Food animals and antimicrobials: impacts on human health

Antimicrobial Resistance Trends of Escherichia coli Isolates: A Three-Year Prospective Study of Poultry Production in Spain

Antimicrobial resistance (AMR) poses a major threat to health worldwide. Poultry products are one of the main threats, due to the transmission of antimicrobial resistance genes throughout the food chain. Escherichia coli is the main cause of mortality in the poultry industry, mainly mitigated with antibiotics, but due to the high genetic strain variability, recurrent outbreaks of multidrug resistant E. coli take place. The major challenge to tackling AMR is understanding the burden of resistance. For this reason, one of the main strategies is monitoring AMR by phenotypic characterisation. Our study aimed to monitor the resistance of E. coli strains isolated from the poultry sector over a period of three years (2019–2021) to provide information on the resistance magnitude and trends. Promising results have been found concerning the low frequency of resistance to cephalosporins, polymyxin, and fluoroquinolones. However, levels of resistance found to antimicrobials such as erythromycin (100%), tylosin (98%), or penicillin (97%) suggest the need to continue working on the limitation of use of antimicrobials in poultry to achieve the demise of MDR.

Antibiotics in Dairy Production: Where Is the Problem?

Antibiotics have long been used for the prevention and treatment of common diseases and for prophylactic purposes in dairy animals. However, in recent decades it has become a matter of concern due to the widespread belief that there has been an abuse or misuse of these drugs in animals and that this misuse has led to the presence of residues in derived foods, such as milk and dairy products. Therefore, this review aims to compile the scientific literature published to date on the presence of antibiotic residues in these products worldwide. The focus is on the reasons that lead to their presence in food, on the potential problems caused by residues in the characteristics of dairy products and in their manufacturing process, on the development and spread of antibiotic-resistant bacteria, and on the effects that both residues and resistant bacteria can cause on human and environmental health.

Characterization and Evaluation of Colombian Propolis on the Intestinal Integrity of Broilers

Nutritional additives such as propolis seek to improve intestinal health as an alternative to the global ban on in-feed antibiotics used as growth promoters (AGP). The objective of this study was to evaluate the effect of propolis supplementation in diet of broilers. Four hundred and fifty straight-run Ross 308 AP broilers were fed with a basal diet (BD) throughout the whole experimental period. Birds were randomly distributed into 5 groups at d 14: negative control without antibiotics nor propolis (AGP-), positive control 500 ppm of Zinc Bacitracin as growth promoter (AGP+), and 3 groups supplemented with 150, 300, and 450 ppm of propolis. Every group included 6 replicates of 15 birds each. Propolis concentration was increased from d 22 to 42, in experimental groups to 300, 600, and 900 ppm of propolis, and 10% of raw soybean was included as a challenge in all groups during the same period. Analysis of productive parameters, intestinal morphometry, and relative quantification of genes associated with epithelial integrity by qPCR were performed at 21 and 42 d. The groups with the greatest weights were those that consumed diets including 150 (21 d) and 900 ppm (42 d) of propolis compared with all treatments. The lowest score of ISI was found at 300 (21 d) and 600 ppm (42 d). A lower degree of injury in digestive system was seen with the inclusion of 300 ppm (21 d) and 900 ppm (42 d). Up-regulation of zonula occludens-1 (ZO-1) was observed in jejunum of broilers supplemented with 150 and 300 ppm at 21 d. Up-regulation of ZO-1 and TGF-β was also evidenced in ileum at all propolis inclusion levels at 42-day-old compared to AGP+ and AGP-. The beneficial effects were evidenced at inclusion levels of 150 ppm in the starter and 900 ppm in the finisher. According to the results, the Colombian propolis inclusion can improve productive performance, physiological parameters, and gene expression associated with intestinal integrity.

An updated review on probiotics as an alternative of antibiotics in poultry - A review

Antibiotics used to be supplemented to animal feeds as growth promoter and as an effective strategy to reduce the burden of pathogenic bacteria present in the gastro-intestinal tract. However, in-feed antibiotics also kill bacteria that may be beneficial to the animal. Secondly, unrestricted use of antibiotics enhanced the antibiotic resistance in pathogenic bacteria. To overcome above problems, scientists are taking a great deal of measures to develop alternatives of antibiotics. There is convincing evidence that probiotics could replace in-feed antibiotics in poultry production. Because they have beneficial effects on growth performance, meat quality, bone health and eggshell quality in poultry. Better immune responses, healthier intestinal microflora and morphology which help the birds to resist against disease attack were also identified with the supplementation of probiotics. Probiotics establish cross-feeding between different bacterial strains of gut ecosystem and reduce the blood cholesterol level via bile salt hydrolase activity. The action mode of probiotics was also updated according to recently published literatures, i.e antimicrobial substances generation or toxin reduction. This comprehensive review of probiotics is aimed to highlight the beneficial effects of probiotics as a potential alternative strategy to replace the antibiotics in poultry.

Administration of probiotic lactic acid bacteria to modulate fecal microbiome in feedlot cattle

Modulation of animal gut microbiota is a prominent function of probiotics to improve the health and performance of livestock. In this study, a large-scale survey to evaluate the effect of lactic acid bacteria probiotics on shaping the fecal bacterial community structure of feedlot cattle during three experimental periods of the fattening cycle (163 days) was performed. A commercial feedlot located in northwestern Argentina was enrolled with cattle fed mixed rations (forage and increasing grain diet) and a convenience-experimental design was conducted. A pen (n = 21 animals) was assigned to each experimental group that received probiotics during three different periods. Groups of n = 7 animals were sampled at 40, 104 and 163 days and these samples were then pooled to one, thus giving a total of 34 samples that were subjected to high-throughput sequencing. The microbial diversity of fecal samples was significantly affected (p < 0.05) by the administration period compared with probiotic group supplementation. Even though, the three experimental periods of probiotic administration induced changes in the relative abundance of the most representative bacterial communities, the fecal microbiome of samples was dominated by the Firmicutes (72–98%) and Actinobacteria (0.8–27%) phyla, while a lower abundance of Bacteroidetes (0.08–4.2%) was present. Probiotics were able to modulate the fecal microbiota with a convergence of Clostridiaceae, Lachnospiraceae, Ruminococcaceae and Bifidobacteriaceae associated with health and growth benefits as core microbiome members. Metabolic functional prediction comparing three experimental administration periods (40, 104 and 163 days) showed an enrichment of metabolic pathways related to complex plant-derived polysaccharide digestion as well as amino acids and derivatives during the first 40 days of probiotic supplementation. Genomic-based knowledge on the benefits of autochthonous probiotics on cattle gastrointestinal tract (GIT) microbiota composition and functions will contribute to their selection as antibiotic alternatives for commercial feedlot.

Evidence of Virulent Multi-Drug Resistant and Biofilm-Forming Listeria Species Isolated from Various Sources in South Africa

Listeriosis is a foodborne disease caused by Listeria monocytogenes species and is known to cause severe complications, particularly in pregnant women, young children, the elderly, and immunocompromised individuals. The aim of this study was to investigate the presence of Listeria species in food and water using both biochemical and species-specific PCR analysis. L. monocytogenes isolates were further screened for the presence of various antibiotic resistance, virulence, and biofilm-forming determinants profiles using phenotypic and genotypic assays. A total of 207 samples (composed of meat, milk, vegetables, and water) were collected and analyzed for presence of L. monocytogenes using species specific PCR analysis. Out of 267 presumptive isolates, 53 (19.85%) were confirmed as the Listeria species, and these comprised 26 L. monocytogenes, 3 L. innocua, 2 L. welshimeri, and 1 L. thailandensis. The remaining 21 Listeria species were classified as uncultured Listeria, based on 16SrRNA sequence analysis results. A large proportion (76% to 100%) of the L. monocytogenes were resistant to erythromycin (76%), clindamycin (100%), gentamicin (100%), tetracycline (100%), novobiocin (100%), oxacillin (100%), nalidixic acid (100%), and kanamycin (100%). The isolates revealed various multi-drug resistant (MDR) phenotypes, with E-DA-GM-T-NO-OX-NA-K being the most predominant MDR phenotypes observed in the L. monocytogenes isolates. The virulence genes prfA, hlyA, actA, and plcB were detected in 100%, 68%, 56%, and 20% of the isolates, respectively. In addition, L. monocytogenes isolates were capable of forming strong biofilm at 4 °C (%) after 24 to 72 h incubation periods, moderate for 8% isolates at 48 h and 20% at 72 h (p < 0.05). Moreover, at 25 °C and 37 °C, small proportions of the isolates displayed moderate (8−20%) biofilm formation after 48 and 72 h incubation periods. Biofilm formation genes flaA and luxS were detected in 72% and 56% of the isolates, respectively. These findings suggest that proper hygiene measures must be enforced along the food chain to ensure food safety.

