Pathogenic and multidrug-resistant Escherichia fergusonii from broiler chicken

Impact of Nanoencapsulated Rosemary Essential Oil as a Novel Feed Additive on Growth Performance, Nutrient Utilization, Carcass Traits, Meat Quality and Gene Expression of Broiler Chicken

This study evaluated the effect of free and nanoencapsulated rosemary essential oil (REO) as an antibiotic alternative in broiler diets on growth performance, nutrient digestibility, carcass traits, meat quality and gene expression. Four hundred twenty day-old commercial broiler chicks (VENCOBB) were randomly allocated to seven dietary treatments, each having four replicates of fifteen chicks. The dietary treatments comprised control (CON) fed a basal diet only, AB (basal diet + 10 mg enramycin/kg), CS (basal diet + 150 mg chitosan nanoparticles/kg), REOF100 and REOF200 (basal diet + 100 mg and 200 mg free REO/kg, respectively), and REON100 and REON200 (basal diet + 100 mg and 200 mg nanoencapsulated REO/kg, respectively). Overall (7-42 d), REON200 showed the highest (p < 0.001) body weight gain (1899 g/bird) and CON had the lowest gain (1742 g/bird), while the CS, REOF100 and REOF200 groups had a similar gain, but lower than that of the AB and REON100 groups. Feed intake was not affected by dietary treatments. Overall, the feed efficiency increased (p = 0.001) by 8.47% in the REON200 group and 6.21% in the AB and REON100 groups compared with the CON. Supplementation of REO improved (p < 0.05) dry matter and crude protein digestibility, with the highest values in REON100 and REON200. Ether extract, crude fiber, calcium and phosphorus digestibility values showed no difference among the groups. The dressing, breast, thigh % increased (p < 0.05) and abdominal fat % decreased (p < 0.001) more in the REON200 group than with other treatments and CON. In breast meat quality, water holding capacity and extract reserve volume increased (p < 0.05) while drip loss and cholesterol content decreased (p < 0.05) in REON100 and REON200. No change was observed in the breast meat color among dietary treatments and CON. The REON100 and REON200 groups had reduced (p < 0.05) meat lipid peroxidation as depicted by the decreased levels of TBARS, free fatty acids and peroxide value compared to other treatments and CON. The expression of the Mucin 2, PepT1 and IL-10 genes was upregulated (p < 0.001) and TNF-α downregulated (p < 0.001) by dietary addition of REO particularly in the nanoencapsulated form compared with the CON. In conclusion, nanoencapsulated REO, especially at 200 mg/kg diet, showed promising results as an antibiotic alternative in improving the performance, nutrient digestibility, carcass traits, meat quality and upregulation of growth and anti-inflammatory genes.

Effects of pomegranate (Punica granatum L.) peel on the growth performance and intestinal microbiota of broilers challenged with Escherichia coli

The effects of pomegranate peel on the growth performance, intestinal morphology, and the cecal microbial community were investigated in broilers challenged with avian pathogenic Escherichia coli (APEC) O78. A total of 240 one-day-old chicks (120 males and 120 females) were randomly and evenly allotted into 4 treatment groups (each with 6 biological replicates each of 10 chicks), i.e., negative control (NC), positive control (PC), and 2 experimental groups treated with 0.2% fermented pomegranate peel (FP) and 0.2% unfermented pomegranate peel (UFP), respectively, with PC, FP, and UFP groups challenged with APEC O78 (5 × 108 CFU) on day 14. Results showed that the challenge of APEC O78 decreased the body weight (BW) and average daily gain (ADG) of broilers from 1 to 28 d (P < 0.01). These broilers exhibited more pathological conditions in the heart and liver and higher mortality rates in 28 d compared to the NC group. Diet supplemented with pomegranate peel (either fermented or unfermented) significantly increased BW, ADG, and the villus height/crypt depth ratio (VCR) of small intestine in 28 d compared to the NC group (P < 0.05). Results of the taxonomic structure of the gut microbiota showed that compared to the NC group, the APEC challenge significantly decreased the relative abundance of Bacteroidetes and increased the relative abundance of Firmicutes (P < 0.01). Compared to the PC group, the relative abundance of Ruminococcus_torques_group in FP group was increased, while the relative abundance of Alistipes was decreased. In summary, our study showed that the dietary supplementation of pomegranate peel could maintain the intestinal microbiota at a state favorable to the host, effectively reduce the abnormal changes in the taxonomic structure of the intestinal microbiota, and improve the growth performance in broilers treated with APEC.

