine, food (raw meat, raw chicken, raw egg surface, and fresh vegetables), water, and air. Twenty-four E. coli isolates were tested for susceptibility to 26 antibiotics. The air sample isolates were most resistant to amoxicillin, ampicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, piperacillin/tazobactam, cefalotin, cefuroxime, cefoxitin, cefixime, nitrofurantoin, and trimethoprim/sulfamethoxazol. The isolates from vegetable samples were resistant to amoxicillin, ampicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, cefalotin, cefuroxime, cefoxitin, and cefixime. By contrast, the isolates from the water samples were resistant only to amoxicillin and ampicillin. The isolates from the human urine samples were most frequently resistant to norfloxacin (80%) followed by amoxicillin and ampicillin (70%), trimethoprim/sulfamethoxazole (55%), ciprofloxacin and ofloxacin (50%), cefalotin (30%), cefuroxime, cefixime and cefotaxime (25%), ceftazidime, ceftriaxone, cefepime and aztreonam (20%), amoxicillin/clavulanic acid, piperacillin/tazobactam and gentamicin (10%), and amoxicillin/sulbactam and cefoxitin (5%). Almost all (23/25, 95.8%) (n = 23) of the isolates were multi-drug resistant (MDR) (i.e., resistant to 3 or more classes of antibiotics), and 16.7% (n = 4) of those were positive for extended spectrum β-lactamase (ESBL). Of the 4 ESBL-producers, 3 were positive for blaCTX-M-15 and blaCTX-M1group, 2 were positive for blaCMY-2, and 1 each was positive for blaCTX-M-2 group, blaSHV, and blaOXA-47. The quinolone resistance gene qnrS was detected in 25% (n = 6) of the E. coli strains isolated from urine (N = 5) and air (N = 1) samples. The considerable number of antimicrobial resistance genes detected among E. coli isolates tested here is alarming and should raise public health concern.

Assessing Environmental Factors within the One Health Approach

Background: One Health is a comprehensive and multisectoral approach to assess and examine the health of animals, humans and the environment. However, while the One Health approach gains increasing momentum, its practical application meets hindrances. This paper investigates the environmental pillar of the One Health approach, using two case studies to highlight the integration of environmental considerations. The first case study pertains to the Danish monitoring and surveillance programme for antimicrobial resistance, DANMAP. The second case illustrates the occurrence of aflatoxin M1 (AFM1) in milk in dairy-producing ruminants in Italian regions. Method: A scientific literature search was conducted in PubMed and Web of Science to locate articles informing the two cases. Grey literature was gathered to describe the cases as well as their contexts. Results: 19 articles and 10 reports were reviewed and informed the two cases. The cases show how the environmental component influences the apparent impacts for human and animal health. The DANMAP highlights the two approaches One Health and farm to fork. The literature provides information on the comprehensiveness of the DANMAP, but highlights some shortcomings in terms of environmental considerations. The AFM1 case, the milk metabolite of the carcinogenic mycotoxin aflatoxin B1, shows that dairy products are heavily impacted by changes of the climate as well as by economic drivers. Conclusions: The two cases show that environmental conditions directly influence the onset and diffusion of hazardous factors. Climate change, treatment of soils, water and standards in slaughterhouses as well as farms can have a great impact on the health of animals, humans and the environment. Hence, it is important to include environmental considerations, for example, via engaging environmental experts and sharing data. Further case studies will help to better define the roles of environment in One Health scenarios.

A history of antimicrobial drugs in animals: Evolution and revolution

The evolutionary process of antimicrobial drug (AMD) uses in animals over a mere eight decades (1940-2020) has led to a revolutionary outcome, and both evolution and revolution are ongoing, with reports on a range of uses, misuses and abuses escalating logarithmically. As well as veterinary therapeutic perspectives (efficacy, safety, host toxicity, residues, selection of drug, determination of dose and measurement of outcome in treating animal diseases), there are also broader, nontherapeutic uses, some of which have been abandoned, whilst others hopefully will soon be discontinued, at least in more developed countries. Although AMD uses for treatment of animal diseases will continue, it must: (a) be sustainable within the One Health paradigm; and (b) devolve into more prudent, rationally based therapeutic uses. As this review on AMDs is published in a Journal of Pharmacology and Therapeutics, its scope has been made broader than most recent reviews in this field. Many reviews have focused on negative aspects of AMD actions and uses, especially on the question of antimicrobial resistance. This review recognizes these concerns but also emphasizes the many positive aspects deriving from the use of AMDs, including the major research-based advances underlying both the prudent and rational use of AMDs. It is structured in seven sections: (1) Introduction; (2) Sulfonamide history; (3) Nontherapeutic and empirical uses of AMDs (roles of agronomists and veterinarians); (4) Rational uses of AMDs (roles of pharmacologists, clinicians, industry and regulatory controls); (5) Prudent use (residue monitoring, antimicrobial resistance); (6) International and inter-disciplinary actions; and (7) Conclusions.

Impact of antibiotics on fluorescent Pseudomonas group and Bacillus cereus group isolated from soils exposed to effluent or waste from conventional and organic pig farming

AIMS

To determine if antibiotics associated with conventional pig farming have a direct role in altering the populations of key soil micro-organisms isolated from piggery environments with and without exposure to antibiotics.

METHODS AND RESULTS

Fluorescent Pseudomonas sp. and the Bacillus cereus group from soils adjacent to four conventional piggeries (use of antibiotics) exposed to effluent (via irrigation) and two organic piggeries (non-use of antibiotics) were assessed against nine relevant antibiotics using disc diffusion. The focus of the study was not to determine antibiotic resistance (or sensitivity) of isolates based on the manufacturer-defined sensitive break point, instead this point was used as the interpretation point to compare the populations (i.e. farm/organism combination) for the antibiotics tested. Each population was statistically analysed to determine whether the mean diameters were significantly above this selected interpretation point. Bacterial species from both environments did not show a distinct population pattern linked to the antibiotics.