Molecular Characterization of pBOq-IncQ and pBOq-95LK Plasmids of Escherichia coli BOq 01, a New Isolated Strain from Poultry Farming, Involved in Antibiotic Resistance

The increase in antimicrobial resistance has raised questions about how to use these drugs safely, especially in veterinary medicine, animal nutrition, and agriculture. Escherichia coli is an important human and animal pathogen that frequently contains plasmids carrying antibiotic resistance genes. Extra chromosomal elements are required for various functions or conditions in microorganisms. Several phage-like plasmids have been identified, which are important in antibiotic resistance. In this work, the molecular characterization of the pBOq-IncQ (4.5 kb) and pBOq-95LK (95 kb) plasmids found in the E. coli strain BOq 01, a multidrug resistant bacteria isolated from a poultry farm, are considered. Plasmid pBOq-IncQ belongs to the incQ incompatibility plasmid family and is involved in sulfonamide resistance. Plasmid pBOq-95LK is a lytic phage-like plasmid that is involved in the lysis of the E. coli BOq 01 strain and carries a bleomycin resistance gene and a strain cured of this plasmid shows bleomycin sensitivity. Induction of the lytic cycle indicates that this phage-like plasmid is an active phage. This type of plasmid has been reported to acquire genes such as mcr-1, which codes for colistin resistance and bacterial persistence and is a significant public health threat. A genome comparison, a pangenomic and phylogenomic analysis with other phage-like plasmids reported in the literature were performed to understand better the evolution of this kind of plasmid in bacteria and its potential importance in antibiotic resistance.

Metabolites in Milk after Enrofloxacin Treatment and Their Persistence to Temperature

In this work, metabolomic profile changes in milk from cows affected by mastitis and treated with enrofloxacin (ENR) have been studied using LC-HRMS techniques. Principal component analysis was applied to the obtained results, and the interest was focused on changes affecting compounds without a structural relationship to ENR. Most of the compounds, whose concentrations were modified as a result of the pharmacological treatment and/or the pathological status, were related to amino acids and peptides. Compounds that may become possible biomarkers for either disease or treatment have been detected. Additionally, the alterations caused by thermal processes, such as those applied to milk before consumption, on the identified metabolites have also been considered.

Differential Overlap in Human and Animal Fecal Microbiomes and Resistomes in Rural versus Urban Bangladesh

While the development of antibiotic resistance in animal gut microbiomes and subsequent transmission to humans has been demonstrated in intensive farming environments and high-income countries, evidence of zoonotic exchange of antibiotic resistance in LMIC communities is lacking. This research provides genomic evidence of overlap of antibiotic resistance genes between humans and animals, especially in urban communities, and highlights chickens as important reservoirs of antibiotic resistance.

Genomic Investigation of Proteus mirabilis Isolates Recovered From Pig Farms in Zhejiang Province, China

Proteus mirabilis is a common opportunistic zoonotic pathogen, and its ongoing acquisition of antimicrobial resistance genes poses challenges to clinical treatments. Human-sourced whole genomic sequencing of human P. mirabilis isolates has been reported, but pig-sourced isolates have not been thoroughly investigated even though these animals can serve as reservoirs for human infections. In the current study, we report a molecular epidemiological investigation to unravel the antimicrobial and virulence gene risk factors for P. mirabilis contamination in 9 pig farms in 3 different cities in Zhejiang Province, China. We collected 541 swab samples from healthy pigs and 30 were confirmed as P. mirabilis. All 30 isolates were resistant to tetracyclines, macrolides, sulfonamides, β-lactams and chloramphenicol, and all were multiple drug-resistant and 27 were strong biofilm formers. Phylogenetic analyses indicated these 30 isolates clustered together in 2 major groups. Whole genome sequencing demonstrated that the isolates possessed 91 different antimicrobial resistance genes belonging to 30 antimicrobial classes including rmtB, sul1, qnrS1, AAC(6′) − Ib − cr, blaCTX − M − 65 and blaOXA − 1. All isolates contained mobile genetic elements including integrative conjugative elements (ICEs) and integrative and mobilizable elements (IMEs). Minimum inhibitory concentration (MIC) testing indicated direct correlates between cognate genes and antimicrobial resistance. We also identified 95 virulence factors, almost all isolates contained 20 fimbrial and flagellar operons, and this represents the greatest number of these operon types found in a single species among all sequenced bacterial genomes. These genes regulate biofilm formation and represent a confounding variable for treating P. mirabilis infections. Our P. mirabilis isolates were present in healthy animals, and multiple drug resistance in these isolates may serve as a reservoir for other intestinal and environmental Enterobacteriaceae members. This prompts us to more strictly regulate veterinary antibiotic use.

Resistome Analysis of Global Livestock and Soil Microbiomes

Antimicrobial resistance (AMR) is a serious threat to public health globally; it is estimated that AMR bacteria caused 1.27 million deaths in 2019, and this is set to rise to 10 million deaths annually. Agricultural and soil environments act as antimicrobial resistance gene (ARG) reservoirs, operating as a link between different ecosystems and enabling the mixing and dissemination of resistance genes. Due to the close interactions between humans and agricultural environments, these AMR gene reservoirs are a major risk to both human and animal health. In this study, we aimed to identify the resistance gene reservoirs present in four microbiomes: poultry, ruminant, swine gastrointestinal (GI) tracts coupled with those from soil. This large study brings together every poultry, swine, ruminant, and soil shotgun metagenomic sequence available on the NCBI sequence read archive for the first time. We use the ResFinder database to identify acquired antimicrobial resistance genes in over 5,800 metagenomes. ARGs were diverse and widespread within the metagenomes, with 235, 101, 167, and 182 different resistance genes identified in the poultry, ruminant, swine, and soil microbiomes, respectively. The tetracycline resistance genes were the most widespread in the livestock GI microbiomes, including tet(W)_1, tet(Q)_1, tet(O)_1, and tet(44)_1. The tet(W)_1 resistance gene was found in 99% of livestock GI tract microbiomes, while tet(Q)_1 was identified in 93%, tet(O)_1 in 82%, and finally tet(44)_1 in 69%. Metatranscriptomic analysis confirmed these genes were “real” and expressed in one or more of the livestock GI tract microbiomes, with tet(40)_1 and tet(O)_1 expressed in all three livestock microbiomes. In soil, the most abundant ARG was the oleandomycin resistance gene, ole(B)_1. A total of 55 resistance genes were shared by the four microbiomes, with 11 ARGs actively expressed in two or more microbiomes. By using all available metagenomes we were able to mine a large number of samples and describe resistomes in 37 countries. This study provides a global insight into the diverse and abundant antimicrobial resistance gene reservoirs present in both livestock and soil microbiomes.

African smallholder farmers and the treatment of livestock diseases using ethnoveterinary medicine: A commentary

Often touted as an ancient and sustainable practice among indigenous livestock farmers in developing countries, the use of ethno-veterinary medicine is examined within the context of its efficacy. While there are undoubtedly positive implications for adopting knowledge and practice that align with nature, there is both prevalence and ambivalence to the adoption of indigenous plant knowledge and resources for the treatment of livestock infections and diseases. This situation is due to the lack of validation and standardization of the practice in low-income countries, requiring scholarly efforts in developing this indigenous knowledge system. This is a short communication piece that provides a commentary on the issues that pertain to ethno-veterinary practice among rural livestock farmers in sub-Saharan Africa.

Paternal transgenerational nutritional epigenetic effect: A new insight into nutritional manipulation to reduce the use of antibiotics in animal feeding

The use of antibiotics in animal feeding has been banned in many countries because of increasing concerns about the development of bacterial resistance to antibiotics and potential issues on food safety. Searching for antibiotic substitutes is essential. Applying transgenerational epigenetic technology to animal production could be an alternative. Some environmental changes can be transferred to memory-like responses in the offspring through epigenetic mechanisms without changing the DNA sequence. In this paper, we reviewed those nutrients and non-nutritional additives that have transgenerational epigenetic effects, including some amino acids, vitamins, and polysaccharides. The paternal transgenerational nutritional epigenetic regulation was particularly focused on mechanism of the substantial contribution of male stud animals to the animal industries. We illustrated the effects of paternal transgenerational epigenetics on the metabolism and immunity in farming animals and proposed strategies to modulate male breeding livestock or poultry.

Removal of Diverse and Abundant ARGs by MF-NF Process from Pig Manure and Digestate

Antimicrobial resistances are emerging as one main threat to worldwide human health and are expected to kill 10 million people by 2050. Intensive livestock husbandry, along with biogas digestate, are considered as one of the biggest ARG reservoirs. Despite major concerns, little information is available on the diversity and abundance of various ARGs in small to large scale pig farms and biogas digestate slurry in Germany, followed by their consequent removal using microfiltration (MF)-nanofiltration (NF) process. Here, we report the identification and quantification of 189 ARGs in raw manure and digestate samples, out of which 66 ARGs were shared among manures and 53 ARGs were shared among both manure and digestate samples. The highest reported total ARG copy numbers in a single manure sampling site was 1.15 × 10⁸ copies/100 µL. In addition, we found the absolute concentrations of 37 ARGs were above 10⁵ copies/100 μL. Filtration results showed that the highly concentrated ARGs (except aminoglycoside resistance ARGs) in feed presented high log retention value (LRV) from 3 to as high as 5 after the MF-NF process. Additionally, LRV below 2 was noticed where the initial absolute ARG concentrations were ≤10³ copies/100 μL. Therefore, ARG removal was found to be directly proportional to its initial concentration in the raw manure and in digestate samples. Consequently, some ARGs (tetH, strB) can still be found within the permeate of NF with up to 10⁴ copies/100 μL.