Identification of acacia gum fermenting bacteria from pooled human feces using anaerobic enrichment culture

Commercial acacia gum (AG) used in this study is a premium-grade free-flowing powder. It is a gummy exudate composed of arabinogalactan branched polysaccharide, a biopolymer of arabinose and galactose. Also known as food additive, acacia gum (E414), which is presently marketed as a functional dietary fiber to improve overall human gut health. The health effects may be related to the luminal pH regulation from the short-chain fatty acids (SCFA) production. Studies suggested that amylolytic and butyrogenic pathways are the major factors determining the SCFA outcome of AG in the lower gut. However, the primary bacteria involved in the fermentation have not been studied. This study aimed to investigate the putative primary degraders of acacia gum in the gut ecosystem. Isolation and identification of gum-fermenting bacteria were performed through enrichment culture fermentation. The experiment was conducted in an anaerobic chamber for 144 h in three stages. The study was conducted in triplicate using an anaerobic chamber system. This culture system allows specific responses to support only bacteria that are responsible for gum fermentation among the gut microbiota. Five bacterial strains were isolated and found to be gum-fermenting bacteria. Based on the 16s RNA sequence, the isolates matched to butyrate-producing Escherichia fergusonii, ATCC 35469.

Characterization of two novel lytic bacteriophages having lysis potential against MDR avian pathogenic Escherichia coli strains of zoonotic potential

Avian pathogenic E. coli (APEC) is associated with local and systemic infections in poultry, ducks, turkeys, and many other avian species, leading to heavy economical losses. These APEC strains are presumed to possess zoonotic potential due to common virulence markers that can cause urinary tract infections in humans. The prophylactic use of antibiotics in the poultry sector has led to the rapid emergence of Multiple Drug Resistant (MDR) APEC strains that act as reservoirs and put human populations at risk. This calls for consideration of alternative strategies to decrease the bacterial load. Here, we report isolation, preliminary characterization, and genome analysis of two novel lytic phage species (Escherichia phage SKA49 and Escherichia phage SKA64) against MDR strain of APEC, QZJM25. Both phages were able to keep QZJM25 growth significantly less than the untreated bacterial control for approximately 18 h. The host range was tested against Escherichia coli strains of poultry and human UTI infections. SKA49 had a broader host range in contrast to SKA64. Both phages were stable at 37 °C only. Their genome analysis indicated their safety as no recombination, integration and host virulence genes were identified. Both these phages can be good candidates for control of APEC strains based on their lysis potential.

Conditions Necessary for the Transfer of Antimicrobial Resistance in Poultry Litter

Animal manures contain a large and diverse reservoir of antimicrobial resistance (AMR) genes that could potentially spillover into the general population through transfer of AMR to antibiotic-susceptible pathogens. The ability of poultry litter microbiota to transmit AMR was examined in this study. Abundance of phenotypic AMR was assessed for litter microbiota to the antibiotics: ampicillin (Ap; 25 μg/mL), chloramphenicol (Cm; 25 μg/mL), streptomycin (Sm; 100 μg/mL), and tetracycline (Tc; 25 μg/mL). qPCR was used to estimate gene load of streptomycin-resistance and sulfonamide-resistance genes aadA1 and sul1, respectively, in the poultry litter community. AMR gene load was determined relative to total bacterial abundance using 16S rRNA qPCR. Poultry litter contained 10⁸ CFU/g, with Gram-negative enterics representing a minor population (<10⁴ CFU/g). There was high abundance of resistance to Sm (10⁶ to 10⁷ CFU/g) and Tc (10⁶ to 10⁷ CFU/g) and a sizeable antimicrobial-resistance gene load in regards to gene copies per bacterial genome (aadA1: 0.0001-0.0060 and sul1: 0.0355-0.2455). While plasmid transfer was observed from Escherichia coli R100, as an F-plasmid donor control, to the Salmonella recipient in vitro, no AMR Salmonella were detected in a poultry litter microcosm with the inclusion of E. coli R100. Confirmatory experiments showed that isolated poultry litter bacteria were not interfering with plasmid transfer in filter matings. As no R100 transfer was observed at 25 °C, conjugative plasmid pRSA was chosen for its high plasmid transfer frequency (10^-4 to 10^-5) at 25 °C. While E. coli strain background influenced the persistence of pRSA in poultry litter, no plasmid transfer to Salmonella was ever observed. Although poultry litter microbiota contains a significant AMR gene load, potential to transmit resistance is low under conditions commonly used to assess plasmid conjugation.