CONCLUSIONS

Antibiotics associated with conventional pig farming do not have a direct role in altering the environmental populations of Pseudomonas and Bacillus sp. when assessed by population shifts.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study confirms that an understanding of the resident soil microbiota, as compared to the transient bacteria of pig origin, is important in addressing the impact of antibiotic usage on the food-chain as a consequence of effluent re-use in, and around, pig farms.

Plasmid Sequences of Four Large Plasmids Carrying Antimicrobial Resistance Genes in Escherichia coli Strains Isolated from Beef Cattle in Japan

Escherichia coli is a common reservoir for antimicrobial resistance genes that can be easily transformed to possess multidrug resistance through plasmid transfer. To understand multidrug resistance plasmids, we report the plasmid sequences of four large plasmids carrying a number of genes related to antimicrobial resistance that were found in E. coli strains isolated from beef cattle.

Resistance to multiple first-line antibiotics among Escherichia coli from poultry in Western Algeria

BACKGROUND AND AIM

Escherichia coli can cause a number of serious infections both in human and veterinary medicine. Their management is increasingly complicated by the emergence and dissemination of multiresistance to various first-line antimicrobial agents. This study aimed to evaluate the resistance level to the commonly used antibiotics, with a focus on the first-line antimicrobial agents, in E. coli strains isolated from poultry in Western Algeria.

MATERIALS AND METHODS

E. coli culture was done on MacConkey agar and their identification was determined by AP20E system. For susceptibility testing, disk diffusion method to 14 antimicrobials, including first-line antibiotics, was used according to Kirby-Bauer disk diffusion method in Mueller-Hinton agar and the results were interpreted according to the Clinical and Laboratory Standards Institute guidelines. E. coli isolates were considered as multidrug resistance (MDR) when found resistant to at least one antimicrobial agent of three different families of antibiotics. Double-disk synergy and combination disk tests were used for initial screening and confirmation for extended-spectrum β-lactamases (ESBLs) production, respectively.

RESULTS

A total of 145 E. coli strains were isolated in this study. High resistance levels to various antibiotics, including commonly used first-line antimicrobial agents, were recorded in this study. The highest resistance level was observed against nalidixic acid (90.34%, n=131), followed by tetracycline (86.89%, n=126), ampicillin (82.75%, n=120), enrofloxacin (80.68%, n=117) and neomycin (80.68%, n=117), trimethoprim/sulfamethoxazole (73.79%, n=107), norfloxacin (72.41%, n=105) and cephalothin (72.41%, n=105), amoxicillin/clavulanic acid (51.72%, n=75), chloramphenicol (22.75%, n=33), nitrofurantoin (17.24%, n=25), gentamicin (13.10%, n=19), and ceftiofur (3.44%, n=5). Moreover, resistance to multiple first-line antibiotics was also demonstrated in the present study. Overall, 139 out of 145 isolates (95.86%) demonstrated MDR (resistant to at least three antibiotics). In addition, five E. coli isolates (3.44%) were confirmed to be ESBL producers.

CONCLUSION

The alarming rate of E. coli resistant to multiple first-line antibiotics in poultry demands intensified surveillance. These results call for taking drastic measures to preserve antibiotic effectiveness and reduce the emergence risks of extensively drug-resistant and pandrug-resistant E. coli isolates.

Antibiotic resistance in porcine pathogenic bacteria and relation to antibiotic usage

BACKGROUND

Optimal treatment and prudent use of antimicrobials for pigs is imperative to secure animal health and prevent development of critical resistance. An important step in this one-health context is to monitor resistance patterns of important animal pathogens. The aim of this study was to investigate the antimicrobial resistance patterns of five major pathogens in Danish pigs during a period from 2004 to 2017 and elucidate any developments or associations between resistance and usage of antibiotics.

RESULTS

The minimum inhibitory concentration (MIC) for Escherichia coli, Actinobacillus pleuropneumoniae, Streptococcus suis, Bordetella bronchiseptica, and Staphylococcus hyicus was determined to representatives of antibiotic classes relevant for treatment or surveillance. Escherichia coli isolates were mostly sensitive to fluoroquinolones and colistin, whereas high levels of resistance were observed to ampicillin, spectinomycin, streptomycin, sulfonamides and tetracycline. While resistance levels to most compounds remained relatively stable during the period, resistance to florfenicol increased from 2.1% in 2004 to 18.1% in 2017, likely in response to a concurrent increase in usage. A temporal association between resistance and usage was also observed for neomycin. E. coli serovars O138 and O149 were generally more resistant than O139. For A. pleuropneumoniae, the resistance pattern was homogenous and predictable throughout the study period, displaying high MIC values only to erythromycin whereas almost all isolates were susceptible to all other compounds. Most S. suis isolates were sensitive to penicillin whereas high resistance levels to erythromycin and tetracycline were recorded, and resistance to erythromycin and trimethoprim increasing over time. For S. hyicus, sensitivity to the majority of the antimicrobials tested was observed. However, penicillin resistance was recorded in 69.4-88.9% of the isolates. All B. bronchiseptica isolates were resistant to ampicillin, whereas all but two isolates were sensitive to florfenicol. The data obtained have served as background for a recent formulation of evidence-based treatment guidelines for pigs.

CONCLUSIONS

Antibiotic resistance varied for some pathogens over time and in response to usage. Resistance to critically important compounds was low. The results emphasize the need for continuous surveillance of resistance patterns also in pig pathogenic bacteria.