Antimicrobial resistance in commensal Staphylococcus aureus from wild ungulates is driven by agricultural land cover and livestock farming

Staphylococcus aureus is a human pathobiont (i.e., a commensal microorganism that is potentially pathogenic under certain conditions), a nosocomial pathogen and a leading cause of morbidity and mortality in humans. S. aureus is also a commensal and pathogen of companion animals and livestock. The dissemination of antimicrobial resistant (AMR) S. aureus, particularly methicillin-resistant (MRSA), has been associated to its ability for establishing new reservoirs, but limited attention has been devoted to the role of the environment. To fill this gap, we aimed to characterize animal carrier status, AMR phenotypes, predominant clonal lineages and their relationship with clinical and food-chain settings, as well as to find predictors of AMR occurrence. Nasal swabs (n = 254) from wild boar (n = 177), red deer (n = 54) and fallow deer (n = 23) hunted in Portugal, during the season 2019/2020, yielded an overall carrier proportion of 35.8%, ranging from 53.7% for red deer and 32.2% for wild boar to 21.7% for fallow deer. MRSA from wild boar and phenotypically linezolid-resistant S. aureus from wild boar and red deer were isolated, indicating that resistance to antimicrobials restricted to clinical practice also occurs in wildlife. The most prevalent genotypes were t11502/ST2678 (29.6%) and t12939/ST2678 (9.4%), previously reported in wild boar from Spain. Clonal lineages reported in humans and livestock, like CC1, CC5 or CC8 (19.1%) and ST425, CC133 or CC398 (23.5%), respectively, were also found. The sequence type ST544, previously restricted to humans, is described in wildlife for the first time. We also identified that land use (agricultural land cover), human driven disturbance (swine abundance) and host-related factors (sex) determine resistance occurrence. These findings suggest that antibiotics used in clinical settings, agriculture and livestock farming, spill over to wildlife, leading to AMR emergence, with potential biological, ecological, and human health effects. This work is one of the most comprehensive surveys in Europe of S. aureus occurrence and determinants among widely distributed wild ungulates.

Changes in antibiotic consumption patterns after the implementation of the National Action Plan according to the Access, Watch, Reserve (AWaRe) classification system

OBJECTIVE

The Korean government published the first National Action Plan (NAP) on antimicrobial resistance (AMR) in August 2016, followed by a second plan in November 2021. The objective of this study was to analyze changes in antibiotic use patterns after the implementation of the NAP in South Korea.

METHODS

We analyzed National Health Insurance claims data for hospitals and clinics from January 2011 to December 2020. Consumption was measured using a defined daily dose per 1000 inhabitants per day (DID). We analyzed data for each year, dimension, and category of the Access, Watch, Reserve classification system by the World Health Organization. Monthly inpatient and outpatient antibiotic use were calculated, and an interrupted time-series (ITS) analysis to assess the trend in antibiotic use was conducted.

RESULTS

The consumption of antibiotics increased from 25.78 DID in 2011 to 29.06 DID in 2016, then decreased in 2017 after the implementation of the NAP on AMR. The watch group showed a temporal decrease after the implementation of the NAP; however, these figures increased until 2019, and the reserve group showed a downward trend beginning in 2017. According to the ITS analysis, the level (β₂) and the slope of the trend (β₃) of total antibiotic use decreased by 0.17 and 0.001, respectively. After implementation of the NAP, antibiotic use was reduced from 7.18 DID in 2016 to 4.84 DID in 2017 for amoxicillin and beta-lactamase inhibitors, 0.86 DID to 0.70 DID for ciprofloxacin, and 0.66 DID to0.66 DID for levofloxacin.

CONCLUSION

After the implementation of the NAP in South Korea, antibiotic use in terms of total antibiotics and fluoroquinolone in the watch and reserve groups decreased. Further policies to improve the use of antibiotics in the watch and reserve groups are needed.

A highly sensitive impedimetric sensor based on a MIP biomimetic for the detection of enrofloxacin

The benefits of molecularly imprinted polymer (MIP) technology in creating artificial receptors to replace natural counterparts have piqued the interest of numerous researchers in recent years. We propose a biomimetic enrofloxacin-MIP for enrofloxacin (ENRO) antigen detection using gold nanoparticles (AuNPs) and MIP methodologies in this study. A self-assembled monomer layer of aminothiophenol was used to immobilize a pre-formed complex of the anti-enrofloxacin monoclonal antibody and enrofloxacin antigen onto the surface of an AuNP coated screen-printed carbon ink electrode (SPCE). The poly-(aminothiophenol) layer thickness was adjusted to entrap and restrict enrofloxacin antigens near the surface. The imprinting and removal of the enrofloxacin antigen in the MIP film were strongly validated by the Raman spectra. The final mAb-MIP sensor had better sensitivity (302 Ω mL ng^-1) and a better detection limit (0.05 ng mL^-1) than self-assembled monolayer (SAM)-based immunosensors, which had 102 Ω mL ng^-1 and 0.1 ng mL^-1, respectively.

Association of human milk oligosaccharides and nutritional status of young infants among Bangladeshi mother-infant dyads

Human milk oligosaccharides (HMOs) support the development of a healthy gut microbiome and the growth of infants. We aimed to determine the association of different HMOs with severe acute malnutrition (SAM) among Bangladeshi young infants. This study was nested within a single-blind, randomized, pilot clinical trial (NCT0366657). A total of 45 breastmilk samples from mothers of < 6 months old infants who had SAM (n = 26) or were non-malnourished (n = 19) and were analyzed for constituent HMOs. Of the infants with SAM, 14 (53.85%) had secretor mothers, and 11 (57.89%) of the non-malnourished infants had secretor mothers. A one-unit increase in the relative abundance of sialylated HMOs was associated with higher odds of SAM in age and sex adjusted model (aOR = 2.00, 90% CI 1.30, 3.06), in age, sex, and secretor status adjusted model (aOR = 1.96, 90% CI 1.29, 2.98), and also in age and sex adjusted model among non-secretor mothers (aOR = 2.86, 90% CI 1.07, 7.62). In adjusted models, there was no evidence of a statistically significant association between SAM and fucosylated or undecorated HMOs. Our study demonstrates that a higher relative abundance of sialylated HMOs in mothers’ breastmilk may have a negative impact on young infants’ nutritional status.

Occurrence and Antibiotic Resistance Profiles of Methicillin-Resistant Staphylococcus Aureus (Mrsa) in Layer Chickens in Kebbi, Nigeria

Antimicrobial resistance (AMR) is a global health threat, and antimicrobial use in animal production for growth enhancement or prophylaxis contributes to the development of AMR. A cross-sectional study was conducted to investigate the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in poultry and farm attendants in Kebbi, North-Western Nigeria. A total of 207 cloacal and nasal swabs were randomly collected from four farms comprising 50 samples from each poultry farm and only 7 samples from farm attendants. The samples were analysed using routine bacteriological culture and identification techniques. Presumptive MRSA isolates were confirmed by PCR assay and AMR profiles of the isolates were evaluated using the Kirby-Bauer disk diffusion method. Of the 207 samples examined, 37.5 % (75/200) of layer birds tested positive for MRSA and 71.4 % (5/7) of farm attendants were MRSA positive. All the isolates were susceptible to vancomycin, with an AMR index ˃ 0.3. The findings of this study indicated colonization of layer chickens and humans by multidrug resistant MRSA, thus highlighting the potential role of poultry sources of transmission of multidrug-resistant MRSA strains to humans and vice versa.

Antimicrobial resistance in commensal Escherichia coli from humans and chickens in the Mekong Delta of Vietnam is driven by antimicrobial usage and potential cross-species transmission

Objectives

To investigate phenotypic antimicrobial resistance (AMR) in relation to antimicrobial use (AMU) and potential inter-species transmission among Escherichia coli from humans and chickens located in the same households in the Mekong Delta of Vietnam.

Methods

We collected data on AMU and faecal swabs from humans (N = 426) and chickens (N = 237) from 237 small-scale farms. From each sample, one E. coli strain was isolated and tested for its susceptibility against 11 antimicrobials by Sensititre AST. The association between AMR and AMU was investigated by logistic regression modelling. Using randomization, we compared the degree of similarity in AMR patterns between human and chicken E. coli from the same farms compared with isolates from different farms.

Results

The AMU rate was ∼19 times higher in chickens (291.1 per 1000 chicken-days) than in humans (15.1 per 1000 person-days). Isolates from chickens also displayed a higher prevalence of multidrug resistance (63.3%) than those of human origin (55.1%). AMU increased the probability of resistance in isolates from human (ORs between 2.1 and 5.3) and chicken (ORs between 1.9 and 4.8). E. coli from humans and chickens living on same farms had a higher degree of similarity in their AMR patterns than isolates from humans and chicken living on different farms.

