Pathotype and antibiotic resistance gene distributions of Escherichia coli isolates from broiler chickens raised on antimicrobial-supplemented diets

Prevalence, antimicrobial resistance and detection of virulence genes of Escherichia coli and Salmonella spp. isolated from white-lipped peccaries and collared peccaries

Salmonella spp. and Escherichia coli are implicated in human and animal infections and require antimicrobial treatment in many situations. Faecal samples of healthy white-lipped peccaries (Pecari tajacu) (n = 30) and collared peccaries (Tayassu pecari ) (n = 60) obtained in three farms located in the Midwest Brazil. The antimicrobial profiles of commensal E. coli from P. tajacu and T. pecari from commercial herds in Brazil were isolated and analyzed and virulence genes were detected. Among 90 healthy animals, no Salmonella spp. were isolated. However, 30 samples (27%) tested positive for E. coli, with 18 isolates from P. tajacu and 12 from T. pecari, representing frequencies of 58.0% and 38.7%, respectively. Additionally, other Enterobacteriaceae family bacteria were detected but not included in this analysis. However, individual samples from 30 animals tested positive for E. coli, of which 16 were isolated from P. tajacu presenting multidrug resistance and six were isolated from T. pecari presenting a similar pattern. The E. coli virulence genes detected were papC (pilus-associated pyelonephritis) in five isolates, tsh (temperature-sensitive hemagglutinin) in one isolate, and eae (enteric attachment and effacement) in one isolate. The serum resistance gene, iss (increased serum survival), was detected in four isolates. An association between these genes and the presence of hemolysin was also observed in one isolate. Thus, T. pecari and P. tajacu are potential reservoirs of pathogenic and multidrug-resistant and E. coli. Faecal E. coli of healthy P. tajacu and T. pecari could act as a possible reservoir of antimicrobial resistance genes in environment.

In vitro evaluation of two novel Escherichia bacteriophages against multiple drug resistant avian pathogenic Escherichia coli

BACKGROUND

In recent years, there has been a growing interest in phage therapy as an effective therapeutic tool against colibacillosis caused by avian pathogenic Escherichia coli (APEC) which resulted from the increasing number of multidrug resistant (MDR) APEC strains.

METHODS

In the present study, we reported the characterization of a new lytic bacteriophage (Escherichia phage AG- MK-2022. Basu) isolated from poultry slaughterhouse wastewater. In addition, the in vitro bacteriolytic activity of the newly isolated phage (Escherichia phage AG- MK-2022. Basu) and the Escherichia phage VaT-2019a isolate PE17 (GenBank: MK353636.1) were assessed against MDR- APEC strains (n = 100) isolated from broiler chickens with clinical signs of colibacillosis.

RESULTS

Escherichia phage AG- MK-2022. Basu belongs to the Myoviridae family and exhibits a broad host range. Furthermore, the phage showed stability under a wide range of temperatures, pH values and different concentrations of NaCl. Genome analysis of the Escherichia phage AG- MK-2022. Basu revealed that the phage possesses no antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and any E. coli virulence associated genes. In vitro bacterial challenge tests demonstrated that two phages, the Escherichia phage VaT-2019a isolate PE17 and the Escherichia phage AG- MK-2022. Basu exhibited high bactericidal activity against APEC strains and lysed 95% of the tested APEC strains.

CONCLUSIONS

The current study findings indicate that both phages could be suggested as safe biocontrol agents and alternatives to antibiotics for controlling MDR-APEC strains isolated from broilers.

Exploring Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli in Food-Producing Animals and Animal-Derived Foods

Antimicrobials serve as crucial treatments in both veterinary and human medicine, aiding in the control and prevention of infectious diseases. However, their misuse or overuse has led to the emergence of antimicrobial resistance, posing a significant threat to public health. This review focuses on extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in animals and their associated food products, which contribute to the proliferation of antimicrobial-resistant strains. Recent research has highlighted the presence of ESBL-producing E. coli in animals and animal-derived foods, with some studies indicating genetic similarities between these isolates and those found in human infections. This underscores the urgent need to address antimicrobial resistance as a pressing public health issue. More comprehensive studies are required to understand the evolving landscape of ESBLs and to develop strategic public health policies grounded in the One Health approach, aiming to control and mitigate their prevalence effectively.

Urinary tract infection and sepsis causing potential of multidrug-resistant Extraintestinal pathogenic E. coli isolated from plant-origin foods

The dissemination of Extraintestinal pathogenic Escherichia coli (ExPEC) in food is a critical concern for human health and food safety. The present study is the first to systematically examine the diverse plant-origin foods such as cucumber, carrot, tomato, radish, chilli, fenugreek, coriander, peppermint, spring onion, cabbage, and spinach for the presence of ExPEC or specific putative ExPEC pathotypes with an in-depth assessment of their phylogenetics, virulence, and drug resistance. A total of 77 (15.9 %) ExPEC isolates were recovered from 1780 samples of the diverse plant-origin foods of distinct environments. Specific putative ExPEC pathotypes such as Uropathogenic E. coli (UPEC, 23.3 %) and Septicemia-associated E. coli (SEPEC, 24.6 %) were identified among ExPEC isolates. The Clermont revisited new phylotyping method revealed the varied distribution (1-27 %) of specific putative ExPEC pathotypes in the different phylogenetic lineages such as A, D/E, B1, and Clade 1, etc. All putative ExPEC pathotypes possess multiple genes (4.3-92.8 %) or phenotypes (3.3-100 %) associated with their virulence. In-vitro antimicrobial susceptibility testing of all putative ExPEC pathotypes demonstrated the presence of 100 % multidrug resistance with moderate to high (52-100 %) resistance to drugs used as last-resorts (chloramphenicol, colistin) or frontline (nitrofurantoin, sulfamethoxazole, ampicillin, gentamicin) in ExPEC-associated infections in humans. Overall, the present findings significantly contribute to our better understanding of the presence of ExPEC in the non-clinical niche, such as plant-origin foods with a possible consequence on human health and food safety.

Genomic diversity, pathogenicity and antimicrobial resistance of Escherichia coli isolated from poultry in the southern United States

Escherichia coli (E. coli) are typically present as commensal bacteria in the gastro-intestinal tract of most animals including poultry species, but some avian pathogenic E. coli (APEC) strains can cause localized and even systematic infections in domestic poultry. Emergence and re-emergence of antimicrobial resistant isolates (AMR) constrain antibiotics usage in poultry production, and development of an effective vaccination program remains one of the primary options in E. coli disease prevention and control for domestic poultry. Thus, understanding genetic and pathogenic diversity of the enzootic E. coli isolates, particularly APEC, in poultry farms is the key to designing an optimal vaccine candidate and to developing an effective vaccination program. This study explored the genomic and pathogenic diversity among E. coli isolates in southern United States poultry. A total of nine isolates were recovered from sick broilers from Mississippi, and one from Georgia, with epidemiological variations among clinical signs, type of housing, and bird age. The genomes of these isolates were sequenced by using both Illumina short-reads and Oxford Nanopore long-reads, and our comparative analyses suggested data from both platforms were highly consistent. The 16 s rRNA based phylogenetic analyses showed that the 10 bacteria strains are genetically closer to each other than those in the public database. However, whole genome analyses showed that these 10 isolates encoded a diverse set of reported virulence and AMR genes, belonging to at least nine O:H serotypes, and are genetically clustered with at least five different groups of E. coli isolates reported by other states in the United States. Despite the small sample size, this study suggested that there was a large extent of genomic and serological diversity among E. coli isolates in southern United States poultry. A large-scale comprehensive study is needed to understand the overall genomic diversity and the associated virulence, and such a study will be important to develop a broadly protective E. coli vaccine.

Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: a review

Economic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poultry producers, despite substantial efforts in prevention and control. Antibiotics have been used not only for the treatment and prevention of such diseases, but also for growth promotion. Consequently, these practices have been linked to the selection and spread of antimicrobial resistant bacteria which constitute a significant global threat to humans, animals, and the environment. To break down the antimicrobial resistance (AMR), poultry producers are restricting the antimicrobial use (AMU) while adopting the antibiotic-free (ABF) and organic production practices to satisfy consumers' demands. However, it is not well understood how ABF and organic poultry production practices influence AMR profiles in the poultry gut microbiome. Various Gram-negative (Salmonella enterica serovars, Campylobacter jejuni/coli, E. coli) and Gram-positive (Enterococcus spp., Staphylococcus spp. and C. perfringens) bacteria harboring multiple AMR determinants have been reported in poultry including organically- and ABF-raised chickens. In this review, we discussed major poultry production systems (conventional, ABF and organic) and their impacts on AMR in some potential pathogenic Gram-negative and Gram-positive bacteria which could allow identifying issues and opportunities to develop efficient and safe production practices in controlling pathogens.