Macleaya cordata helps improve the growth-promoting effect of chlortetracycline on broiler chickens

Chlortetracycline (CTC), one kind of common antibiotic for prevention and treatment of various diseases, also exhibits good performance in accelerating the growth of livestock. Macleaya cordata, a traditional Chinese medicine, is usually used as a natural additive in livestock because of its anti-microbial, anti-fungal, anti-inflammatory, and pesticidal activity. In this work, we studied whether M. cordata helps regulate the growth-promoting effect of CTC on broiler chickens. It is demonstrated that M. cordata improves the growth-promoting effect of CTC on growth performance indices of broiler chickens, such as survival rate, daily weight, and feed to weight rate. M. cordata also delays the maximum of CTC residues in plasma. It may depend on the higher values of operational taxonomic unit (OTU) and the indices of α diversity driven by simultaneous use of CTC and M. cordata.

Present and Future Surveillance of Antimicrobial Resistance in Animals: Principles and Practices

There is broad consensus internationally that surveillance of the levels of antimicrobial resistance (AMR) occurring in various systems underpins strategies to address the issue. The key reasons for surveillance of resistance are to determine (i) the size of the problem, (ii) whether resistance is increasing, (iii) whether previously unknown types of resistance are emerging, (iv) whether a particular type of resistance is spreading, and (v) whether a particular type of resistance is associated with a particular outbreak. The implications of acquiring and utilizing this information need to be considered in the design of a surveillance system. AMR surveillance provides a foundation for assessing the burden of AMR and for providing the necessary evidence for developing efficient and effective control and prevention strategies. The codevelopment of AMR surveillance programs in humans and animals is essential, but there remain several key elements that make data comparisons between AMR monitoring programs, and between regions, difficult. Currently, AMR surveillance relies on uncomplicated in vitro antimicrobial susceptibility methods. However, the lack of harmonization across programs and the limitation of genetic information of AMR remain the major drawbacks of these phenotypic methods. The future of AMR surveillance is moving toward genotypic detection, and molecular analysis methods are expected to yield a wealth of information. However, the expectation that these molecular techniques will surpass phenotypic susceptibility testing in routine diagnosis and monitoring of AMR remains a distant reality, and phenotypic testing remains necessary in the detection of emerging resistant bacteria, new resistance mechanisms, and trends of AMR.

A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds

OBJECTIVES

Reliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring.

METHODS

We evaluated the ability of: (i) MIC determination for Escherichia coli; (ii) cfu counting of E. coli; (iii) cfu counting of aerobic bacteria; and (iv) metagenomic shotgun sequencing to predict expected tetracycline resistance based on known antimicrobial consumption in 10 Danish integrated slaughter pig herds. In addition, we evaluated whether fresh or manure floor samples constitute suitable proxies for intestinal sampling, using cfu counting, qPCR and metagenomic shotgun sequencing.

RESULTS

Metagenomic read-mapping outperformed cultivation-based techniques in terms of predicting expected tetracycline resistance based on antimicrobial consumption. Our metagenomic approach had sufficient resolution to detect antimicrobial-induced changes to individual resistance gene abundances. Pen floor manure samples were found to represent rectal samples well when analysed using metagenomics, as they contain the same DNA with the exception of a few contaminating taxa that proliferate in the extraintestinal environment.

CONCLUSIONS

We present a workflow, from sampling to interpretation, showing how resistance monitoring can be carried out in swine herds using a metagenomic approach. We propose metagenomic sequencing should be part of routine livestock resistance monitoring programmes and potentially of integrated One Health monitoring in all reservoirs.

Type 3 Fimbriae Encoded on Plasmids Are Expressed from a Unique Promoter without Affecting Host Motility, Facilitating an Exceptional Phenotype That Enhances Conjugal Plasmid Transfer

Horizontal gene transfer (HGT), the transmission of genetic material to a recipient that is not the progeny of the donor, is fundamental in bacterial evolution. HGT is often mediated by mobile genetic elements such as conjugative plasmids, which may be in conflict with the chromosomal elements of the genome because they are independent replicons that may petition their own evolutionary strategy. Here we study differences between type 3 fimbriae encoded on wild type plasmids and in chromosomes. Using known and newly characterized plasmids we show that the expression of type 3 fimbriae encoded on plasmids is systematically different, as MrkH, a c-di-GMP dependent transcriptional activator is not needed for strong expression of the fimbriae. MrkH is required for expression of type 3 fimbriae of the Klebsiella pneumoniae chromosome, wherefrom the fimbriae operon (mrkABCDF) of plasmids is believed to have originated. We find that mrkABCDFs of plasmids are highly expressed via a unique promoter that differs from the original Klebsiella promoter resulting in fundamental behavioral consequences. Plasmid associated mrkABCDFs did not influence the swimming behavior of the host, that hereby acquired an exceptional phenotype being able to both actively swim (planktonic behavior) and express biofilm associated fimbriae (sessile behavior). We show that this exceptional phenotype enhances the conjugal transfer of the plasmid.

Multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from a dairy farm

Escherichia coli strains were isolated from a single dairy farm as a sentinel organism for the persistence of antibiotic resistance genes in the farm environment. Selective microbiological media were used to obtain 126 E. coli isolates from slurry and faeces samples from different farm areas. Antibiotic resistance profiling for 17 antibiotics (seven antibiotic classes) showed 57.9% of the isolates were resistant to between 3 and 15 antibiotics. The highest frequency of resistance was to ampicillin (56.3%), and the lowest to imipenem (1.6%), which appeared to be an unstable phenotype and was subsequently lost. Extended spectrum β-lactamase (ESBL) resistance was detected in 53 isolates and blaCTX-M, blaTEM and blaOXA genes were detected by PCR in 12, 4 and 2 strains, respectively. Phenotypically most isolates showing resistance to cephalosporins were AmpC rather than ESBL, a number of isolates having both activities. Phenotypic resistance patterns suggested co-acquisition of some resistance genes within subsets of the isolates. Genotyping using ERIC-PCR demonstrated these were not clonal, and therefore co-resistance may be associated with mobile genetic elements. These data show a snapshot of diverse resistance genes present in the E. coli population reservoir, including resistance to historically used antibiotics as well as cephalosporins in contemporary use.

