Antimicrobial Susceptibility of Escherichia coli and Salmonella spp. Isolates From Healthy Pigs in Australia: Results of a Pilot National Survey

Antimicrobial Resistance in Selected Bacteria from Food Animals in New Zealand 2018-2022

Antimicrobial resistance (AMR) presents a significant threat to human health worldwide. One important source of antimicrobial-resistant infections in humans is exposure to animals or animal products. In a phased survey, we investigated AMR in 300 Escherichia coli isolates and 300 enterococci (Enterococcus faecalis and E. faecium) isolates each from the carcasses of poultry, pigs, very young calves, and dairy cattle (food animals); all Salmonella isolates from poultry, very young calves, and dairy cattle; and 300 Campylobacter (Campylobacter jejuni and C. coli) isolates from poultry. The highest resistance levels in E. coli were found for sulfamethoxazole, tetracycline, and streptomycin, for all food animals. Cefotaxime-resistant E. coli were not found and low resistance to ciprofloxacin, colistin, and gentamicin was observed. The majority of enterococci isolates from all food animals were bacitracin-resistant. Erythromycin- and/or tetracycline-resistant enterococci isolates were found in varying proportions from all food animals. Ampicillin- or vancomycin-resistant enterococci isolates were not identified, and ciprofloxacin-resistant E. faecalis were not found. Salmonella isolates were only recovered from very young calves and all eight isolates were susceptible to all tested antimicrobials. Most Campylobacter isolates were susceptible to all tested antimicrobials, although 16.6% of C. jejuni were resistant to quinolones and tetracycline. Results suggest that AMR in E. coli, enterococci, Salmonella, and Campylobacter isolates from food animals in New Zealand is low, and currently, AMR in food animals poses a limited public health risk. Despite the low prevalence of AMR in this survey, ongoing monitoring of antimicrobial susceptibility in bacteria from food animals is recommended, to ensure timely detection of AMR with potential impacts on animal and human health.

Meningitis and Bacteremia by Unusual Serotype of Salmonella enterica Strain: A Whole Genome Analysis

Background

Although meningitis caused by Salmonella species is relatively rare and accounts for <1% of the confirmed cases in neonates, it is associated with case complications and fatality rates up to 50-70% when compared to other forms of Gram-negative bacilli meningitis.

Objectives

We conducted an investigation into the first reported case of neonatal meningitis caused by nontyphoidal S. enterica in Jazan, a region in the southwestern part of Saudi Arabia.

Methods

CSF and blood culture were collected from a female neonate patient to confirm the presence of bacterial meningitis. WGS was conducted to find out the comprehensive genomic characterization of S. enterica isolate.

Results

A 3-week-old infant was admitted to a local hospital with fever, poor feeding, and hypoactivity. She was diagnosed with Salmonella meningitis and bacteremia caused by S. enterica, which was sensitive to all antimicrobials tested. WGS revealed the specific strain to be S. enterica serotype Johannesburg JZ01, belonging to ST515 and cgMLST 304742.

Conclusions

We presented a genomic report of rare case of NTS meningitis in an infant who is living in a rural town in Jazan region, Saudi Arabia. Further research is required to understand the impact of host genetic factors on invasive nontyphoidal Salmonella infection.

Phage vB_Ec_ZCEC14 to treat antibiotic-resistant Escherichia coli isolated from urinary tract infections

Escherichia coli is a commensal bacterial species in the human gastrointestinal tract; however, it could be pathogenic and cause severe infections in intra and extra-intestinal sites. Uropathogenic E. coli accounts for 80-90% of urinary tract infections that can result in urosepsis and septic shock. Consequently, multidrug-resistant uropathogenic E. coli poses a considerable risk to the healthcare system worldwide. Phage therapy is demonstrated as an optimistic solution to over-the-counter antibiotics that contribute to the global issue of multidrug-resistant bacteria. This study aims to isolate a novel phage that could be implemented to cure urinary tract infections mediated by multidrug-resistant E. coli. Twenty-seven E. coli isolates were collected from patients with urinary tract infections to assess the antibacterial efficacy of phage vB_Ec_ZCEC14. Phage kinetics were encountered against the E. coli strain (EC/4), in addition to evaluating phage stability under various temperatures, pH values, and UV exposure periods. Full genome sequencing and morphological analysis were conducted for further phage characterization, which revealed that phage vB_Ec_ZCEC14 belongs to the family Straboviridae. Phage vB_Ec_ZCEC14 showed thermal tolerance at 80 ℃, pH stability between pH 3 and pH 12, and endurance to UV exposure for 45 min. The phage-host interaction results revealed that phage vB_Ec_ZCEC14 has strong and steady antibacterial action at lower concentrations (MOI 0.1). The study findings strongly indicate that phage vB_Ec_ZCEC14 holds significant promise as a potential therapeutic alternative for treatment of antibiotic-resistant uropathogenic E. coli.

Antimicrobial Resistance in Commensal Escherichia coli of the Porcine Gastrointestinal Tract

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

Artificial intelligence-accelerated high-throughput screening of antibiotic combinations on a microfluidic combinatorial droplet system

Microfluidic platforms have been employed as an effective tool for drug screening and exhibit the advantages of lower reagent consumption, higher throughput and a higher degree of automation. Despite the great advancement, it remains challenging to screen complex antibiotic combinations in a simple, high-throughput and systematic manner. Meanwhile, the large amounts of datasets generated during the screening process generally outpace the abilities of the conventional manual or semi-automatic data analysis. To address these issues, we propose an artificial intelligence-accelerated high-throughput combinatorial drug evaluation system (AI-HTCDES), which not only allows high-throughput production of antibiotic combinations with varying concentrations, but can also automatically analyze the dynamic growth of bacteria under the action of different antibiotic combinations. Based on this system, several antibiotic combinations displaying an additive effect are discovered, and the dosage regimens of each component in the combinations are determined. This strategy not only provides useful guidance in the clinical use of antibiotic combination therapy and personalized medicine, but also offers a promising tool for the combinatorial screenings of other medicines.

Effect of N-Acetyl-L-cysteine on Activity of Doxycycline against Biofilm-Forming Bacterial Strains

Biofilm-forming bacteria are associated with difficult-to-cure bacterial infections in veterinary patients. According to previous studies, N-acetyl-L-cysteine (NAC) showed an inhibitory effect on biofilm formation when it was applied in combination with beta-lactam antibiotics and fluoroquinolones. The lack of information about the effect of NAC on doxycycline activity against biofilm-forming strains was the reason for conducting this study. Staphylococcus aureus (S. aureus) ATCC 25923, Staphylococcus aureus O74, Escherichia coli (E. coli) ATCC 25922 and Pseudomonas aeruginosa (P. aeruginosa) ATCC 27853 were used to evaluate the activity of doxycycline with and without addition of NAC on planktonic bacteria and on biofilm formation. The minimum inhibitory concentrations (MICs) of doxycycline were not affected by NAC for Gram-negative strains and were found to be two times higher for the strains of S. aureus. The minimum biofilm inhibitory concentrations (MBICs) for Gram-negative bacteria (2 μg/mL for E. coli ATCC 25922 and 32 μg/mL for P. aeruginosa ATCC 27853), determined using a standard safranin colorimetric assay, were higher than the MICs (0.5 and 4 μg/mL, respectively). The data suggest that the combinations of doxycycline and NAC could stimulate the growth of planktonic cells of S. aureus and biofilm-forming E. coli ATCC 25922. NAC did not affect the strong inhibitory effect of doxycycline on the biofilm formation by the strains of S. aureus.

