The application of antibiotics in broiler production and the resulting antibiotic resistance in Escherichia coli: A global overview

A Cross-Sectional Survey of the Knowledge, Attitudes, and Practices of Antimicrobial Users and Providers in an Area of High-Density Livestock-Human Population in Western Kenya

Background: Antimicrobial resistance (AMR) is one of the most important global health crises in recent times and is driven primarily by antimicrobial consumption. In East Africa, there is a paucity of data regarding the knowledge, attitudes, and practices (KAP) related to antimicrobial use (AMU). We investigate the ways in which antimicrobial users in the veterinary sector accessed veterinary antimicrobials, and common behaviors of veterinary antimicrobial users and prescribers associated with AMU and AMR.

Methods: In total, 70 farmers, staff at 49 agricultural-veterinary antimicrobial shops (agrovet staff) and 28 veterinary animal healthcare workers or veterinary surgeons (veterinary professionals) were interviewed in Busia county, western Kenya in 2016 using a standard questionnaire as a framework for structured interviews. Data recorded included participant demographics, level of education, access to and sources of veterinary antimicrobials, prescribing patterns, and knowledge of AMR and antimicrobial withdrawal periods.

Results: The majority of antimicrobials were accessed through informal means, purchased from agroveterinary shops; more than half of staff did not hold nationally mandated qualifications to advise on or sell veterinary antimicrobials. Approximately 40% of veterinary antimicrobials were sold without a prescription and it was noted that both price and customer preference were important factors when selling antimicrobials in almost all agrovet shops. Knowledge of the dangers associated with AMR and AMU were mostly superficial. Treatment failure occurred often, and there was a lack of differentiation between AMR and simply treatment failure.

Conclusion: In this study area in East Africa with high-density human and livestock populations, AMU was primarily for maintenance of livestock health. These findings have highlighted several aspects surrounding inappropriate access to antimicrobials, and as such require attention from policy makers concerned with AMR in both livestock and human medicine sectors. Improving prescribing practices and ensuring a minimum level of general education and awareness of prescribers, as well as expanding the role of agrovet staff in antimicrobial stewardship programmes, may help begin to mitigate the maintenance and transmission of AMR, particularly amongst livestock.

The Influencing Factors of Bacterial Resistance Related to Livestock Farm: Sources and Mechanisms

Bacterial resistance is a complex scientific issue. To manage this issue, we need to deeply understand the influencing factors and mechanisms. Based on the background of livestock husbandry, this paper reviews the factors that affect the acquisition of bacterial resistance. Meanwhile, the resistance mechanism is also discussed. “Survival of the fittest” is the result of genetic plasticity of bacterial pathogens, which brings about specific response, such as producing adaptive mutation, gaining genetic material or changing gene expression. To a large extent, bacterial populations acquire resistance genes directly caused by the selective pressure of antibiotics. However, mobile resistance genes may be co-selected by other existing substances (such as heavy metals and biocides) without direct selection pressure from antibiotics. This is because the same mobile genetic elements as antibiotic resistance genes can be co-located by the resistance determinants of some of these compounds. Furthermore, environmental factors are a source of resistance gene acquisition. Here, we describe some of the key measures that should be taken to mitigate the risk of antibiotic resistance. We call on the relevant governments or organizations around the world to formulate and improve the monitoring policies of antibiotic resistance, strengthen the supervision, strengthen the international cooperation and exchange, and curb the emergence and spread of drug-resistant strains.

Evaluation of Antibiotic Resistance in Bacterial Strains Isolated from Sewage of Slaughterhouses Located in Sicily (Italy)

Antimicrobial resistance is presently one of the most public health critical concerns. The frequent and often incorrect use of antibiotics in animal husbandry has led to the spread of antimicrobial resistance in this setting. Wastewater from slaughterhouses can be contaminated with multidrug-resistant bacteria, representing a possible cross-contamination route. We evaluated the presence of antibiotic-resistant bacteria in wastewater samples from slaughterhouses located in an Italian region. Specifically, 18 slaughterhouses were included in the study. Of the tested samples, 40 bacterial strains were chosen, identified, and tested for antibiotic susceptibility. Pseudomonas spp., Proteus spp., Enterobacter spp., Aeromonas spp., and Citrobacter spp. were the most detected genera. The most resistant strains were on average those belonging to Enterobacter spp. The highest resistance rate was recorded for macrolides. Among β-lactams, penicillins and cephalosporins were by far the molecules towards which the highest resistance was detected. A very interesting finding is the difference found in strains detected in wastewater from poultry slaughterhouses, in which higher levels for almost all the considered drugs were detected compared to those from ungulates slaughterhouses. Our results indicate wastewater from slaughterhouses as a potential vehicle of resistant bacteria and highlight the importance of correct management of these kinds of waters.

Aluminosilicates at different levels in rye litter and feed affect the growth and meat quality of broiler chickens

Litter sanitation treatments and feed supplements that stimulate bird growth. The aim of this study was to analyse the effects of zeolite (z) and halloysite (h) in feed and rye straw litter on growth performance, meat quality in chickens. 500 males Ross 308 were allocated to 5 groups (10 replicates). Feed for groups 2–5 was supplemented with halloysite and zeolite (25:75). The content of aluminosilicates in the feed was different depending on the feeding phase: 0.5, 1, 1.5, or 2%. The following doses were used in litter: 2, 0.800 kg/m² h; 3, 0.400 kg/m² h and 0.400 kg/m² z; 4, 0.800 kg/m² z; 5, 0.200 kg/m² h, and 0.600 kg/m² z. Growth, and meat quality were analysed. Body weight and body weight gain were higher in groups 2–5 than in group 1, while feed intake was lower in groups 1 and 2 (p < 0.05). Body weight, the weight of carcass, and most of its elements were higher in the experimental groups (p < 0.05). Breast muscles from group 1 were characterised by better water-holding capacity and higher protein content, while those from 4 had higher content of collagen and water (p < 0.05). Breast muscles from group 3 were characterized by lower yellowness than in 2 (p < 0.05). Leg muscles from group 1 were characterized by lower redness than in 4 (p < 0.05). Water-holding capacity was better in group 3 and protein content was higher in 2 (p < 0.05). The content of fat in leg muscle was lower in all experimental groups compared to control (p < 0.05). This indicates the suitability of aluminosilicates in poultry management practice, with better growth and meat quality.

Onion leaf and synthetic additives in broiler diet: impact on splenic cytokines, serum immunoglobulins, cecal bacterial population, and muscle antioxidant status

BACKGROUND

The disadvantages associated with the use of synthetic additives in animal production could threaten human and animal health, and the safety of animal-derived foods. This study assessed the growth performance, blood chemistry, immune indices, selected caeca bacterial population, muscle antioxidant enzyme activities, and meat quality in broiler chickens fed diet supplemented with antibiotic (70% oxytetracycline +30% neomycin), tert-butylhydroxytoluene or onion leaf powder (OLP). One day old Ross 308 chicks (n = 240) were assigned randomly to either D-1, control diet (CD) without additives; D-2, CD + 0.3 g kg^-1 antibiotic +0.15 g kg^-1 tert-butylhydroxytoluene; D-3, CD + 2.5 g kg^-1 OLP; or D-4, CD + 5 g kg^-1 OLP for 42 days.

RESULTS

The D-2 and D-4 diets improved (P < 0.05) bodyweight gain and feed efficiency in broilers. Platelet and cecal Lactobacillus spp. counts were higher (P < 0.05) whereas muscle cholesterol was lower (P < 0.05) in the OLP-supplemented birds. Supplemented birds had higher (P < 0.01) splenic interleukin-10 and lower (P < 0.01) splenic tumor necrosis factor-α, immunoglobulin A, cecal E. coli and C. perfringens counts compared with the D-1 birds. The D-4 birds had the least (P < 0.05) splenic interleukin-1β. Dietary supplements increased (P < 0.05) catalase, glutathione peroxidase, and total antioxidant capacity, and lowered (P < 0.05) drip loss, malondialdehyde and carbonyl content in breast meat.

CONCLUSION

Dietary supplementation of 5 g kg^-1 OLP exerted antimicrobial, immunomodulatory, and antioxidant effects that were comparable to those of antibiotics and tert-butylhydroxytoluene in broiler chickens. © 2021 Society of Chemical Industry.

Assessing Class 1 Integron Presence in Poultry Litter Amended with Wood Biochar and Wood Vinegar

Class 1 integrons are mobile genetic elements that facilitate the spread of antibiotic resistance genes among bacteria. The use of prophylactic antibiotics has resulted in the rise of antibiotic resistance genes accumulating in a wide range of settings, including poultry houses and the agricultural fields where poultry litter is applied as a fertilizer. Biochar and wood vinegar are forest products wastes that have generated increasing attention as additives to agricultural soils. The objectives of this study were to observe the prevalence of class 1 integrons in poultry litter blended with biochar and wood vinegar over time and to verify a modified class 1 integron screening assay. Poultry litter blends were sampled and screened for class 1 integrons using polymerase chain reaction, and 80 products, 79 of which showed positive, were sent for DNA sequencing. The GenBank® BLAST database was used to verify the presence of the class 1 integron-integrase gene (intI1). There was no change in prevalence over time in poultry litter blends. Out of 79 PCR products that were intI1 positive, 78 showed at least 95% sequence identity to intI1 encoding bacteria and 64 showed at least 97% sequence identity. This indicates that this method was effective for conducting baseline surveillance of class 1 integrons in poultry litter and poultry litter-blended biochar and/or wood vinegar. Most significantly, class 1 integron prevalence did not decrease over time, further supporting the recalcitrance of these elements and the need for improved monitoring systems.

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes

BACKGROUND

Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the spread of antibiotic-resistant bacteria from food animals to humans, and the environment, but there is a lack of comprehensive experimental data supporting this. We investigated the effects of growth promotor (bacitracin) and therapeutic (enrofloxacin) antibiotic administration on AMR in broilers for the duration of a production cycle, using a holistic approach that integrated both culture-dependent and culture-independent methods. We specifically focused on pathogen-harboring families (Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae).