Characterization of Escherichia coli and other bacteria isolated from condemned broilers at a Danish abattoir

Meat inspection is important to ensure food safety and protect public health. Visual inspection of slaughtered carcasses for pathological changes should be supported by bacteriological analysis to determine whether the entire carcass or parts of it should be condemned. The aim of this study was to determine the bacterial species present in different sample types from condemned broiler carcasses. Furthermore, we investigated the genetic characteristics, zoonotic potential, and relatedness of Escherichia coli, the predominant bacterial species isolated from the carcasses. A total of 400 broiler carcasses condemned because of cellulitis (100), scratches (100), hepatitis (100), and healthy control carcasses (100) were selected. Samples of meat, pathological lesion, and bone marrow of each carcass were obtained for microbial analysis. From the analyzed samples, 469 bacterial isolates were recovered with E. coli accounting for 45.8%, followed by Aeromonas spp. (27.9%), in particular A. veronii. The highest rate of bacterial isolation was observed in carcasses condemned with cellulitis, whereas carcasses with hepatitis had the lowest rate of bacterial isolation. Forty-four E. coli isolates originating from different sample types were selected for whole genome sequencing. A clonal relationship was shown between E. coli from different sample types of the same carcass condemned with cellulitis and scratches. A major clade of E. coli was found in carcasses condemned with cellulitis with isolates containing mdf(A), tet(A), and bla TEM-1B genes that confer resistance to macrolides, tetracycline, and ampicillin, respectively. E. coli in this clade all belonged to ST117 and clustered with E. coli isolates previously collected from dead chickens and carcasses condemned due to cellulitis in Denmark, Finland, and the United Kingdom. Bacterial evaluation results of carcasses condemned with cellulitis, scratches (moderate to severe skin lesion), and acute hepatitis confirmed the need for total condemnation of carcasses with these pathological findings. A similar evaluation should be done for carcasses affected with chronic hepatitis, and minor scratches lesions.

Relationship between Phylogenetic Groups of Escherichia coli and Pathogenicity Among Isolates from Chickens with Colibacillosis and Healthy Chickens

Avian pathogenic Escherichia coli (APEC) is closely related to extraintestinal pathogenic E. coli, which are frequently assigned to specific phylogenetic groups (phylogroups). Therefore, we investigated the association between phylogroups of E. coli isolates and those recovered from commercial broiler and layer chickens with colibacillosis. We used 104 E. coli isolates from chickens with colibacillosis (hereafter referred to as “colibacillosis-related isolates”), 56 E. coli isolates obtained from fecal samples of clinically healthy broiler chickens, and 58 isolates obtained from environmental samples of layer chicken housing facilities where clinically healthy layer chickens were reared (hereafter referred to as “healthy chicken-related isolates”). The prevalence of phylogroup F among colibacillosis-related isolates was significantly (P < 0.05) higher than that among healthy chicken-related isolates, while phylogroups A and B1 were more frequently distributed in healthy chicken-related isolates. Fifty-seven (87%) of 65 colibacillosis-related isolates belonging to phylogroup F were defined as APEC based on the presence of virulence-associated genes according to a previously established criterion. In contrast, none of the healthy chicken-related isolates were defined as APEC. As evidenced by the chicken embryo lethality assay, 87 of the 92 healthy chicken-related isolates tested had embryo lethality rates of <30% and were considered avirulent, whereas 59 of the 104 colibacillosis-related isolates were considered virulent. Nonetheless, among isolates exhibiting embryo lethality rates of <30%, the mean lethality rate of embryos inoculated with colibacillosis-related isolates was significantly higher than that of embryos inoculated with healthy chicken-related isolates. These observations suggest that phylogroup F predicts colibacillosis among E. coli strains with virulence-associated genes.

Antimicrobial drug resistance against Escherichia coli and its harmful effect on animal health

Multidrug resistance among pathogenic bacteria is imperilling the worth of antibiotic infection, which has become an emerging problem, which previously transformed the veterinary sciences. Since its discovery, many antibiotics have been effective in treating bacterial infections in animals. Escherichia coli, a bacterium, is one of the reservoirs of antibiotic resistance genes in a community. The current use of antibiotics and demographic factors usually increase multidrug resistance. Genetically, the continuous adoption of environmental changes by E. coli allows it to acquire many multidrug resistance. During the host's life, antimicrobial resistance rarely poses a threat to the E. coli strain and pressure, similar to that of a flexible animal lower intestine. In this review, we describe the E. coli antibiotic drug–resistance mechanism driving transmission, the causes of transmission and the harmful effects on animal health.

Rumen Microbial Metabolic Responses of Dairy Cows to the Honeycomb Flavonoids Supplement Under Heat-Stress Conditions

Flavonoids played critical roles in stabilizing microbial homoeostasis when animals suffered exoteric stresses. However, whether flavonoids attenuated heat stress of dairy cows is still not clear. Therefore, in the present article, flavonoids extracted from honeycomb were supplemented to investigate the production, digestibility, and rumen microbial metabolism responses of cows under heat stress conditions. A total of 600 multiparous dairy herds were randomly allotted into the control treatment (CON), the heat stress (HS) treatment, and the honeycomb flavonoids supplement under heat stress conditions (HF) treatment for a 30-day-long trial. Each treatment contains 4 replicates, with 50 cows in each replicate. Production performances including dry matter intake (DMI), milk production, and milk quality were measured on the basis of replicate. Furthermore, two cows of each replicate were selected for the measurement of the nutrient digestibility, the ruminal fermentable parameters including ruminal pH, volatile fatty acids, and ammonia-N, and the rumen microbial communities and metabolism. Results showed that HF effectively increased DMI, milk yield, milk fat, and ruminal acetate content (p < 0.05) compared with HS. Likewise, digestibility of NDF was promoted after HF supplement compared with HS. Furthermore, relative abundances of rumen microbial diversities especially Succiniclasticum, Pseudobutyrivibrio, Acetitomaculum, Streptococcus, and Succinivibrio, which mainly participated in energy metabolism, significantly improved after HF supplement. Metabolomic investigation showed that HF supplement significantly upregulated relative content of lipometabolic-related metabolites such as phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, and phosphatidylethanolamine, while it downregulated biogenic amines. In summary, HF supplement helps proliferate microbial abundances, which further promoted fiber digestibility and energy provision, and ultimately enhances the production performances of dairy cows under heat stress conditions.

Virulence Genotype and Phenotype of Multiple Antimicrobial-Resistant Escherichia coli Isolates from Broilers Assessed from a "One-Health" Perspective

ABSTRACT

Extraintestinal pathogenic Escherichia coli (ExPEC) include several serotypes that have been associated with colibacillosis in poultry and with urinary tract infections (UTIs) and newborn meningitis in humans. In this study, 57 antimicrobial-resistant E. coli from apparently healthy broiler chickens were characterized for their health and safety risks. These isolates belonged to 12 serotypes, and isolates of the same serotype were clonal based on single nucleotide variant analysis. Most of the isolates harbored plasmids; IncC and IncFIA were frequently detected. The majority of the resistant isolates harbored plasmid-mediated resistance genes, including aph(3″)-Ib, aph(6)-Id, blaCMY-2, floR, sul1, sul2, tet(A), and tet(B), in agreement with their resistant phenotypes. The class 1 integron was detected in all E. coli serotypes except O124:H25 and O7:H6. Of the 57 broiler E. coli isolates, 27 were avian pathogenic, among which 18 were also uropathogenic E. coli and the remainder were other ExPEC. The two isolates of serotype O161:H4 (ST117) were genetically related to the control avian pathogenic strains and a clinical isolate associated with UTIs. A strain of serotype O159:H45 (ST101) also was closely related to a UTI isolate. The detected virulence factors included adhesins, invasins, siderophores, type III secretion systems, and toxins in combination with other virulence determinants. A broiler isolate of serotype O7:H18 (ST38) carried the ibeA gene encoding a protein involved in invasion of brain endothelium on a 102-kbp genetic island. This isolate moderately adhered and invaded Caco-2 cells and induced mortality (42.5%) in a day-old-chick infection model. The results of this study suggest that multiple antimicrobial-resistant E. coli isolates recovered from apparent healthy broilers can be pathogenic and act as reservoirs for antimicrobial resistance genes, highlighting the necessity of their assessment in a "One-Heath" context.