Comparison of Antimicrobial Resistance among Commensal Escherichia coli Isolated from Retail Table Eggs Produced by Laying Hens from the Cage and Non-Cage Housing Systems in Western Australia

Antimicrobial resistance (AMR) has become a global public health concern in recent decades. Although several investigations evaluated AMR in commensal and pathogenic bacteria from different foods of animal origin in Australia, there is a lack of studies that compared AMR in commensal E. coli isolated from retail table eggs obtained from different laying hen housing systems. This study aimed to determine AMR and differences in AMR patterns among E. coli isolates recovered from retail table eggs sourced from caged and non-caged housing systems in Western Australia. Commensal E. coli isolates were tested for susceptibility to 14 antimicrobials using a broth microdilution method. Clustering analyses and logistic regression models were applied to identify patterns and differences in AMR. Overall, there were moderate to high frequencies of resistance to the antimicrobials of lower importance used in Australian human medicine (tetracycline, ampicillin, trimethoprim, and sulfamethoxazole) in the isolates sourced from the eggs of two production systems. All E. coli isolates were susceptible to all critically important antimicrobials except the very low level of resistance to ciprofloxacin. E. coli isolates from eggs of non-caged systems had higher odds of resistance to tetracycline (OR = 5.76, p < 0.001) and ampicillin (OR = 3.42, p ≤ 0.01) compared to the isolates from eggs of caged systems. Moreover, the number of antimicrobials to which an E. coli isolate was resistant was significantly higher in table eggs from non-caged systems than isolates from caged systems’ eggs. Considering the conservative approach in using antimicrobials in the Australian layer flocks, our findings highlight the potential role of the environment or human-related factors in the dissemination and emergence of AMR in commensal E. coli, particularly in retail table eggs of non-cage system origin. Further comprehensive epidemiological studies are required to better understand the role of different egg production systems in the emergence and dissemination of AMR in commensal E. coli.

Antibacterial, Antifungal and Algicidal Activity of Phlorotannins, as Principal Biologically Active Components of Ten Species of Brown Algae

Marine seaweeds synthesize a plethora of bioactive metabolites, of which phlorotannins of brown algae currently attract special attention due to their high antibiotic and cytotoxic capacities. Here we measured the minimum inhibitory concentrations (MICs) of several semi-purified phlorotannin preparations of different origins and molecular composition using a set of model unicellular organisms, such as Escherichia coli, Saccharomyces cerevisiae, Chlamydomonas reinhardtii, etc. For the first time, MIC values were evaluated for phlorotannin-enriched extracts of brown algae of the orders Ectocarpales and Desmarestiales. Phlorotannin extracts of Desmarestia aculeata, Fucus vesiculosus, and Ectocarpus siliculosus showed the lowest MIC values against most of the treated organisms (4-25 μg/mL for bacteria and yeast). Analysis of the survival curves of E. coli showed that massive loss of cells started after 3-4 h of exposure. Microalgae were less susceptible to activity of phlorotannin extracts, with the highest MIC values (≥200 µg/mL) measured for Chlorella vulgaris cells. D. aculeata, E. siliculosus, and three fucalean algae accumulate considerable amounts (4-16% of dry weight) of phlorotannins with MIC values similar to those widely used antibiotics. As these species grow abundantly in polar and temperate seas and have considerable biomass, they may be regarded as promising sources of phlorotannins.

Hydrocinnamic Acid and Perillyl Alcohol Potentiate the Action of Antibiotics against Escherichia coli

The treatment of bacterial infections has been troubled by the increased resistance to antibiotics, instigating the search for new antimicrobial therapies. Phytochemicals have demonstrated broad-spectrum and effective antibacterial effects as well as antibiotic resistance-modifying activity. In this study, perillyl alcohol and hydrocinnamic acid were characterized for their antimicrobial action against Escherichia coli. Furthermore, dual and triple combinations of these molecules with the antibiotics chloramphenicol and amoxicillin were investigated for the first time. Perillyl alcohol had a minimum inhibitory concentration (MIC) of 256 µg/mL and a minimum bactericidal concentration (MBC) of 512 µg/mL. Hydrocinnamic acid had a MIC of 2048 µg/mL and an MBC > 2048 µg/mL. Checkerboard and time-kill assays demonstrated synergism or additive effects for the dual combinations chloramphenicol/perillyl alcohol, chloramphenicol/hydrocinnamic acid, and amoxicillin/hydrocinnamic acid at low concentrations of both molecules. Combenefit analysis showed synergism for various concentrations of amoxicillin with each phytochemical. Combinations of chloramphenicol with perillyl alcohol and hydrocinnamic acid revealed synergism mainly at low concentrations of antibiotics (up to 2 μg/mL of chloramphenicol with perillyl alcohol; 0.5 μg/mL of chloramphenicol with hydrocinnamic acid). The results highlight the potential of combinatorial therapies for microbial growth control, where phytochemicals can play an important role as potentiators or resistance-modifying agents.

Antimicrobial Resistance Profiles and Molecular Characteristics of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Healthy Cattle and Pigs in Korea

Antimicrobial-resistant bacteria isolated from food animals pose a major health threat to the public on this planet. This study aimed to determine the susceptibility profiles of Escherichia coli isolated from cattle and pig fecal samples and investigate the molecular characteristics of extended-spectrum β-lactamase (ESBL)-producing E. coli using gene identification, conjugation, and Southern blot approach. Overall 293 E. coli were recovered from cattle (120 isolates) and pigs (173 isolates) in 7 provinces of Korea during 2017-2018. Ampicillin, chloramphenicol, streptomycin, and sulfisoxazole resistance rates were the highest in pigs' isolates (>60%, p ≤ 0.001) compared to that in cattle (3-39%). Multidrug resistance (MDR) was higher in pig isolates (73%) than in cattle (31%), and the MDR profile usually includes streptomycin, sulfisoxazole, and tetracycline. Resistance to critically important antimicrobials such as ceftiofur, colistin, and ciprofloxacin was higher in weaners than those from finishers in pigs. The qnrS gene was detected in 13% of the pig isolates. Eight isolates from pigs and one isolate from cattle were identified as ESBL-producers and ESBL genes belonged to bla_CTX-M-55 (n = 4), bla_CTX-M-14 (n = 3), and bla_CTX-M-65 (n = 2). Notably, the bla_CTX-M-65 and qnrS1 genes were found to be carried together in an identical plasmid (IncHI2) in two isolates from finisher pigs. The bla_CTX-M-carrying isolates belonged to phylogenetic groups B1 (n = 4), B2 (n = 2), A (n = 2), and D (n = 1). The bla_CTX-M genes and non-β-lactam resistance traits were transferred to the E. coli J53 recipient from seven bla_CTX-M-positive strains isolated from pigs. The bla_CTX-M genes belonged to the IncI1α, IncFII, and IncHI2 plasmids and are also associated with the ISEcp1, IS26, IS903, and orf477 elements. These findings suggested the possibility of bla_CTX-M-carrying E. coli transmission to humans through direct contact with cattle and pigs or contamination of food products.