Conclusions

We demonstrated the co-influence of AMU and potential transmission on observed phenotypic AMR patterns among E. coli isolates from food-producing animals and in-contact humans. Restricting unnecessary AMU alongside limiting interspecies contact (i.e. increasing hygiene and biocontainment) are essential for reducing the burden of AMR.

The use of common antimicrobial agents in US veal calves

The use of antimicrobials in food animals and the selection of antimicrobial-resistant pathogens continue to be prominent concerns for human food safety and public health. To provide optimal stewardship programs, antimicrobial use in animal production operations must be quantified and standardized for benchmarking and creating goals, monitoring temporal trends, and identifying causes of emerging resistance. In the United States, quantified estimates of antimicrobial use are available in dairy and beef cattle, but these data have not been generated for veal calf herds. Therefore, the objective of this study was to estimate the treatment incidence (TI) of antimicrobials for eight US veal calf farms in one rearing cycle. Treatment incidences were compared between calculated doses defined by the labeled daily dose (LDD), animal-defined daily dose (ADD) from the European Medicines Agency (EMA) guideline, and the used daily dose (UDD) from the farm treatment protocols. Among eight farms, veal calves received a mean of 34.40 LDD, 34.88 ADD, and 28.68 UDD of an antimicrobial per 100 days. The lower TI based on the UDD administration was a result of higher farm protocol dosing relative to the labeled and EMA daily doses. Higher quantities of antimicrobial administration were observed in the first three weeks (day 1-21) of rearing (Tukey-adjusted p < .05). This study is the first to quantitatively estimate the TI of antimicrobials on the US veal calf operations and serves as an important step toward the development of antimicrobial stewardship programs.

Antagonistic activity and mode of action of trypacidin from marine-derived Aspergillus fumigatus against Vibrio parahaemolyticus

This study aimed to investigate the antagonistic activity and mode of action of trypacidin from marine-derived Aspergillus fumigatus against Vibrio parahaemolyticus. Results indicated that the minimal inhibitory concentration and minimal bactericidal concentration of trypacidin against V. parahaemolyticus were 31.25 and 62.5 μg/mL, respectively, which was better than that of streptomycin sulfate. Trypacidin remarkably inhibited the growth of V. parahaemolyticus and had a strong destructive effect on cell wall permeability and integrity, cell membrane permeability, and morphological alterations. Its potential as an antibacterial agent for aquatic products must be further explored.

Antibiotic Resistance Profiles of Bacteria Isolated from Hotspot Environments in Bahir Dar City, Northwestern Ethiopia

Background

Wastes generated from hotspot environments contain a wide range of antibiotics and pathogens that play a significant role in the dissemination of antibiotic-resistant bacteria in the environment. This study was carried out to isolate bacteria from hotspot environments and determine their resistance profiles to commonly used antibiotics in Bahir Dar city, Ethiopia.

Methods

A cross-sectional study was conducted from October 2020 to June 2021 in Bahir Dar City. A total of 126 waste and wastewater samples were aseptically collected, transported, and processed for bacteriological isolation and susceptibility testing following standard procedures.

Results

A total of 411 bacterial isolates were recovered and the highest value of 122 (29.7%) bacterial isolates were obtained from medical wastewater samples, and the most frequently isolated bacteria were assigned to the species Escherichia coli with 82 strains (19.5%). The results revealed that the highest resistance profile of 69 (95.8%) was obtained in Staphylococcus aureus against ampicillin and 46 (86.8%) Citrobacter spp. against tetracycline. Two hundred and sixteen (52.6%) of bacteria showed multi-drug resistance and the highest multi-drug resistance was observed in Pseudomonas spp. 47 (65.3%), followed by Escherichia coli 51 (62.2%). The highest resistance profile of 12 (85.7%) and 60 (74.1%) for tetracycline were obtained from beef waste and wastewater and medical wastewater samples. The highest multi-drug resistance was recorded in isolates isolated from beef waste and wastewater samples 11 (64.7%), followed by medical wastewater samples 84 (64.1%). Even though a higher (>0.2) multi-antibiotic resistance index was found in all hotspot environments, the highest multi-antibiotic resistance index (0.477) was recorded in bacteria isolated from medical wastewater.

Conclusion

It was concluded that wastes generated from hotspot environments and released in the environment contain large numbers of antibiotic-resistant, multidrug, extensively, and pan-drug-resistant bacteria. Proper waste management strategies should be established.

Conurbation size drives antibiotic resistance along the river

With growing concerns about antibiotic resistance, the tracking of antibiotic resistance genes (ARGs) in urban waterways will facilitate our increased understanding of the impact of urbanization on ARGs dissemination. In the current study, we assessed the ARGs profiles and antibiotic resistome in water samples along the Jiulong River basin, a distance of 250 km, to better understand the impact of anthropogenic activities. A total of 244 ARGs and 12 MGEs were detected from 21 sampling sites. Both relative and absolute abundance of the observed resistome decreased with increasing distance from urban areas. Ordinary least-squares (OLS) regression revealed that both the relative and absolute resistome abundance were positively correlated with city size. The resistome had several inputs and outputs and Fast Expectation Maximization Microbial Source Tracking (FEAST), suggested that the majority of the antibiotic resistome originated from anthropogenic activities. A total of 8 ARGs and 20 microbial OTUs were considered as biomarkers that differentiated the location of sampling sites. Bacterial communities were significantly correlated with ARGs according to Procrustes analysis and Mantel test, which was also supported by a co-occurrence network. Variation partitioning analysis revealed that ARG profiles were driven by multiple factors. Although antibiotic resistome abundance significantly increased near urban conurbations, overall resistome abundance decreased as the river flowed downstream. Our study highlights the effect of conurbation size on antibiotic resistance profiles within the river basin and the potential resilience of rivers to recover from ARGs contamination.

A Review of the Effectiveness of Current US Policies on Antimicrobial Use in Meat and Poultry Production

PURPOSE

Industrial food animal production accounts for most animal-source protein consumed in the USA. These operations rely on an array of external inputs, which can include antimicrobials of medical importance. The use of these drugs in this context has been the subject of public health debate for decades because their widespread use contributes to the selection for and proliferation of drug-resistant bacteria and their genetic determinants. Here, we describe legislative and regulatory efforts, at different levels of governance in the USA, to curtail food animal consumption of medically important antimicrobials.

RECENT FINDINGS

The features and relative success of the US efforts are examined alongside those of selected member states (Denmark and the Netherlands) of the European Union. Evaluation of efforts at all levels of US governance was complicated by shortcomings in prescribed data collection; nevertheless, available information suggests deficiencies in policy implementation and enforcement compromise the effectiveness of interventions pursued to date. The political will, robust systems for collecting and integrating data on antimicrobial consumption and use, and cross-sectoral collaboration that have been integral to the success of efforts in Denmark and The Netherlands have been notably absent in the USA, especially at the federal level.

Plasma colorimetric aptasensor for the detection of chloramphenicol in honey based on cage Au@AuNPs and cascade hybridization chain reaction

A plasma colorimetric aptasensor was developed for rapid determination of chloramphenicol (CAP) in honey on site. Herein, cage gold shell@core nanoparticles (Au@AuNPs) were synthesized to enhance signal response and broaden the linear range. In addition, aptamer-based cascade hybridization chain reaction (cHCR), consisting of HP1, HP2, HP3, and HP4, was also designed for signal amplification and specific analysis. In this assay, HP1 and HP4 were immobilized on the surface of cage Au@AuNPs. In the presence of CAP, cHCR was triggered, and frond-like DNA products were formed, which made the distance among the cage Au@AuNPs closer and the system color changed from red to deep purple. Qualitative and quantitative analysis were carried out according to color changes and UV-Vis spectra. Under the optimized conditions, the wavelength of UV-Vis absorption peak exhibited a good linear relationship with CAP concentration in the range of 5.0 to 500 nmol/L with the detection limit of 1.2 nmol/L (S/N = 3). This aptasensor also showed good specificity for CAP detection compared with other antibiotics similar to the target analyte. Furthermore, the colorimetric aptasensor was successfully applied to the detection of CAP in honey with recoveries of 88.0-107.6%. This cHCR-based aptasensing for CAP possesses high sensitivity, good selectivity, low cost and excellent stability, and could be extended to detect a wide variety of other small molecular analytes, nucleic acids or proteins. Therefore, the versatile method might become a potential alternative tool in food analysis and environmental monitoring.