HIGHLIGHTS

Impact of chicken litter pre-application treatment on the abundance, field persistence, and transfer of antibiotic resistant bacteria and antibiotic resistance genes to vegetables

Treatment of manures prior to land application can potentially reduce the abundance of antibiotic resistance genes and thus the risk of contaminating crops or water resources. In this study, raw and composted chicken litter were applied to field plots that were cropped to carrots, lettuce and radishes. Vegetables were washed per normal culinary practice before downstream analysis. The impact of composting on manure microbial composition, persistence of antibiotic resistant bacteria in soil following application, and distribution of antibiotic resistance genes and bacteria on washed vegetables were determined. A subset of samples that were thought likely to reveal the most significant effects were chosen for shotgun sequencing. The absolute abundance of all target genes detected by qPCR decreased after composting except sul1, intI1, incW and erm(F) that remained stable. The shotgun sequencing revealed that some integron integrases were enriched by composting. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. Manure-amended soil showed significantly higher abundances of sul1, str(A), str(B), erm(B), aad(A), intI1 and incW compared to unmanured soil. At harvest, those genes that were detected in soil samples before the application of manure (intI1, sul1, strA and strB) were quantifiable by qPCR on vegetables, with a larger number of gene targets detected on the radishes than in the carrots or lettuce. Shotgun metagenomic sequencing suggested that the increase of antibiotic resistance genes on radishes produced in soil receiving raw manure may be due to changes to soil microbial communities following manure application, rather than transfer to the radishes of enteric bacteria. Overall, under field conditions there was limited evidence for transfer of antibiotic resistance genes from composted or raw manure to vegetables that then persisted through washing.

High Prevalence of Multidrug Resistance and Biofilm-Formation Ability Among Avian Escherichia coli Isolated from Broilers in Iran

The present study was conducted to determine the antimicrobial resistance pattern and biofilm-formation ability in 100 Avian-Pathogenic Escherichia coli (APEC) isolated from colibacillosis-suspected broilers and 100 Avian Fecal E. coli (AFEC) isolates from healthy broilers in Hamedan, Iran. All isolates were screened by polymerase chain reaction for antimicrobial resistance genes, class 1 and 2 integrons, and biofilm-associated genes. Besides, we assessed the possible relationship between biofilm-formation ability antibiotic resistance patterns, genetic background, and the pathogenicity of APEC strains. 81% of APEC and 73% of AFEC isolates showed multidrug resistance (MDR) phenotype; in addition, 45% of the APEC and 21% of the AFEC strains showed biofilm-formation ability. This is the first report of the biofilm formation ability in E. coli isolated from broilers in Iran. The most prevalent antibiotic resistance gene in APEC strains was tetA (68%), followed by sul1 (63%), dfrA1-like (51%), and bla_TEM (30%), whereas in AFEC strains, the frequencies of the antibiotic resistance genes were tetA (63%), sul1 (58%), dfrA1-like (49%), and bla_TEM (22%). Out of 81 MDR APEC isolates, 53 (65.4%) and 38 (46.91%) isolates were positive for intI1 and intI2 genes, respectively. In the AFEC strains intI1 and intI2 genes were presented in 57 and 33 isolates, respectively. All APEC isolates belonging to phylogenetic groups B1, B2, and C were MDR. The results of the present study indicate that isolates with biofilm-forming ability show more MDR properties and probably have more pathogenicity to broilers.

Gastrointestinal Development and Microbiota Responses of Geese to Honeycomb Flavonoids Supplementation

Background: Geese are conventionally considered to be herbivorous, which could also be raised with concentrate feeding diets without green grass because of the similar gastrointestinal tract with other poultry. However, the geese gut microbiota profiles and their interactions with epithelial cells are still of limited study. Flavonoids were well-documented to shape gut microbiota and promote epithelial barrier functions individually or cooperatively with other metabolites. Therefore, in the present study, honeycomb flavonoids (HF) were supplemented to investigate the effects on growth performances, intestinal development, and gut microbiome of geese.

Material and Methods: A total of 400 1-day-old male lion-head geese with similar birth weight (82.6 ± 1.4 g) were randomly divided into five treatments: the control treatment (CON) and the HF supplementation treatments, HF was supplemented arithmetically to increase from 0.25 to 1%. Growth performance, carcass performances, and intestines' development parameters were measured to determine the optimum supplement. Junction proteins including ZO-1 and ZO-2 and cecal microbiota were investigated to demonstrate the regulatory effects of HF on both microbiota and intestinal epithelium.

Results: Results showed that 0.5% of HF supplement had superior growth performance, carcass performance, and the total parameters of gastrointestinal development to other treatments. Further research showed that tight junction proteins including ZO-1 and ZO-2 significantly up-regulated, while Firmicutes and some probiotics including Clostridiales, Streptococcus, Lachnoclostridium, and Bifidobacterium, remarkably proliferated after HF supplement. In conclusion, HF supplement in concentrate-diet feeding geese effectively increased the growth performances by regulating the gut microbiota to increase the probiotic abundance to promote the nutrient digestibility and fortify the epithelial development and barrier functions to facilitate the nutrient absorption and utilization.

Effects of the prebiotic lactoferrin on multidrug-resistant Escherichia coli infections in broiler chickens

Background and Aim

Increased multidrug resistance in Escherichia coli has created challenges for the poultry industry. Consequently, new antimicrobial agents should preferentially be utilized for the prevention and treatment of E. coli outbreaks. This study aimed to evaluate the effects of lactoferrin (LF) as a prebiotic on broiler chicks challenged with multidrug-resistant E. coli in comparison with antibiotics.

Materials and Methods

A total of 70 diseased flocks from Egypt were collected for E. coli isolation and identification, serotyping, and antimicrobial susceptibility pattern determination. E. coli was isolated and characterized phenotypically and one isolate that showed multidrug-resistance was selected. A challenge trial was performed to evaluate the effectiveness of LF as a prebiotic on the isolated multidrug-resistant E. coli. Liver samples were collected from the experimental chicks and subjected to E. coli enumeration to illustrate the effectiveness of LF on the liver cells and bacteria using an electron microscope. Serum samples were also collected to estimate lysozyme and nitric oxide (NO) concentrations.

Results

After isolation of E. coli with a percentage of 54.3% from the diseased broilers, the strain was serotyped (identified serotypes: O2, O18, O55, O78, O86a, O111, O125, O126, O127, O157, O159, and O166). Multi-antibiotic resistance was found to be harbored in a high percentage among 11 antibiotic discs. The LF in the prophylactic and treated groups was found to have a significant effect in comparison with the group treated with the drug of choice (ciprofloxacin). Furthermore, a significant difference in the NO (one of non-specific immune response) and a non-significant difference in lysozyme concentrations were reported in the group fed on rations with LF in comparison with the non-fed group.

Conclusion

LF was thus identified as an effective prebiotic that can improve chick performance, help them to overcome multidrug-resistant E. coli and stimulate immunity.

Growth performances, gastrointestinal epithelium and bacteria responses of Yellow-feathered chickens to kudzu-leaf flavonoids supplement

The objective of this study was to investigate the effects of replacing antibiotics with Kudzu-leaf flavonoids (KLF) on the growth performances, gut epithelial development, and gastrointestinal bacteria diversities of Yellow-feathered broilers. For this purpose, total of 216 1-day-old male Yellow-feathered chickens with the similar birth weight (31.0  ±  1.0 g) were randomly divided into 3 treatments: the control treatment (CON), the kudzu-leaf flavonoids supplement treatment (KLF), and the antibiotics supplement treatment (AGP). All birds were provided with a 56 d-feeding procedure, followed by the measurement of production performances, immune organs, blood anti-oxidant parameters, intestine epithelium development, and cecal microbiota. Results showed the feed conversion ratio significantly decreased after KLF supplement compared with CON (P  <  0.05). KLF supplement partly promoted the anti-oxidant capacity on account of the increased activity of Superoxide dismutase (SOD) and the decrease content of malondialdehyde (MDA). Further, as referred to the gastrointestinal development and bacteria, ratio of villus/crypt significantly increased of ileum in KLF treatment (P  <  0.05) while a significant promition of bacterial diversity and partial representative probiotic bacteria (P  <  0.05) after KLF supplementation. Moreover, correlation analysis indicated that probitics including Bifidobacterium, Butyricimonas, Lactobacillus and Streptococcus positively correlated with production performances. In conclusion, KLF supplement may promote feed efficiency and benefit the gastrointestinal health through improving gut bacterial diversity and probiotic bacteria. The KLF might be applied as a proper antibiotic alternative.