Phenotypic and Genotypic Analysis of Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Beef Cattle in Australia

This study investigated the antimicrobial resistance (AMR) profile of fecal Escherichia coli isolates from beef cattle (n = 150) at entry and exit from an Australian feedlot. Sample plating on MacConkey agar and Brilliance ESBL agar differentiated generic from extended-spectrum β-lactamase (ESBL)-producing E. coli, respectively. Resistance profiles were determined by minimum inhibitory concentration (MIC) testing and further analyzed by whole-genome sequencing (WGS). At entry, the prevalence of antimicrobial resistance to amoxicillin/clavulanic acid, ampicillin, streptomycin, and trimethoprim/sulfamethoxazole was very low (0.7%, each). At the exit, the resistance prevalence was moderate to tetracycline (17.8%) and low to ampicillin (5.4%), streptomycin (4.7%), and sulfisoxazole (3.9%). The most common AMR genes observed in phenotypically resistant isolates were tet(B) (43.2%), aph(3″)-Ib and aph(6)-Id (32.4%), blaTEM-1B, and sul2 (24.3%, each), which are responsible for resistance to tetracyclines, aminoglycosides, β-lactams, and sulfonamides, respectively. The ESBL-producing E. coli were recovered from one sample (0.7%) obtained at entry and six samples (4.0%) at the exit. The ESBL-producing E. coli harbored blaTEM (29.7%), blaCTX m(13.5%), and blaCMY (5.4%). The resistance phenotypes were highly correlated with resistance genotypes (r ≥ 0.85: p < 0.05). This study demonstrated that E. coli isolated from feedlot beef cattle can harbour AMR genes, but the low incidence of medically important resistance reflected the prudent antimicrobial use in the Australian industry.

Identifying Associations in Minimum Inhibitory Concentration Values of Escherichia coli Samples Obtained From Weaned Dairy Heifers in California Using Bayesian Network Analysis

Objective

Many antimicrobial resistance (AMR) studies in both human and veterinary medicine use traditional statistical methods that consider one bacteria and one antibiotic match at a time. A more robust analysis of AMR patterns in groups of animals is needed to improve on traditional methods examining antibiotic resistance profiles, the associations between the patterns of resistance or reduced susceptibility for all isolates in an investigation. The use of Bayesian network analysis can identify associations between distributions; this investigation seeks to add to the growing body of AMR pattern research by using Bayesian networks to identify relationships between susceptibility patterns in Escherichia coli (E. coli) isolates obtained from weaned dairy heifers in California.

Methods

A retrospective data analysis was performed using data from rectal swab samples collected from 341 weaned dairy heifers on six farms in California and selectively cultured for E. coli. Antibiotic susceptibility tests for 281 isolates against 15 antibiotics were included. Bayesian networks were used to identify joint patterns of reduced susceptibility, defined as an increasing trend in the minimum inhibitory concentration (MIC) values. The analysis involved learning the network structure, identifying the best fitting graphical mode, and learning the parameters in the final model to quantify joint probabilities.

Results

The graph identified that as susceptibility to one antibiotic decreases, so does susceptibility to other antibiotics in the same or similar class. The following antibiotics were connected in the final graphical model: ampicillin was connected to ceftiofur; spectinomycin was connected with trimethoprim-sulfamethoxazole, and this association was mediated by farm; florfenicol was connected with tetracycline.

Conclusions

Bayesian network analysis can elucidate complex relationships between MIC patterns. MIC values may be associated within and between drug classes, and some associations may be correlated with farm of sample origin. Treating MICs as discretized variables and testing for joint associations in trends may overcome common research problems surrounding the lack of clinical breakpoints.

Antimicrobial susceptibility, plasmid replicon typing, phylogenetic grouping, and virulence potential of avian pathogenic and faecal Escherichia coli isolated from meat chickens in Australia

Globally, avian colibacillosis is a leading cause of morbidity and mortality in poultry, associated with economic losses and welfare problems. Here, clinical avian pathogenic E. coli isolates (CEC; n=50) and faecal E. coli isolates from healthy (FEC; n=187) Australian meat chickens collected between 2006 and 2014 were subjected to antimicrobial susceptibility testing, phylogenetic grouping, plasmid replicon (PR) typing, multilocus sequence typing, and virulence gene (VG) profiling. Extended-spectrum cephalosporin (ESC)- and fluoroquinolone (FQ)-resistant E. coli isolates underwent further genetic characterisation. Significant proportions of CEC and FEC were respectively susceptible (13/50 [26%]; 48/187 [26%],) or MDR (9/50 [18%]; 26/187 [14%]) to 20 tested antimicrobials. Phylogenetic groups A and C, and PR types IncFIB and IncFrep were most commonly represented. Five tested CEC-associated VGs were more prevalent in CEC (≥90%) compared to FEC isolates (≤58%). Some isolates (CEC n=3; FEC n=7) were resistant to ESCs and/or FQs and possessed signature mutations in chromosomal FQ target genes and plasmid-mediated qnrS, bla_CMY-2, and bla_DHA-1 genes. Sequence type 354 (n=4), associated with extraintestinal infections in a broad range of hosts, was prevalent among the ESC- and/or FQ-resistant FEC.This study confirmed the existence of a small reservoir of ESC- and FQ-resistant E. coli in Australian commercial meat chickens despite the absence of use in the industry of these drug classes. Otherwise, a diversity of VGs and PR types in both faecal and clinical E. coli populations were identified. It's hypothesised that the source of ESC- and FQ-resistant E. coli may be external to poultry production facilities.Highlights1. Low-level resistance to older and newer generation antimicrobial drugs detected2. The most common sequence type (ST) associated with FQ resistance was ST354 (4/10)3. A small proportion of CEC (n=3) and FEC (n=7) were resistant to ESCs and/or FQs.

Global Distribution of Fluoroquinolone and Colistin Resistance and Associated Resistance Markers in Escherichia coli of Swine Origin - A Systematic Review and Meta-Analysis

Background

Fluoroquinolones and polymyxins (colistin) are considered as critical drugs for human medicine. Antimicrobials of these classes are also used in swine production worldwide and this usage can contribute to selection of antimicrobial resistance (AMR), which is a threat to both human and animal health. Given the dynamic epidemiology of AMR, updating our knowledge regarding distribution and trends in the proportion of resistant bacteria is of critical importance.

Objectives

The aim of this systematic review and meta-analysis was to describe the global prevalence of phenotypic and genotypic resistance to fluoroquinolones and colistin in Escherichia coli collected from swine.