Naturalized Escherichia coli in Wastewater and the Co-evolution of Bacterial Resistance to Water Treatment and Antibiotics

Antibiotic resistance represents one of the most pressing concerns facing public health today. While the current antibiotic resistance crisis has been driven primarily by the anthropogenic overuse of antibiotics in human and animal health, recent efforts have revealed several important environmental dimensions underlying this public health issue. Antibiotic resistant (AR) microbes, AR genes, and antibiotics have all been found widespread in natural environments, reflecting the ancient origins of this phenomenon. In addition, modern societal advancements in sanitation engineering (i.e., sewage treatment) have also contributed to the dissemination of resistance, and concerningly, may also be promoting the evolution of resistance to water treatment. This is reflected in the recent characterization of naturalized wastewater strains of Escherichia coli-strains that appear to be adapted to live in wastewater (and meat packing plants). These strains carry a plethora of stress-resistance genes against common treatment processes, such as chlorination, heat, UV light, and advanced oxidation, mechanisms which potentially facilitate their survival during sewage treatment. These strains also carry an abundance of common antibiotic resistance genes, and evidence suggests that resistance to some antibiotics is linked to resistance to treatment (e.g., tetracycline resistance and chlorine resistance). As such, these naturalized E. coli populations may be co-evolving resistance against both antibiotics and water treatment. Recently, extraintestinal pathogenic strains of E. coli (ExPEC) have also been shown to exhibit phenotypic resistance to water treatment, seemingly associated with the presence of various shared genetic elements with naturalized wastewater E. coli. Consequently, some pathogenic microbes may also be evolving resistance to the two most important public health interventions for controlling infectious disease in modern society-antibiotic therapy and water treatment.

Possible Acquisition of ESBL-mediated Antimicrobial Resistance by Farmers from Aquatic Reservoir used for Bathing and Cleaning of Water Buffalos (Bubalus bubalis) with Intestinal Carriage of ESBL Producing Escherichia coli

Little information is available on the risk of human subjects for acquisition of antimicrobial resistance (AMR) from aquatic environment other than those treated with antimicrobials for aquaculture. Carriage of extended-spectrum beta-lactamase (ESBL) and carbapenemase categories of AMR by enteric bacteria in livestock have been frequently reported. Dissemination of these categories of AMR to the environment thus poses a threat for their transmission to farmers engaged in livestock care posing a severe public health hazard. A study on the prevalence of ESBL- and carbapenemase-mediated AMR among Escherichia coli isolated from earth pond environment used for bathing and cleaning of buffalos (Bubalus bubalis) and from human subjects engaged in such activity revealed isolation rate of ESBL positivity to be higher in human subjects engaged in washing and bathing of buffalos (37.5%) compared to those without engagement in such activities (20.7%) with CTX-M type ESBL, a group of class A ESBL, as the predominant molecular type (97.4%). While no carbapenemase positivity could be detected among E. coli isolated from pond environment or buffalos, small percentage of carbapenemase could be detected among the E. coli isolated from human subjects although the risk was not higher than those not associated with bathing and cleaning of buffalos. Bathing and cleaning of buffalos could potentially facilitate transmission of ESBL resistance from livestock to human subjects in pond environment.

Silver Nanoparticles Targeting the Drug Resistance Problem of Streptococcus dysgalactiae: Susceptibility to Antibiotics and Efflux Effect

The present work is a continuation of our translational research focusing on the use of silver nanoparticles (AgNPs) to solve the global problem of antibiotic resistance. In vivo fieldwork was done with 300 breeding farm cows with serous mastitis. Ex vivo assays revealed that after cow treatment with the antibiotic drug Spectromast LC^TM, S.dysgalactiae susceptibility to 31 antibiotics dropped by 22.9%, but after treatment with Argovit-C^TM AgNPs, it was raised by 13.1%. This was explained by the fact that the percentage of isolates with an efflux effect after Spectromast LC treatment resulted in an 8% increase, while Argovit-C-treatment caused a 19% decrease. The similarity of these results to our previous results on S. aureus isolates from mastitis cows treated with the antibiotic drug Lactobay and Argovit-C^TM AgNPs was shown. So, mastitis treatments with Argovit-C^TM AgNPs can partially return the activity of antibiotics towards S.dysgalactiae and S. aureus, while, in contrast, treatments with antibiotic drugs such as Spectromast LC and Lactobay enhance bacterial resistance to antibiotics. The results of this work strengthen the hope that in the future the use of AgNPs as efflux pump inhibitors will recover the activity of antibiotics, and thus will preserve the wide spectrum of antibiotics on the market.

Following the route of veterinary antibiotics tiamulin and tilmicosin from livestock farms to agricultural soils

Veterinary antibiotics (VAs) are not completely metabolized in the animal body. Hence, when animal excretes are used as soil manures, VA residues are dispersed with potential implications for environmental quality and human health. We studied the persistence of tiamulin (TIA) and tilmicosin (TLM) along their route from pig administration to fecal excretion and to agricultural soils. TLM was detected in feces at levels folds higher (4.27-749.6 μg g^-1) than TIA (0.55-5.99 μg g^-1). Different administration regimes (feed or water) showed different excretion patterns and residual levels for TIA and TLM, respectively. TIA and TLM (0.5, 5 and 50 μg g^-1) dissipated gradually from feces when stored at ambient conditions (DT₅₀ 5.85-35.9 and 23.5-49.8 days respectively), while they persisted longer during anaerobic digestion (DT₉₀ >365 days) with biomethanation being adversely affected at VA levels > 5 μg g^-1. When applied directly in soils, TLM was more persistent than TIA with soil fumigation extending their persistence suggesting microbial degradation, while soil application through feces increased their persistence, probably due to increased sorption to the fecal organic matter. The use of TIA- and TLM-contaminated feces as manures is expected to lead to VAs dispersal with unexplored consequences for the environment and human health.

Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives

The emergence of resistance against common antibiotics in the gut microbiota is a major issue for both human and livestock health. This highlights the need for understanding the impact of such application on the reservoir of antibiotic resistance genes in poultry gut and devising means to circumvent the potential resistome expansion. Phytogenic feed additives (PFAs) are potential natural alternative to antibiotic to improve animal health and performance, supposedly via positively affecting the gut microbial ecosystem, but there is little systematic information available. In this time-course study, we applied a shotgun meta-transcriptomics approach to investigate the impact of a PFA product as well as the commonly used antibiotic, zinc bacitracin either at AGP concentration or therapeutic concentration on the gut microbiome and resistome of broiler chickens raised for 35 days. Over the course of the trial, PFA treatments increased the abundance of Firmicutes such as Lactobacillus and resulted in a lower abundance of Escherichia, while the latter group increased significantly in the feces of chickens that received either AGP or AB doses of bacitracin. Tetracycline resistance and aminoglycoside resistance were the predominant antibiotic resistance gene (ARG) classes found, regardless of the treatment. PFA application resulted in a decrease in abundance of ARGs compared to those in the control group and other antibiotic treatment groups. In summary, the findings from this study demonstrate the potential of phytogenic feed additives could be an alternative to antibiotics in poultry farming, with the added benefit of counteracting antimicrobial resistance development.

Effect of Bacillus species–fermented products and essential oils on growth performance, gut morphology, cecal short-chain fatty acid levels, and microbiota community in broilers

In this study, the effects of Bacillus species–fermented products (synbiotics [SYNs]) and essential oils (EOs) on the growth performance, gut morphology, cecal short-chain fatty acid (SCFA) levels, and microbiota of broilers were investigated. A total of 180 one-day-old unsexed broiler chicks (Ross 308) were randomly assigned to 5 dietary treatments as follows: basal diet (control group), basal diet plus enramycin (10 mg/kg; A group), basal diet plus SYNs (3 × 10¹¹ CFU spore/kg of feed; SYN group), basal diet plus EOs (100 mg/kg; EO group), and basal diet plus SYNs and EOs (SYN + EO group), with 6 replicate cages per treatment group and 6 birds per cage. The SYN+EO treatment resulted in a higher (P = 0.003) average daily gain at 1 to 14 d of age than did the control and EO treatments. SYNs had a significant effect on the average daily gain at 1 to 14 d (P < 0.001) and 1 to 35 d (P = 0.045) of age. EOs had a significant effect on the villus height of the duodenum (P = 0.015) and jejunum (P = 0.027). Superoxide dismutase (SOD) and mucin 2 (MUC2) mRNA expression in the duodenum, jejunum, and ileum in the SYN + EO group was higher (P < 0.001) than that in any of the other groups. The SYN+EO treatment resulted in higher (P < 0.001) 2-methylbutyric acid and 3-methylbutyric acid levels in the cecal digesta of the broilers than did the control treatment. Cecal species evenness in the SYN + EO group was higher (P < 0.001) than that in the control group. The abundance of the phylum Firmicutes in the cecal digesta of the broilers was higher (P < 0.001) in the SYN+EO group than in the control group. SYNs had a significant effect (P < 0.001) on the abundance of the genus Lactobacillus in the cecal digesta of the broilers. The abundance of the genus Lactobacillus was positively associated with 2-methylbutyric acid and 3-methylbutyric acid levels. The 2-methylbutyric acid and 3-methylbutyric acid levels were positively correlated with the villus height of the duodenum and ileum. These results suggest that simultaneous supplementation with SYNs and EOs can increase the average daily gain, improve gut health–associated gene expression, increase SCFA levels, and modulate the gut microbiota composition of broilers.