Antimicrobial resistance in humans, livestock and the wider environment

Antimicrobial resistance (AMR) in humans is inter-linked with AMR in other populations, especially farm animals, and in the wider environment. The relatively few bacterial species that cause disease in humans, and are the targets of antibiotic treatment, constitute a tiny subset of the overall diversity of bacteria that includes the gut microbiota and vast numbers in the soil. However, resistance can pass between these different populations; and homologous resistance genes have been found in pathogens, normal flora and soil bacteria. Farm animals are an important component of this complex system: they are exposed to enormous quantities of antibiotics (despite attempts at reduction) and act as another reservoir of resistance genes. Whole genome sequencing is revealing and beginning to quantify the two-way traffic of AMR bacteria between the farm and the clinic. Surveillance of bacterial disease, drug usage and resistance in livestock is still relatively poor, though improving, but achieving better antimicrobial stewardship on the farm is challenging: antibiotics are an integral part of industrial agriculture and there are very few alternatives. Human production and use of antibiotics either on the farm or in the clinic is but a recent addition to the natural and ancient process of antibiotic production and resistance evolution that occurs on a global scale in the soil. Viewed in this way, AMR is somewhat analogous to climate change, and that suggests that an intergovernmental panel, akin to the Intergovernmental Panel on Climate Change, could be an appropriate vehicle to actively address the problem.

The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks, effects of interventions and the way forward

The purpose of this review was to provide an updated overview on the use of antimicrobial agents in livestock, the associated problems for humans and current knowledge on the effects of reducing resistance in the livestock reservoir on both human health and animal production. There is still limiting data on both use of antimicrobial agents, occurrence and spread of resistance as well as impact on human health. However, in recent years, emerging issues related to methicillin-resistant Staphylococcus aureus, Clostridium difficile, Escherichia coli and horizontally transferred genes indicates that the livestock reservoir has a more significant impact on human health than was estimated 10 years ago, where the focus was mainly on resistance in Campylobacter and Salmonella. Studies have indicated that there might only be a marginal if any benefit from the regular use of antibiotics and have shown that it is possible to substantially reduce the use of antimicrobial agents in livestock production without compromising animal welfare or health or production. In some cases, this should be done in combination with other measures such as biosecurity and use of vaccines. To enable better studies on both the global burden and the effect of interventions, there is a need for global harmonized integrated and continuous surveillance of antimicrobial usage and antimicrobial resistance, preferably associated with data on production and animal diseases to determine the positive and negative impact of reducing antimicrobial use in livestock.

Molecular analysis of β-lactamase genes to understand their differential expression in strains of Yersinia enterocolitica biotype 1A

Beta-lactams are used as major therapeutic agents against a number of infectious agents. Due to widespread use of β-lactams, β-lactamases have evolved at a rapid pace leading to treatment failures. Yersinia enterocolitica causes many gastrointestinal problems. It is an extremely heterogeneous species comprising more than fifty serotypes and six biotypes which differ in their ecological niches, geographical distribution and pathogenic potential. Though biotype 1A strains have been associated with outbreaks of Yersiniosis, there has been a controversy regarding their pathogenicity. The strains of Y. enterocolitica isolated from India belonged to biotype 1A and possessed genes for two β-lactamases namely, blaA and blaB. An earlier study by us reported differential expression of blaA by strains of Y. enterocolitica biotype 1A. The present study has been carried out to understand the molecular bases which regulate the expression of blaA in Y. enterocolitica biotype 1A. We concluded that six types of blaA variants were present in strains of biotype 1A. Neither amino acid substitutions in blaA nor mutations in promoter regions of blaA contributed to differential expression of blaA in Y. enterocolitica biotype 1A. Rather, the secondary structures attained by mRNA of blaA might underlie the differential expression of blaA in Y. enterocolitica.

Characterization of multi-antibiotic-resistant Escherichia coli Isolated from beef cattle in Japan

The emergence of multiple-antibiotic-resistance bacteria is increasing, which is a particular concern on livestock farms. We previously isolated 1,347 antimicrobial-resistant (AMR) Escherichia coli strains from the feces of beef cattle on 14 Japanese farms. In the present study, the genetic backgrounds and phylogenetic relationships of 45 AMR isolates were characterized by the chromosome phylotype, AMR phenotype, AMR genotype, and plasmid type. These isolates were classified into five chromosome phylotypes, which were closely linked to the farms from which they were isolated, suggesting that each farm had its own E. coli phylotype. AMR phenotype and plasmid type analyses yielded 8 and 14 types, all of which were associated with the chromosomal phylotype and, thus, to the original farms. AMR genotype analysis revealed more variety, with 16 types, indicating both inter- and intra-farm diversity. Different phylotype isolates from the same farm shared highly similar plasmid types, which indicated that plasmids with AMR genes could be transferred between phylotypes, thereby generating multi-antibiotic-resistant microorganisms. This ecological study demonstrated that the chromosome phylotype was strongly correlated with the farm from which they were isolated, while the AMR phenotype, genotype, and plasmid type were generally correlated with the chromosome phylotype and farm source.

Antimicrobial resistance, virulence factors and genetic diversity of Escherichia coli isolates from household water supply in Dhaka, Bangladesh

Background

Unsafe water supplies continue to raise public health concerns, especially in urban areas in low resource countries. To understand the extent of public health risk attributed to supply water in Dhaka city, Bangladesh, Escherichia coli isolated from tap water samples collected from different locations of the city were characterized for their antibiotic resistance, pathogenic properties and genetic diversity.