Results

Four databases (PubMed, PubAg, Web of Science, and CAB abstracts) and reports of national surveillance programs were scanned and 360 articles were included in the analysis. We identified higher prevalence levels of fluoroquinolone and colistin resistance in isolates from pig populations in Asia compared to Europe. The heterogeneity of pooled estimates was also higher in Asian countries suggesting that prevalence of AMR is still not fully characterized. There was a major knowledge gap about the situation of AMR in South American and African countries. We also identified key deficiencies in how AMR data was reported in the studies. A meta-analysis using 6,167 publicly available genomes of swine E. coli established the prevalence and global distribution of genetic determinants that can lead to fluoroquinolone and colistin resistance.

Conclusion

This study provides the most comprehensive information on prevalence of phenotypic and genotypic resistance to key antimicrobials in pig populations globally. There is a need to establish national surveillance programs and effective policies, particularly in certain world regions, to curtail the threat of evolution of resistant isolates in swine production that can potentially contribute to public health detrimentally.

Phenotypic and Genotypic Assessment of Antimicrobial Resistance in Escherichia coli from Australian Cattle Populations at Slaughter

ABSTRACT

Australia relies on periodic antimicrobial resistance (AMR) surveys to determine trends and changes in AMR in animal production systems. This study is a follow-up to a survey of Escherichia coli from healthy cattle at slaughter conducted in 2013, which provided baseline data on AMR prevalence across cattle groups and production practices. In this study, 591 beef cattle, 194 dairy cattle, and 216 veal calf fecal samples were collected from 25 beef and veal processing establishments in Australia, representing approximately 77% of total export volume. A total of 969 matrix-assisted laser desorption-ionization results confirmed commensal E. coli isolates from 574 beef cattle, 186 dairy cattle, and 209 veal calves were recovered, and antimicrobial susceptibility testing was carried out by microbroth dilution to 16 drugs from 10 classes interpreted against epidemiological cutoff breakpoints. Overall, a high proportion of E. coli isolates (83.8%) were wild type for all antimicrobials assessed. In addition, isolates that were non-wild type (NWT) for three or more classes of antimicrobial did not exceed 4% for any of the cattle groups. The prevalence of E. coli that were NWT for antimicrobials that are critical or of high importance to human health was very low, with 1.4% of all isolates tested determined to be NWT for fluoroquinolones, third-generation cephalosporins, or polymyxins. Genomic analysis of NWT isolates identified one beef cattle isolate (ST-10) harboring blaCMY-2 and a dairy isolate (ST-58) and two veal calf isolates (ST-58 and ST-394) that had qnrS1, which confer resistance to extended-spectrum cephalosporins and fluoroquinolones, respectively. The low levels of AMR reported in this study confirm previous Australian studies, which indicated that there is minimal evidence that specific production practices lead to widespread disproportionate development of NWT isolates.

HIGHLIGHTS

Antimicrobial resistance and population genomics of multidrug-resistant Escherichia coli in pig farms in mainland China

The expanding use of antimicrobials in livestock is an important contributor to the worldwide rapid increase in antimicrobial resistance (AMR). However, large-scale studies on AMR in livestock remain scarce. Here, we report findings from surveillance of E. coli AMR in pig farms in China in 2018–2019. We isolated E. coli in 1,871 samples from pigs and their breeding environments, and found AMR in E. coli in all provinces in mainland China. We detected multidrug-resistance in 91% isolates and found resistance to last-resort drugs including colistin, carbapenems and tigecycline. We also identified a heterogeneous group of O-serogroups and sequence types among the multidrug-resistant isolates. These isolates harbored multiple resistance genes, virulence factor-encoding genes, and putative plasmids. Our data will help to understand the current AMR profiles of pigs and provide a reference for AMR control policy formulation for livestock in China.

Use of antimicrobials in livestock contributes to development of antimicrobial resistance but there are few large-scale surveillance studies. Here, the authors describe E. coli surveillance in pig farms in China, reporting high levels of multidrug-resistance across all mainland provinces.

Molecular epidemiology and antimicrobial resistance profiles of Salmonella isolates from dairy heifer calves and adult lactating cows in a Mediterranean pasture-based system of Australia

Dairy cows can be reservoirs of foodborne pathogens such as Salmonella that pose serious public health risks to humans. The study was designed to examine the molecular epidemiology and antimicrobial resistance profiles of Salmonella isolates from dairy heifer calves and adult lactating cows in the pasture-based system of Australia. A total of 838 animals (328 heifer calves and 510 lactating cows) from 22 farms were sampled. Overall, 54 Salmonella isolates were recovered (calves 28/328 and cows 26/510). A herd-level Salmonella prevalence of 50% (95% confidence interval: 31%-69%) was recorded. Within-herd prevalence for Salmonella ranged between 4%-29% and 4%-45% among the heifer calves and adult lactating cows, respectively. Three different serovars were identified with Salmonella Infantis being the most common serovar (n = 33, 61%) followed by Salmonella Kiambu (n = 20, 37.0%) and one isolate of Salmonella Cerro (2%). The highest antimicrobial resistance prevalence of Salmonella isolates was found against streptomycin (n = 31, 57%), followed by cefoxitin (n = 12, 22%), ceftriaxone (n = 2, 4%), and chloramphenicol (n = 1, 2%). Multiple class resistance was observed on 4 isolates against cefoxitin, chloramphenicol, and streptomycin. Multilocus sequence types ST32 (61%), ST309 (37%), and ST367 (2%) were strongly linked to the serovars Salmonella Infantis, Salmonella Kiambu, and Salmonella Cerro, respectively. Whole genome sequencing of Salmonella isolates detected only 2 resistance genes: aac(6') gene that confers resistance against aminoglycosides among 40.7% of the isolates, and a single isolate positive for the blaDHA-16 gene. Two distinct clusters among the serovars were observed suggesting 2 independent sources of spread. Despite the low prevalence of antimicrobial resistance among Salmonella from the dairy farms, our findings contribute to the regional and national understanding of antimicrobial resistance in dairy herds in Australia. There is need for continued antimicrobial resistance stewardship and surveillance programs to ensure the production of high-quality food products and the long-term protection of both animal and human health.

Neonatal calf diarrhea: A potent reservoir of multi-drug resistant bacteria, environmental contamination and public health hazard in Pakistan