Fattening Pigs Are a Reservoir of Florfenicol-Resistant Enterococci Harboring Oxazolidinone Resistance Genes

ABSTRACT

The use of florfenicol in farm animals may select enterococci that carry resistance genes that confer resistance to linezolid, a critically important oxazolidinone antibiotic used in human medicine. This cross-sectional study aimed to assess the occurrence of oxazolidinone resistance genes in florfenicol-resistant enterococci from fattening pigs in Switzerland and to characterize a subset of the isolates using whole genome sequencing. A total of 31 florfenicol-resistant enterococcal isolates were obtained from 27 (5%) of 565 cecal samples of fattening pigs from seven (11%) of 62 farms. Screening by PCR revealed the presence of cfr-poxtA in 1 of 31, optrA in 15 of 31, and poxtA in 15 of 31 enterococcal isolates. One randomly selected isolate per PCR-positive Enterococcus species and positive farm was selected for further analysis (n = 10). In nine of the 10 isolates, the presence of oxazolidinone resistance genes did not result in phenotypic resistance. Whole genome sequencing analysis showed the presence of E. faecalis (n = 1), E. faecium (n = 1), and E. hirae (n = 1), harboring optrA18, optrA7, and a new optrA allele, respectively. E. durans (n = 1), E. faecium (n = 4), and E. hirae (n = 1) carried the wild-type poxtA, and E. faecalis (n = 1) coharbored cfr(D) and poxtA2. Except for optrA7, all oxazolidinone resistance genes were found on plasmids. Multilocus sequence typing analysis identified E. faecalis ST19 and ST376, E. faecium ST80 belonging to hospital-adapted clade A1, and E. faecium ST21, ST55, ST269, and ST416 belonging to clade A2, which represents human commensals and animal strains. The occurrence of cfr(D), optrA, and poxtA in various porcine Enterococcus spp. demonstrates the spread of oxazolidinone resistance genes among enterococci from fattening pigs in Switzerland. The presence in one sample of poxtA-carrying E. faecium ST80 emphasizes the potential risk to human health through dissemination of strains carrying oxazolidinone resistance genes into the food chain.

HIGHLIGHTS

Current Knowledge on the Bioavailability of Thymol as a Feed Additive in Humans and Animals with a Focus on Rabbit Metabolic Processes

Simple Summary

This review provides general information on the possible health benefits in animals and humans of herbal additives, particularly thymol, whose phenolic group is responsible for the neutralisation of free radicals, and information concerning its detection through body action, bioavailability and mechanisms in rabbits. Plants containing thymol have been used in traditional medicine for the treatment of various diseases, such as cardiovascular diseases, cancer and diabetes. Although a great number of in vitro studies of cardiovascular and cancer diseases are available, in vivo studies that confirm these findings have not been sufficiently reported. To determine the beneficial dose, further clinical studies are necessary, with preclinical comprehensive research on animal models.

Abstract

The aim of this review is to describe the therapeutic effect of thymol on various human diseases, followed by its bioavailability in humans and animals. Based on our knowledge from the current literature, after thymol addition, thymol metabolites—mostly thymol sulphate and glucuronide—are detected in the plasma and urine of humans and in the plasma, intestinal content, faeces and tissues in rats, pigs, chickens, horses and rabbits after enzymatic cleavage. In rabbits, thymol absorption from the gastrointestinal tract, its distribution within the organism, its accumulation in tissues and its excretion from the organism have been described in detail. It is necessary and important for these studies to suggest the appropriate dose needed to achieve the required health benefits not only for animals but also for humans. Information from this review concerning the mode of action of thymol in animal organisms could also be applied to human medicine and may help in the utilisation of herbal medicine in humans and in veterinary healthcare. This review summarises the important aspects of thymol’s effects on health and its bioavailability in organisms, particularly in rabbits. In future, herbal-based drugs must be extensively investigated in terms of their mode of action, efficiency of administration and clinical effect.

Antibiotics Resistance in Escherichia coli Isolated from Livestock in the Emirate of Abu Dhabi, UAE, 2014–2019

Escherichia coli (E. coli) is a zoonotic pathogen that showed growing resistance to antibiotics. No descriptive analysis highlights the threat of antimicrobial-resistant (AMR) of E. coli among livestock in the United Arab Emirates (UAE). Herein, we conducted phenotypic and genotypic resistance studies on E. coli isolates from livestock samples in the Emirate of Abu Dhabi based on routine diagnosis between the periods 2014–2019. Bacterial culture and disk diffusion methods were used for bacterial isolation and phenotypic resistance analysis. Resistance mechanism was studied by PCR targeting the most commonly resistance genes: ampicillin (blaSHV, blaCMY, and blaTEM-1B), tetracyclines (tetA and tetB), co-trimoxazole [sulfamethoxazole (sul1, sul2, and sul3) + trimethoprim (dfrA1 and dfrA17)], aminoglycosides [aph(3'')-Ia, aph(6)-Id, and aac(3)-IV], and fluoroquinolones (qnrA and aac(6’)-Ib-cr). Analysis of 165 E. coli isolates showed resistant to ampicillin, tetracycline, co-trimoxazole, gentamicin, and enrofloxacin by 157/165 (95.4%), 154/165 (93.6%), 141/165 (86%), 139/165 (85%), and 135/165 (82.7%), respectively. Predominant resistance gene/s detected by PCR were blaCMY (119/160, 72%) and blaTEM-1B (154/160, 96.3%) for ampicillin; tetA (162/164, 98.8%) and tetB (112/164, 68.3%) for tetracyclines; sul2 (156/164, 95%), sul3 (138/164, 84%), and dfra17 (74/164, 44.5%) for co-trimoxazole; aph(3'')-Ia (134/164, 82.1%) and aph(6)-Id (161/164, 98.2%) for aminoglycosides; and aac(6’)-Ib-cr (61/61, 100%) for enrofloxacin. Both phenotypic and genotypic analyses revealed that all E. coli isolates were multidrug-resistant (resistance to 3, 4, and 5 antibiotics classes by 3.6%, 57.6%, and 38.8%, respectively) carrying one or more resistance gene/s for the same antibiotic. PCR profiling confirmed the presence of resistance genes corresponding to their antibiotic profile. Results of the study will highlight the knowledge based on E. coli AMR related to livestock in UAE that may call for interventions.

Pattern of Antibiotic Consumption in Two Italian Production Chains Differing by the Endemic Status for Porcine Reproductive and Respiratory Syndrome

The aim of this case study was to quantify antibiotic (AB) use in Italian weaning (W) and fattening (F) units differentiated for porcine reproductive and respiratory syndrome (PRRS) occurrence. Farms were classified as either PRRS negative (–) or PRRS positive (+) based on the circulation of the virus among the animals. In all the farms, the modified live PRRS virus (PRRSV) vaccine was provided to all the animals. In the PRRS– farms, the level of circulating antibodies was low, and the disease, in its clinical form, did not occur. In the PRRS+ farms, the level of circulating antibodies against the virus was high, and the disease was recurrent. Data regarding AB consumption were collected from 2017 to 2020, and the active compounds (ACs) were expressed as milligrams of AC/total kilogram of body weight (BW) produced. Each AC was classified into one of four categories according to the European Medicines Agency classification of ABs for prudent and responsible use in animals: Avoid, Restrict, Caution, and Prudence. Data regarding the ACs in each category were analyzed using a linear model that included production phase, PRRS status, and their interaction as factors. Performance parameters, average age of the pigs at the end of each phase, daily live weight gain, feed-to-gain ratio, total losses, cost index, and medication costs were significantly influenced by the PRRS chain. The use of class B ABs was not affected by production phase or PRRS status. Conversely, for class C ABs, interaction between the two factors (p = 0.02) was observed; W/PRRS+ and F/PRRS+ showed the greatest AB use for this class (p = 0.003). For class D ABs, the interaction was significant (p = 0.01); class C and D ABs were used more in the weaning (p = 0.07) than in the fattening phase (p = 0.003). For the weaning phase, the use of class C and D ABs was greater in the PRRS+ than in the PRRS– chain (p < 0.01). In conclusion, PRRS status affected the growth of pigs and economic performance. Moreover, PRRS status significantly influenced the use of ABs during all the growing periods with the greatest impact being on the weaning phase.

Prevalence and characterisation of antimicrobial resistance genes and class 1 and 2 integrons in multiresistant Escherichia coli isolated from poultry production

A global increase in the populations of drug resistant bacteria exerts negative effects on animal production and human health. Our study has been focused on the assessment of resistance determinants in relation to phenotypic resistance of the 74 commensal E. coli isolates present in different ecological environments. The samples were collected from poultry litter, feces, and neck skin. Among the microorganisms isolated from the poultry litter (group A), the highest resistance was noted against AMP and DOX (100%). In the E. coli extracts from the cloacal swabs (group B), the highest resistance was observed against AMP (100%) and CIP (92%). The meat samples (group C) were characterized by resistance to AMP (100%) and STX (94.7%). Genes encoding resistance to β-lactams (bla_TEM, bla_CTX-M), fluoroquinolones (qnrA, qnrB, qnrS), aminoglycosides (strA-strB, aphA1, aac(3)-II), sulfonamides (sul1, sul2, sul3), trimethoprim (dfr1, dfr5, dfr7/17) and tetracyclines (tetA, tetB) were detected in the studied bacterial isolates. The presence of class 1 and 2 integrons was confirmed in 75% of the MDR E. coli isolates (plasmid DNA), of which 60% contained class 1 integrons, 15% contained class 2 integrons, and 11.7% carried integrons of both classes. Thus, it may be concluded that integrons are the common mediators of antimicrobial resistance among commensal multidrug resistant Escherichia coli at important stages of poultry production.