Antimicrobial Resistance Phenotypes and Genotypes of Escherichia coli Isolates from Broiler Chickens Fed Encapsulated Cinnamaldehyde and Citral

ABSTRACT

This study was conducted to investigate the effects of in-feed encapsulated cinnamaldehyde (CIN) and citral (CIT) alone or in combination on antimicrobial resistance (AMR) phenotypes and genotypes of Escherichia coli isolates recovered from feces of 6-, 16-, 23-, and 27-day-old broiler chickens. The five dietary treatments including the basal diet (negative control [NC]) and the basal diet supplemented with 55 ppm of bacitracin (BAC), 100 ppm of encapsulated CIN, 100 ppm of encapsulated CIT, or 100 ppm each of encapsulated CIN and encapsulated CIT (CIN+CIT). Antimicrobial susceptibility testing of 240 E. coli isolates revealed that the most common resistance was to β-lactams, aminoglycosides, sulfonamides, and tetracycline; however, the prevalence of AMR decreased (P < 0.05) as birds aged. The prevalence of resistance to amoxicillin-clavulanic acid, ceftiofur, ceftriaxone, cefoxitin, gentamicin, and sulfonamide was lower (P < 0.05) in isolates from the CIN or CIN+CIT groups than in isolates from the NC or BAC groups. Whole genome sequencing of 227 of the 240 isolates revealed 26 AMR genes and 19 plasmids, but the prevalence of some AMR genes and the number of plasmids were lower (P < 0.05) in E. coli isolated from CIN or CIN+CIT birds than in isolates from NC or BAC birds. The most prevalent resistance genes were tet(A) (108 isolates), aac(3)-VIa (91 isolates), aadA1 (86 isolates), blaCMY-2 (78 isolates), sul1 (77 isolates), aph(3)-Ib (58 isolates), aph(6)-Id (58 isolates), and sul2 (24 isolates). The numbers of most virulence genes carried by isolates increased (P < 0.05) in chickens from 6 to 27 days of age. The prevalence of E. coli O21:H16 isolates was lower (P < 0.05) in CIN and CIN+CIT, and the colibacillosis-associated multilocus sequence type (ST117) was most prevalent in isolates from 23-day-old chickens. A phylogenetic tree of whole genome sequences revealed a close relationship between 25 of the 227 isolates and human or broiler extraintestinal pathogenic E. coli strains. These findings indicate that AMR and virulence genotypes of E. coli could be modulated by providing encapsulated CIN or CIN+CIT feed supplements, but further investigation is needed to determine the mechanisms of the effects of these supplements.

HIGHLIGHTS

Poultry-origin extraintestinal Escherichia coli strains carrying the traits associated with urinary tract infection, sepsis, meningitis and avian colibacillosis in India

AIM

In-depth 'One Health' risk assessment of extraintestinal pathogenic Escherichia coli (ExPEC) strains carrying the traits of urinary tract infection, sepsis, meningitis and avian colibacillosis in poultry of India.

METHODS AND RESULTS

A total of 230 E. coli isolates were recovered from chicken samples representing the different sources (faeces vs caeca), stages (poultry farms vs retails butcher shop) or environments (rural vs urban) of poultry in India. Among all poultry-origin E. coli isolates, 49 (21·1%) strains were identified as ExPEC possessing multiple virulence determinants regardless of their association with any specific phylogenetic lineages. Of particular, potentially virulent ExPEC pathotypes, that is, uropathogenic E.coli (UPEC, 20·4%), avian pathogenic E. coli (APEC, 34·6%), septicaemia-associated E. coli (SEPEC, 47·0%) and neonatal meningitis-causing E.39 coli (NMEC, 2·0%) were also detected among all ExPEC strains.

CONCLUSIONS

Our study is the first to assess ExPEC strains circulating in the different settings of poultry in India and significantly demonstrates their potential ability to cause multiple extraintestinal infections both in humans and animals.

SIGNIFICANCE AND IMPACT OF THE STUDY

The data of our study are in favour of the possibility that poultry-origin putative virulent ExPEC pathotypes consequently constitute a threat risk to 'One Health' or for food safety and a great concern for poultry production of India.

Effects of replacing dietary Aureomycin with a combination of plant essential oils on production performance and gastrointestinal health of broilers

The objective of this study was to investigate the effects of replacing antibiotics with a combination of plant essential oils on the growth performances and gastrointestinal health of broilers. A total of 720 1-day-old male AA broilers were randomly divided into 3 treatments: the control treatment (CON), the Aureomycin supplementation treatment (AGP), and the combined plant oils supplementation treatment (POC), with a 42-D period feeding procedure. Growth performances, carcass performances, intestinal sections, and cecal microbiota were investigated. Results indicated that POC supplementation decreased the feed conversion ratio compared with CON and AGP treatments, though not significantly. No significant differences were found for feed intake, BW gain, and culling rate among the 3 treatments (P > 0.05). In addition, no significant differences were seen on carcass performance. For the aspects of intestinal section, POC supplementation did not make significant effects on intestinal wall thickness, villus heights, crypt depths, and the ratio of villus heights/crypt depths compared with CON and AGP treatments. Cecal microbiota results demonstrated that bacterial diversity and some representative probiotic bacteria were significantly increased in numbers (P < 0.05) after POC supplementation. In conclusion, the combination of essential oils promoted intestinal health through improving gut bacterial diversity and probiotic bacteria, as well as improving feed conversion ratio of broilers. These results indicated that the combination of essential oils may benefit the gastrointestinal health and be applied as an antibiotic alternative.

Occurrence of Escherichia coli in captive psittaciformes: antimicrobial susceptibility and virulence genes

Abstract Captive Psittaciformes may harbor Gram-negative bacteria in their digestive tract, mainly due to poor hygienic conditions and confinement. The present study was carried out with the objective of isolating and identifying Escherichia coli in samples collected from Psittaciformes cages in 50 commercial establishments in the metropolitan region of Goiania, with subsequent antimicrobial susceptibility testing and detection of virulence genes. A total of 141 samples of excreta and swab samples from feeders and water bowls were collected, totaling 423 samples. Escherichia coli was isolated from 9.7% (41/423) samples: 12% (17/141) in excreta, 8.5% (12/141) in feed, and 8.5% (12 /141) in waterers. To determine the susceptibility profile of E. coli isolates, resistance to ciprofloxacin 4.9% (2/41), gentamicin 17.0% (7/41), doxycycline 34.1% (14/41), florfenicol 34.1% (14/41), trimethoprim 39.0% (16/41), tetracycline 41.5% (17/41), enrofloxacin 43.9% (18/41), amoxicillin 48.8% (20/41), neomycin 61.0% (25/41), and sulfonamide 90.2% (37/41) was determined. In 20 isolates, resistance was determined at 4 or more antimicrobials, seven of excreta (7/17), five of feed (5/12), and eight of waterers (8/12). One of the isolates from the waterers showed resistance to all antimicrobials. The iss gene was detected in three isolates, the tsh gene in three, the papC gene in two, traT and eae genes were not detected. In this study, it can be concluded that Psittaciformes commercialized as pet are carry E. coli isolates resistant to most commonly used antimicrobials, mainly sulfonamides and neomycin, besides having virulence and serum resistance genes, which highlights the possibility of the to cause disease in humans.

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

The increase in antibiotic resistance is a global concern for human and animal health. Resistant microorganisms can spread between food-producing animals and humans. The objective of this review was to identify the type and amount of antibiotics used in poultry production and the level of antibiotic resistance in Escherichia coli isolated from broilers. Isolate information was obtained from national monitoring programs and research studies conducted in large poultry-producing regions: US, China, Brazil, and countries of EU-Poland, United Kingdom, Germany, France, and Spain. The survey results clearly display the absence of a harmonized approach in the monitoring of antibiotics per animal species and the evaluation of resistances using the same methodology. There is no public long-term quantitative data available targeting the amount of antibiotics used in poultry, with the exception of France. Data on antibiotic-resistant E. coli are available for most regions but detection of resistance and number of isolates in each study differs among regions; therefore, statistical evaluation was not possible. Data from France indicate that the decreased use of tetracyclines leads to a reduction in the detected resistance rates. The fluoroquinolones, third-generation cephalosporins, macrolides, and polymyxins ("highest priority critically important" antibiotics for human medicine according to WHO) are approved for use in large poultry-producing regions, with the exception of fluoroquinolones in the US and cephalosporins in the EU. The approval of cephalosporins in China could not be evaluated. Tetracyclines, aminoglycosides, sulfonamides, and penicillins are registered for use in poultry in all evaluated countries. The average resistance rates in E. coli to representatives of these antibiotic classes are higher than 40% in all countries, with the exception of ampicillin in the US. The resistance rates to fluoroquinolones and quinolones in the US, where fluoroquinolones are not registered for use, are below 5%, while the average of resistant E. coli is above 40% in Brazil, China, and EU, where use of fluoroquinolones is legalized. However, banning of fluoroquinolones and quinolones has not totally eliminated the occurrence of resistant populations.

Characterization of multidrug-resistant Gram-negative bacilli isolated from hospitals effluents: first report of a blaOXA-48-like in Klebsiella oxytoca, Algeria

The antibiotic susceptibility profile and antimicrobial resistance determinants were characterized on Gram-negative bacilli (GNB) isolated from Algerian hospital effluents. Among the 94 isolates, Enterobacteriaceae was the predominant family, with Escherichia coli and Klebsiella pneumoniae being the most isolated species. In non-Enterobacteriaceae, Acinetobacter and Aeromonas were the predominant species followed by Pseudomonas, Comamonas, Pasteurella, and Shewanella spp. The majority of the isolates were multidrug-resistant (MDR) and carried different antimicrobial resistance genes including bla_CTX-M, bla_TEM, bla_SHV, bla_OXA-48-like, bla_OXA-23, bla_OXA-51, qnrB, qnrS, tet(A), tet(B), tet(C), dfrA1, aac(3)-IIc (aacC2), aac(6')-1b, sul1, and sul2. The qacEΔ1-sul1 and intI2 signatures of class 1 and class 2 integrons, respectively, were also detected. Microarray hybridization on MDR E. coli revealed additional resistance genes (aadA1 and aph3strA, tet30, mphA, dfrA12, bla_cmy2, bla_ROB1, and cmlA1) and classified the tested strains as commensals, thus highlighting the potential role of humans in antibiotic resistance dissemination. This study is the first report of bla_OXA-48-like in Klebsiella oxytoca in Algeria and bla_OXA-23 in A. baumannii in Algerian hospital effluents. The presence of these bacteria and resistance genes in hospital effluents represents a serious public health concern since they can be disseminated in the environment and can colonize other hosts.