Though emergence of multi-drug resistant bacteria in the environment is a demonstrated worldwide phenomenon, limited research is reported about the prevalence of resistant bacteria in fecal ecology of neonatal calf diarrhea (NCD) animals in Pakistan. The present study aimed to identify and assess the prevalence of bacterial pathogens and their resistance potential in the fecal ecology of NCD diseased animals of Pakistan. The presence of antibiotic resistance genes (bla_TEM, bla_NDM-1, bla_CTX-M, qnrS) was also investigated. A total of 51 bacterial isolates were recovered from feces of young diarrheic animals (n = 11), collected from 7 cities of Pakistan and identified on the basis of 16S rRNA gene sequence and phylogenetic analysis. Selected isolates were subjected to antimicrobial susceptibility by disc diffusion method while polymerase chain reaction (PCR) was used to characterize the bla_TEM, bla_NDM-1, bla_CTX-M, qnrS and mcr-1 antibiotic resistance genes. Based on the 16S rRNA gene sequences (Accession numbers: LC488898 to LC488948), all isolates were identified that belonged to seventeen genera with the highest prevalence rate for phylum Proteobacteria and genus Bacillus (23%). Antibiotic susceptibility explained the prevalence of resistance in isolates ciprofloxacin (100%), ampicillin (100%), sulfamethoxazole-trimethoprim (85%), tetracycline (75%), amoxicillin (55%), ofloxacin (50%), ceftazidime (45%), amoxicillin/clavulanic acid (45%), levofloxacin (30%), cefpodoxime (25%), cefotaxime (25%), cefotaxime/clavulanic acid (20%), and imipenem (10%). MICs demonstrated that almost 90% isolates were multi-drug resistant (against at least three antibiotics), specially against ciprofloxacin, and tetracycline with the highest resistance levels for Shigella sp. (NCCP-421) (MIC-CIP up to 75 μg mL^-1) and Escherichia sp. (NCCP-432) (MIC-TET up to 250 μg mL^-1). PCR-assisted detection of antibiotic resistance genes showed that 54% isolates were positive for bla_TEM gene, 7% isolates were positive for bla_CTX-M gene, 23% isolates were positive for each of qnrS and mcr-1 genes, 23% isolates were co-positive in combinations of qnrS and mcr-1 genes and bla_TEM and mcr-1 genes, whereas none of the isolate showed presence of bla_NDM-1 gene.

Diversity detected in commensals at host and farm level reveals implications for national antimicrobial resistance surveillance programmes

BACKGROUND

A key component to control of antimicrobial resistance (AMR) is the surveillance of food animals. Currently, national programmes test only limited isolates per animal species per year, an approach tacitly assuming that heterogeneity of AMR across animal populations is negligible. If the latter assumption is incorrect then the risk to humans from AMR in the food chain is underestimated.

OBJECTIVES

To demonstrate the extent of phenotypic and genetic heterogeneity of Escherichia coli in swine to assess the need for improved protocols for AMR surveillance in food animals.

METHODS

Eight E. coli isolates were obtained from each of 10 pigs on each of 10 farms. For these 800 isolates, AMR profiles (MIC estimates for six drugs) and PCR-based fingerprinting analysis were performed and used to select a subset (n = 151) for WGS.

RESULTS

Heterogeneity in the phenotypic AMR traits of E. coli was observed in 89% of pigs, with 58% of pigs harbouring three or more distinct phenotypes. Similarly, 94% of pigs harboured two or more distinct PCR-fingerprinting profiles. Farm-level heterogeneity was detected, with ciprofloxacin resistance detected in only 60% of pigs from a single farm. Furthermore, 58 STs were identified, with the dominant STs being ST10, ST101, ST542 and ST641.

CONCLUSIONS

Phenotypic and genotypic heterogeneity of AMR traits in bacteria from animal populations are real phenomena posing a barrier to correct interpretation of data from AMR surveillance. Evolution towards a more in-depth sampling model is needed to account for heterogeneity and increase the reliability of inferences.

Validation of Selective Agars for Detection and Quantification of Escherichia coli Strains Resistant to Critically Important Antimicrobials

Success in the global fight against antimicrobial resistance (AMR) is likely to improve if surveillance can be performed on an epidemiological scale. An approach based on agars with incorporated antimicrobials has enormous potential to achieve this. However, there is a need to identify the combinations of selective agars and key antimicrobials yielding the most accurate counts of susceptible and resistant organisms. A series of experiments involving 1,202 plates identified the best candidate combinations from six commercially available agars and five antimicrobials, using 18 Escherichia coli strains as either pure cultures or inocula-spiked feces. The effects of various design factors on colony counts were analyzed in generalized linear models. Without antimicrobials, Brilliance E. coli and CHROMagar ECC agars yielded 28.9% and 23.5% more colonies, respectively, than MacConkey agar. The order of superiority of agars remained unchanged when fecal samples with or without spiking of resistant E. coli strains were inoculated onto agars with or without specific antimicrobials. When antimicrobials were incorporated at various concentrations, it was revealed that ampicillin, tetracycline, and ciprofloxacin were suitable for incorporation into Brilliance and CHROMagar agars at all defined concentrations. Gentamicin was suitable for incorporation only at 8 and 16 μg/ml, while ceftiofur was suitable only at 1 μg/ml. CHROMagar extended-spectrum β-lactamase (ESBL) agar supported growth of a wider diversity of extended-spectrum-cephalosporin-resistant E. coli strains. The findings demonstrate the potential for agars with incorporated antimicrobials to be combined with laboratory-based robotics to deliver AMR surveillance on a vast scale with greater sensitivity of detection and strategic relevance.

IMPORTANCE Established models of surveillance for AMR in livestock typically have a low sampling intensity, which creates a tremendous barrier to understanding the variation of resistance among animal and food enterprises. However, developments in laboratory robotics now make it possible to rapidly and affordably process large volumes of samples. Combined with modern selective agars incorporating antimicrobials, this forms the basis of a novel surveillance process for identifying resistant bacteria by chromogenic reactions, including accurately detecting and quantifying the presence of bacteria even when they are present at low concentrations. Because Escherichia coli is a widely preferred indicator bacterium for AMR surveillance, this study identifies the optimal selective agar for quantifying resistant E. coli strains by assessing the growth performance on agars with antimicrobials. The findings are the first step toward exploiting laboratory robotics in an up-scaled approach to AMR surveillance in livestock, with wider adaptations in food, clinical microbiology, and public health.

Characterization of beta-lactam-resistant Escherichia coli from Australian fruit bats indicates anthropogenic origins

Antimicrobial-resistant Escherichia coli, particularly those resistant to critically important antimicrobials, are increasingly reported in wildlife. The dissemination of antimicrobial-resistant bacteria to wildlife indicates the far-reaching impact of selective pressures imposed by humans on bacteria through misuse of antimicrobials. The grey-headed flying fox (GHFF; Pteropus poliocephalus), a fruit bat endemic to eastern Australia, commonly inhabits urban environments and encounters human microbial pollution. To determine if GHFF have acquired human-associated bacteria, faecal samples from wild GHFF (n=287) and captive GHFF undergoing rehabilitation following illness or injury (n=31) were cultured to detect beta-lactam-resistant E. coli. Antimicrobial susceptibility testing, PCR and whole genome sequencing were used to determine phenotypic and genotypic antimicrobial resistance profiles, strain type and virulence factor profiles. Overall, 3.8 % of GHFF carried amoxicillin-resistant E. coli (wild 3.5 % and captive 6.5 %), with 38.5 % of the 13 GHFF E. coli isolates exhibiting multidrug resistance. Carbapenem (bla_NDM-5) and fluoroquinolone resistance were detected in one E. coli isolate, and two isolates were resistant to third-generation cephalosporins (bla_CTX-M-27 and ampC). Resistance to tetracycline and trimethoprim plus sulfamethoxazole were detected in 69.2% and 30.8 % of isolates respectively. Class 1 integrons, a genetic determinant of resistance, were detected in 38.5 % of isolates. Nine of the GHFF isolates (69.2 %) harboured extraintestinal virulence factors. Phylogenetic analysis placed the 13 GHFF isolates in lineages associated with humans and/or domestic animals. Three isolates were human-associated extraintestinal pathogenic E. coli (ST10 O89:H9, ST73 and ST394) and seven isolates belonged to lineages associated with extraintestinal disease in both humans and domestic animals (ST88, ST117, ST131, ST155 complex, ST398 and ST1850). This study provides evidence of anthropogenic multidrug-resistant and pathogenic E. coli transmission to wildlife, further demonstrating the necessity for incorporating wildlife surveillance within the One Health approach to managing antimicrobial resistance.