RESULTS

Antibiotic-resistant bacteria and antibiotic resistance genes were ubiquitous in chicken cloaca and litter regardless of antibiotic administration. Environment (cloaca vs. litter) and growth stage were the primary drivers of variation in the microbiomes and resistomes, with increased bacterial diversity and a general decrease in abundance of the pathogen-harboring families with age. Bacitracin-fed groups had higher levels of bacitracin resistance genes and of vancomycin-resistant Enterococcaceae (total Enterococcaceae counts were not higher). Although metagenomic analyses classified 28-76% of the Enterococcaceae as the commensal human pathogens E. faecalis and E. faecium, culture-based analysis suggested that approximately 98% of the vancomycin-resistant Enterococcaceae were avian and not human-associated, suggesting differences in the taxonomic profiles of the resistant and non-resistant strains. Enrofloxacin treatments had varying effects, but generally facilitated increased relative abundance of multidrug-resistant Enterobacteriaceae strains, which were primarily E. coli. Metagenomic approaches revealed a diverse array of Staphylococcus spp., but the opportunistic pathogen S. aureus and methicillin resistance genes were not detected in culture-based or metagenomic analyses. Camphylobacteriaceae were significantly more abundant in the cloacal samples, especially in enrofloxacin-treated chickens, where a metagenome-assembled C. jejuni genome harboring fluoroquinolone and β-lactam resistance genes was identified.

CONCLUSIONS

Within a "farm-to-fork, one health" perspective, considering the evidence that bacitracin and enrofloxacin used in poultry production can select for resistance, we recommend their use be regulated. Furthermore, we suggest routine surveillance of ESBL E. coli, vancomycin-resistant E. faecalis and E. faecium, and fluoroquinolone-resistant C. jejuni strains considering their pathogenic nature and capacity to disseminate AMR to the environment. Video Abstract.

Antibiotic Resistance and Virulence Profiles of Escherichia coli Strains Isolated from Wild Birds in Poland

Wild animals are increasingly reported as carriers of antibiotic-resistant and pathogenic bacteria including Enterobacteriaceae. However, the role of free-living birds as reservoirs for potentially dangerous microbes is not yet thoroughly understood. In our work, we examined Escherichia coli strains from wild birds in Poland in relation to their antimicrobial agents susceptibility, virulence and phylogenetic affiliation. Identification of E. coli was performed using MALDI-TOF mass spectrometry. The antibiotic susceptibility of the isolates was determined by the broth microdilution method, and resistance and virulence genes were detected by PCR. E. coli bacteria were isolated from 32 of 34 samples. The strains were most often classified into phylogenetic groups B1 (50%) and A (25%). Resistance to tetracycline (50%), ciprofloxacin (46.8%), gentamicin (34.3%) and ampicillin (28.1%) was most frequently reported, and as many as 31.2% of E. coli isolates exhibited a multidrug resistance phenotype. Among resistance genes, sul2 (31.2% of isolates) and bla_TEM (28.1%) were identified most frequently, while irp-2 (31.2%) and ompT (28.1%) were the most common virulence-associated genes. Five strains were included in the APEC group. The study indicates that wild birds can be carriers of potentially dangerous E. coli strains and vectors for the spread of resistant bacteria and resistance determinants in the environment.

Erythromycin loaded by tetrahedral framework nucleic acids are more antimicrobial sensitive against Escherichia coli (E. coli)

Erythromycin is a commonly used broad-spectrum antibiotic, but resistance to this antibiotic makes its use less effective. Considerable efforts, beside finding alternatives, are needed to enhance its antimicrobial effect and stability against bacteria. Tetrahedral framework nucleic acids (tFNAs), a novel delivery vehicle with a three-dimensional nanostructure, have been studied as a carrying platform of antineoplastic drugs. In this study, the use of tFNAs in delivering erythromycin into Escherichia coli (E. coli) was investigated for the first time. The tFNAs vehicle increased the bacterial uptake of erythromycin and promoted membrane destabilization. Moreover, it increased the permeability of the bacterial cell wall, and reduced drug resistance by improving the movement of the drug across the membrane. The tFNAs-based delivery system enhanced the effects of erythromycin against E. coli. It may therefore provide an effective delivery vehicle for erythromycin in targeting antibiotic-resistant bacteria with thick cell wall.

Prescribers' Knowledge, Attitudes and Behaviors on Antibiotics, Antibiotic Use and Antibiotic Resistance in Jordan

More research is needed on the drivers of irrational antibiotic prescribing among healthcare professionals and to ensure effective prescribing and an adequate understanding of the issue of antibiotic resistance. This study aimed at evaluating prescribers’ knowledge, attitudes and behaviors about antibiotic use and antibiotic resistance. A cross-sectional study was conducted utilizing an online questionnaire and included physicians and dentists from all sectors in Jordan. A total of 613 prescribers were included (physicians n = 409, dentists n = 204). Respondents’ knowledge on effective use, unnecessary use or associated side effects of antibiotics was high (>90%), compared with their knowledge on the spread of antibiotic resistance (62.2%). For ease of access to the required guidelines on managing infections, and to materials that advise on prudent antibiotic use and antibiotic resistance, prescribers agreed in 62% and 46.1% of cases, respectively. 28.4% of respondents had prescribed antibiotics when they would have preferred not to do so more than once a day or more than once a week. Among respondents who prescribed antibiotics, 63.4% would never or rarely give out resources on prudent use of antibiotics for infections. The findings are of importance to inform antibiotic stewardships about relevant interventions aimed at changing prescribers’ behaviors and improving antibiotic prescribing practices.

Prevalence and Characteristics of Multidrug-Resistant Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) CC398 Isolated from Quails (Coturnix Coturnix Japonica) Slaughtered for Human Consumption

Simple Summary

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen in both humans and animals worldwide. MRSA associated with livestock is a zoonotic pathogen that has been reported in several animals and, although its infections in humans are rare, this strain is recognized as an occupational hazard for people working in direct contact with livestock. Thus, we aimed to isolate MRSA from quails and to characterize their antimicrobial resistance and genetic lineages. One hundred swab samples were recovered from quails at the slaughterhouse. To investigate the prevalence and antimicrobial resistance of MRSA in poultry, we conducted this study on 100 quails slaughtered for human consumption. The antimicrobial resistance was investigated in all isolates as well as virulence genes and genetic lineages. Twenty-nine MRSA were isolated. The results showed that all MRSA isolates had resistance to multiple antibiotics. All strains were classified as livestock-associated. Most strains belonged to a well-known livestock-associated lineage: CC398.

Abstract

Livestock-associated MRSA (LA-MRSA) is a zoonotic pathogen that has been reported in several animals, and it is often associated with clonal complex (CC) 398. We aimed to isolate MRSA from quails and to characterize their antimicrobial resistance and genetic lineages. One hundred swab samples were recovered from quails at the slaughterhouse. The swabs were inoculated onto CHROMagar™ MRSA agar plates for MRSA isolation. The presence of antimicrobial-resistant genes and virulence factors was investigated by PCR. All strains were typed by MLST, SCCmec-, spa- and agr-typing. From the 100 samples, 29 MRSA were isolated. All strains were resistant to penicillin, cefoxitin, ciprofloxacin, erythromycin and clindamycin and carried the blaZ, mecA, ermB and ermC genes. All strains, except one, showed resistance to tetracycline and harbored the tetM, tetK and tetL genes in different combinations. Twenty strains belonged to ST398 and SCCmec type V, and nine strains belonged to the new ST6831. Twenty-eight out of twenty-nine strains were ascribed to t011 and one to t108. As far as we know, this is the first report of MRSA from quails slaughtered for human consumption. Most strains belonged to ST398-t011, which is the most common LA-MRSA clone found in livestock in Europe.

A stick-like intelligent multicolor nano-sensor for the detection of tetracycline: The integration of nano-clay and carbon dots

In recent years, the overuse of antibiotics has caused more and more serious environmental pollution, the uncontrolled abuse of antibiotics makes bacteria produce resistance to antibiotics faster than the replacement rate of antibiotics themselves, leading to the emergence of super drug-resistant bacteria. Therefore, it is of great practical significance to establish a simple, rapid and sensitive method for the detection of antibiotics. By integrating natural nano-clay (Atta) and carbon dots (CDs), the real-time and rapid visual detection of tetracycline (TC) in the sample can be realized by chromaticity pick-up APP on smartphone. The nano-sensor can detect tetracycline in the concentration between 25 nM and 20 μM with the detection limit of 8.7 nM. The low detection limit coupled with good accuracy, sensitivity and specificity meets the requirements for the detection of tetracycline in food. More importantly, the test paper and fluorescent stick-like nano-sensor are designed to detect tetracycline by polychromatic fluorescence changes. In addition, a logic gate for semi-quantitative identification of the concentration of tetracycline is designed, which makes it possible for the application of the nano-sensor in the field of smart devices.