An evaluation of multidrug-resistant Escherichia coli isolates in urinary tract infections from Aguascalientes, Mexico: cross-sectional study

BACKGROUND

Uropathogenic Escherichia coli (UPEC) are one of the main bacteria causing urinary tract infections (UTIs). The rates of UPEC with high resistance towards antibiotics and multidrug-resistant bacteria have increased dramatically in recent years and could difficult the treatment.

METHODS

The aim of the study was to determine multidrug-resistant bacteria, antibiotic resistance profile, virulence traits, and genetic background of 110 E. coli isolated from community (79 isolates) and hospital-acquired (31 isolates) urinary tract infections. The plasmid-mediated quinolone resistance genes presence was also investigated. A subset of 18 isolates with a quinolone-resistance phenotype was examined for common virulence genes encoded in diarrheagenic and extra-intestinal pathogenic E. coli by a specific E. coli microarray.

RESULTS

Female children were the group most affected by UTIs, which were mainly community-acquired. Resistance to trimethoprim-sulfamethoxazole, ampicillin, and ampicillin-sulbactam was most prevalent. A frequent occurrence of resistance toward ciprofloxacin (47.3%), levofloxacin (43.6%) and cephalosporins (27.6%) was observed. In addition, 63% of the strains were multidrug-resistant (MDR). Almost all the fluoroquinolone (FQ)-resistant strains showed MDR-phenotype. Isolates from male patients were associated to FQ-resistant and MDR-phenotype. Moreover, hospital-acquired infections were correlated to third generation cephalosporin and nitrofurantoin resistance and the presence of kpsMTII gene. Overall, fimH (71.8%) and fyuA (68.2%), had the highest prevalence as virulence genes among isolates. However, the profile of virulence genes displayed a great diversity, which included the presence of genes related to diarrheagenic E. coli. Out of 110 isolates, 25 isolates (22.7%) were positive to qnrA, 23 (20.9%) to qnrB, 7 (6.4%) to qnrS1, 7 (6.4%) to aac(6')lb-cr, 5 (4.5%) to qnrD, and 1 (0.9%) to qnrC genes. A total of 12.7% of the isolates harbored blaCTX-M genes, with blaCTX-M-15 being the most prevalent.

CONCLUSIONS

Urinary tract infection due to E. coli may be difficult to treat empirically due to high resistance to commonly used antibiotics. Continuous surveillance of multidrug resistant organisms and patterns of drug resistance are needed in order to prevent treatment failure and reduce selective pressure. These findings may help choosing more suitable treatments of UTI patients in this region of Mexico.

Different loci and mRNA copy number of the increased serum survival gene of Escherichia coli

The increased serum survival gene (iss) has been identified as a virulence trait associated with the virulence of Escherichia coli, causing colibacillosis in poultry. However, it remains unclear as to whether iss mRNA copy number and sequence affect virulence. To examine these influences, we assessed the presence of iss, sequence analysis, iss mRNA copy number, and serum resistance. The iss gene was detected in 88 (all) E. coli isolates from different sources, and sequencing identified 16 alleles (32 different loci) and 10 amino acid sequences (10 different loci). Nested polymerase chain reaction improved iss detection. The isolates from sick chickens had >68% livability in serum resistance tests and higher iss mRNA copy number. The iss mRNA copy number highly correlated with mortality and E. coli livability. Student's t tests confirmed the relationship between the different loci to iss transcription, serum resistance, and virulence. These data suggest that iss mRNA copy number and different loci affect the virulence and serum resistance. These findings could be useful in further studies on the prevalence of iss among E. coli isolates and other virulence factors.

Genomic Analysis of Third Generation Cephalosporin Resistant Escherichia coli from Dairy Cow Manure

The production of extended-spectrum β-lactamases (ESBLs) conferring resistance to new derivatives of β-lactams is a major public health threat if present in pathogenic Gram-negative bacteria. The objective of this study was to characterize ceftiofur (TIO)- or cefotaxime (FOX)-resistant Escherichia coli isolated from dairy cow manure. Twenty-four manure samples were collected from four farms and incubated under anaerobic conditions for 20 weeks at 4 °C or at 25 °C. A total of 37 TIO- or FOX-resistant E. coli were isolated from two of the four farms to determine their susceptibility to 14 antibiotics. Among the 37 resistant E. coli, 10 different serotypes were identified, with O8:H1 being the predominant serotype (n = 17). Five isolates belonged to each of serotypes O9:NM and O153:H42, respectively. All 37 cephalosporin resistant isolates were multi-resistant with the most prevalent resistance spectrum being amoxicillin-clavulanic acid-ampicillin-cefoxitin-ceftiofur-ceftriaxone-chloramphenicol-streptomycin-sulfisoxazole-tetracycline-trimethoprim-sulfamethoxazole. The genomes of 18 selected isolates were then sequenced and compared to 14 selected human pathogenic E. coli reference genomes obtained from public repositories using different bioinformatics approaches. As expected, all 18 sequenced isolates carried at least one β-lactamase bla gene: TEM-1, TEM-81, CTX-M115, CTX-M15, OXA-1, or CMY-2. Several other antibiotic resistance genes (ARGs) and virulence determinants were detected in the sequenced isolates and all of them harbored antimicrobial resistance plasmids belonging to classic Inc groups. Our results confirm the presence of diverse ESBL producing E. coli isolates in dairy cow manure stored for a short period of time. Such manure might constitute a reservoir of resistance and virulence genes for other bacteria that share the same environment.

Genetic diversity of Escherichia coli isolates from surface water and groundwater in a rural environment

The genetic characteristics among Escherichia coli strains can be grouped by origin of isolation. Then, it is possible to use the genotypes as a tool to determine the source of water contamination. The aim of this study was to define water aptitude for human consumption in a rural basin and to assess the diversity of E. coli water populations. Thus, it was possible to identify the main sources of fecal contamination and to explore linkages with the hydrogeological environment and land uses. The bacteriological analysis showed that more than 50% of samples were unfit for human consumption. DNA fingerprinting analysis by BOX-PCR indicated low genotypic diversity of E. coli isolates taken from surface water and groundwater. The results suggested the presence of a dominant source of fecal contamination. The relationship between low genotypic diversity and land use would prove that water contamination comes from livestock. The genetic diversity of E. coli isolated from surface water was less than that identified in groundwater because of the different hydraulic features of both environments. Furthermore, each one of the two big strain groups identified in this basin is located in different sub-basins, showing that hydrological dynamics exerts selective pressure on bacteria DNA.

Physiology and pathogenicity of cpdB deleted mutant of avian pathogenic Escherichia coli

Avian colibacillosis is one of the most common infectious diseases caused partially or entirely by avian pathogenic Escherichia coli (APEC) in birds. In addition to spontaneous infection, APEC can also cause secondary infections that result in greater severity of illness and greater losses to the poultry industry. In order to assess the role of 2', 3'-cyclic phosphodiesterase (cpdB) in APEC on disease physiology and pathogenicity, an avian pathogenic Escherichia coli-34 (APEC-34) cpdB mutant was obtained using the Red system. The cpdB mutant grew at a slower rate than the natural strain APEC-34. Scanning electron microscopy (SEM) indicated that the bacteria of the cpdB mutant were significantly longer than the bacteria observed in the natural strain (P<0.01), and that the width of the cpdB mutant was significantly smaller than its natural counterpart (P<0.01). In order to evaluate the role of cpdB in APEC in the colonization of internal organs (lung, liver and spleen) in poultry, seven-day-old SPF chicks were infected with 10⁹CFU/chick of the cpdB mutant or the natural strain. No colonizations of cpdB mutants were observed in the internal organs 10days following the infection, though numerous natural strains were observed at 20days following infection. Additionally, the relative expression of division protein ftsZ, outer membrane protein A ompA, ferric uptake regulator fur and tryptophanase tnaA genes in the mutant strain were all significantly lower than in the natural strain (P<0.05 or P<0.01). These results suggested that cpdB is involved in the long-term colonization of APEC in the internal organs of the test subjects. The deletion of the cpdB gene also significantly affected the APEC growth and morphology.