Extended-Spectrum ß-Lactamase-Producing Escherichia coli Among Humans, Beef Cattle, and Abattoir Environments in Nigeria

Introduction

Beef cattle, one of the food-producing animals, are linked to humans through a shared environment and the food chain as a major source of animal protein. Antimicrobial drugs are readily accessible for use in food animal production in Nigeria. Beef cattle and abattoir environments harbor pathogenic bacteria such as Escherichia coli (E. coli) which have developed resistance to antimicrobial agents used for prophylaxis or treatment. This study investigated the zoonotic transmission of extended-spectrum beta-lactamase-producing E. coli (ESBL-EC) among humans, beef cattle, and abattoir environments in Abuja and Lagos, Nigeria.

Materials and Methods

We conducted a cross-sectional study among abattoir workers, beef cattle, and abattoir environments in Abuja and Lagos. Stool, cecal, and environmental samples were collected from apparently healthy workers, slaughtered cattle, and abattoir environments from May to December 2020. Data were collected electronically using open data kit app installed on a mobile phone. Antimicrobial susceptibility patterns were determined using the Kirby–Bauer disk diffusion method against a panel of 16 antimicrobial agents. Phenotypic and genotypic characterizations of the isolates were conducted. Data were analyzed with descriptive statistics.

Results

From 21.7% (n = 97) of 448 samples, ESBL-EC were isolated and further characterized. Prevalence of ESBL-EC was highest in cattle (45.4%; n = 44), abattoir workers (41.2%; n = 40), and abattoir environment (13.4%; n = 13). Whole-genome sequencing of ESBL-EC showed dissemination of blaCTX-M-15 (90.7%; n = 88); blaCTX-M-14 (5.2%; n = 5); and blaCTX-M-55 (2.1%; n = 2) genes. The blaCTX-M-15 coexisted with blaCTX-M-14 and blaTEM-1 genes in 2.1% (n = 2) and 39.2% (n = 38) of the isolates, respectively. The presence of blaCTX-M-14 and blaCTX-M-15 genes was significantly associated with isolates originating from abattoir workers when compared with beef cattle isolates (p = 0.05; p < 0.01). The most prevalent sequence types (ST) were ST10 (n = 11), ST215 (n = 7), ST4684 (n = 7), and ST2178 (n = 6). ESBL-EC strain (ST205/B1) harbored mcr-1.1 and blaCTX-M15 and was isolated from a worker at Lagos abattoir. In 91 ESBL-EC isolates, 219 mobile genetic elements (MGEs) harbored resistance genes out of which β-lactam genes were carried on 64 different MGEs. Isolates showed equal distribution of insertion sequences and miniature inverted repeats although only a few composite transposons were detected (humans n = 12; cattle n = 9; environment n = 4). Two isolates of human and cattle origin (ST46/A) harboring ESBL genes and carried by MGEs were clonally related.

Conclusions

This is the first report of blaCTX-M-55 gene in humans and cattle in Nigeria. This study demonstrates the horizontal transfer of ESBL genes possibly by MGEs and buttresses the importance of genomic surveillance. Healthcare workers should be sensitized that people working closely with cattle or in abattoir environments are a high-risk group for fecal carriage of ESBL-EC when compared with the general population.

Anti-Salmonella and Antibiofilm Potency of Salvia officinalis L. Essential Oil against Antibiotic-Resistant Salmonella enterica

Raw milk is a significant vehicle for the transmission of different infections. In the present study, we focused on Salmonella enterica from raw milk and its resistance to various antibacterial drugs. Furthermore, we have investigated the antimicrobial and antibiofilm effects of essential oil (EO) obtained from Salvia officinalis L. leaves that were collected from the Aljouf region, Saudi Arabia, against S. enterica. One-dozen strains of S. enterica were found in a batch of a hundred milk samples, and those S. enterica strains were shown to be resistant to several antibiotics, particularly the β-lactam group of antimicrobial drugs. Against multidrug-resistant S. enterica, the inhibitory zones for EO from S. officinalis leaves were found to be 21 mm in diameter. S. officinalis EO at 5% concentration showed a remarkable in vitro inhibitory activity toward the biofilm growth of different S. enterica isolates. Analysis of EO by GC–MS identified 21 distinct components, accounting for 89.94% of the total oil component. The most prominent compounds were 1,8-cineole (39.18%), β-caryophyllene (12.8%), and α--terpineol (10.3%). Taken together, our results unequivocally confirm that the S. officinalis EOs exert numerous bioactivities. Thus, the well-deserved attention on S. officinalis EO usage as a food preservative and adjunctive remedy for bacterial food-borne diseases is justified.

Exposure of Buffalo Milkers to Pathogenic Bacteria and Characterization of Isolated Methicillin-Resistant Staphylococcus spp

The research was focused on the surveillance of the exposure of buffalo milkers in contact with both animals and potentially contaminated equipment, pointing attention on the diffusion of antibiotic-resistant Staphylococcus spp. The monitoring was performed for 12 months, allowing the collection of 600 raw milk and buffalo udder surface samples, 192 milking lanes, 400 milking clusters, 160 personal protective equipment (PPEs) and electronic devices surface samples in contact with the workers of four milking parlors located in Southern Italy. The analysis of the milk samples evidenced the highest exposure to the bacteria considered (and mainly to S. aureus) from late winter-spring seasons onward. The possible risk arising from buffalo udder, milking clusters, and lines were instead considered rather stable along the entire period of sampling. The PPEs turned out to be a source of contamination for milkers mainly during the spring and summer periods. The analysis for oxacillin/methicillin resistance revealed in all the farms enrolled an overall amount of 37.5% of Staphylococci strains (belonging to S. aureus, S. haemolyticus, S. pseudintermedius, S. chromogenes species) resistant both to methicillin and oxacillin. The investigation demonstrated that the potential transfer of pathogenic bacteria to humans would have a better chance to occur at milk resumption time (since late winter-spring onward) when the number of animals to be milked is greater and the activity in the milking parlor is more challenging. At the same time, the findings seem to point out that the potential risk may be worsened by a significant presence of oxacillin/methicillin-resistant Staphylococci, potentially resulting from irrational use of antibiotics.

Antimicrobial Resistance Patterns of Fecal Escherichia coli in Wildlife, Urban Wildlife, and Livestock in the Eastern Region of Sri Lanka, and Differences between Carnivores, Omnivores, and Herbivores

Antimicrobial resistance (AMR) is a major public health concern. We identified AMR in fecal Escherichia coli of wildlife (WL), urban wildlife (UWL), and livestock in the eastern region in Sri Lanka and compared the prevalence of AMR bacteria from carnivores, omnivores, and herbivores. Fecal samples were collected from 165 animals: WL (n=47), UWL (n=54), and livestock (n=64). Esherichia coli was cultured from 129 samples, with isolation rates of 76% from WL (36/47), 70% from UWL (45/54), and 75% from livestock (48/64). Testing E. coli isolates against 12 antimicrobials using the disk diffusion method revealed that the proportions of E. coli isolates resistant to at least one antimicrobial were WL 52.7%, UWL 20%, and livestock 52%. Multidrug-resistant E. coli isolates were detected in WL, UWL, and livestock. Overall, the prevalence of E. coli isolates with AMR was significantly lower in UWL compared with WL and livestock. The number of isolates showed AMR was significantly higher in E. coli from carnivores than in isolates from omnivores and in herbivores. We conclude that AMR E. coli in Sri Lanka is widespread in WL, UWL, and livestock. The higher incidence of AMR bacteria in carnivores compared with herbivores and omnivores suggest that the mechanisms of spread of AMR may vary among wild animals, which requires further investigation.

Prevalence and Phylodiversity of ESBL-Producing Coliforms Isolated from Ruminant Mastitis in Nigeria

The public health threat posed by Extended-spectrum beta-lactamase producing E. coli (ESBL-EC) in food animal production systems has attracted global attention. Data on the prevalence, diversity and genetic characteristics of ESBL-producing coliforms are key to advocacy on promoting responsible antimicrobial stewardship and proper planning of control strategies. The coliforms were isolated from 1052 milk samples of 160 cows, 103 ewes and 103 does with mastitis in Plateau State, Nigeria and analysed for ESBL production by phenotypic, biochemical, antimicrobial sensitivity and genetic characterization. The percentage of occurrence of clinical mastitis in cows, ewes, and does were 0.2 %, 0 %, 1.5 % respectively, while the percentage occur-rence of subclinical mastitis in ruminants were 18.1 %, 28.2 % and 38.3 % respectively. From the 677 isolates, 31.3 % (n = 212) were ESBL producing coliforms, with a prevalence of 48.6 %, 18.4 %, 12.7 %, 8.9 %, 5.7 %, 3.8 % and 1.9 % for E. coli, K. pneumoniae, C. freundii, K. aerogenes, S. marcescens, K. oxytoca and E. cloacae, respectively. The genetic characterization revealed a higher prevalence of bla CTX-M than bla TEM in the samples analysed (24.39 % vs. 12.19 %). High pairwise identity was observed among the bla CTX-M and bla TEM gene sequences obtained in this study, but they displayed high phylodiversity with sequences from ruminants and humans from other climes. The bla SHV gene was not detected. Multidrug resistances especially to the commonly used antimicrobials; ofloxacin, gentamycin and streptomycin in veterinary practice in Nigeria were observed. This has public health implications considering the fact that consumption of raw unpasteurized milk is a common practice in some cultures in Nigeria. Such practise will facilitate the transfer of multidrug resistant coliforms to humans resulting in the complications of treatment outcomes. To the best of our knowledge this is the first genetic characterization of ESBL-producing agents from ruminant mastitis in Nigeria.