Effects of Bacillus subtilis and Bacillus licheniformis on growth performance, immunity, short chain fatty acid production, antioxidant capacity, and cecal microflora in broilers

This study investigated the effects of dietary supplementation with Bacillus subtilis (B. subtilis) or Bacillus licheniformis (B. licheniformis) on growth performance, immunity, antioxidant capacity, short chain fatty acid (SCFA) production, and the cecal microflora in broiler chickens. In total, 360 male, 1-day-old Cobb 500 birds were randomly divided into 3 groups: the control group was fed a basal diet; the B. subtilis group was fed a basal diet supplemented with 1.5 × 10⁹ CFU/kg B. subtilis; the B. licheniformis group was fed a basal diet supplemented with 1.5 × 10⁹ CFU/kg B. licheniformis. Results showed that chickens supplemented with either B. subtilis or B. licheniformis had comparatively higher (P < 0.05) body weight and average daily gain, whereas no difference (P > 0.05) was observed in feed efficiency. Concentrations of serum IgA, IgY, and IgM, as well as anti-inflammatory IL-10 were significantly increased (P < 0.05), and proinflammatory IL-1β and IL-6 were significantly decreased (P < 0.05) by B. subtilis or B. licheniformis supplementation. Moreover, chickens fed with diets supplemented by either B. subtilis or B. licheniformis had greater antioxidant capacity, indicated by the notable increases (P < 0.05) in glutathione peroxidase, superoxide dismutase, and catalase, along with decrease (P < 0.05) in malondialdehyde. Compared to the control group, levels of SCFA, excluding acetic and propionic acid, in cecal content had improved (P < 0.05) by adding B. licheniformis, and significant increase (P < 0.05) in acetic and butyric acid was observed with B. subtilis supplementation. Microbial analysis showed that both B. subtilis or B. licheniformis supplementation could increase butyrate-producing bacteria such as Alistipes and Butyricicoccus, and decrease pathogenic bacteria such as the Synergistetes and Gammaproteobacteria. In summary, dietary supplemented with B. subtilis or B. licheniformis improved growth performance, immune status, and antioxidant capacity, increased SCFA production, and modulated cecal microbiota in chickens. Moreover, B. licheniformis was more effective than B. subtilis with the same supplemental amount.

Pharmacokinetics of Colistin in the Gastrointestinal Tract of Poultry Following Dosing via Drinking Water and Its Bactericidal Impact on Enteric Escherichia coli

Colistin, a last-line antibiotic of major importance in veterinary medicine and of critical importance in human medicine, is authorized to treat gastrointestinal (enteric) infections caused by non-invasive Escherichia coli in multiple veterinary species including poultry. Its use in veterinary medicine has been implicated in the widespread prevalence of mobilized colistin resistance. The objectives of this study were to determine the intestinal content reached in broiler chickens during 72-h treatment with colistin, to evaluate the associated impact on intestinal E. coli density, and to select less susceptible E. coli populations. In this study, 94 broiler chickens were administered a dose of 75,000 IU/kg/day via drinking water. Intestinal samples were collected pre-, during-, and post-dosing. Luminal intestinal content was assessed for colistin content by ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), and E. coli were isolated and enumerated on UriSelect agar™. Minimum inhibitory concentration (MIC, for eight isolates per intestine per animal) was determined, and when higher than the epidemiological cutoff (ECOFF 2 mg/l), isolates were screened for mobilized colistin resistance (mcr)-1 to 5. Colistin content increased during treatment to a maximum of 5.09 mg/kg. During this time, the total population of E. coli showed an almost 1,000-fold reduction. An apparent increase in the relative abundance of E. coli with an MIC ≥ ECOFF, either mcr-negative (6.25–10.94%) or mcr-1-positive (4.16–31.25%) was observed, although this susceptibility shift was not maintained post-treatment. Indeed, following cessation of dosing, colistin was eliminated from the intestine, and content was below the limit of quantification (LOQ, 1.1 mg/kg) within 4 h, and the median MIC of E. coli isolates returned below baseline thereafter. Few isolates with a lower susceptibility (mcr-1-positive or negative) were however observed at the end of the study period, indicating maintained sub-populations in the chicken gut. The results of this study show a limited impact on long-term maintenance of less susceptible E. coli populations as a direct result of colistin treatment in individual birds.

Identification of Bacterial Profiles and Their Interactions with Selected Quality, Oxidative, and Immunological Parameters of Turkey Semen

Simple Summary

Overbreeding—and its associated increase in the chest areas of turkeys—has led to the loss of their natural ability to reproduce. Therefore, commercial production of turkey meat relies on artificial insemination. However, along with the physiology of the genital tract of turkeys, there is high potential for bacterial contamination of ejaculates. These bacteria may affect crucial semen quality parameters required for successful fertilization. As such, it is important to pay close attention to the bacteria present in turkey ejaculates and possible solutions to eliminate their adverse effects on avian spermatozoa.

Abstract

This study focused on the identification of naturally occurring bacteria in the reproductive fluid and impact on the quality of ejaculates obtained from the turkey breed British United Turkeys (BUT) Big 6 (n = 60). We determined possible relationships between the bacterial load and advanced sperm quality parameters that are important for effective artificial insemination and high fertility, as well as the concentration of selected antimicrobial proteins and pro-inflammatory markers of turkey semen. Sperm motility was assessed with computer-assisted sperm analysis (CASA), while the membrane and acrosome integrity were examined with smearing and staining methods. Reactive oxygen species (ROS) generation was quantified via luminometry, sperm DNA fragmentation was evaluated using the TUNEL assay, and the JC-1 assay was applied to evaluate the mitochondrial membrane potential. Cell lysates were prepared to investigate the extent of lipid and protein oxidation. Furthermore, levels of interleukins 1 and 6 (IL-1, IL-6), C-reactive protein, cathelicidin, and β-defensin were quantified in the seminal plasma using the ELISA method. The most dominant species identified by the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry was Escherichia coli, Proteus mirabilis, Staphylococcus lentus, and Citrobacter braakii. The bacterial load had a negative effect on the sperm motility (p < 0.001), as well as membrane (p < 0.05) and acrosome integrity (p < 0.01). A strong positive relationship between the bacterial load and DNA fragmentation (p < 0.001) was detected as well. Positive associations were recorded between the increasing presence of bacteria, ROS overgeneration (p < 0.001), and a subsequent oxidative damage to the proteins (p < 0.001) and lipids (p < 0.01). It was revealed that the antimicrobial peptides β-defensin (p < 0.001) and cathelicidin (p < 0.001) had a positive relationship with the motility. In contrast, pro-inflammatory markers, such as IL-1 (p < 0.001) and IL-6 (p < 0.001), had a negative impact on the motion behavior of turkey spermatozoa. Our results suggest that the semen quality may be notably affected by the bacterial quantity as well as quality. It seems that bacteriospermia is associated with inflammatory processes, oxidative stress, sperm structural deterioration, and a subsequent risk for a failed artificial insemination in turkey breeding.

Oxytetracycline induces anxiety-like behavior in adult zebrafish

Oxytetracycline (OTC) is one of the broad-spectrum antibiotics widely used for the treatment of fish-farm infection. Considering that behavior is directly related to reproduction, individual fitness, and survival, it is important to evaluate the impact of antibiotics on the behavioral repertoire in fish. Zebrafish (Danio rerio) presents a well-described behavioral repertoire to reliably demonstrate complex responses to chemical compound exposure. This work aims to identify the role of OTC in comprehensive behavioral parameters and whole-body cortisol levels in adult zebrafish. Here we report that OTC exposure (10, 20, and 100 mg/L) induces an anxiogenic-like phenotype in the novel tank test. OTC exposure also changes the behavior of social interaction with a shoal of unknown zebrafish - characterized as a stimulus group. Zebrafish exposed to OTC (10 mg/L) remains a longer period in the stimulus zone when compared to the control group. Clonazepam (0.006 mg/L) was able to reverse anxiogenic-like behavior and the changes in social behavior induced by OTC. We also demonstrated that cortisol levels were significantly decreased after exposure to OTC (10, 20, and 100 mg/L), which were not reversed by clonazepam. These findings highlight the growing utility of zebrafish as a model to understand the impact of antibiotics on behavior and their underlying mechanisms.

Determination of five antimicrobial families in droppings of therapeutically treated broiler chicken by high-performance liquid chromatography-tandem mass spectrometry

Antimicrobials are currently used in poultry for disease treatment. However, their excretion in bird feces may contaminate the environment. Considering this, the objective of this work was to quantify antimicrobials residues concentrations in therapeutically treated broiler chicken droppings throughout the post-treatment period. For this aim a multiresidue method using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was validated. Forty-eight male broiler chickens were distributed and treated with commercial formulations of 5 different antimicrobials. Results showed that oxytetracycline and 4-epi-oxytetracycline, presented the highest concentrations during all sampling period, detecting concentrations of 1471.41 µg kg⁻¹ at the last sampling point (day 22 post-treatment). Florfenicol, tylosin, enrofloxacin, and ciprofloxacin were eliminated and detected in treated chicken droppings until d 18 post-treatment. Sulfachloropyridazine decrease gradually during post-treatment period until day 30. Results demonstrate that studied antimicrobials in treated chicken droppings were eliminated for prolonged periods, therefore becoming a significant route of residues dissemination into the environment.

Effect of Goji Berry (Lycium barbarum) Supplementation on Reproductive Performance of Rabbit Does

Simple Summary

Infectious diseases represent serious problems for the reproductive performance of livestock animals because they negatively affect not only the welfare of the animals, but also the profitability of the farm. Moreover, the European Community continues to promote the reduction of the use of antibiotics and hormones in animal breeding. In this context, it is necessary to find new nutritional approaches to reduce the negative energy balance, and at the same time, to reinforce the immune system of the animals. In this research, the effect of goji berry supplementation on the reproductive activity and productive performance of rabbits is evaluated. Lycium barbarum fruit is considered a nutraceutical natural product containing various biologically active substances that show health benefits for both humans and animals. In particular, the berry can modulate hormones and metabolites involved in energy balance and reproduction, stimulate and balance the immune system activity, contributing to the defense of the organism against pathogens. Our results suggest that the integration with goji berry in the rabbit diet at 1% affects the reproductive activity, influencing the pattern secretion of luteinizing hormone (LH) and estrogens, as well as the sexual receptivity. Moreover, the fruit induced a higher milk production, improving the productive performance of young rabbits.