First case report of pustules associated with Escherichia fergusonii in the chinese pangolin (Manis pentadactyla aurita)

BACKGROUND

Escherichia fergusonii is a common conditionally pathogenic bacterium that infects humans and animals. E. fergusonii has been reported to cause diarrhea, respiratory disease, and septicemia, but it is rarely reported to cause skin infections in animals. E. fergusonii has been isolated from the skin and muscular tissue of Chinese pangolin (Manis pentadactyla aurita). To date, there have been no reports of Chinese pangolins with clinical signs of skin diseases.

CASE PRESENTATION

This case report describes the clinical case of a subadult (bodyweight: 1.1 kg) female Chinese pangolin from wild rescue with pustules and subcutaneous suppurative infection due to E. fergusonii in the abdominal skin. Bacterial culture, Biochemical analysis, PCR and histopathology were utilized to identify the bacteria in the pustule puncture fluid and infected tissue. To the best of our knowledge, this is the first report of E. fergusonii-related pustules on a Chinese pangolin.

CONCLUSION

This case report presents the first observed skin infection in a Chinese pangolin. E. fergusonii infection should be considered as a possible differential diagnosis of pustules and subcutaneous suppurative skin conditions in Chinese pangolins, and we also provide several recommendations for the diagnosis and treatment of this disease.

Antimicrobial resistance and molecular epidemiological analysis of Escherichia fergusonii harboring the mcr gene in pigs and broiler chickens in Okinawa, Japan

The dissemination of mcr-harboring Enterobacteriaceae, e.g., Escherichia fergusonii, with resistance to colistin via animal products is a public health concern. In our previous study, E. fergusonii harboring the mcr gene were isolated from 11 pigs and 43 chickens. To understand the spread of mcr-harboring E. fergusonii in Okinawa, Japan, and to gain further insights into how they can be controlled, an antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), a conjugation test for the transferability of mcr-harboring plasmids, and PCR-based replicon typing (PBRT) were performed using the 54 strains. According to the disk-diffusion and broth microdilution methods, 9 of the 11 strains from pigs and 9 of the 43 strains from chickens had multidrug resistance (MDR). The broth microdilution method showed that all strains were resistant to colistin, and the minimum inhibitory concentration of colistin was 4-16 μg/mL. PFGE suggested identical PFGE types were being transmitted within one pig farm, within one chicken farm, and among several chicken farms. These findings showed that some mcr-harboring E. fergusonii in Okinawa exhibited MDR, and these had spread within farms and between farms. In the mcr gene conjugation test and PBRT, a type IncI2 plasmid replicon was detected in all mcr-1-harboring transconjugants. Therefore, evidence suggests that the IncI2 plasmid is probably involved in the transmission of the mcr-1 gene. It is important to monitor the antimicrobial resistance profile and dissemination of the IncI2 plasmid in mcr-harboring E. fergusonii.

Avian strains of emerging pathogen Escherichia fergusonii are phylogenetically diverse and harbor the greatest AMR dissemination potential among different sources: Comparative genomic evidence

Introduction

Escherichia fergusonii is regarded as an emerging pathogen with zoonotic potential. In the current study, we undertook source-wise comparative genomic analyses (resistome, virulome, mobilome and pangenome) to understand the antimicrobial resistance, virulence, mobile genetic elements and phylogenetic diversity of E. fergusonii.

Methods

Six E. fergusonii strains (5 multidrug resistant strains and 1 biofilm former) were isolated from poultry (duck faeces and retail chicken samples). Following confirmation by phenotypic and molecular methods, the isolates were further characterized and their genomes were sequenced. Comparative resisto-virulo-mobilome analyses and pangenomics were performed for E. fergusonii genomes, while including 125 other E. fergusonii genomes available from NCBI database.

Results and discussion

Avian and porcine strains of E. fergusonii were found to carry significantly higher number of antimicrobial resistance genes (p < 0.05) and mobile genetic elements (plasmids, transposons and integrons) (p < 0.05), while the pathogenic potential of bovine strains was significantly higher compared to other strains (p < 0.05). Pan-genome development trends indicated open pan-genome for all strains (0 < γ < 1). Genomic diversity of avian strains was found to be greater than that from other sources. Phylogenetic analysis revealed close clustering among isolates of similar isolation source and geographical location. Indian isolates of E. fergusonii clustered closely with those from Chinese and a singleton Australian isolate. Overall, being the first pangenomic study on E. fergusonii, our analysis provided important cues on genomic features of the emerging pathogen E. fergusonii while highlighting the potential role of avian strains in dissemination of AMR.