Deep Learning for Novel Antimicrobial Peptide Design

Antimicrobial resistance is an increasing issue in healthcare as the overuse of antibacterial agents rises during the COVID-19 pandemic. The need for new antibiotics is high, while the arsenal of available agents is decreasing, especially for the treatment of infections by Gram-negative bacteria like Escherichia coli. Antimicrobial peptides (AMPs) are offering a promising route for novel antibiotic development and deep learning techniques can be utilised for successful AMP design. In this study, a long short-term memory (LSTM) generative model and a bidirectional LSTM classification model were constructed to design short novel AMP sequences with potential antibacterial activity against E. coli. Two versions of the generative model and six versions of the classification model were trained and optimised using Bayesian hyperparameter optimisation. These models were used to generate sets of short novel sequences that were classified as antimicrobial or non-antimicrobial. The validation accuracies of the classification models were 81.6–88.9% and the novel AMPs were classified as antimicrobial with accuracies of 70.6–91.7%. Predicted three-dimensional conformations of selected short AMPs exhibited the alpha-helical structure with amphipathic surfaces. This demonstrates that LSTMs are effective tools for generating novel AMPs against targeted bacteria and could be utilised in the search for new antibiotics leads.

From Farm-to-Fork: E. Coli from an Intensive Pig Production System in South Africa Shows High Resistance to Critically Important Antibiotics for Human and Animal Use

Antibiotic resistance profiles of Escherichia coli were investigated in an intensive pig production system in the uMgungundlovu District, South Africa, using the 'farm-to-fork' approach. Four hundred seventeen (417) samples were collected from pig and pig products at different points (farm, transport, and abattoir). E. coli was isolated and enumerated using the Colilert^® 18/Quanti-Tray^® 2000 system. Ten isolates from each Quanti-tray were selected randomly and putatively identified on eosin methylene blue agar. Real-time PCR targeting the uidA gene was used to confirm isolates to the genus level. The Kirby-Bauer disc diffusion method was used to determine the isolates' antibiotic susceptibility profiles against 20 antibiotics. A total of 1044 confirmed E. coli isolates were obtained across the three critical points in the food chain. Resistance was observed to all the antibiotics tested with the highest and lowest rates obtained against tetracycline (88.5%) and meropenem (0.2%), respectively. Resistance was also observed to chloramphenicol (71.4%), ampicillin (71.1%), trimethoprim-sulfamethoxazole (61.3%), amoxicillin-clavulanate (43.8%), cephalexin (34.3%), azithromycin (23.9%), nalidixic acid (22.1%), cefoxitin (21.1%), ceftriaxone (18.9%), ciprofloxacin (17.3%), cefotaxime (16.9%), gentamicin (15.5%), cefepime (13.8%), ceftazidime (9.8%), amikacin (3.4%), piperacillin-tazobactam (1.2%), tigecycline (0.9%), and imipenem (0.3%). Multidrug resistance (MDR) was observed in 71.2% of the resistant isolates with an overall multiple antibiotic resistance (MAR) index of 0.25, indicating exposure to high antibiotic use environments at the farm level. A high percentage of resistance was observed to growth promoters and antibiotics approved for veterinary medicine in South Africa. Of concern was resistance to critically important antibiotics for animal and human use and the watch and reserve categories of antibiotics. This could have adverse animal and human health consequences from a food safety perspective, necessitating efficient antibiotic stewardship and guidelines to streamline antibiotic use in the food-animal production chain.

Antimicrobial resistance and genomic characterisation of Escherichia coli isolated from caged and non-caged retail table eggs in Western Australia

Foodborne exposure to antimicrobial-resistant bacteria is a growing global health concern. Escherichia coli (E. coli) is well recognised as an indicator of food contamination with faecal materials. In the present study, we investigated the occurrence of E. coli in table eggs sold at retail supermarkets in Western Australia (WA). A total of 2172 visually clean and intact retail eggs were purchased between October 2017 and June 2018. A single carton containing a dozen eggs was considered as a single sample resulting a total of 181 samples. The shells and contents of each sample were separately pooled and tested using standard culture-based methods. Overall, generic E. coli was detected in 36 (19.8%; 95% confidence interval: 14.3; 26.4) of the 181 tested retail egg samples. We characterised 100 of the recovered E. coli isolates for their phenotypic antimicrobial resistance using minimum inhibitory concentration (MIC). A subset of E. coli isolates (n = 14) were selected on the basis of their MIC patterns, and were further characterised using whole genome sequencing (WGS). Fifty-seven (57%) of the recovered generic E. coli isolates (n = 100) were resistant to at least one of the 14 antimicrobials included in the MIC testing panel, of which 22 isolates (22%) showed multi-class resistance. The highest frequencies of non-susceptibility of E. coli isolated from WA retailed eggs were against tetracycline (49%) and ampicillin (36%). WGS revealed that tet(A) and bla_TEM-1B genes were present in most of the isolates exhibiting phenotypic resistance to tetracycline and ampicillin, respectively. The majority (98%) of the characterised E. coli isolates were susceptible to ciprofloxacin and azithromycin, and none were resistant to the cephalosporin antimicrobials included in the MIC panel. Two isolates demonstrated reduced susceptibility to ciprofloxacin, with MICs of 0.125 and 0.25 mg/L, and WGS revealed the presence of plasmid mediated qnrs1 gene in both isolates. This is the first report on detection of non-wild-type resistance to fluoroquinolones in supermarket eggs in Australia; one of the two isolates was from a cage-laid eggs sample while the other was from a barn-laid retail eggs sample. Fluoroquinolones have never been permitted for use in poultry farms in Australia. Thus, the detection of low-level ciprofloxacin-resistant E. coli in the absence of local antimicrobial selection pressure at the Australian layer farms warrants further research on the potential role of the environment or human-related factors in the transmission of antimicrobial resistance. The results of this study add to the local and global understanding of antimicrobial resistance spread in foods of animal origin.