Abstract

Goji berry shows a wide range of beneficial properties in human health, but only a few studies evaluated its effects in livestock animals. The objective of this research was to assess the effects of goji berry supplementation on the hormonal profile, productive, and reproductive performance of does. Two months before artificial insemination, 105 nulliparous does were randomly divided into three groups (n = 35) based on the dietary treatment: commercial diet (C), or a diet supplemented with either 1% (G1), or 3% (G3) of goji berry, respectively. The results showed that receptivity was higher in G1 than in the C group (p < 0.05). Trends toward significance for differences between the G1 and G3 groups in marginal means of LH concentrations (p = 0.059), and between G1 and C in LH AUC values (p = 0.078), were evidenced. Estrogen concentrations showed a more fluctuating trend but a significant interaction effect (p < 0.001). The G1 group showed higher litter weight than C at birth (p = 0.008) and weaning (p < 0.001), as well as higher litter size at weaning (p = 0.020). The G1 group also exhibited the highest mean milk production (p < 0.01). In conclusion, goji berry influenced reproductive and productive performance, probably via modulating hormonal patterns and milk production in rabbits. However, further studies are needed to validate these preliminary results.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

Campylobacter jejuni ST50, a pathogen of global importance: A comparative genomic analysis of isolates from Australia, Europe and North America

Campylobacter jejuni is the leading cause of bacterial gastroenteritis globally, and infections are often transmitted through consumption of raw or undercooked poultry. Campylobacter jejuni ST50 is among the top ten sequence types (STs) reported in the collected isolates listed at PubMLST records from poultry, food and clinical sources for Asia, Europe, North America, Oceania and South America. This study was designed to determine the most commonly reported C. jejuni STs globally using the PubMLST database and assess similarities between genomes of C. jejuni ST50 isolates from geographically distinct locations. To gain a better understanding of C. jejuni diversity, we compared draft genome sequences of 182 ST50 isolates recovered from retail or caecal poultry samples in Oceania, Europe and North America that were collected over a period of 9 years (2010 to 2018). Overall, phylogenetic analysis revealed that isolates from geographically distinct locations tended to cluster based on the continent where the sample was collected. Among ST50 isolates from Europe and North America, we identified resistance determinants associated with phenotypic resistance to beta-lactams (EU: 55%; GB: 43.1%), tetracyclines (CA: 77.3%; EU: 37.5%; GB: 9.8%; US: 43.5%) and fluoroquinolones (EU: 60.0%; GB: 15.7%); no resistance determinants were identified in isolates from Australia. In general, the majority of the virulence genes, with rare exceptions such as wlaN, cj1138, hddA and rfbC, were evenly distributed throughout the genomes of all ST50 isolates in this study. Genomic-based characterization of C. jejuni ST50 isolates from poultry on three continents highlighted that geographically distinct isolates have evolved independently but only represent a glimpse into the diversity of C. jejuni.

Prevalence of 16S rRNA Methylation Enzyme Gene armA in Salmonella From Outpatients and Food

Salmonella is the primary cause of community-acquired foodborne infections, so its resistance to antimicrobials, such as aminoglycosides, is a public health issue. Of concern, aminoglycoside resistance in Salmonella is increasing rapidly. Here, we performed a retrospective study evaluating the prevalence of Salmonella harboring armA-mediated aminoglycoside resistance in community-acquired infections and in food or environmental sources. The prevalence rates of armA-harboring Salmonella strains were 1.1/1,000 (13/12,095) and 8.7/1,000 (32/3,687) in outpatient and food/environmental isolates, respectively. All the armA-harboring Salmonella strains were resistant to multiple drugs, including fluoroquinolone and/or extended-spectrum cephalosporins, and most (34/45) belonged to serovar Indiana. The armA gene of these strains were all carried on plasmids, which spanned five replicon types with IncHI2 being the dominant plasmid type. All the armA-carrying plasmids were transferable into Escherichia coli and Acinetobacter baumannii recipients. The conjugation experiment results revealed that the armA-harboring S. Indiana strains had a relatively higher ability to acquire armA-carrying plasmids. The low similarity of their pulsed field gel electrophoresis patterns indicates that the armA-harboring Salmonella strains were unlikely to have originated from a single epidemic clone, suggesting broad armA spread. Furthermore, the genetic backgrounds of armA-harboring Salmonella strains isolated from outpatients exhibited higher similarity to those isolated from poultry than to those isolated from swine, suggesting that poultry consumption maybe an infection source. These findings highlight an urgent need to monitor the prevalence and transmission of armA-harboring Salmonella, especially S. Indiana, to better understand the potential public health threat and prevent the further spread of these strains.

The Use of Lavender (Lavandula angustifolia) Essential Oil as an Additive to Drinking Water for Broiler Chickens and Its In Vitro Reaction with Enrofloxacin

Biological activity of lavender essential oil is a property that can potentially find an application in poultry nutrition. Nowadays, the use of bioactive compounds is encouraged in many areas of industry and agriculture, since these substances have similar properties as withdrawn antibiotic growth promoters. Additionally, antibiotic resistance bacteria are one of the most important current threats to animal health. The purpose of the study was to determine the influence of lavender essential oil on the production parameters and blood parameters in broiler chickens and to assess the lavender oil's in vitro reaction in a combination with enrofloxacin towards Escherichia coli. One-day-old non-sexed chicks (Ross 308) were divided into three experimental groups, each consisting of 100 individuals (five replicate of 20 boiler chicken each). The chickens in the control group received drinking water with no addition of lavender essential oil. In the experimental groups, lavender oil was added to the drinking water at a concentration of 0.4 mL/L, in the LEO_1-42 from 1 to 42 days of age and the LEO_22-42 group from the 22 to 42 days of age. The chickens' body weight, feed consumption, water consumption, deaths and elimination due to health reasons were determined in the experiment. On day 42 of the chickens' lives, blood samples were collected based on which selected parameters were identified. An in vitro experiment of lavender oil in combination with enrofloxacin was investigated with a checkerboard method. The results of the experiment showed the antimicrobial and antioxidant activity of lavender essential oil and its positive effect on the production results of broiler chickens. The study results proved that the addition of lavender oil positively impacted the chickens' final body weight and feed conversion ratio (p < 0.01). No differences were observed between the groups for water consumption, death rate and the examined biochemical and immunological blood serum indices. Lavender essential oil was demonstrated to increase the blood serum's total antioxidant status. A synergistic reaction in vitro was observed for lavender oil combined with enrofloxacin against resistant strains of Escherichia coli. Based on our study, a health-promoting effect of adding LEO to water for broiler chickens was found. Moreover, in vitro studies indicate a significant effect of lavender essential oil on the inhibition of the resistant strains of Escherichia coli growth and synergistic reaction with enrofloxacin.

Dietary effect of licorice (Glycyrrhiza glabra) on quail performance, carcass, blood metabolites and intestinal microbiota

This study aimed to assess the impacts of licorice (Glycyrrhiza glabra) on the growth performance, carcass traits, intestinal microbiota, liver and kidney functions, immunity, oxidative status, and lipid profile of Japanese quails. A total of 200 one-week-old unsexed Japanese quails with an average initial body weight of 26.24 ± 0.2 g were randomly distributed into 5 equal groups of 40 birds and further subdivided into 5 replicates. The first (control) group was fed a diet without any licorice, while licorice powder was added at levels of 250, 500, 750, and 1000 mg per kg diet in the second, third, fourth, and fifth groups, respectively. At the age of 3 wk, the group of quail fed on a diet supplemented with 750 and 1000 mg licorice/kg of diet gained the highest body weight (BW) and daily body weight (DBW), while attaining the lowest feed conversion ratio (FCR) compared to other groups. Meanwhile, groups fed diets with licorice at levels of 0 and 250 mg/kg showed the highest feed intake. After the 5-wk feeding trial, the highest BW and DBW values, and the lowest FCR were recorded in the group fed with 750 mg licorice/kg diet. The different treatments produced no significant differences (P > 0.05) in quail carcass characteristics, including percentages of carcass, liver, gizzard, heart, giblets, and dressing. The blood of the group fed a 750 mg licorice diet had higher contents of total protein and GLOB, while its contents of A/G%, lactate dehydrogenase (LDH), total cholesterol, triglyceride (TG), and low density lipoprotein (LDL) were lower. Apart from the high level of licorice (1000 mg/kg), the MDA level was linearly and quadratically (P = 0.0413 and 0.001) decreased with different licorice groups, while superoxide dismutase (SOD), total antioxidant capacity (TAC), immunoglobulin G (IgG), and M (IgM) were quadratically increased when compared to the control group. Licorice supplementation resulted in marked reductions in the number of total bacteria, coliforms, E. coli, and Salmonella, compared to those in the control. In conclusion, the inclusion of licorice at levels of 750 and 1000 mg/kg into the diet of Japanese quail enhances the animal's performance, immunity, antioxidant capacity, and maintains a healthy gut microbiota.

Extended-spectrum cephalosporin resistance in Escherichia coli from broiler chickens raised with or without antibiotics in Ontario, Canada

Extended-spectrum cephalosporin (ESC)-resistant Escherichia coli were isolated from fecal samples enriched in ESC-containing broth over two years from broiler chickens raised with and without therapeutic antimicrobials. Pooled samples were obtained from 13 different farms in Canada over two rearing cycles each. Resistant isolates were screened for bla_CMY, bla_CTX-M, and bla_SHV by PCR, and several isolates were sequenced and assembled using Oxford Nanopore MinION technology. Flocks raised with or without antimicrobials contained similar ESC-resistant E. coli. Some plasmids were found in isolates from both farm types and many shared replicon types (IncI1, F, C, and B/O/K/Z) and resistance determinants. Although the use of cephalosporins has stopped in poultry production in Canada, the prevalence of ESC-resistant E. coli found in this study remained high; therefore, further studies are required to determine routes of transmission and persistence.

Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile

During a field experiment applying broiler manure for fertilization of agricultural land, we detected viable Clostridioides (also known as Clostridium) difficile in broiler faeces, manure, dust and fertilized soil. A large diversity of toxigenic C. difficile isolates was recovered, including PCR ribotypes common from human disease. Genomic relatedness of C. difficile isolates from dust and from soil, recovered more than 2 years after fertilization, traced their origins to the specific chicken farm that had delivered the manure. We present evidence of long-term contamination of agricultural soil with manure-derived C. difficile and demonstrate the potential for airborne dispersal of C. difficile through dust emissions during manure application. Clostridioides genome sequences virtually identical to those from manure had been recovered from chicken meat and from human infections in previous studies, suggesting broiler-associated C. difficile are capable of zoonotic transmission.

Detection of Antimicrobial Residues in Poultry Litter: Monitoring a Risk through a Selective and Sensitive HPLC-MS/MS Method

Simple Summary

After administration of antimicrobials, poultry excrete significant concentrations of antimicrobials through their droppings, which accumulate in the litter where poultry are housed. Poultry litter, which consists mainly of wood shavings, feathers, and droppings, is widely used as an agricultural fertilizer worldwide. The period that antimicrobials persist in agricultural soils could present various environmental and public health concerns. Thus, in this research, a method to identify different families of antimicrobials in poultry litter was developed. Results show that HPLC–MS/MS can reliably detect nine different compounds from three families of antimicrobials. This method was used to identify antimicrobials from commercial poultry flocks, providing a valuable and specific tool to monitor these residues in poultry litter prior to its use as an agricultural fertilizer.

Abstract

Tetracyclines, sulphonamides, and quinolones are families of antimicrobials (AMs) widely used in the poultry industry and can excrete up to 90% of AMs administrated, which accumulate in poultry litter. Worryingly, poultry litter is widely used as an agriculture fertilizer, contributing to the spread AMs residues in the environment. The aim of this research was to develop a method that could simultaneously identify and quantify three AMs families in poultry litter by high-performance liquid chromatography–tandem mass spectrometry (HPLC–MS/MS). Samples of AMs free poultry litter were used to validate the method according to 657/2002/EC and VICH GL49. Results indicate that limit of detection (LOD) ranged from 8.95 to 20.86 μg kg⁻¹, while limits of quantitation (LOQ) values were between 26.85 and 62.58 µg kg⁻¹ of tetracycline, 4-epi-tetracycline, oxytetracycline, 4-epi-oxytetracycline, enrofloxacin, ciprofloxacin, flumequine, sulfachloropyridazine, and sulfadiazine. Recoveries obtained ranged from 93 to 108%. The analysis of field samples obtained from seven commercial poultry flocks confirmed the adequacy of the method since it detected means concentrations ranging from 20 to 10,364 μg kg⁻¹. This provides us an accurate and reliable tool to monitor AMs residues in poultry litter and control its use as agricultural fertilizer.

Comparison of Antibiotic Resistance Profile of Escherichia coli between Pristine and Human-Impacted Sites in a River

Information on the actual existence of antibiotic-resistant bacteria in rivers where sewage, urban wastewater, and livestock wastewater do not load is essential to prevent the spread of antibiotic-resistant bacteria in water environments. This study compared the antibiotic resistance profile of Escherichia coli upstream and downstream of human habitation. The survey was conducted in the summer, winter, and spring seasons. Resistance to one or more antibiotics at upstream and downstream sites was on average 18% and 20%, respectively, and no significant difference was observed between the survey sites. The resistance rates at the upstream site (total of 98 isolated strains) to each antibiotic were cefazolin 17%, tetracycline 12%, and ampicillin 8%, in descending order. Conversely, for the downstream site (total of 89 isolated strains), the rates were ampicillin 16%, cefazolin 16%, and tetracycline 1% in descending order. The resistance rate of tetracycline in the downstream site was significantly lower than that of the upstream site. Furthermore, phylogenetic analysis revealed that many strains showed different resistance profiles even in the same cluster of the Pulsed-Field Gel Electrophoresis (PFGE) pattern. Moreover, the resistance profiles differed in the same cluster of the upstream and the downstream sites. In flowing from the upstream to the downstream site, it is plausible that E. coli transmitted or lacked the antibiotic resistance gene.

Antibiotic Resistance and Virulence Gene Patterns Associated with Avian Pathogenic Escherichia coli (APEC) from Broiler Chickens in Qatar

Avian Pathogenic Escherichia coli (APEC) is the contributing agent behind the avian infectious disease colibacillosis, which causes substantial fatalities in poultry industries that has a significant impact on the economy and food safety. Several virulence genes have been shown to be concomitant with the extraintestinal survival of APEC. This study investigates the antibiotic resistance patterns and APEC-associated virulence genes content in Escherichia coli isolated from non-healthy and healthy broiler chickens from a commercial poultry farm in Qatar. A total of 158 E. coli strains were isolated from 47 chickens from five different organs (air sac, cloacal, kidney, liver, and trachea). Based on genetic criteria, 65% were APEC strains containing five or more virulence genes, and 34% were non-pathogenic E. coli (NPEC) strains. The genes ompT, hlyF, iroN, tsh, vat, iss, cvi/cva, and iucD were significantly prevalent in all APEC strains. E. coli isolates showed 96% resistance to at least one of the 18 antibiotics, with high resistance to ampicillin, cephalothin, ciprofloxacin, tetracycline, and fosfomycin. Our findings indicate high antibiotic resistance prevalence in non-healthy and healthy chicken carcasses. Such resistant E. coli can spread to humans. Hence, special programs are required to monitor the use of antibiotics in chicken production in Qatar.

Longitudinal study on antibiotic susceptibility in commensal E. coli from geese raised in free-range production systems

The transmission of antimicrobial resistance bacteria from animals to humans has become an important concern. The extended-spectrum beta-lactamase (ESBL) -AmpC- producing Escherichia coli (ESBL-AmpC EC) and quinolones resistant E. coli are of particular interest. The present study aimed to evaluate the load and prevalence of antibiotic-resistant commensal E. coli along the goose production cycle on 2 free-range farms in central Italy. On A farm, oxytetracycline was administered, while the B farm did not use antibiotics during the geese productive cycle. One hundred geese of 1-day-old from the same batch were divided into the two farms. At hatching, the animals showed an average of E. coli loads was 6.83 ± 0.48 log CFU/g, and 0.28 ± 0.28, 0, 5.12 ± 0.54 log CFU/g for E. coli resistant to nalidixic acid (E. coli^nal), to cefotaxime (E. coli^cef) and to tetracyclines (E. coli^tet), respectively. The loads of E. coli, E. coli^nal, E. coli^cef and E. coli^tet on 224 environmental faecal pools were determined at 8 time points. Antimicrobial susceptibility and molecular characterization of E. coli^cef isolates were performed. The ANOVA was used to assess the difference in bacterial loads between the two farms. We described more than 50% of resistances for tetracyclines in both farms, and sulphonamides and cephazolin in the A farm. The loads of E. coli and E. coli^nal in faeces were estimated at approximately 6–7 log (CFU/g) and 5–6 log (CFU/g) in the two farms, respectively. The average load of extended-spectrum beta-lactamase Escherichia coli (ESBL EC) in goose faeces varied broadly along the production cycle: in the first weeks, a sharp increase was observed in both farms, while later on A farm, the burden of ESBL EC remained steady until the end of the production cycle and on B farm the load dramatically decreased from 6 wk of age onward. An increase in the proportion of E. coli^nal was observed on A farm shortly after the antibiotic administration. Our study shows that the dynamics of antibiotic-resistant E. coli in farmed geese are similar to the ones observed in broilers. However, the risk of the emergence of antibiotic-resistant commensal E. coli, might be mitigated by the adoption of good management practices, including prudent use of antibiotics.

Antimicrobial resistance clusters in commensal Escherichia coli from livestock

To combat antimicrobial resistance (AMR), policymakers need an overview of evolution and trends of AMR in relevant animal reservoirs, and livestock is monitored by susceptibility testing of sentinel organisms such as commensal E. coli. Such monitoring data are often vast and complex and generates a need for outcome indicators that summarize AMR for multiple antimicrobial classes. Model-based clustering is a data-driven approach that can help to objectively summarize AMR in animal reservoirs. In this study, a model-based cluster analysis was carried out on a dataset of minimum inhibitory concentrations (MIC), recoded to binary variables, for 10 antimicrobials of commensal E. coli isolates (N = 12,986) derived from four animal species (broilers, pigs, veal calves and dairy cows) in Dutch AMR monitoring, 2007-2018. This analysis revealed four clusters in commensal E. coli in livestock containing 201 unique resistance combinations. The prevalence of these combinations and clusters differs between animal species. Our results indicate that to monitor different animal populations, more than one indicator for multidrug resistance seems necessary. We show how these clusters summarize multidrug resistance and have potential as monitoring outcome indicators to benchmark and prioritize AMR problems in livestock.

Antimicrobial Resistance Gene Detection Methods for Bacteria in Animal-Based Foods: A Brief Review of Highlights and Advantages

Antimicrobial resistance is a major public health problem and is mainly due to the indiscriminate use of antimicrobials in human and veterinary medicine. The consumption of animal-based foods can contribute to the transfer of these genes between animal and human bacteria. Resistant and multi-resistant bacteria such as Salmonella spp. and Campylobacter spp. have been detected both in animal-based foods and in production environments such as farms, industries and slaughterhouses. This review aims to compile the techniques for detecting antimicrobial resistance using traditional and molecular methods, highlighting their advantages and disadvantages as well as the effectiveness and confidence of their results.

Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Escherichia coli Strains From Healthy Food Animals Across Europe

The role of livestock animals as a putative source of ESBL/pAmpC E. coli for humans is a central issue of research. In a large-scale pan-European surveillance, 2,993 commensal Escherichia spp. isolates were recovered from randomly collected fecal samples of healthy cattle, pigs and chickens in various abattoirs. One-hundred Escherichia spp. isolates (0.5% from cattle, 1.3% pigs, 8.0% chickens) fulfilled the criteria for cefotaxime and ceftazidime non-wildtype (EUCAST). In silico screening of WGS data of 99 isolates (98 E. coli and 1 E. fergusonii) revealed bla_SHV–12 (32.3%), bla_CTX–M–1 (24.2%), and bla_CMY–2 (22.2%) as predominant ESBL/pAmpC types. Other types were bla_SHV–2 (1.0%), bla_{CTX–M–2/–14/–15} (1.0/6.1/1.0%), and bla_TEM–52 (5.1%). Six isolates revealed AmpC-promoter mutations (position −42 (C > T) and one carried mcr-1. The majority (91.3%) of ESBL/pAmpC genes were located on plasmids. SHV-12 was mainly (50%) encoded on IncI1α plasmids (pST-3/-26/-95), followed by IncX3 (12.5%) and IncK2 (3.1%). The bla_TEM–52 genes were located on IncI1α-pST-36 (60%) and IncX1 plasmids (20%). The dominant plasmid lineage among CTX-M-1 isolates was IncI1α (pST-3/-295/-317) (87.5%), followed by IncN-pST-1 (8.3%). CMY-2 was mostly identified on IncI1α (pST-12/-2) (54.5%) and IncK2 (31.8%) plasmids. Several plasmids revealed high similarity to published plasmids from human and animal Enterobacteriaceae. The isolates were assigned to phylogroups A/C (34.7/7.1%), B1 (27.6%), B2 (3.1%), D/F (9.2/10.2%), E (5.1%), and to E. clades (3.0%). With 51 known and 2 novel MLST types, a wide variety of STs was found, including STs previously observed in human isolates (ST10/38/117/131/648). ESBL/AmpC types or STs were rarely correlated with the geographic origin of the isolates or animal species. Virulence gene typing identified extraintestinal pathogenic E. coli (ExPEC; 2.0%), avian pathogenic E. coli (APEC; 51.5%), and atypical enteropathogenic E. coli (EPEC; 6.1%). In conclusion, the high diversity of STs and phylogenetic groups provides hardly any hint for clonal spread of single lineages but hints toward the dissemination of cephalosporin resistance genes in livestock via distinct, globally successful plasmid lineages. Even though a number of isolates could not be assigned to a distinct pathotype, our finding of combined multidrug-resistance and virulence in this facultative pathogen should be considered an additional threat to public health.

Antibiotics and Antibiotic Resistance Genes in Animal Manure - Consequences of Its Application in Agriculture

Antibiotic resistance genes (ARGs) are a relatively new type of pollutant. The rise in antibiotic resistance observed recently is closely correlated with the uncontrolled and widespread use of antibiotics in agriculture and the treatment of humans and animals. Resistant bacteria have been identified in soil, animal feces, animal housing (e.g., pens, barns, or pastures), the areas around farms, manure storage facilities, and the guts of farm animals. The selection pressure caused by the irrational use of antibiotics in animal production sectors not only promotes the survival of existing antibiotic-resistant bacteria but also the development of new resistant forms. One of the most critical hot-spots related to the development and dissemination of ARGs is livestock and poultry production. Manure is widely used as a fertilizer thanks to its rich nutrient and organic matter content. However, research indicates that its application may pose a severe threat to human and animal health by facilitating the dissemination of ARGs to arable soil and edible crops. This review examines the pathogens, potentially pathogenic microorganisms and ARGs which may be found in animal manure, and evaluates their effect on human health through their exposure to soil and plant resistomes. It takes a broader view than previous studies of this topic, discussing recent data on antibiotic use in farm animals and the effect of these practices on the composition of animal manure; it also examines how fertilization with animal manure may alter soil and crop microbiomes, and proposes the drivers of such changes and their consequences for human health.

Molecular Characterization of Enterococcus Isolates From Different Sources in Estonia Reveals Potential Transmission of Resistance Genes Among Different Reservoirs

In this study, we aimed to characterize the population structure, drug resistance mechanisms, and virulence genes of Enterococcus isolates in Estonia. Sixty-one Enterococcus faecalis and 34 Enterococcus faecium isolates were collected between 2012 and 2014 across the country from various sites and sources, including farm animals and poultry (n = 53), humans (n = 12), environment (n = 24), and wild birds (n = 44). Clonal relationships of the strains were determined by whole-genome sequencing and analyzed by multi-locus sequence typing. We determined the presence of acquired antimicrobial resistance genes and 23S rRNA mutations, virulence genes, and also the plasmid or chromosomal origin of the genes using dedicated DNA sequence analysis tools available and/or homology search against an ad hoc compiled database of relevant sequences. Two E. faecalis isolates from human with vanB genes were highly resistant to vancomycin. Closely related E. faecalis strains were isolated from different host species. This indicates interspecies spread of strains and potential transfer of antibiotic resistance. Genomic context analysis of the resistance genes indicated frequent association with plasmids and mobile genetic elements. Resistance genes are often present in the identical genetic context in strains with diverse origins, suggesting the occurrence of transfer events.

Synthesis of Escherichia coli OmpA Oral Nanoparticles and Evaluation of Immune Functions against the Major Etiologic Agent of Cow Mastitis

Escherichia coli is a major etiologic agent of cow mastitis, a condition that results in huge economic losses. There is a lack of an oral vaccine for cow mastitis. Previous studies have confirmed that the outer membrane protein A (OmpA) of E. coli is immunogenic and can be used for vaccine design. In the present study, OmpA was encapsulated into nanoparticles (NP-OmpA) for an oral vaccine for cow mastitis. Methods: OmpA was purified with Ni-NTA flow resin and encapsulated with chitosan (CS) to prepare NP-OmpA nanoparticles. The gastrointestinal tract was simulated in vitro (PBS, pH 1.2) to measure the protein release rate. The optimal preparation conditions for NP-OmpA were determined by analyzing the concentrations of OmpA and CS, magnetic mixing speed, mixing time, and the ratio of tripolyphosphate (TPP)/CS (w/w). NP-OmpA safety was assessed by function factors and histopathological examination of livers and kidneys. The immune activity of NP-OmpA was determined using qRT-PCR to assess immune-related gene expression, leukocyte phagocytosis of Staphylococcus aureus, ELISA to evaluate antiserum titer and immune recognition of E. coli, and the organ index. The immune protection function of NP-OmpA was assessed by the protection rate of NP-OmpA to E. coli in mice, qRT-PCR for inflammation-related gene expression, assay kits for antioxidant factors, and visceral injury in the histopathological sections. Results: NP-OmpA nanoparticles had a diameter of about 700 nm, loading efficiency (LE) of 79.27%, and loading capacity (LC) of 20.31%. The release rate of NP-OmpA (0~96 h) was less than 50% in vitro. The optimal preparation conditions for NP-OmpAs were OmpA protein concentration of 2 mg/mL, CS concentration of 5 mg/mL, TPP/CS (w/w) of 1:1, magnetic mixing speed of 150 r/min, and mixing time of 15 min. Histopathological sections and clinical analytes of uric acid (UA), creatinine (Cr), alanine aminotransferase (ALT), aspartate transaminase (AST), catalase (CAT), glutathione (GSH), and malondialdehyde (MDA) showed NP-OmpA did not damage mice livers or kidneys. NP-OmpA could enhance the immune-related gene expression of IFN-γ and HSP70 in the spleen, liver, and kidney and the leukocyte phagocytosis of S. aureus. The antiserum titer (1:3200) was obtained from mice immunized with NP-OmpA, which had an immune recognition effect to E. coli. The immune protection rate of NP-OmpA was 71.43% (p < 0.05) to E. coli. NP-OmpA could down-regulate the inflammation-related gene expression of TNF-a, IL-6, and IL-10 in the spleen, liver, and kidney, and the antioxidant factors MDA and SOD in the liver, and reduce injury in the liver and kidney of mice induced by E. coli. Conclusions: A novel NP-OmpA nanoparticle was encapsulated, and the optimal preparation conditions were determined. The NP-OmpA was safe and had good immune functions. They are expected to induce a response that resists infection with the major etiologic agent (E. coli) of cow mastitis.

Evaluation of Antibiotic Dissemination into the Environment and Untreated Animals, by Analysis of Oxytetracycline in Poultry Droppings and Litter

Simple Summary

Oxytetracycline (OTC) is an antibiotic used mainly in feed and drinking water. OTC is poorly absorbed in the gastrointestinal tract of poultry; making droppings a potential route of dissemination of this antibiotic. The aim of this study was to evaluate the dissemination of oxytetracycline excreted from treated birds to the environment and other untreated animals (sentinels), through the analysis of their droppings and litter by HPLC-MS/MS following the end of treatment. In treated bird droppings, the average concentration of OTC+4-epi-OTC ranged from 347.63 to 2244.66 µg kg⁻¹. OTC+4-epi-OTC in litter reached concentrations of 22,741.68 µg kg⁻¹. Traces of OTC+4-epi-OTC were detected in the droppings and litter from sentinels. Therefore, OTC+4-epi-OTC can persist in the litter of treated animals at high concentrations and can be transferred to untreated birds that share the same environment. This exposure has the potential to increase the likelihood of selection of resistant bacteria in the environment.

Abstract

Oxytetracycline (OTC) is widely used in broiler chickens. During and after treatment a fraction of OTC is excreted in its original form and as its epimer, 4-epi-OTC in droppings. To address the transfer of OTC into the environment, we evaluated the dissemination of OTC and 4-epi-OTC from treated birds to the environment and sentinels, through the simultaneous analysis of broiler droppings and litter. Male broiler chickens were bred in controlled conditions. One group was treated by orogastric tube with 80 mg kg⁻¹ of OTC and two groups received no treatment (sentinels). OTC+4-epi-OTC were analyzed and detected by a HPLC-MS/MS post the end of treatment. The highest concentrations of OTC+4-epi-OTC were detected in the droppings of treated birds 14-days following the end of treatment (2244.66 µg kg⁻¹), and one day following the end of treatment in the litter (22,741.68 µg kg⁻¹). Traces of OTC+4-epi-OTC were detected in the sentinels’ droppings and litter (<12.2 µg kg⁻¹). OTC+4-epi-OTC can be transferred from treated birds to the environment and to other untreated birds. The presence and persistence of OTC+4-epi-OTC in litter could contribute to the selection of resistant bacteria in the environment, increasing the potential hazard to public and animal health.