Antimicrobial Resistance of Escherichia fergusonii Isolated from Broiler Chickens

The objective of this study was to investigate the antibiotic resistance of Escherichia fergusonii isolated from commercial broiler chicken farms. A total of 245 isolates from cloacal and cecal samples of 28- to 36-day-old chickens were collected from 32 farms. Isolates were identified using PCR, and their susceptibility to 16 antibiotics was determined by disk diffusion assay. All isolates were susceptible to meropenem, amikacin, and ciprofloxacin. The most common resistances were against ampicillin (75.1%), streptomycin (62.9%), and tetracycline (57.1%). Of the 184 ampicillin-resistant isolates, 127 were investigated using a DNA microarray carrying 75 probes for antibiotic resistance genetic determinants. Of these 127 isolates, the β-lactamase blaCMY2, blaTEM, blaACT, blaSHV, and blaCTX-M-15 genes were detected in 120 (94.5%), 31 (24.4%), 8 (6.3%), 6 (4.7%), and 4 (3.2%) isolates, respectively. Other detected genes included those conferring resistance to aminoglycosides (aadA1, strA, strB), trimethoprims (dfrV, dfrA1), tetracyclines (tetA, tetB, tetC, tetE), and sulfonamides (sul1, sul2). Class 1 integron was found in 35 (27.6%) of the ampicillin-resistant isolates. However, our data showed that the tested E. fergusonii did not carry any carbapenemase blaOXA genes. Pulsed-field gel electrophoresis revealed that the selected ampicillin-resistant E. fergusonii isolates were genetically diverse. The present study indicates that the monitoring of antimicrobial-resistant bacteria should include enteric bacteria such as E. fergusonii, which could be a reservoir of antibiotic resistance genes. The detection of isolates harboring extended-spectrum β-lactamase genes, particularly blaCTX-M-15, in this work suggests that further investigations on the occurrence of such genes in broilers are warranted.

Chitosan Nanoparticles as Carriers for the Delivery of ΦKAZ14 Bacteriophage for Oral Biological Control of Colibacillosis in Chickens

The use of chitosan as a delivery carrier has attracted much attention in recent years. In this study, chitosan nanoparticles (CS-NP) and chitosan-ΦKAZ14 bacteriophage-loaded nanoparticles (C-ΦKAZ14 NP) were prepared by a simple coercavation method and characterized. The objective was to achieve an effective protection of bacteriophage from gastric acids and enzymes in the chicken gastrointestinal tract. The average particle sizes for CS-NP and C-ΦKAZ14 NP were 188 ± 7.4 and 176 ± 3.2 nm, respectively. The zeta potentials for CS-NP and C-ΦKAZ14 NP were 50 and 60 mV, respectively. Differential scanning calorimetry (DSC) of C-ΦKAZ14 NP gave an onset temperature of -17.17 °C with a peak at 17.32 °C and final end set of 17.41 °C, while blank chitosan NP had an onset of -20.00 °C with a peak at -19.78 °C and final end set at -20.47. FT-IR spectroscopy data of both CS-NP and C-ΦKAZ14 NP were the same. Chitosan nanoparticles showed considerable protection of ΦKAZ14 bacteriophage against degradation by enzymes as evidenced in gel electrophoresis, whereby ΦKAZ14 bacteriophage encapsulated in chitosan nanoparticles were protected whereas the naked ΦKAZ14 bacteriophage were degraded. C-ΦKAZ14 NP was non-toxic as shown by a chorioallantoic membrane (CAM) toxicity assay. It was concluded that chitosan nanoparticles could be a potent carrier of ΦKAZ14 bacteriophage for oral therapy against colibacillosis in poultry.

Antibiotic Resistance in Animal and Environmental Samples Associated with Small-Scale Poultry Farming in Northwestern Ecuador

In developing countries, small-scale poultry farming employing antibiotics as growth promoters is being advanced as an inexpensive source of protein and income. Here, we present the results of a large ecoepidemiological study examining patterns of antibiotic resistance (AR) in E. coli isolates from small-scale poultry production environments versus domestic environments in rural Ecuador, where such backyard poultry operations have become established over the past decade. Our previous research in the region suggests that introduction of AR bacteria through travel and commerce may be an important source of AR in villages of this region. This report extends the prior analysis by examining small-scale production chicken farming as a potential source of resistant strains. Our results suggest that AR strains associated with poultry production likely originate from sources outside the study area and that these outside sources might be a better place to target control efforts than local management practices.

The effects of animal agriculture on the spread of antibiotic resistance (AR) are cross-cutting and thus require a multidisciplinary perspective. Here we use ecological, epidemiological, and ethnographic methods to examine populations of Escherichia coli circulating in the production poultry farming environment versus the domestic environment in rural Ecuador, where small-scale poultry production employing nontherapeutic antibiotics is increasingly common. We sampled 262 “production birds” (commercially raised broiler chickens and laying hens) and 455 “household birds” (raised for domestic use) and household and coop environmental samples from 17 villages between 2010 and 2013. We analyzed data on zones of inhibition from Kirby-Bauer tests, rather than established clinical breakpoints for AR, to distinguish between populations of organisms. We saw significantly higher levels of AR in bacteria from production versus household birds; resistance to either amoxicillin-clavulanate, cephalothin, cefotaxime, and gentamicin was found in 52.8% of production bird isolates and 16% of household ones. A strain jointly resistant to the 4 drugs was exclusive to a subset of isolates from production birds (7.6%) and coop surfaces (6.5%) and was associated with a particular purchase site. The prevalence of AR in production birds declined with bird age (P < 0.01 for all antibiotics tested except tetracycline, sulfisoxazole, and trimethoprim-sulfamethoxazole). Farming status did not impact AR in domestic environments at the household or village level. Our results suggest that AR associated with small-scale poultry farming is present in the immediate production environment and likely originates from sources outside the study area. These outside sources might be a better place to target control efforts than local management practices.

IMPORTANCE In developing countries, small-scale poultry farming employing antibiotics as growth promoters is being advanced as an inexpensive source of protein and income. Here, we present the results of a large ecoepidemiological study examining patterns of antibiotic resistance (AR) in E. coli isolates from small-scale poultry production environments versus domestic environments in rural Ecuador, where such backyard poultry operations have become established over the past decade. Our previous research in the region suggests that introduction of AR bacteria through travel and commerce may be an important source of AR in villages of this region. This report extends the prior analysis by examining small-scale production chicken farming as a potential source of resistant strains. Our results suggest that AR strains associated with poultry production likely originate from sources outside the study area and that these outside sources might be a better place to target control efforts than local management practices.

Characterization and antimicrobial resistance patterns of Escherichia coli isolated from feces of healthy broiler chickens

ABSTRACT: Avian pathogenic Escherichia coli (APEC) strains are isolated from lesions of poultry presenting colibacillosis, which is a disease that causes either systemic or localized clinical signs. Such strains share many characteristics with E. coli strains that cause extra-intestinal illness in humans. There is not a consensus on how to define the APEC pathotype with regard to the presence of virulence traits. On the other hand, in the past few years, five minimal predictors for APEC detection were proposed. The E. coli isolates in this work were tested through polymerase chain reaction (PCR) to the five proposed minimal predictors and cva C. The strains presenting them were categorized as potential APEC. The APEC and non-APEC categories showed high resistance (> 50%) to cephalotin, erythromycin, streptomycin, sulphametoxazol/trimethoprim, ampicillin, and amoxicillin. Potential APEC strains were significantly more resistant to cephalotin (p < 0.05) and neomcycin (p < 0.01) than non-APEC. These latter were significantly more resistant to tetracycline (p < 0.01) than the potential APEC strains. These results demonstrate that feces of poultry present E. coli strains with resistant features, showing or not the potential of causing colibacillosis in poultry. Because APEC and extra-intestinal illness in humans may be similar, these resistant strains are of interest to public health.

Comparison of Antibiotic Resistance and Virulence Factors among Escherichia coli Isolated from Conventional and Free-Range Poultry

Microbiological contamination in commercial poultry production has caused concerns for human health because of both the presence of pathogenic microorganisms and the increase in antimicrobial resistance in bacterial strains that can cause treatment failure of human infections. The aim of our study was to analyze the profile of antimicrobial resistance and virulence factors of E. coli isolates from chicken carcasses obtained from different farming systems (conventional and free-range poultry). A total of 156 E. coli strains were isolated and characterized for genes encoding virulence factors described in extraintestinal pathogenic E. coli (ExPEC). Antimicrobial susceptibility testing was performed for 15 antimicrobials, and strains were confirmed as extended spectrum of β-lactamases- (ESBLs-) producing E. coli by phenotypic and genotypic tests. The results indicated that strains from free-range poultry have fewer virulence factors than strains from conventional poultry. Strains from conventionally raised chickens had a higher frequency of antimicrobial resistance for all antibiotics tested and also exhibited genes encoding ESBL and AmpC, unlike free-range poultry isolates, which did not. Group 2 CTX-M and CIT were the most prevalent ESBL and AmpC genes, respectively. The farming systems of poultries can be related with the frequency of virulence factors and resistance to antimicrobials in bacteria.