Growth studies in commercial broiler birds offered citric acid in formulated feed with low mineral density

Study of 35 days was conducted to evaluate citric acid (CA) as an additive in poultry broiler feed with lower mineral content of calcium (Ca) and total phosphorus (TP) in commercial broiler poultry birds for its effect on growth, nutrient utilization, carcass characteristics, and economics. Vancobb-400 strain day old broiler chicks were divided into four main treatment groups T_0, T₁, T₂, and T_3. Treatment groups were further divided into eight replicates with ten chicks in each. T₀ served as control, given standard corn-soy flakes-based ration (Pre-starter %: Crude protein (CP)-23, Ca-1.00, TP-0.70; Starter %: CP-22, Ca-1.10, TP-0.72, and Finisher %: CP-20, Ca-0.99, TP-0.70). Treatment T₁ served as positive control with added 0.5% CA (Pre-starter %: CP-23, Ca-1.00, TP-0.70; Starter %: CP-22, Ca-1.10, TP-0.72 and Finisher %: CP-20, Ca-0.99, TP-0.70). Treatment T₂ was given feed containing 0.5% CA with low Ca and TP content (Pre-starter %: CP-23, Ca-0.90, TP-0.66; Starter %: CP-22, Ca-0.99, TP-0.71 and Finisher %: CP-20, Ca-0.90, TP-0.69), whereas treatment T₃ was given feed containing 0.5% CA with moderately low Ca and TP content (Pre-starter %: CP-23, Ca-0.80, TP-0.65; Starter %: CP-22, Ca-0.88, TP-0.70 and Finisher %: CP-20, Ca-0.79, TP-0.68). Birds offered moderately low Ca and TP with 0.5% CA addition, exhibited higher growth rate (P < 0.05), better nutrient utilization with positive influence on dressing percentage and forequarters weight. Economics of broiler feeding revealed that 0.5% CA supplementation fetched highest gross return above feed cost in broiler birds offered feed with moderately low Ca and TP content whereas lowest profit was recorded in feed with low content of Ca and TP. In conclusion, supplementation of 0.5% CA in feed with low and moderately low Ca and TP content positively influenced overall growth, and carcass characteristics. Economics of broiler feeding with moderately low Ca and TP content revealed highest profit with CA (0.5%) supplementation.

Effects of Total Sulfur Amino Acids on Growth Performance, Immunity, and Meat Yield in Broilers Fed Diets With and Without Antibiotics

Two experiments were conducted to evaluate the effects of digestible sulfur amino acids (SAA) on performance, carcass yield, immunity, and amino acid transporters in broilers fed diets with or without an antibiotic growth promoter (AGP). In experiment 1, a total of 250 1-day-old Cobb500 male chicks were assigned to battery cages with two levels of AGP (0 and 0.05% bacitracin) and five levels of SAA (0.7, 0.8, 0.9, 1.0, and 1.1%) for 21 d. In experiment 2, a total of 900 1-day-old Cobb500 male chicks were assigned to floor pens with two levels of AGP and three levels of SAA for the starter (0.7, 0.8, and 0.9%) or finisher phase (0.52, 0.62, and 0.72%) for 42 d. In experiment 1, from 0 to 7 d, the body weight gain (BWG) was the lowest for birds fed 0.7% SAA. The AGP significantly decreased the feed conversion ratio (FCR), and birds fed 0.9 and 1.1% SAA had significantly lower FCR than 0.7% SAA. From 8 to 14 d, for the AGP-fed birds, the lowest BWG was observed in the 0.7% SAA group. In birds not fed AGP, birds fed 0.8% SAA had higher BWG than 0.7 and 1.1% SAA. Birds fed 0.7% SAA diet had lower feed intake (FI) than 0.8% SAA and higher FCR than 0.8, 0.9, and 1.0% SAA. In experiment 2, from 0 to 21 d, the lowest BWG and the highest FCR were observed in birds fed 0.7% SAA, whereas birds fed 0.9% SAA had the highest BWG and lowest FCR. From 22 to 42 d, FCR was lower for birds fed AGP, and for birds fed 0.72%. Interactions between the factors were found for FI and BWG. The whole thigh and wing weights were the highest for 0.62% SAA, and the pectoralis major weight was higher for birds fed 0.62% SAA than those fed 0.52% SAA. There was an interaction between SAA and AGP for Lat1 (large neutral amino acid transporter) expression, and AGP-fed birds had higher expression of ileal interleukin 1β (Il−1β gene). The interleukin 10 (Il-10) expression was upregulated in the ileum. There was an interaction between factors for sodium-dependent neutral amino acid transporter B [0] AT1 (SLC6A19) expression. The results suggested that both AGP and SAA supplementation would affect the growth performance of the broilers.