High-throughput sequencing-based analysis of the intestinal microbiota of broiler chickens fed with compound small peptides of Chinese medicine

The objective of this study was to determine the effects of compound small peptides of Chinese medicine (CSPCM) on the intestinal microbiota of broilers. A total of thirty-six 1-day-old Arbor Acres broilers were assigned to 6 dietary treatments that include 250, 500, and 750 g/T of CSPCM in feed, 100 g/T of Bacillus subtilis and Clostridium butyricum in feed, and 100 g/T of 50,000 IU xylanase in feed. Each treatment had 2 replicates with 2 cages (3 birds per cage). The jejunal digesta samples were collected from chickens at 42 d. Operational taxonomic unit analysis showed that adding CSPCM at a concentration of 750 g/T of feed can increase the number of operational taxonomic unit samples than other groups. Compared with the control group, adding 250 g/T of CSPCM of feed can improve content of Lactobacillus, Cupriavidus, Ochrobactrum, Candidatus_Arthromitus, Acinetobacter, and Sphingomonas. Adding 500 g/T of CSPCM in feed resulted in varying degrees of improvement in Candidatus_Arthromitus, Acinetobacter, and Sphingomonas. Adding 750 g/T of CSPCM in feed can increase the content of Lactobacillus and Candidatus_Arthromitus. In PICRUSt function prediction analysis, CSPCM acts on the body by creating an environment suitable for the growth of beneficial bacteria. Adding 250 g/T of CSPCM in feed can improve amino acid metabolism, endocrine system function, membrane transport, and cell mobility function. Adding 500 g/T of CSPCM in feed can improve replication and repair and membrane transport function. Adding 750 g/T of CSPCM in feed can increase carbohydrate metabolism, replication and repair, and membrane transport function. Adding B. subtilis and C. butyricum in feed increased replication and repair and membrane transport function. Adding xylanase in feed increased membrane transport function. In conclusion, this study demonstrated that dietary supplementation of CSPCM to broiler diets increased beneficial flora content, metabolism of carbohydrates, amino acid metabolism, the deposition of proteins, renewal of bacteria, and maintenance of vigorous vitality. Among the 3 additive quantities of 250 g/t, 500 g/t, and 750 g/t of CSPCM in feed, 250 g/t of CSPCM improved parameters that are necessary for improved growth and production.

Antimicrobial Resistance Profiles of Salmonella Isolates on Chickens Processed and Retailed at Outlets of the Informal Market in Gauteng Province, South Africa

The study determined the antimicrobial resistance profiles of Salmonella on chickens processed and retailed at outlets of the informal markets in Gauteng province, South Africa. The study also investigated the relationship of antimicrobial resistant Salmonella to the source and type of samples and their serotypes. Carcass swabs, cloacal swabs and carcass drips were randomly collected from each of 151 slaughtered chickens from six townships. Isolation and identification were performed using standard and polymerase chain reaction (PCR) methods. The disc diffusion method was used to determine the resistance of Salmonella isolates to 16 antimicrobial agents and PCR to determine their serovars. Ninety-eight (64.9%) of the 151 chickens were contaminated with Salmonella of which 94.9% (93/98) were resistant serovars. The frequency of antimicrobial resistance of Salmonella isolates was high to erythromycin (94.9%) and spectinomycin (82.7%) but was low to ciprofloxacin (1.0%) and norfloxacin (1.0%) (p < 0.05). All 170 isolates of Salmonella tested exhibited resistance to one or more antimicrobial agents and the frequency varied significantly (p < 0.05) across the townships, the type of samples and the serovars. The prevalence of multidrug resistance (MDR) in Salmonella was 81.8% (139/170). Our findings pose zoonotic, food safety and therapeutic risks to workers and consumers of undercooked, contaminated chickens from these outlets.

Poultry and Wild Birds as a Reservoir of CMY-2 Producing Escherichia coli: The First Large-Scale Study in Greece

Resistance mediated by β-lactamases is a globally spread menace. The aim of the present study was to determine the occurrence of Escherichia coli producing plasmid-encoded AmpC β-lactamases (pAmpC) in animals. Fecal samples from chickens (n = 159), cattle (n = 104), pigs (n = 214), and various wild bird species (n = 168), collected from different Greek regions during 2018-2020, were screened for the presence of pAmpC-encoding genes. Thirteen E. coli displaying resistance to third-generation cephalosporins and a positive AmpC confirmation test were detected. bla_CMY-2 was the sole pAmpC gene identified in 12 chickens' and 1 wild bird (Eurasian magpie) isolates and was in all cases linked to an upstream ISEcp1-like element. The isolates were classified into five different sequence types: ST131, ST117, ST155, ST429, and ST1415. Four chickens' stains were assigned to ST131, while five chickens' strains and the one from the Eurasian magpie belonged to ST117. Seven pAmpC isolates co-harbored genes conferring resistance to tetracyclines (tetM, tetB, tetC, tetD), 3 carried sulfonamide resistance genes (sulI and sulII), and 10 displayed mutations in the quinolone resistance-determining regions of gyrA (S83L+D87N) and parC (S80I+E84V). This report provides evidence of pAmpC dissemination, describing for the first time the presence of CMY-2 in chickens and wild birds from Greece.

Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli

Introduction

Commensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants.

Objectives

In order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S. Infantis and E. coli from broiler sources.

Results

The core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers.

Conclusion

This is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S. Infantis.

Genome evolution and the emergence of pathogenicity in avian Escherichia coli

Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.

Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

Recent findings on Antibiotic Resistance (AR) have brought renewed attention to the comparison of data on AR from human and animal sectors. This is however a major challenge since the data is not harmonized. This study performs a comparative analysis of data on resistance combinations in Escherichia coli (E. coli) from different routine surveillance and monitoring systems for human and different animal populations in Germany. Data on E. coli isolates were collected between 2014 and 2017 from human clinical isolates, non-clinical animal isolates from food-producing animals and food, and clinical animal isolates from food-producing and companion animals from national routine surveillance and monitoring for AR in Germany. Sixteen possible resistance combinations to four antibiotics—ampicillin, cefotaxime, ciprofloxacin and gentamicin–for these populations were used for hierarchical clustering (Euclidian and average distance). All analyses were performed with the software R 3.5.1 (Rstudio 1.1.442). Data of 333,496 E. coli isolates and forty-one different human and animal populations were included in the cluster analysis. Three main clusters were detected. Within these three clusters, all human populations (intensive care unit (ICU), general ward and outpatient care) showed similar relative frequencies of the resistance combinations and clustered together. They demonstrated similarities with clinical isolates from different animal populations and most isolates from pigs from both non-clinical and clinical isolates. Isolates from healthy poultry demonstrated similarities in relative frequencies of resistance combinations and clustered together. However, they clustered separately from the human isolates. All isolates from different animal populations with low relative frequencies of resistance combinations clustered together. They also clustered separately from the human populations. Cluster analysis has been able to demonstrate the linkage among human isolates and isolates from various animal populations based on the resistance combinations. Further analyses based on these findings might support a better one-health approach for AR in Germany.

Bacteriophages Against Pathogenic Bacteria and Possibilities for Future Application in Africa

Bacteriophages (phages) are viruses that infect prokaryotic cells. Phages exist in many shapes and sizes with the majority of them being less than 100 nm in size. Essentially, the majority of phages identified are double-stranded DNA virions with the remaining few being found as RNA or single-stranded DNA viruses. These biological entities are plentiful in different environments, especially in wet sources. Treatment of a bacterial disease using phage application has been documented in the pre-antibiotic era. Different studies have emerging to value the efficacy of phage use in in-vitro and in-vivo based systems against specific bacterial agents of humans, animals or plant diseases. The process represents a natural and nontoxic framework to avert infections due to pathogenic and antimicrobial-resistant bacteria. Most of the published researches on the usefulness of phages against disease-causing bacteria (including antimicrobial-resistant strains) of humans, animals or plants are emerging from the US and European countries with very few studies available from Africa. This review assesses published articles in the area of phage applications against pathogenic or antimicrobial-resistant bacteria from experimental, clinical and field settings. The knowledge and skill of isolating lytic phages against bacteria can be operational for its simpler procedures and economic benefit. Future studies in Africa and other emerging countries may consider in-house phage preparations for effective control and eradication of pathogenic and multidrug resistant bacteria of humans, animals and plants.

Effects of hulless barley and exogenous beta-glucanase levels on ileal digesta soluble beta-glucan molecular weight, digestive tract characteristics, and performance of broiler chickens

The reduced use of antibiotics in poultry feed has led to the investigation of alternatives to antibiotics, and one such substitution is fermentable carbohydrates. Exogenous β-glucanase (BGase) is commonly used in poultry fed barley-based diets to reduce digesta viscosity. The effects of hulless barley (HB) and BGase levels on ileal digesta soluble β-glucan molecular weight, digestive tract characteristics, and performance of broiler chickens were determined. A total of 360 day-old broilers were housed in battery cages (4 birds per cage) and fed graded levels of high β-glucan HB (CDC Fibar; 0, 30, and 60% replacing wheat) and BGase (Econase GT 200 P; 0, 0.01, and 0.1%) in a 3 × 3 factorial arrangement. Beta-glucan peak molecular weight in the ileal digesta was lower with 30 and 60 than 0% HB, whereas the peak decreased with increasing BGase. The weight average molecular weight was lower at 0.1 than 0% BGase in wheat diets, whereas in HB diets, it was lower at 0.01 and 0.1 than 0% BGase. The maximum molecular weight was lower with 0.01 and 0.1 than 0% BGase regardless of the HB level. The maximum molecular weight was lower with HB than wheat at 0 or 0.01% BGase. Overall, empty weights and lengths of digestive tract sections increased with increasing HB, but there was no BGase effect. Hulless barley decreased the duodenum and jejunum contents, whereas increasing the gizzard (diets with BGase), ileum, and colon contents. The jejunum and small intestine contents decreased with increasing BGase. Ileal and colon pH increased with increasing HB, but there was no BGase effect. Treatment effects were minor on short-chain fatty acids levels and performance. In conclusion, exogenous BGase depolymerized the ileal digesta soluble β-glucan in broiler chickens in a dose-dependent manner. Overall, feed efficiency was impaired by increasing HB levels. However, HB and BGase did not affect carbohydrate fermentation in the ileum and ceca, although BGase decreased ileal viscosity and improved feed efficiency at the 0.1% dietary level.