Zoonotic potential of Escherichia coli isolates from retail chicken meat products and eggs

Chicken products are suspected as a source of extraintestinal pathogenic Escherichia coli (ExPEC), which causes diseases in humans. The zoonotic risk to humans from chicken-source E. coli is not fully elucidated. To clarify the zoonotic risk posed by ExPEC in chicken products and to fill existing knowledge gaps regarding ExPEC zoonosis, we evaluated the prevalence of ExPEC on shell eggs and compared virulence-associated phenotypes between ExPEC and non-ExPEC isolates from both chicken meat and eggs. The prevalence of ExPEC among egg-source isolates was low, i.e., 5/108 (4.7%). Based on combined genotypic and phenotypic screening results, multiple human and avian pathotypes were represented among the chicken-source ExPEC isolates, including avian-pathogenic E. coli (APEC), uropathogenic E. coli (UPEC), neonatal meningitis E. coli (NMEC), and sepsis-associated E. coli (SEPEC), as well as an undefined ExPEC group, which included isolates with fewer virulence factors than the APEC, UPEC, and NMEC isolates. These findings document a substantial prevalence of human-pathogenic ExPEC-associated genes and phenotypes among E. coli isolates from retail chicken products and identify key virulence traits that could be used for screening.

Dissemination of antibiotic resistance genes in representative broiler feedlots environments: identification of indicator ARGs and correlations with environmental variables

Livestock operations are known to harbor elevated levels of antibiotic resistance genes (ARGs) that may pose a threat to public health. Broiler feedlots may represent an important source of ARGs in the environment. However, the prevalence and dissemination mechanisms of various types of ARGs in the environment of broiler feedlots have not previously been identified. We examined the occurrence, abundance and variation of ARGs conferring resistance to chloramphenicols, sulfonamides and tetracyclines in the environments of two representative types of broiler feedlots (free range and indoor) by quantitative PCR, and assessed their dissemination mechanisms. The results showed the prevalence of various types of ARGs in the environmental samples of the broiler feedlots including manure/litter, soil, sediment, and water samples, with the first report of five chloramphenicol resistance genes (cmlA, floR, fexA, cfr, and fexB) in broiler feedlots. Overall, chloramphenicol resistance genes and sulfonamides sul genes were more abundant than tetracyclines tet genes. The ARG abundances in the samples from indoor boiler feedlots were generally different to the free range feedlots, suggesting the importance of feeding operations in ARG dissemination. Pearson correlation analysis showed significant correlations between ARGs and mobile genetic element genes (int1 and int2), and between the different classes of ARGs themselves, revealing the roles of horizontal gene transfer and coselection for ARG dissemination in the environment. Further regression analysis revealed that fexA, sul1 and tetW could be reliable indicator genes to surrogate anthropogenic sources of ARGs in boiler feedlots (correlations of fexA, sul1 and tetW to all ARGs: R = 0.95, 0.96 and 0.86, p < 0.01). Meanwhile, significant correlations were also identified between indicator ARGs and their corresponding antibiotics. In addition, some ARGs were significantly correlated with typical metals (e.g., Cu, Zn, and As with fexA, fexB, cfr, sul1, tetW, tetO, tetS: R = 0.52-0.71) and some environmental parameters (e.g., TOC, TN, TP, NH3-N with fexA, fexB, cfr, sul1, tetW, tetO, tetQ, tetS: R = 0.53-0.87) (p < 0.01). Further redundancy analysis demonstrated that the distribution and transportation of ARGs from the boiler feedlots to the receiving environments were correlated with environmental variables. The findings highlight the contribution of some chemicals such as antibiotics and metals to the development of ARGs in broiler feedlots environments; and the observed ARG dissemination mechanism in the broiler feedlots facilitates the development of effective mitigation measures.

Detection of pathogens, indicators, and antibiotic resistance genes after land application of poultry litter

Poultry litter (PL) is a by-product of broiler production. Most PL is land applied. Land-applied PL is a valuable nutrient source for crop production but can also be a route of environmental contamination with manure-borne bacteria. The objective of this study was to characterize the fate of pathogens, fecal indicator bacteria (FIB), and bacteria containing antibiotic resistance genes (ARGs) after application of PL to soils under conventional till or no-till management. This 2-yr study was conducted in accordance with normal agricultural practices, and microbial populations were quantified using a combination of culture and quantitative, real-time polymerase chain reaction analysis. Initial concentrations of in PL were 5.4 ± 3.2 × 10 cells g PL; sp. was not detected in the PL but was enriched periodically from PL-amended soils. was detected in PL (1.5 ± 1.3 × 10 culturable or 1.5 ± 0.3 × 10 genes g) but was rarely detected in field soils, whereas enterococci (1.5 ± 0.5 × 10 cells g PL) were detected throughout the study. These results suggest that enterococci may be better FIB for field-applied PL. Concentrations of ARGs for sulfonamide, streptomycin, and tetracycline resistance increased up to 3.0 orders of magnitude after PL application and remained above background for up to 148 d. These data provide new knowledge about important microbial FIB, pathogens, and ARGs associated with PL application under realistic field-based conditions.

Antibiotics in Canadian poultry productions and anticipated alternatives

The use of antibiotics in food-producing animals has significantly increased animal health by lowering mortality and the incidence of diseases. Antibiotics also have largely contributed to increase productivity of farms. However, antibiotic usage in general and relevance of non-therapeutic antibiotics (growth promoters) in feed need to be reevaluated especially because bacterial pathogens of humans and animals have developed and shared a variety of antibiotic resistance mechanisms that can easily be spread within microbial communities. In Canada, poultry production involves more than 2600 regulated chicken producers who have access to several antibiotics approved as feed additives for poultry. Feed recipes and mixtures vary greatly geographically and from one farm to another, making links between use of a specific antibiotic feed additive and production yields or selection of specific antibiotic-resistant bacteria difficult to establish. Many on-farm studies have revealed the widespread presence of antibiotic-resistant bacteria in broiler chickens. While some reports linked the presence of antibiotic-resistant organisms to the use of feed supplemented with antibiotics, no recent studies could clearly demonstrate the benefit of antimicrobial growth promoters on performance and production yields. With modern biosecurity and hygienic practices, there is a genuine concern that intensive utilization of antibiotics or use of antimicrobial growth promoters in feed might no longer be useful. Public pressure and concerns about food and environmental safety (antibiotic residues, antibiotic-resistant pathogens) have driven researchers to actively look for alternatives to antibiotics. Some of the alternatives include pre- and probiotics, organic acids and essential oils. We will describe here the properties of some bioactive molecules, like those found in cranberry, which have shown interesting polyvalent antibacterial and immuno-stimulatory activities.

Characterization of Extraintestinal Pathogenic Escherichia coli isolated from retail poultry meats from Alberta, Canada

Extraintestinal Pathogenic Escherichia coli (ExPEC) have the potential to spread through fecal waste resulting in the contamination of both farm workers and retail poultry meat in the processing plants or environment. The objective of this study was to characterize ExPEC from retail poultry meats purchased from Alberta, Canada and to compare them with 12 human ExPEC representatives from major ExPEC lineages. Fifty-four virulence genes were screened by a set of multiplex PCRs in 700 E. coli from retail poultry meat samples. ExPEC was defined as the detection of at least two of the following virulence genes: papA/papC, sfa, kpsMT II and iutA. Genetic relationships between isolates were determined using pulsed field gel electrophoresis (PFGE). Fifty-nine (8.4%) of the 700 poultry meat isolates were identified as ExPEC and were equally distributed among the phylogenetic groups A, B1, B2 and D. Isolates of phylogenetic group A possessed up to 12 virulence genes compared to 24 and 18 genes in phylogenetic groups B2 and D, respectively. E. coli identified as ExPEC and recovered from poultry harbored as many virulence genes as those of human isolates. In addition to the iutA gene, siderophore-related iroN and fyuA were detected in combination with other virulence genes including those genes encoding for adhesion, protectin and toxin while the fimH, ompT, traT, uidA and vat were commonly detected in poultry ExPEC. The hemF, iss and cvaC genes were found in 40% of poultry ExPEC. All human ExPEC isolates harbored concnf (cytotoxic necrotizing factor 1 altering cytoskeleton and causing necrosis) and hlyD (hemolysin transport) genes which were not found in poultry ExPEC. PFGE analysis showed that a few poultry ExPEC isolates clustered with human ExPEC isolates at 55-70% similarity level. Comparing ExPEC isolated from retail poultry meats provides insight into their virulence potential and suggests that poultry associated ExPEC may be important for retail meat safety. Investigations into the ability of our poultry ExPEC to cause human infections are warranted.