Absence of high priority critically important antimicrobial resistance in Salmonella sp. isolated from Australian commercial egg layer environments

The development of antimicrobial resistance in foodborne pathogens is a growing public health concern. This study was undertaken to determine the antimicrobial susceptibility of Salmonella enterica subspecies enterica isolated from the Australian commercial egg layer industry. S. enterica subspecies enterica (n=307) isolated from Australian commercial layer flock environments (2015-2018) were obtained from reference, research and State Government laboratories from six Australian states. All Salmonella isolates were serotyped. Antimicrobial susceptibility testing (AST) for 16 antimicrobial agents was performed by broth microdilution. Antimicrobial resistance genes and sequence types (STs) were identified in significant isolates by whole genome sequencing (WGS). Three main serotypes were detected, S. Typhimurium (n=61, 19.9%), S. Senftenburg (n=45, 14.7%) and S. Agona (n=37, 12.1%). AST showed 293/307 (95.4%) isolates were susceptible to all tested antimicrobial agents and all isolates were susceptible to amoxicillin-clavulanate, azithromycin, ceftiofur, ceftriaxone, ciprofloxacin, colistin, florfenicol, gentamicin, kanamycin and trimethoprim-sulfamethoxazole. Low levels of non-susceptibility were observed to streptomycin (2.3%, n=7), sulfisoxazole (2.0%, n=6), chloramphenicol (1.3%, n=4) and tetracycline (1.0%, n=3). Very low levels of non-susceptibility were observed to ampicillin (2/307; 0.7%) and cefoxitin (2/307; 0.7%). Two isolates (S. Havana and S. Montevideo), exhibited multidrug-resistant phenotypes to streptomycin, sulfisoxazole and tetracycline and possessed corresponding antimicrobial resistance genes (aadA4, aac(6')-Iaa, sul1, tetB). One S. Typhimurium isolate was resistant to ampicillin and tetracycline, and possessed both tetA and bla_TEM-1B. WGS also identified these isolates as belonging to ST4 (S. Montevideo), ST578 (S. Havana) and ST19 (S. Typhimurium). The absence of resistance to highest priority critically important antimicrobials as well as the extremely low level of AMR generally among Australian commercial egg layer Salmonella isolates likely reflect Australia's conservative antimicrobial registration policy in food-producing animals and low rates of antimicrobial use within the industry.

3D microfluidic gradient generator for combination antimicrobial susceptibility testing

Microfluidic concentration gradient generators (µ-CGGs) have been utilized to identify optimal drug compositions through antimicrobial susceptibility testing (AST) for the treatment of antimicrobial-resistant (AMR) infections. Conventional µ-CGGs fabricated via photolithography-based micromachining processes, however, are fundamentally limited to two-dimensional fluidic routing, such that only two distinct antimicrobial drugs can be tested at once. This work addresses this limitation by employing Multijet-3D-printed microchannel networks capable of fluidic routing in three dimensions to generate symmetric multidrug concentration gradients. The three-fluid gradient generation characteristics of the fabricated 3D µ-CGG prototype were quantified through both theoretical simulations and experimental validations. Furthermore, the antimicrobial effects of three highly clinically relevant antibiotic drugs, tetracycline, ciprofloxacin, and amikacin, were evaluated via experimental single-antibiotic minimum inhibitory concentration (MIC) and pairwise and three-way antibiotic combination drug screening (CDS) studies against model antibiotic-resistant Escherichia coli bacteria. As such, this 3D µ-CGG platform has great potential to enable expedited combination AST screening for various biomedical and diagnostic applications.

Resistance to critically important antimicrobials in Australian silver gulls (Chroicocephalus novaehollandiae) and evidence of anthropogenic origins

OBJECTIVES

Antimicrobial resistance (AMR) to critically important antimicrobials (CIAs) amongst Gram-negative bacteria can feasibly be transferred amongst wildlife, humans and domestic animals. This study investigated the ecology, epidemiology and origins of CIA-resistant Escherichia coli carried by Australian silver gulls (Chroicocephalus novaehollandiae), a gregarious avian wildlife species that is a common inhabitant of coastal areas with high levels of human contact.

METHODS

Sampling locations were widely dispersed around the perimeter of the Australian continent, with sites separated by up to 3500 km. WGS was used to study the diversity and molecular characteristics of resistant isolates to ascertain their epidemiological origin.

RESULTS

Investigation of 562 faecal samples revealed widespread occurrence of extended-spectrum cephalosporin-resistant (21.7%) and fluoroquinolone-resistant (23.8%) E. coli. Genome sequencing revealed that CIA-resistant E. coli isolates (n = 284) from gulls predominantly belonged to human-associated extra-intestinal pathogenic E. coli (ExPEC) clones, including ST131 (17%), ST10 (8%), ST1193 (6%), ST69 (5%) and ST38 (4%). Genomic analysis revealed that gulls carry pandemic ExPEC-ST131 clades (O25:H4 H30-R and H30-Rx) and globally emerging fluoroquinolone-resistant ST1193 identified among humans worldwide. Comparative analysis revealed that ST131 and ST1193 isolates from gulls overlapped extensively with human clinical isolates from Australia and overseas. The present study also detected single isolates of carbapenem-resistant E. coli (ST410-blaOXA-48) and colistin-resistant E. coli (ST345-mcr-1).

CONCLUSIONS

The carriage of diverse CIA-resistant E. coli clones that strongly resemble pathogenic clones from humans suggests that gulls can act as ecological sponges indiscriminately accumulating and disseminating CIA-resistant bacteria over vast distances.

Non-Typhoidal Salmonella at the Human-Food-of-Animal-Origin Interface in Australia

Non-typhoidal Salmonella is a major zoonotic pathogen that plays a significant role in foodborne human salmonellosis worldwide through the consumption of contaminated foods, particularly those of animal origin. Despite a considerable reduction in human salmonellosis outbreaks in developed countries, Australia is experiencing a continuous rise of such outbreaks in humans. This review of the literature highlights the reported non-typhoidal Salmonella outbreaks in humans as well as the occurrence of the pathogen in foods from animal sources throughout Australia. Non-typhoidal Salmonella infections from food animals are more often associated with at-risk people, such as immunocompromised and aged people or children. Although several animal-sourced foods were recognised as the catalysts for salmonellosis outbreaks in Australia, egg and egg-based products remained the most implicated foods in the reported outbreaks. This review further highlights the antimicrobial resistance trends of non-typhoidal Salmonella isolates at the human-food interface, with a focus on clinically important antimicrobials in humans, by collating evidence from previous investigations in Australia. The rise in antimicrobial-resistant Salmonella, especially to antimicrobials commonly prescribed to treat human salmonellosis, has become a significant global public health concern. However, the overall prevalence of antimicrobial resistance in Australia is considerably lower than in other parts of the world, particularly in terms of critically important antimicrobials for the treatment of human salmonellosis. The present review adds to our understanding of the global epidemiology of non-typhoidal Salmonella with emphasis on the past few decades in Australia.

Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring

Intensive pig production systems often rely on the use of antimicrobials and heavy metal feed additives to maintain animal health and welfare. To gain insight into the carriage of antimicrobial resistance genes (ARGs) in the faecal flora of commercially reared healthy swine, we characterised the genome sequences of 117 porcine commensal E. coli that carried the class 1 integrase gene (intI1⁺). Isolates were sourced from 42 healthy sows and 126 of their offspring from a commercial breeding operation in Australia in 2017. intI1⁺ E. coli was detected in 28/42 (67%) sows and 90/126 (71%) piglets. Phylogroup A, particularly clonal complex 10, and phylogroup B1 featured prominently in the study collection. ST10, ST20, ST48 and ST361 were the dominant sequence types. Notably, 113/117 isolates (96%) carried three or more ARGs. Genes encoding resistance to -lactams, aminoglycosides, trimethoprim, sulphonamides, tetracyclines and heavy metals were dominant. ARGs encoding resistance to last-line agents, such as carbapenems and third generation cephalosporins, were not detected. IS26, an insertion sequence noted for its ability to capture and mobilise ARGs, was present in 108/117 (92%) intI1⁺ isolates, and it played a role in determining class 1 integron structure. Our data shows that healthy Australian pig faeces are an important reservoir of multidrug resistant E. coli that carry genes encoding resistance to multiple first-generation antibiotics and virulence-associated genes.