Methodology/Principal Findings

A total of 233 E. coli isolates obtained from 175 tap water samples were analysed for susceptibility to 16 different antibiotics and for the presence of genes associated with virulence and antibiotic resistance. Nearly 36% (n = 84) of the isolates were multi-drug(≥3 classes of antibiotics) resistant (MDR) and 26% (n = 22) of these were positive for extended spectrum β-lactamase (ESBL). Of the 22 ESBL-producers, 20 were positive for bla_CTX-M-15, 7 for bla_OXA-1-group (all had bla_OXA-47) and 2 for bla_CMY-2. Quinolone resistance genes, qnrS and qnrB were detected in 6 and 2 isolates, respectively. Around 7% (n = 16) of the isolates carried virulence gene(s) characteristic of pathogenic E. coli; 11 of these contained lt and/or st and thus belonged to enterotoxigenic E. coli and 5 contained bfp and eae and thus belonged to enteropathogenic E. coli. All MDR isolates carried multiple plasmids (2 to 8) of varying sizes ranging from 1.2 to >120 MDa. Ampicillin and ceftriaxone resistance were co-transferred in conjugative plasmids of 70 to 100 MDa in size, while ampicillin, trimethoprim-sulfamethoxazole and tetracycline resistance were co-transferred in conjugative plasmids of 50 to 90 MDa. Pulsed-field gel electrophoresis analysis revealed diverse genetic fingerprints of pathogenic isolates.

Significance

Multi-drug resistant E. coli are wide spread in public water supply in Dhaka city, Bangladesh. Transmission of resistant bacteria and plasmids through supply water pose serious threats to public health in urban areas.

High prevalence of antimicrobial-resistant Escherichia coli from animals at slaughter: a food safety risk

BACKGROUND

There has been concern about the increase of antimicrobial resistant bacteria and protection of animal and public health, along with food safety. In the present study, we evaluate the incidence of antimicrobial resistance among 192 strains of Escherichia coli isolated from faecal samples of healthy food-producing animals at slaughter in Portugal.

RESULTS

Ninety-seven % of the pig isolates, 74% from sheep and 55% from cattle were resistant to one or more antimicrobial agents, with the resistances to ampicillin, streptomycin, tetracycline and trimethoprim-sulfamethoxazole the most common phenotype detected. Genes encoding resistance to antimicrobial agents were detected in most of the resistant isolates. Ninety-three % of the resistant isolates were included in the A or B1 phylogenetic groups, and the virulence gene fimA (alone or in association with papC or aer genes) was detected in 137 of the resistant isolates. Five isolates from pigs belonging to phylogroup B2 and D were resistant to five different antimicrobial agents.

CONCLUSION

Our data shows a high percentage of antibiotic resistance in E. coli isolates from food animals, and raises important questions in the potential impact of antibiotic use in animals and the possible transmission of resistant bacteria to humans through the food chain.

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

OBJECTIVES

Antimicrobial susceptibility testing of bacterial isolates is essential for clinical diagnosis, to detect emerging problems and to guide empirical treatment. Current phenotypic procedures are sometimes associated with mistakes and may require further genetic testing. Whole-genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures.

METHODS

Antimicrobial susceptibility tests were performed on 200 isolates originating from Danish pigs, covering four bacterial species. Genomic DNA was purified from all isolates and sequenced as paired-end reads on the Illumina platform. The web servers ResFinder and MLST (www.genomicepidemiology.org) were used to identify acquired antimicrobial resistance genes and MLST types (where MLST stands for multilocus sequence typing). ResFinder results were compared with phenotypic antimicrobial susceptibility testing results using EUCAST epidemiological cut-off values and MLST types.

RESULTS

A total of 3051 different phenotypic tests were performed; 482 led to the categorizing of isolates as resistant and 2569 as susceptible. Seven cases of disagreement between tested and predicted susceptibility were observed, six of which were related to spectinomycin resistance in Escherichia coli. Correlation between MLST type and resistance profiles was only observed in Salmonella Typhimurium, where isolates belonging to sequence type (ST) 34 were more resistant than ST19 isolates.

CONCLUSIONS

High concordance (99.74%) between phenotypic and predicted antimicrobial susceptibility was observed. Thus, antimicrobial resistance testing based on WGS is an alternative to conventional phenotypic methods.

Antibiotic use in animal feed and its impact on human healt

Antibiotic resistance in bacteria that cause disease in man is an issue of major concern. Although misuse of antibiotics in human medicine is the principal cause of the problem, antibiotic-resistant bacteria originating in animals are contributory factors, with some types of resistance in some species of bacteria. Antibiotics are added to animal feeds to treat and prevent infections and to improve growth and production. Until recently, the major concerns about incorporation of antibiotics in animal feeds related to antibiotic residues in products from treated animals. Although, in 1969, the Swann (1969) report drew attention to the potential for antibiotic-resistant bacteria to spread from treated animals via the food chain, there was little response until the detection of vancomycin-resistant enterococci in animals fed a related glycopeptide, avoparcin. Subsequently, attention started to focus on the issue and other examples of transfer of resistant bacteria through the food chain, such as enterococci resistant to quinupristin-dalfopristin or to everninomicin, fluoroquinolone-resistant campylobacters and multiresistant Escherichia coli, and salmonella such as Salmonella typhimurium DT104. Reviews and committees in many countries have highlighted the need for better control of licensing of antibiotics, and codes for prudent use of antibiotics by veterinary practitioners and farmers. The continued use of antibiotic growth promoters has been questioned and there is a need to ensure that antibiotics important in human medicine are not used therapeutically or prophylactically in animals.