Duplex PCR methods for the molecular detection of Escherichia fergusonii isolates from broiler chickens

Escherichia fergusonii is an emerging pathogen that has been isolated from a wide range of infections in animals and humans. Primers targeting specific genes, including yliE (encoding a conserved hypothetical protein of the cellulose synthase and regulator of cellulose synthase island), EFER_1569 (encoding a hypothetical protein, putative transcriptional activator for multiple antibiotic resistance), and EFER_3126 (encoding a putative triphosphoribosyl-dephospho-coenzyme A [CoA]), were designed for the detection of E. fergusonii by conventional and real-time PCR methods. Primers were screened by in silico PCR against 489 bacterial genomic sequences and by both PCR methods on 55 reference and field strains. Both methods were specific and sensitive for E. fergusonii, showing amplification only for this bacterium. Conventional PCR required a minimum bacterial concentration of approximately 10(2) CFU/ml, while real-time PCR required a minimum of 0.3 pg of DNA for consistent detection. Standard curves showed an efficiency of 98.5%, with an R(2) value of 0.99 for the real-time PCR assay. Cecal and cloacal contents from 580 chickens were sampled from broiler farms located in the Fraser Valley (British Columbia, Canada). Presumptive E. fergusonii isolates were recovered by enrichment and plating on differential and selective media. Of 301 total presumptive isolates, 140 (46.5%) were identified as E. fergusonii by biochemical profiling with the API 20E system and 268 (89.0%) using PCR methods. E. fergusonii detection directly from cecal and cloacal samples without preenrichment was achieved with both PCR methods. Hence, the PCR methods developed in this work significantly improve the detection of E. fergusonii.

Antibiotic resistance and diversity of Salmonella enterica serovars associated with broiler chickens

The objective of this study was to analyze the antibiotic resistance phenotype and genotype of Salmonella isolated from broiler production facilities. A total of 193 Salmonella isolates recovered from commercial farms in British Columbia, Canada, were evaluated. Susceptibility to antibiotics was determined with the Sensititre system. Virulence and antibiotic resistance genes were detected by PCR assay. Genetic diversity was determined by pulse-field gel electrophoresis (PFGE) typing. Seventeen serovars of Salmonella were identified. The most prevalent Salmonella serovars were Kentucky (29.0% of isolates), Typhimurium (23.8%), Enteritidis (13.5%), and Hadar (11.9%); serovars Heidelberg, Brandenburg, and Thompson were identified in 7.7, 4.1, and 3.6% of isolates, respectively. More than 43% of the isolates were simultaneously resistant to ampicillin, amoxicillin-clavulanic acid, ceftiofur, cefoxitim, and ceftriaxone. This β-lactam resistance pattern was observed in 33 (58.9%) of the Salmonella Kentucky isolates; 2 of these isolates were also resistant to chloramphenicol, streptomycin, sulfisoxazole, and tetracycline. Genes associated with resistance to aminoglycosides (aadA1, aadA2, and strA), β-lactams (blaCMY-2, blaSHV, and blaTEM), tetracycline (tetA and tetB), and sulfonamide (sul1) were detected among corresponding resistant isolates. The invasin gene (invA) and the Salmonella plasmid virulence gene (spvC) were found in 97.9 and 25.9% of the isolates, respectively, with 33 (71.7%) of the 46 Salmonella Typhimurium isolates and 17 (65.4%) of the 26 Salmonella Enteritidis isolates carrying both invA and spvC. PGFE typing revealed that the antibiotic-resistant serovars were genetically diverse. These data confirm that broiler chickens can be colonized by genetically diverse antibiotic-resistant Salmonella isolates harboring virulence determinants. The presence of such strains is highly relevant to food safety and public health.

Effect of 3',5'-cyclic diguanylic acid in a broiler Clostridium perfringens infection model

In an effort to explore strategies to control Clostridium perfringens, we investigated the synergistic effect of a ubiquitous bacterial second messenger 3',5'-cyclic diguanylic acid (c-di-GMP) with penicillin G in a broiler challenge model. All chicks were inoculated in the crop by gavage on d 14, 15, and 16 with a mixture of 4 C. perfringens strains. Birds were treated with saline (control group) or 20 nmol of c-di-GMP by gavage or intramuscularly (IM) on d 24, all in conjunction with penicillin G in water for 5 d. Weekly samplings of ceca and ileum were performed on d 21 to 35 for C. perfringens and Lactobacillus enumeration. On d 35 of age, the IM treatment significantly (P < 0.05) reduced C. perfringens in the ceca, suggesting possible synergistic activity between penicillin G and c-di-GMP against C. perfringens in broiler ceca. Moreover, analysis of ceca DNA for the presence of a series of C. perfringens virulence genes showed a prevalence of 30% for the Clostridium perfringens alpha-toxin gene (cpa) from d 21 to 35 in the IM-treated group, whereas the occurrence of the cpa gene increased from 10 to 60% in the other 2 groups (control and gavage) from d 21 to 35. Detection of β-lactamase genes (blaCMY-2, blaSHV, and blaTEM) indicative of gram-negative bacteria in the same samples from d 21 to 35 did not show significant treatment effects. Amplified fragment-length polymorphism showed a predominant 92% similarity between the ceca of 21-d-old control birds and the 35-d-old IM-treated c-di-GMP group. This suggests that c-di-GMP IM treatment might be effective at restoring the normal microflora of the host on d 35 after being challenged by C. perfringens. Our results suggest that c-di-GMP can reduce the colonization of C. perfringens in the gut without increasing the selection pressure for some β-lactamase genes or altering the commensal bacterial population.

Multidrug resistant commensal Escherichia coli in animals and its impact for public health

After the era of plentiful antibiotics we are alarmed by the increasing number of antibiotic resistant strains. The genetic flexibility and adaptability of Escherichia coli to constantly changing environments allows to acquire a great number of antimicrobial resistance mechanisms. Commensal strains of E. coli as versatile residents of the lower intestine are also repeatedly challenged by antimicrobial pressures during the lifetime of their host. As a consequence, commensal strains acquire the respective resistance genes, and/or develop resistant mutants in order to survive and maintain microbial homeostasis in the lower intestinal tract. Thus, commensal E. coli strains are regarded as indicators of antimicrobial load on their hosts. This chapter provides a short historic background of the appearance and presumed origin and transfer of antimicrobial resistance genes in commensal intestinal E. coli of animals with comparative information on their pathogenic counterparts. The dynamics, development, and ways of evolution of resistance in the E. coli populations differ according to hosts, resistance mechanisms, and antimicrobial classes used. The most frequent tools of E. coli against a variety of antimicrobials are the efflux pumps and mobile resistance mechanisms carried by plasmids and/or other transferable elements. The emergence of hybrid plasmids (both resistance and virulence) among E. coli is of further concern. Co-existence and co-transfer of these "bad genes" in this huge and most versatile in vivo compartment may represent an increased public health risk in the future. Significance of multidrug resistant (MDR) commensal E. coli seem to be highest in the food animal industry, acting as reservoir for intra- and interspecific exchange and a source for spread of MDR determinants through contaminated food to humans. Thus, public health potential of MDR commensal E. coli of food animals can be a concern and needs monitoring and more molecular analysis in the future.

Presence of multi-drug resistant pathogenic Escherichia coli in the San Pedro River located in the State of Aguascalientes, Mexico

Contamination of surface waters in developing countries is a great concern. Treated and untreated wastewaters have been discharged into rivers and streams, leading to possible waterborne infection outbreaks and may represent a significant dissemination mechanism of antibiotic resistance genes. In this study, the water quality of San Pedro River, the main river and pluvial collector of the Aguascalientes State, Mexico was assessed. Thirty sample locations were tested throughout the River. The main physicochemical parameters of water were evaluated. Results showed high levels of fecal pollution as well as inorganic and organic matter abundant enough to support the heterotrophic growth of microorganisms. These results indicate poor water quality in samples from different locations. One hundred and fifty Escherichia coli were collected and screened by PCR for several virulence genes. Isolates were classified as either pathogenic (n = 91) or commensal (n = 59). The disc diffusion method was used to determine antimicrobial susceptibility to 13 antibiotics. Fifty-two percent of the isolates were resistant to at least one antimicrobial agent and 30.6% were multi-resistant. Eighteen E. coli strains were quinolone resistant of which 16 were multi-resistant. Plasmid-mediated quinolone resistance (PMQR) genes were detected in 12 isolates. Mutations at the Ser-83→Leu and/or Asp-87→Asn in the gyrA gene were detected as well as mutations at the Ser-80→Ile in parC. An E. coli microarray (Maxivirulence V 3.1) was used to characterize the virulence and antimicrobial resistance genes profiles of the fluoroquinolone-resistant isolates. Antimicrobial resistance genes such as bla TEM, sulI, sulII, dhfrIX, aph3 (strA), and tet (B) as well as integrons were found in fluoroquinolone (FQ) resistance E. coli strains. The presence of potential pathogenic E. coli and antibiotic resistance in San Pedro River such as FQ resistant E. coli could pose a potential threat to human and animal health.