Detection of fluoroquinolone and sulfonamide residues in poultry eggs in Kunming city, southwest China

Antibiotic residues contained in poultry eggs pose threat to human health. However, the classes and concentrations of antibiotics in poultry egg in southwestern China is unknown due to insufficient monitoring and research. A total of 513 egg samples were collected from supermarkets and farm markets in Kunming city in 2020 and the levels of 7 antibiotics were analyzed using ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method. The linear correlation coefficients were above 0.990 for all antibiotics tested. The limits of detection and limits of quantification in poultry eggs were 0.002 to 0.010 μg/g and 0.007 to 0.033 μg/g, respectively. The average recoveries of the 7 analytes from poultry egg samples were 80.00 to 128.01%, with relative standard deviations of less than 13.97%. A total of 93 (18.13%) samples tested positive for antibiotics, with the highest concentration being 2.48 μg/g. The concentration range of ofloxacin, danofloxacin, difloxacin, sulfadimethoxine, sulfamonomethoxine, sulfamethoxypyridazine, and sulfamethoxazole in poultry eggs was 0.01 to 0.37 μg/g, 0.06 to 0.48 μg/g, 0.05 to 0.29 μg/g, 0.03 to 0.16 μg/g, 0.06 to 1.00 μg/g, 0.05 to 0.37, and 0.07 to 2.48 μg/g, respectively. Sulfamonomethoxine was detected from hen eggs with the highest concentration level at 1.00 μg/g. Sulfamethoxazole was detected with the highest concentration level from both duck and quail eggs, at 1.87 and 2.48 μg/g, respectively. The antibiotic with the highest residue level in pheasant eggs was danofloxacin, which was 0.37 μg/g. Sulfamethoxypyridazine was identified in 30 samples with the highest positive rate of 5.85%, sulfadimethoxine was identified in 3 samples with the lowest positive rate of 0.58%. We observed that 7 targeted antibiotic residues in quail eggs and 3 targeted antibiotic residues in pheasant eggs. We also found that there were antibiotic residues in free-range hen eggs and the concentration was not low. The antibiotic with the highest residue level in free-range eggs was sulfamonomethoxine, which was 1.00 μg/g. These findings suggest that continual antibiotic residue monitoring of poultry eggs is essential in China.

Recent Trends and Advances of Co3O4 Nanoparticles in Environmental Remediation of Bacteria in Wastewater

Antibiotic resistance is a formidable global threat. Wastewater is a contributing factor to the prevalence of antibiotic-resistant bacteria and genes in the environment. There is increased interest evident from research trends in exploring nanoparticles for the remediation of antibiotic-resistant bacteria. Cobalt oxide (Co3O4) nanoparticles have various technological, biomedical, and environmental applications. Beyond the environmental remediation applications of degradation or adsorption of dyes and organic pollutants, there is emerging research interest in the environmental remediation potential of Co3O4 nanoparticles and its nanocomposites on antibiotic-resistant and/or pathogenic bacteria. This review focuses on the recent trends and advances in remediation using Co3O4 nanoparticles and its nanocomposites on antibiotic-resistant or pathogenic bacteria from wastewater. Additionally, challenges and future directions that need to be addressed are discussed.

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

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

A Survey on Knowledge, Attitude, and Practices of Large-Animal Farmers towards Antimicrobial Use, Resistance, and Residues in Mymensingh Division of Bangladesh

The widespread and indiscriminate use of antimicrobials in food animals is a key contributor to antimicrobial resistance and antimicrobial residue, which have become a growing public and animal health concern in developing countries such as Bangladesh. This study was aimed to assess the knowledge, attitude, and practices (KAP) of large-animal farmers towards antimicrobial use (AMU), antimicrobial resistance (AMR), and antimicrobial residue (AR) with their correlation. A cross-sectional survey was conducted with a structured and pretested questionnaire in the Mymensingh division of Bangladesh. A total of 212 large-animal farmers (dairy, beef fattening, buffalo, sheep, and goat farmers) were surveyed. Results showed that most of the farmers are male (85.8%) and belong to the 18–30 age group (37.3%). About 20.3% had no formal education, and nearly half of the participants (48.1%) received training regarding antibiotic use and resistance. Penicillin is the most common class of antibiotic used (61.8%) in the study area, followed by other antimicrobials. Only 37.7% of the farmers used antimicrobials on the recommendation of their veterinarian. Overall, 41.5%, 42.5%, and 21.7% of farmers possess adequate knowledge and a satisfactory attitude and perform desirable practices, respectively. Farmers in the 31–40 age group have adequate knowledge, attitude, and ability to implement desired practices compared to farmers in the 18–30 age group. Farmers having a graduate or post-graduate degree scored better in relation to knowledge, attitude, and practice than other farmers. Analysis revealed that farmers who received training on AMU and AMR had 10.014 times (OR = 10.014, 95% CIs: 5.252–19.094), 9.409 times (OR = 9.409, 95% CIs: 4.972–17.806), and 25.994 times (OR = 25.994, 95% CIs: 7.73–87.414) better knowledge, attitude, and performance, respectively, compared to their counterparts. A significant proportion of farmers (97.2%) dispose of leftover antibiotics inappropriately. The findings of the present study will be used to intervene in the education and training of the farmers, which will help to limit the indiscriminate and irrational use of antimicrobials, leading to reducing the chances of developing AMR.

The Intestinal Microbiota May Be a Potential Theranostic Tool for Personalized Medicine

The human intestine is colonized by a huge number of microorganisms from the moment of birth. This set of microorganisms found throughout the human body, is called the microbiota; the microbiome indicates the totality of genes that the microbiota can express, i.e., its genetic heritage. Thus, microbiota participates in and influences the proper functioning of the organism. The microbiota is unique for each person; it differs in the types of microorganisms it contains, the number of each microorganism, and the ratio between them, but mainly it changes over time and under the influence of many factors. Therefore, the correct functioning of the human body depends not only on the expression of its genes but also on the expression of the genes of the microorganisms it coexists with. This fact makes clear the enormous interest of community science in studying the relationship of the human microbiota with human health and the incidence of disease. The microbiota is like a unique personalized “mold” for each person; it differs quantitatively and qualitatively for the microorganisms it contains together with the relationship between them, and it changes over time and under the influence of many factors. We are attempting to modulate the microbial components in the human intestinal microbiota over time to provide positive feedback on the health of the host, from intestinal diseases to cancer. These interventions to modulate the intestinal microbiota as well as to identify the relative microbiome (genetic analysis) can range from dietary (with adjuvant prebiotics or probiotics) to fecal transplantation. This article researches the recent advances in these strategies by exploring their advantages and limitations. Furthermore, we aim to understand the relationship between intestinal dysbiosis and pathologies, through the research of resident microbiota, that would allow the personalization of the therapeutic antibiotic strategy.

Lagoon, Anaerobic Digestion, and Composting of Animal Manure Treatments Impact on Tetracycline Resistance Genes

Increased demand for animal protein is met by increased food animal production resulting in large quantities of manure. Animal producers, therefore, need sustainable agricultural practices to protect environmental health. Large quantities of antimicrobials are used in commercial food animal production. Consequently, antimicrobial-resistant bacteria and the resistance genes emerge and are excreted through feces. Manure management is essential for the safe disposal of animal waste. Lagoons, with or without covers, and anaerobic digesters, with the primary purpose of methane production, and composting, with the primary purpose of producing organic fertilizer, are widely used methods of manure treatment. We reviewed manure management practices and their impact on tetracycline resistance genes. Lagoons are maintained at ambient temperatures; especially uncovered lagoons are the least effective in removing tetracycline resistance genes. However, some modifications can improve the performance of lagoons: sequential use of uncovered lagoons and the use of covered lagoons resulted in a one-log reduction, while post-treatments such as biofiltration following covered lagoon treatment resulted in 3.4 log reduction. Mesophilic digestion of animal manure did not have any significant effect; only a 0.7 log reduction in tet(A) was observed in one study. While thermophilic anaerobic digesters are effective, if properly operated, they are expensive for animal producers. Aerobic thermophilic composting is a promising technology if optimized with its economic benefits. Composting of raw animal manure can result in up to a 2.5 log reduction, and postdigestion composting can reduce tetracycline resistance gene concentration by >80%. In general, manure management was not designed to mitigate antimicrobial resistance; future research is needed to optimize the economic benefits of biogas or organic fertilizer on the one hand and for the mitigation of foodborne pathogens and antimicrobial resistance on the other.