Antibiotic resistance, phylogenetic grouping and virulence potential of Escherichia coli isolated from the faeces of intensively farmed and free range poultry

Antibiotic use in poultry production is a risk factor for promoting the emergence of resistant Escherichia coli. To ascertain differences in different classes of chickens, the resistance profile, some virulence genes and phylogenetic grouping on 251 E. coli isolates from intensive meat (free range and indoor commercial) and free range egg layer chickens collected between December 2008 and June 2009 in South Australia were performed. Among the 251 strains, 102 (40.6%) and 67 (26.7%) were found to be resistant to tetracycline and ampicillin respectively. Resistance was also observed to trimethoprim-sulfamethoxazole (12.4%), streptomycin (10.8%), spectinomycin (9.6%), neomycin (6.0%) and florfenicol (2.0%) but no resistance was found to ceftiofur, ciprofloxacin or gentamicin. Amplification of DNA of the isolates by polymerase chain reaction revealed the presence of genes that code for resistant determinants: tetracycline (tet(A), tet(B) and tet(C)), ampicillin (bla(TEM) and bla(SHV)), trimethoprim (dhfrV and dhfrXIII), sulphonamide (sulI and sulII), neomycin (aph(3)-Ia(aphA1)), and spectinomycin-streptinomycin (aadA2). In addition, 32.3-39.4% of the isolates were found to belong to commensal groups (A and B1) and 11.2-17.1% belonged to the virulent groups (B2 and D). Among the 251 E. coli isolates, 25 (10.0%) carried two or more virulence genes typical of Extraintestinal pathogenic E. coli (ExPEC). Furthermore, 17 of the isolates with multi-resistance were identified to be groups B2 and D. Although no significant difference was observed between isolates from free range and indoor commercial meat chickens (P>0.05), significant differences was observed between the different classes of meat chickens (free range and indoor commercial) and egg layers (P<0.05). While this study assessed the presence of a limited number of virulence genes, our study re emphasises the zoonotic potential of poultry E. coli isolates.

Comparison of broth microdilution and disk diffusion test for antimicrobial resistance testing in Yersinia enterocolitica 4/O:3 strains

The aim of this study was to compare the results obtained from two methods for the determination of antimicrobial resistance in 110 Yersinia enterocolitica 4/O:3 strains. Ten antimicrobial agents were tested using broth microdilution and disk diffusion. Similar results were determined for six antimicrobials. Very major errors (false-susceptible by disk diffusion test) were detected for ampicillin (at a rate of 1.8%). Major errors (false-resistant by disk diffusion test) were found for streptomycin (0.9%) and sulfamethoxazole (1.8%). Minor errors (intermediate susceptible by disk diffusion and resistant or susceptible by microdilution) were obtained for ampicillin (2.7%) and sulfamethoxazole (13.6%). All Y. enterocolitica were resistant to at least one antimicrobial agent. Resistances to three classes of antimicrobial agents were obtained by 3% of the strains included in the study. A slightly higher frequency of multiresistance was obtained by disk diffusion (3%) compared with broth microdilution (1%). Resistance to streptomycin was found frequently (13%); in contrast, resistance to tetracycline was rare (1%). The disk diffusion test produced unacceptably high rates of very major errors for ampicillin and a high frequency of minor errors for sulfamethoxazole. Susceptibility tests should thus be carried out by the more reliable method of microdilution. Most of the antimicrobials that can be used for therapy were very effective when tested against Y. enterocolitica. In order to identify changes in susceptibilities as early as possible, antimicrobial resistance in Y. enterocolitica should be regularly surveyed.

Antimicrobial resistance in fecal Escherichia coli isolated from growing chickens on commercial broiler farms

To investigate the effects of rearing practices of commercial broiler chickens on the incidence of antimicrobial resistance in commensal Escherichia coli isolates, fecal E. coli isolates obtained in 4 farms were screened for anitimicrobial resistance. Ten E. coli isolates were recovered from each of the fecal samples collected from 10 birds in the farms at the ages of 2 days, 14-17 days, and 47-50 days. In 2 out of the 4 farms, no antimicrobials were used during the rearing period. In the other two farms, following collection of the fecal samples at 14 and 15 days of age, oxytetracycline (OTC), sulfadimethoxine (SDMX), and tylosin were given to birds on one farm and SDMX was used in the other. Isolates resistant to ampicillin and OTC that were obtained from an untreated flock at different sampling times were closely related to each other by pulsed-field gel electrophoresis patterns (PFGE) of XbaI-digested chromosomal DNA. PFGE analysis together with in vitro conjugation experiments suggested that diversity of resistance phenotypes within a clone may be resulted from the acquisition and loss of R-plasmids in an untreated and a treated flock. The numbers of resistance phenotypes observed among fecal isolates increased during the growth of the chickens in all the farms. The results in the present study suggest that persistence of commensal E. coli strains resistant to antimicrobials even in the absence of antimicrobial administration. It is also hypothesized that horizontal transmission of resistance determinants resulted in the emergence of different resistance phenotypes in those farms.

Detection, semiquantitative enumeration, and antimicrobial susceptibility of Yersinia enterocolitica in pork and chicken meats in Italy

Yersinia enterocolitica is recognized as an etiological agent of gastroenteritis, lymphadenitis, and chronic sequelae. During 2006 and 2007, 205 samples (125 pork and 80 chicken meats) were collected in Italy and tested for detection and most-probable-number (MPN) enumeration of Y. enterocolitica organisms. The microorganism was isolated from 45 samples (21.9%): 19 (15.2%) pork samples and 26 (32.5%) chicken samples. Y. enterocolitica MPN contamination levels were low, ranging from 0.30 to 1.50/g. Most (94.4%) Y. enterocolitica strains were biotype 1A (serotypes O:3; O:5; O:6,30; O:6,30-6,31; O:7,8-8-8,19; O:8; O:9; O:25,35; O:36; and O nontypeable), and 5.6% of the isolates were bioserotype 2/O:9. All isolates were tested for yadA, ail, inv, ystA, and ystB virulence sequences. The yadA gene was detected in two strains (3.7%) isolated from chicken samples: one Y. enterocolitica 2/O:9 yadA+ ail+ ystA+, and one Y. enterocolitica 1A/O:7,8-8-8,19 yadA+ inv+ ystB+. Two (3.7%) 2/O:9 strains, isolated from pork products, were ail+ ystA+. Most biotype 1A strains were ystB+ (84.3%) and inv+ (39.2%). All strains were sensitive to cefotaxime, ciprofloxacin, chloramphenicol, nalidixic acid, streptomycin, sulfonamide, tetracycline, trimethoprim, and trimethoprim-sulfamethoxazole. Resistance to gentamicin and aztreonam was observed in 1.9% of the isolates. High levels of resistance were detected toward amoxicillin-clavulanic acid (27.8%), ampicillin (75.9%), and erythromycin (100%). The authors hypothesize that Y. enterocolitica pathogenic biotypes are rather uncommon in foods when compared with their isolation rates from animal sources and that chicken meat could be contaminated as well as pig meat and its derived products.