Beneficial Alteration in Growth Performance, Immune Status, and Intestinal Microbiota by Supplementation of Activated Charcoal-Herb Extractum Complex in Broilers

This study aimed to examine the effects of activated charcoal-herb extractum complex (CHC) on the growth performance of broilers, inflammatory status, microbiota, and their relationships. A total of 864 1-day-old Arbor Acres male broilers (41.83 ± 0.64 g) were distributed to eight dietary treatments with six replicates (18 birds per replicate), which were a corn-soybean meal-based diet (NCON); basal diets supplemented with 250, 500, 750, or 1,000 mg/kg CHC, and three positive controls; basal diets supplemented with 200 mg/kg antibacterial peptide (AMP), 200 mg/kg calsporin (Probio) or 500 mg/kg montmorillonite. The study period was 42 days including the starter (day 0-21) and grower (day 22-42) phases. Compared with the NCON group, CHC supplementation (optimal dose of 500 mg/kg) increased (p < 0.05) growth performance and tended to increase feed conversion rate in broilers. CHC (optimal dose of 500 mg/kg) decreased the level of the interleukin-1β (IL-1β) and interferon-γ (IFN-γ) in serum and improved the levels of immunoglobulins A (IgA) and immunoglobulins A (IgM) in serum, and secretory immunoglobulin A (SIgA) in the mucosa of duodenum and jejunum (p < 0.05). In the ileum, CHC supplementation decreased community abundance represented by lower Sobs, Chao 1, Ace, and Shannon compared with NCON (p < 0.05). At the phylum level, CHC supplementation increased the abundance of Firmicutes, while decreasing the abundance of Bacteroidetes in ileum and cecum (p < 0.05). At the genus level, compared with the NCON group, CHC markedly reduced (p < 0.05) the abundances of pathogenic bacteria Alistipes in the ileum, which were negatively associated with the levels of SIgA and IL-1β in ileum mucosa. In conclusion, CHC had beneficial effects on growth performance, immune status, and intestinal microbiota composition. CHC had dual functions of absorption like clays and antibacterial like antibacterial peptides.

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

A Study of the Antimicrobial Activity of Combined Black Pepper and Cinnamon Essential Oils against Escherichia fergusonii in Traditional African Yoghurt

The antimicrobial activity of the essential oils of black pepper (BPE) and cinnamon bark (CE) extracts against E. fergusonii was assessed in pasteurized full cream milk during and post-fermentation. The milk was fermented with 1% (v/v) of Lactobacillus delbrueckii subspecies bulgaricus (NCIMB 11778) and Streptococcus thermophilus (NCIMB 10387) (approx. 10⁶ cfu/mL each) and incubated and stored at 25 °C for 5 days (144 h) or at 43 °C for 24 h and then stored at 25 °C for 120 h. The milk was spiked with E. fergusonii at the start of fermentation by the lactic acid bacteria (pre-fermentation contamination) for after fermentation (post fermentation contamination). BPE and CE were applied at concentrations based on their minimum inhibitory concentration of 0.5% and 0.25% respectively as follows: 0.5% BPE alone; 0.125% BPE with 0.1875% CE; 0.25% BPE with 0.125% CE; 0.375% BPE with 0.0625% CE; 0.25% CE alone. Results showed that during fermentation at 25 °C, E. fergusonii grew to a similar level (approx. 10⁹ CFU/mL) in control samples and 10⁸ CFU/mL when BPE or CE were added alone. Whereas, in the samples with the combined essential oils, the bacterium grew to 10⁶–10⁷ CFU/mL only. During the milk fermentation at 43 °C, E. fergusonii grew to approx. 10⁹ CFU/mL in samples without treatment. However, it was not detected in samples containing mixed BPE with CE after 8, 10 and 12 h of fermentation. Subsequent storage at 25 °C resulted in undetectable levels of the bacterium in all the samples treated with BPE or CE after 24 h of storage. These results indicated that BPE in combination with CE reduced growth during fermentation and was bactericidal during storage.