How antibiotics are used in pig farming: a mixed-methods study of pig farmers, feed mills and veterinarians in Thailand

Background

Rising global concern about antimicrobial resistance has drawn attention to the use of antibiotics in livestock. Understanding the current usage of antibiotics in these animals is essential for effective interventions on the optimisation of antibiotic use. However, to date few studies have been conducted in low- and middle-income countries. This study aimed to explore the use of antibiotics and estimate the total amount of antibiotics used in pig production in Thailand.

Methods

This was a mixed-methods study including a cross-sectional questionnaire-based survey of 84 pig farmers, secondary analysis of data from a survey of 31 feed mills to estimate the amount of antibiotics mixed in pig feed and interviews with five veterinarians involved in the feed mill industry to gain an understanding of medicated feed production.

Findings

Half of the farmers reported using antibiotics for disease prevention. Use was significantly associated with farmers' experience in raising pigs, farm income, having received advice on animal health and belonging to a farm cooperative. The estimated total amount of active ingredients mixed into medicated feed for pigs for the whole country was 843 tonnes in 2017. Amoxicillin was the most commonly used antibiotic reported by both pig farms and feed mills. The use of Critically Important Antimicrobials including colistin was common, with one-third of farmers reporting their use as oral or as injectable medication, and accounting for nearly two-thirds of antibiotics contained in medicated feed.

Conclusion

A majority of antibiotics used in Thai pig farms belonged to the category of Critically Important Antimicrobials. Progressive restriction in the use of antibiotics in pigs is recommended through using prescriptions to control the distribution of certain antibiotics. The government should strengthen veterinary services to improve access of farmers to animal health advice and explore alternative interventions.

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

Background

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

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

Results

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

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

Conclusion

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

Genomic Characterization of Prevalent mcr-1, mcr-4, and mcr-5 Escherichia coli Within Swine Enteric Colibacillosis in Spain

Antimicrobial agents are crucial for the treatment of many bacterial diseases in pigs, however, the massive use of critically important antibiotics such as colistin, fluoroquinolones and 3rd-4th-generation cephalosporins often selects for co-resistance. Based on a comprehensive characterization of 35 colistin-resistant Escherichia coli from swine enteric colibacillosis, belonging to prevalent Spanish lineages, the aims of the present study were to investigate the characteristics of E. coli clones successfully spread in swine and to assess the correlation of the in vitro results with in silico predictions from WGS data. The resistome analysis showed six different mcr variants: mcr-1.1; mcr-1.10; mcr-4.1; mcr-4.2; mcr-4.5; and mcr-5.1. Additionally, bla _{CTX-M- 14}, bla _{CTX-M- 32} and bla _{SHV- 12} genes were present in seven genomes. PlasmidFinder revealed that mcr-1.1 genes located mainly on IncHI2 and IncX4 types, and mcr-4 on ColE10-like plasmids. Twenty-eight genomes showed a gyrA S83L substitution, and 12 of those 28 harbored double-serine mutations gyrA S83L and parC S80I, correlating with in vitro quinolone-resistances. Notably, 16 of the 35 mcr-bearing genomes showed mutations in the PmrA (S39I) and PmrB (V161G) proteins. The summative presence of mechanisms, associated with high-level of resistance to quinolones/fluoroquinolones and colistin, could be conferring adaptive advantages to prevalent pig E. coli lineages, such as the ST10-A (CH11-24), as presumed for ST131. SerotypeFinder allowed the H-antigen identification of in vitro non-mobile (HNM) isolates, revealing that 15 of the 21 HNM E. coli analyzed were H39. Since the H39 is associated with the most prevalent O antigens worldwide within swine colibacillosis, such as O108 and O157, it would be probably playing a role in porcine colibacillosis to be considered as a valuable subunit antigen in the formulation of a broadly protective Enterotoxigenic E. coli (ETEC) vaccine. Our data show common features with other European countries in relation to a prevalent clonal group (CC10), serotypes (O108:H39, O138:H10, O139:H1, O141:H4), high plasmid content within the isolates and mcr location, which would support global alternatives to the use of antibiotics in pigs. Here, we report for first time a rare finding so far, which is the co-occurrence of double colistin-resistance mechanisms in a significant number of E. coli isolates.

Escherichia coli and Salmonella spp. isolated from Australian meat chickens remain susceptible to critically important antimicrobial agents

The World Health Organisation has defined "highest priority critically important antimicrobials" (CIAs) as those requiring the greatest control during food production. Evidence demonstrating that restricted antimicrobial usage prevents the emergence of resistance to CIA's amongst pathogenic and commensal organisms on a production system-wide scale would strengthen international efforts to control antimicrobial resistance (AMR). Therefore, in a designed survey of all major chicken-meat producers in Australia, we investigated the phenotypic AMR of E. coli (n = 206) and Salmonella (n = 53) from caecal samples of chickens at slaughter (n = 200). A large proportion of E. coli isolates (63.1%) were susceptible to all tested antimicrobials. With regards to CIA resistance, only two E.coli isolates demonstrated resistance to fluoroquinolones, attributed to mutations in the quinolone resistance-determining regions of gyrA. Antimicrobial resistance was observed for trimethoprim/sulfamethoxazole (8.7%), streptomycin (9.7%), ampicillin (14.1%), tetracycline (19.4%) and cefoxitin (0.5%). All Salmonella isolates were susceptible to ceftiofur, chloramphenicol, ciprofloxacin, colistin, florfenicol, gentamicin and tetracycline. A low frequency of Salmonella isolates exhibited resistance to streptomycin (1.9%), ampicillin (3.8%), and cefoxitin (11.3%). AMR was only observed among Salmonella Sofia serovars. None of the Salmonella isolates exhibited a multi-class-resistant phenotype. Whole genome sequencing did not identify any known resistance mechanisms for the Salmonella isolates demonstrating resistance to cefoxitin. The results provide strong evidence that resistance to highest priority CIA's is absent in commensal E. coli and Salmonella isolated from Australian meat chickens, and demonstrates low levels of resistance to compounds with less critical ratings such as cefoxitin, trimethoprim/sulfamethoxazole, and tetracycline. Apart from regulated exclusion of CIAs from most aspects of livestock production, vaccination against key bacterial pathogens and stringent biosecurity are likely to have contributed to the favorable AMR status of the Australian chicken meat industry. Nevertheless, industry and government need to proactively monitor AMR and antimicrobial stewardship practices to ensure the long-term protection of both animal and human health.