Isolation of Tn1546-like elements in vancomycin-resistant Enterococcus faecium isolated from wood frogs: an emerging risk for zoonotic bacterial infections to humans

AIM

Isolation and characterization of vancomycin-resistant enterococci (VRE), mainly Enterococcus faecium, from the faecal pellet of wood frogs (Rana sylvatica).

METHODS AND RESULTS

The frog VRE isolates were tested for their susceptibility to various antibiotics and were found resistant to ampicillin (Am), chloramphenicol (Cm), erythromycin (Em), gentamicin (Gm), tetracycline (Tc), teicoplanin (Tp) and vancomycin (Vn). The linkage of multiple antibiotic resistances to Em, Tc, Tp and Vn was observed in 84% of resistant Ent. faecium. Inducible antibiotic resistance (MIC ≥ 512 μg ml(-1) ) to Vn was also detected in these isolates. PCR analysis revealed the presence of vanA in all strains, and none of the strains were positive for vanB, indicating the existence of vanA phenotype. Furthermore, the PCR-RFLP analysis of the frog vanA amplicon with PstI, BamHI and SphI generated identical restriction patterns similar to Tn1546-like elements found in human VRE isolates. DNA homoduplex analysis also confirmed that vanA from the frog VRE has DNA sequence homology with the vanA of Tn1546-like elements of human and animal isolates. Blastx analysis of frog vanA sequence showed similarities with protein sequences generated from protein database of Vn-resistant Ent. faecium, Baccilus circulans, Paenibacillus apiarius and Oerskovia turbata isolates. Horizontal transfer of Vn resistance was not detected in frog isolates as revealed by filter mating conjugal experiment.

CONCLUSIONS

In summary, our results demonstrated that wood frogs carry Vn-resistant bacteria, and resistance genes (vanA) are located on Tn1546-like elements.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study highlights a previously less recognized role of amphibians as sentinels for multidrug-resistant bacteria and alerts the public health workers for an emerging risk of zoonotic bacterial infections to humans.

Prevalence and antimicrobial resistance of Salmonella serotypes in chickens from retail markets in Yaounde (Cameroon)

From February 2006 to January 2007, 150 chickens were collected from eight retail markets in Yaounde, and 90 (60%) tested positive for Salmonella. Seventy-nine chickens were contaminated with only one Salmonella serotype, 10 with two different serotypes, and 1 with four serotypes. The most prevalent serotypes were Enteritidis (47 strains) and Hadar (29 strains). The isolates were tested for their susceptibilities to amoxicillin, amoxicillin/clavulanic acid, cefoxitin, cefotaxime, gentamicin, streptomycin, tetracycline, chloramphenicol, sulfonamides, nalidixic acid, ciprofloxacin, and trimethoprim/sulfamethazole by disk diffusion assay. Minimum inhibitory concentrations of ampicillin, streptomycin, tetracycline, sulfonamides, and nalidixic acid were determined for the resistant strains by agar dilution method. Eleven isolates (10.7%) of the 103 tested were susceptible to all antimicrobials. Resistance was most observed to tetracycline (84.5%), streptomycin (44.7%), and nalidixic acid (34%). Forty-one isolates (39.8%) were multidrug resistant (resistant to three or more antimicrobials from different classes), of which 68.3% were Hadar and 21.9% Enteritidis. The most frequent resistant pattern in Hadar was streptomycin-tetracycline-nalidixic acid. These results highlight once more the need for surveillance of Salmonella contamination in poultry.

Antimicrobial resistance of Staphylococcus aureus isolated from bovine mastitis in China

Mastitis is one of the largest production concerns in the dairy industry worldwide. Mastitis caused by Staphylococcus aureus is a major concern to the dairy industry because of its resistance to antibiotic treatment. In this report, the results of antibiotic susceptibility test, carried out on 236 Staphylococcus aureus isolated from milk samples which were collected from cases of mastitis in cow herds of China, are presented. The regions and number of isolates include Inner Mongolia (112), Hebei (58) and Heilongjiang (66). Susceptibility to ampicillin, penicillin G, amoxicillin, piperacillin, cephalexin, cephazolin, cefotaxime, ceftazidime, cefoxitin, SMZ-TMP, gentamycin, kanamycin, norfloxacin, ciprofloxacin, ofloxacin, furaxone, torlamician, roxithromycin, clindamycin and vancomycin was determined by the disc diffusion method. Antibiotic susceptibility testing showed 87.30% (206 of 236) isolates were resistant to penicillin G. This result compares with the reports from other countries; the overall level of resistance was generally high for all antimicrobial agents tested.

Microbial evaluation and public health implications of urine as alternative therapy in clinical pediatric cases: health implication of urine therapy

BACKGROUND

Cultural means of pediatric treatment during ill health is a mainstay in Africa, and though urine has been known to contain enteric pathogens, urine therapy is still culturally applicable in some health conditions and also advocated as alternative therapy. The study therefore, is to evaluate the microbial contents and safety of urine.

METHODS

Urinary bacteria from cows and healthy children aged 5-11 years were identified by conventional phenotypic methods and antimicrobial susceptibility testing was performed using modified agar disc and well-diffusion methods.