In-Vitro Characterization of Growth Inhibition against the Gut Pathogen of Potentially Probiotic Lactic Acid Bacteria Strains Isolated from Fermented Products

Lactic acid bacteria (LAB) are probiotic candidates that may restore the balance of microbiota populations in intestinal microbial ecosystems by controlling pathogens and thereby promoting host health. The goal of this study was to isolate potential probiotic LAB strains and characterize their antimicrobial abilities against pathogens in intestinal microbiota. Among 54 LAB strains isolated from fermented products, five LAB strains (NSMJ15, NSMJ16, NSMJ23, NSMJ42, and NFFJ04) were selected as potential probiotic candidates based on in vitro assays of acid and bile salt tolerance, cell surface hydrophobicity, adhesion to the intestinal epithelium, and antagonistic activity. Phylogenetic analysis based on 16S rRNA genes showed that they have high similarities of 99.58-100% to Lacticaseibacillus&nbsp;paracasei strains NSMJ15 and NFFJ04, Lentilactobacillus parabuchneri NSMJ16, Levilactobacillus&nbsp;brevis NSMJ23, and Schleiferilactobacillus harbinensis NSMJ42. To characterize their antimicrobial abilities against pathogens in intestinal microbiota, the impact of cell-free supernatant (CFS) treatment in 10% (v/v) fecal suspensions prepared using pooled cattle feces was investigated using in vitro batch cultures. Bacterial community analysis using rRNA amplicon sequencing for control and CFS-treated fecal samples at 8 and 16 h incubation showed the compositional change after CFS treatment for all five LAB strains. The changed compositions were similar among them, but there were few variable increases or decreases in some bacterial groups. Interestingly, as major genera that could exhibit pathogenicity and antibiotic resistance, the members of Bacillus, Escherichia, Leclercia, Morganella, and Vagococcus were decreased at 16 h in all CFS-treated samples. Species-level classification suggested that the five LAB strains are antagonistic to gut pathogens. This study showed the probiotic potential of the five selected LAB strains; in particular, their antimicrobial properties against pathogens present in the intestinal microbiota. These strains would therefore seem to play an important role in modulating the intestinal microbiome of the host.

Extract of neem (Azadirachta indica) leaf exhibits bactericidal effect against multidrug resistant pathogenic bacteria of poultry

The aim of the study was to determine the efficacy of neem leaf extract against multidrug resistant (MDR) pathogenic bacteria. Laboratory stock culture of Pasteurella multocida, Salmonella pullorum, Salmonella gallinarum and Escherichia coli was revived. Antibiogram profiles of these bacteria were determined by disc diffusion method. Ethanolic extract of neem leaf was prepared. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of neem leaf extract (112.5, 100, 50, 25, 12.5, 6.25 and 3.12 mg/ml) against MDR pathogenic bacteria of poultry were determined by double dilution method. The MIC and MBC of the neem leaf extract were 12.5 and 25 mg/ml, respectively for P. multocida, 50 and 100 mg/ml for S. pullorum and S. gallinarum, 100 and 112.5 mg/ml for E. coli. Neem leaf extracts exhibited bactericidal effect against MDR pathogenic bacteria of poultry.

Genome-wide genetic marker analysis and genotyping of Escherichia fergusonii strain OTSVEF-60

Poultry originated Escherichia fergusonii (POEF), an emerging bacterial pathogen, causes a wide range of intestinal and extra-intestinal infections in the poultry industry which incurred significant economic losses worldwide. Chromosomal co-existence of antibiotics and metal resistance genes has recently been the focal point of POEF isolates besides its pathogenic potentials. This study reports the complete genome analysis of POEF strain OTSVEF-60 from the poultry originated samples of Bangladesh. The assembled draft genome of the strain was 4.2 Mbp containing 4503 coding sequences, 120 RNA (rRNA = 34, tRNA = 79, ncRNA = 7), and three intact phage signature regions. Forty-one broad range antibiotic resistance genes (ARGs) including dfrA12, qnrS1, bla_TEM-1, aadA2, tet(A), and sul-2 along with multiple efflux pump genes were detected, which translated to phenotypic resistant patterns of the pathogen to trimethoprim, fluoroquinolones, β-lactams, aminoglycoside, tetracycline, and sulfonamides. Moreover, 22 metal resistance genes were found co-existing within the genome of the POEF strain, and numerous virulence genes (VGs) coding for cit (AB), feo (AB), fep (ABCG), csg (ABCDEFG), fliC, ompA, gadA, ecpD, etc. were also identified throughout the genome. In addition, we detected a class I integron gene cassette harboring dfrA12, ant (3″)-I, and qacEΔ-sul2 genes; 42 copies of insertion sequence (IS) elements; and two CRISPR arrays. The genomic functional analysis predicted several metabolic pathways related to motility, flagellar assembly, epithelial cell invasion, quorum sensing, biofilm formation, and biosynthesis of vitamin, co-factors, and secondary metabolites. We herein for the first time detected multiple ARGs, VGs, mobile genetic elements, and some metabolic functional genes in the complete genome of POEF strain OTSVEF-60, which might be associated with the pathogenesis, spreading of ARGs and VGs, and subsequent treatment failure against this emerging avian pathogen with currently available antimicrobials.