Microbial Contamination of Chicken Litter Manure and Antimicrobial Resistance Threat in an Urban Area Setting in Cameroon

We conducted a pilot study to assess microbiological safety of chicken litter, an affordable organic and main fertilizer used in Cameroon and worldwide. A convenience sampling of 26 farms was done and a questionnaire was administered. Samples of litter were aseptically collected. E. coli and Salmonella spp. were isolated using CLSI standards. Antibiotic susceptibility testing was performed using the disc diffusion method and a micro broth dilution method for colistin. In broiler farms, 90% of participating farmers gave antibiotic prophylaxis. The prevalence of E. coli and Salmonella spp. was 59.1% and 15.5%, respectively. All E. coli isolates were multidrug resistant as well as 36.4% for Salmonella spp. No resistance was found against cefepime and imipenem. All Salmonella spp. tested were found sensitive to colistin while 26.7% of E. coli spp. were colistin resistant. Contamination of chicken litter may be an underestimated source of antimicrobial resistance (AMR) transmission towards animals, humans and the environment with multidrug resistant E. coli and Salmonella spp. This shows the need and opportunity for a One Health approach in AMR surveillance and control in Cameroon. Continued surveillance in chicken litter would enable monitoring of AMR risks and trends.

Phenotypical antimicrobial resistance data of clinical and non-clinical Escherichia coli from poultry in Germany between 2014 and 2017

Antimicrobial resistance (AMR) is a global threat in humans and animals, and antimicrobial usage (AMU) has been identified as a main trigger of AMR. The purpose of this work was to compare data on AMR in clinical and non-clinical isolates of Escherichia coli in German broilers and turkeys between 2014 and 2017. Furthermore, we investigated AMR changes over time and the association of changes in AMU with changes in AMR. Data on clinical and non-clinical isolates together with data on therapy frequency of broilers and turkeys were collected from German monitoring systems. Logistic regression analyses were performed to assess the association between the explanatory factors (AMU, year and isolate type) and the dependent variable (AMR). In broilers, the analysis showed lower resistance proportions of clinical isolates of E. coli to ampicillin and colistin (ampicillin: Odds ratio (OR) and 95% confidence interval (CI) = 0.44 (0.3-0.64), p<0.001; colistin: OR and 95% CI = 0.75 (0.73-0.76), p<0.001) but higher proportions for cefotaxime (OR and 95% CI = 4.58 (1.56-15.1), p = 0.007). Resistance to ampicillin, gentamicin and tetracycline was less frequent in clinical isolates in turkeys (ampicillin: OR and 95% CI = 0.4 (0.29-0.53), p<0.001; gentamicin: OR and 95% CI = 0.5 (0.26-0.94), p = 0.035; tetracycline: OR and 95% CI = 0.4 (0.29-0.55), p<0.001). The analysis found decreasing associations of AMU with resistance to tetracycline in turkeys and to colistin in broilers. Year was associated with a decrease in resistance to colistin in broilers and to tetracycline in turkeys. Differences in resistance found in this study between clinical and non-clinical isolates might play an important role in resistance prevalence. This study indicated that further data analyses over longer time intervals are required to clarify the differences found between clinical and non-clinical isolates and to assess the long-term effects of changes in AMU on the prevalence of AMR.

Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli

Simple Summary

Antimicrobial resistance acquired an endemic status in the Pakistan poultry sector. A cross-sectional study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant Escherichia coli using next-generation sequencing. Results show the widespread presence of diverse antibiotic resistance genes, virulence-associated genes, plasmid replicon types, and dysbiotic fecal microbial communities. Results indicate that antibiotic resistance altered the fecal microbial community structure of broiler chickens. The use of next-generation sequencing in this study documents a robust and cost-effective approach to study the fecal microbiome and resistome diversities of broiler chickens.

Abstract

The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) Escherichia coli (E. coli). Fecal samples (n = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR E. coli. Upon initial screening, thirteen (13) MDR E. coli isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were iroN, iutA, iss, and iucA. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as E. coli, Salmonella enterica, Klebsiella pneumoniae, and Shigella flexneri belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR E. coli of Khyber Pakhtunkhwa for the first time using NGS.

Dietary probiotics as a strategy for improving growth performance, intestinal efficacy, immunity, and antioxidant capacity of white Pekin ducks fed with different levels of CP

The potential impacts of probiotics on the performance and health status of white Pekin ducks fed with optimal or suboptimal dietary CP were evaluated during the growing period. A total of 180 male white Pekin ducks (14-day-old ducks with an initial weight of 415.65 ± 2.20 g) were randomly divided into 4 experimental groups (45 in each group of 5 replicates) in a 2 × 2 factorial design. The main factors included 2 dietary CP levels (18 or 14%) and dietary probiotic addition (with or without probiotics). The probiotic source was supplemented at 0.2 g per kilogram of diet from a blend of Lactobacillus acidophilus and Lactobacillus casei. The results showed that the diet containing 18% CP and probiotics significantly increases the final and total weight gain. Activities of intestinal enzymes (amylase, lipase, and protease), morphometrics (villus length, goblet cell count, and cryptal depth), and carcass percentage were also increased significantly. Total protein content, lysozyme activity, bactericidal activity, nitro blue tetrazolium levels, alternative complement pathway, superoxide dismutase activity, and catalase activity were significantly increased, whereas glucose, cortisol, and total cholesterol levels were decreased when treated with diet containing 18% CP and probiotics. Conversely, the group treated with diet containing 14% CP without probiotics showed the poorest performance, carcass properties, immune response, and antioxidant potential. In conclusion, probiotic addition to the 14% CP diet improved the performance of white Pekin ducks caused by reduced CP diet to performance due to the 18% CP diet without probiotic supplementation.

Longitudinal monitoring of multidrug resistance in Escherichia coli on broiler chicken fattening farms in Shandong, China

The extensive use of antibiotics has, in recent years, caused antimicrobial resistance and multidrug resistance in Escherichia coli to gradually develop into a worldwide problem. These resistant E. coli could be transmitted to humans through animal products and animal feces in the environment, thereby creating a problem for bacterial treatment for humans and animals and resulting in a public health issue. Monitoring the resistance of E. coli throughout the broiler fattening period is therefore of great significance for both the poultry industry and public health. In this longitudinal study, samples were taken from 6 conventional broiler fattening farms in Shandong Province, China, at 3 different times within 1 fattening period. The overall isolation rate of E. coli was 53.04% (375/707). Antibiotic resistance was very common in the E. coli isolated from these farms, and differed for different antibiotics, with ampicillin having the highest rate (92.86%) and cefoxitin the lowest (10.12%). Multidrug resistance was as high as 91.07%. More importantly, both the resistance rate of E. coli to the different drugs and the detection rate of drug resistance genes increased over time. The mobile colistin resistance (mcr-1) gene was detected in 24.40% of the strains, and these strains often carried other drug resistance genes, such as those conferring aminoglycoside, β-lactamase, tetracycline, and sulfonamide resistance. Antimicrobial resistance and drug resistance genes in E. coli were least common in the early fattening stage. The individual detection rates of sul1, sul3, aacC4, aphA3, and mcr-1 were significantly lower (P < 0.05) for the early fattening stage than for the middle and late stages. The rational use of antibiotics, in conjunction with the improvement of the breeding environment during the entire broiler fattening cycle, will be helpful in the development of the poultry industry and the protection of public health.

Antibiotic Resistance and Biofilm-Forming Ability in Enterococcal Isolates from Red Meat and Poultry Preparations

This study investigated the resistance to antibiotics and the capacity to form a biofilm of 200 isolates of enterococci isolated from raw preparations of beef (51 strains), pork (47), chicken (50), and turkey (52) acquired in north-western Spain. Fifteen antimicrobials of clinical importance were tested by the disc diffusion method. The average number of resistances per strain was 4.48 ± 1.59. If resistant strains were taken together with those showing reduced susceptibility, the total number of resistances per strain was 6.97 ± 2.02. Two isolates (1.0% of strains) were resistant to a single antibiotic, twenty-two isolates (11.0%) presented resistance to two, one strain (0.5%) was resistant to three, and 175 isolates (87.5%) showed a multiple drug-resistant phenotype (MDR; defined as no susceptibility to at least one agent from each of three or more antimicrobial categories). The prevalence of resistance varied between 0.5% (gentamicin) and 100% (kanamycin). All strains produced biofilm on polystyrene microwell plates, determined using crystal violet assay. Isolates were classified as having a weak (51 strains; average optical density at 580 nanometers -OD₅₈₀- = 0.206 ± 0.033), moderate (78 strains; average OD₅₈₀ = 0.374 ± 0.068), or strong (71 strains; average OD₅₈₀ = 1.167 ± 0.621) ability to produce biofilm (p < 0.05). Isolates from beef preparations produced the most substantial (p < 0.05) biofilms. The results of this study indicate that meat and poultry preparations are major reservoirs of antibiotic-resistant enterococcal strains capable of forming a biofilm. In order for food-borne infections to be prevented, the importance of careful handling of these foodstuffs during preparation, avoiding cross-contamination, and ensuring thorough cooking, is stressed.