RESULTS

A total of 116 bacterial isolates (n = 77 children; n = 39 cows) were identified as Bacillus (10.4%; 5.1%)), Staphylococcus (2.6%; 2.6%), Citrobacter (3.9%; 12.8%), Escherichia coli (36.4%; 23.1%), Klebsiella (7.8%; 12.8%), Proteus (18.2%; 23.1%), Pseudomonas (9.1%; 2.6%), Salmonella (3.9%; 5.1%) and Shigella (7.8%; 12.8%) spp. Antibiotic resistance rates of the Gram-positive bacteria were high (50.0100%), except in Bacillus strains against chloramphenicol, gentamicin and tetracycline (14.3%), while higher resistance rates were recorded among the Gram-negative bacteria except in Citrobacter (0.0%) and Proteus (8.5%) spp. against gentamicin and tetracycline respectively. The Gram-negative bacteria from ito malu (cow urine) were more resistant bacteria except in Citrobacter (20.0%) and Shigella spp. (0.0%) against tetracycline and Proteus spp. (11.1%), (22.2%) against amoxicillin and tetracycline respectively. Multiple antibiotic resistance (MAR) rates recorded in children urinal bacterial species were 37.5-100% (Gram-positive) and 12.5-100% (Gram-negative), while MAR among the cow urinal bacteria was 12.5-75.0% (Gram-positive) and 25.0-100% (Gram-negative). Similar higher resistance rates were also recorded among the Gram-negative bacterial species from urine specimens against the pediatric antibiotic suspensions.

CONCLUSION

The study reported presence of multiple antibiotic-resistant indicator bacteria in human urine and ito malu used as alternative remedy in pediatric health conditions like febrile convulsion.

Prevalence of antimicrobial resistance among bacterial pathogens isolated from cattle in different European countries: 2002-2004

Background

The project "Antibiotic resistance in bacteria of animal origin – II" (ARBAO-II) was funded by the European Union (FAIR5-QLK2-2002-01146) for the period 2003–2005, with the aim to establish a continuous monitoring of antimicrobial susceptibility among veterinary laboratories in European countries based on validated and harmonised methodologies. Available summary data of the susceptibility testing of the bacterial pathogens from the different laboratories were collected.

Method

Antimicrobial susceptibility data for several bovine pathogens were obtained over a three year period (2002–2004). Each year the participating laboratories were requested to fill in excel-file templates with national summary data on the occurrence of antimicrobial resistance from different bacterial species.

A proficiency test (EQAS – external quality assurance system) for antimicrobial susceptibility testing was conducted each year to test the accuracy of antimicrobial susceptibility testing in the participating laboratories. The data from this testing demonstrated that for the species included in the EQAS the results are comparable between countries.

Results

Data from 25,241 isolates were collected from 13 European countries. For Staphylococcus aureus from bovine mastitis major differences were apparent in the occurrence of resistance between countries and between the different antimicrobial agents tested. The highest frequency of resistance was observed for penicillin. For Mannheimia haemolytica resistance to ampicillin, tetracycline and trimethoprim/sulphonamide were observed in France, the Netherlands and Portugal. All isolates of Pasteurella multocida isolated in Finland and most of those from Denmark, England (and Wales), Italy and Sweden were susceptible to the majority of the antimicrobials. Streptococcus dysgalactiae and Streptococcus uberis isolates from Sweden were fully susceptible. For the other countries some resistance was observed to tetracycline, gentamicin and erythromycin. More resistance and variation of the resistance levels between countries were observed for Escherichia coli compared to the other bacterial species investigated.

Conclusion

In general, isolates from Denmark, England (and Wales), the Netherlands, Norway, Sweden and Switzerland showed low frequencies of resistance, whereas many isolates from Belgium, France, Italy, Latvia and Spain were resistant to most antimicrobials tested. In the future, data on the prevalence of resistance should be used to develop guidelines for appropriate antimicrobial use in veterinary medicine.

Occurrence of antimicrobial resistance among bacterial pathogens and indicator bacteria in pigs in different European countries from year 2002 - 2004: the ARBAO-II study

Background

The project "Antibiotic resistance in bacteria of animal origin – II" (ARBAO-II) was funded by the European Union (FAIR5-QLK2-2002-01146) for the period 2003–05. The aim of this project was to establish a program for the continuous monitoring of antimicrobial susceptibility of pathogenic and indicator bacteria from food animals using validated and harmonised methodologies. In this report the first data on the occurrence of antimicrobial resistance among bacteria causing infections in pigs are reported.

Methods

Susceptibility data from 17,642 isolates of pathogens and indicator bacteria including Actinobacillus pleuropneumoniae, Streptococcus suis and Escherichia coli isolated from pigs were collected from fifteen European countries in 2002–2004.

Results

Data for A. pleuropneumoniae from infected pigs were submitted from five countries. Most of the isolates from Denmark were susceptible to all drugs tested with the exceptions of a low frequency of resistance to tetracycline and trimethoprim – sulphonamide.

Data for S. suis were obtained from six countries. In general, a high level of resistance to tetracycline (48.0 – 92.0%) and erythromycin (29.1 – 75.0%) was observed in all countries whereas the level of resistance to ciprofloxacin and penicillin differed between the reporting countries. Isolates from England (and Wales), France and The Netherlands were all susceptible to penicillin. In contrast the proportion of strains resistant to ciprofloxacin ranged from 12.6 to 79.0% (2004) and to penicillin from 8.1 – 13.0% (2004) in Poland and Portugal.

Data for E. coli from infected and healthy pigs were obtained from eleven countries. The data reveal a high level of resistance to tetracyclines, streptomycin and ampicillin among infected pigs whereas in healthy pigs the frequency of resistance was lower.

Conclusion

Bacterial resistance to some antimicrobials was frequent with different levels of resistance being observed to several antimicrobial agents in different countries. The occurrence of resistance varied distinctly between isolates from healthy and diseased pigs, with the isolates from healthy pigs generally showing a lower level of resistance than those from diseased pigs.

The study suggests that the choice of antimicrobials used for the treatment of diseased animals should preferably be based on knowledge of the local pattern of resistance.