Influence of dietary supplementation of Crassocephalum crepidioides leaf on growth, immune status, caecal microbiota, and meat quality in broiler chickens

The effect of dietary supplementation of Crassocephalum crepidioides leaf powder (CCLP) in comparison with oxytetracycline and butylated hydroxyanisole (BHA) on growth, caecal microbiota, immune status, blood chemistry, carcass traits, meat quality, and oxidative stability in broiler chickens was evaluated. Two hundred and eighty 1-day-old Arbor acre chicks were randomly assigned to a basal diet containing either no additive (control, CON), 400 ppm oxytetracycline + 150 ppm BHA (ANTIBIOX), 1000 ppm CCLP (CCLP-1), or 2000 ppm CCLP (CCLP-2) for 42 days. Each dietary group had seven replicates with ten birds per replicate. Supplemented birds had higher (P < 0.05) feed efficiency, hemoglobin, and hematocrit compared with the CON birds. Diet did not affect feed intake, body weight gain, splenic interleukin-1β, interleukin-6, interleukin-10, and serum IgM. The CCLP-2 birds had lower (P < 0.05) serum total and LDL cholesterol than did birds fed other treatments. Salmonella spp. and Escherichia coli counts and serum IgG were higher in the CON birds than in the supplemented birds. The ANTIBIOX birds had lower (P < 0.05) Lactobacillus spp. count, and higher (P < 0.05) E. coli count compared with the CCLP-supplemented birds. Carcass, muscle pH, and cook loss were not affected by diet. The CON breast meat had higher drip loss and lower redness than did the breast meat of the supplemented birds. Carbonyl content and TBARS value in the thigh and breast meat of the supplemented birds were lower (P < 0.05) than those of the CON birds. These results infer that CCLP exhibited antioxidant and antimicrobial properties that were comparable to those of BHA and oxytetracycline in the diet of broiler chickens.

Whole genome sequence of colistin-resistant Escherichia coli from western India

Background

With virtually dried out new antibiotic discovery pipeline, emergence and spread of antimicrobial resistance is a cause for global concern. Colistin, a cyclic polypeptide antibiotic, often regarded as last resort for multi drug resistance gram-negative bacteria, is also rendered ineffective by horizontal transfer of resistance genes. Surveillance of colistin resistance in GNB is essential to ascertain molecular epidemiology.

Methods

Whole genome sequencing (WGS) of an unusual colistin resistant urinary isolate of Escherichia coli was performed using Illumina MiSeq platform using 2x250bp V2 chemistry by following the manufactures protocol (Illumina Inc. USA). Multiple web-based bio-informatic tools were utilized to ascertain antibiotic resistant genes.

Results

An approximate 5.4 Mb of genome of the urinary isolate AFMC_UC19 was sequenced successfully. Mobile colistin resistance gene (mcr) on the plasmid responsible for horizontal spread was absent in the isolate.

Conclusion

Colistin resistance has been reported previously in Klebsiella pneumoniae and it is a rare occurrence in Escherichia coli in Indian setting. Although the isolate lack mcr mediated colistin resistance, emergence and spread of colistin resistant in gram-negative bacteria pose a threat.

Bacteria and antibiotic resistance detection in fractures of wild birds from wildlife rehabilitation centres in Spain

Anatomic adaptations make birds more prone to open fractures with exposed bone parts losing vascularization. As a result of this exposure, fractures are colonized by different microorganisms, including different types of bacteria, both aerobic and anaerobic, causing osteomyelitis in many cases. For this reason, antibiotic treatment is common. However, carrying out antibiotic treatment without carrying out a previous antibiogram may contribute to increased resistance against antibiotics, especially in migratory wild birds. In this paper, bacterial counts regarding fracture type, bacterial identification and antibiotic resistance have been analysed in wild birds from wildlife rehabilitation centres in Spain. The results obtained showed that open fractures had higher bacterial counts (CFU/mL) than closed ones. Bacteria in family Enterobacteriaceae, identified were Escherichia spp., Enterobacter spp., Shigella spp., Hafnia alvei, Proteus mirabilis, Leclercia adecarboxylata and Pantoea agglomerans. Other bacteria present in wild birds' fractures were Aeromonas spp., Enterococcus spp. Bacillus wiedmannii and Staphylococcus sciuri. All species found presented resistance to at least one of the antibiotics used. Wild birds can be implicated in the introduction, maintenance and global spreading of antibiotic resistant bacteria and represent an emerging public health concern. Results obtained in this paper support the idea that it is necessary to take this fact into account before antibiotic administration to wild animals, since it could increase the number of bacteria resistant to antibiotics.

Letter to the Editor: Escherichia fergusonii Harboring IncHI2 Plasmid Containing mcr-1 Gene-A Novel Reservoir for Colistin Resistance in Brazil

Emergence of colistin-resistant bacteria harboring mobile colistin resistance genes (mcr genes) pose a threat for food-producing animals and humans. In this article, we aim to highlight the emergence of Escherichia fergusonii as an important new reservoir to mcr-1-harboring plasmid in poultry production. Three strains closely related were isolated from cloacal swabs. Their genome contains four plasmids, including a 182,869 bp IncHI2 plasmid harboring the colistin resistance gene mcr-1. These results will contribute to our understanding of plasmid-mediated mcr-1 gene presence and transmission in E. fergusonii.

Rumex nervosus leaves meal improves body weight gain, duodenal morphology, serum thyroid hormones, and cecal microflora of broiler chickens during the starter period

A total of 192 one-day-old Ross 308 broiler chicks were assigned to 4 treatments with 8 replicate cages of 6 chicks (3♀ and 3♂) per cage according to a completely randomized block design. The dietary treatments were a basal diet (control) and a control diet supplemented with 1,000, 3,000, and 5,000 mg/kg Rumex nervosus leaves meal (RN). Gallic acid and some volatile compounds were detected in the RN extract. On day 10 of age, BW was improved (P = 0.016) with supplemental RN (1,000-5,000 mg/kg). On day 14 of age, dietary application of RN up to 3,000 mg/kg increased BWG (P = 0.003) compared with control, while a 1,000 mg/kg RN had the best feed conversion ratio (P = 0.016). On day 10 of age, samples were taken on a single female bird per replicate. The addition of RN (1,000-5,000 mg/kg) increased (P < 0.001) serum albumin and triiodothyronine levels and maximized the relative weight of breast meat (P = 0.003). Feeding a diet with 1,000 mg/kg RN resulted in greater duodenal villus height (P < 0.001) than control and the diet with 5,000 mg/kg RN. Broilers fed diet supplemented with 1,000 mg/kg RN had the best duodenal villus surface area (P < 0.001). Feeding a diet with 1,000 mg/kg RN decreased (P < 0.001) cecal Escherichia coli count compared with control and the diet with 5,000 mg/kg RN. Salmonella spp. count tended to increase with 5,000 mg/kg RN leaves meal (P = 0.069, linear P = 0.026). In conclusion, R. nervosus leaves meal could be considered as a phytogenic feed additive in broiler diets up to a 1,000-mg/kg inclusion rate because of its combined positive effects on BWG, feed conversion ratio, villus height, villus surface area, serum albumin and triiodothyronine hormone, and cecal E. coli during the starter period (day 10-14 of age). Further study is required to elucidate its molecular mechanism.

Contribution of the Broiler Breeders' Fecal Microbiota to the Establishment of the Eggshell Microbiota

In broiler chicken production, microbial populations on the eggshell surface following oviposition are still poorly characterized, though they may significantly impact both poultry and public health. The aim of this study was to describe the microbiota of both broiler breeder hens’ feces and the surface of their eggs to assess the contribution of the parental fecal microbiota to the eggshell microbiota. A total of twelve breeder flocks in Quebec, Canada, were sampled at two different times, and a total of 940 feces and 16,400 egg surface samples were recovered. Using 16S rRNA gene sequencing, we showed that even if the microbiota of both feces and eggshells were mainly composed of the phyla Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes, the bacterial community compositions and structures differed between both types of samples. Our results also showed that both the sampling time and the flock identity significantly influenced the alpha- and the beta-diversities of the studied microbiomes. Using a Venn diagram, we showed that 1790 operational taxonomic units (OTUs) were shared between feces and eggshell samples. Sequences associated with genera of potentially pathogenic and spoilage bacteria, Acinetobacter, Campylobacter, Escherichia/Shigella, Helicobacter, Listeria, Proteus, Pseudomonas, Salmonella, and Staphylococcus, were shared between sample types. Some OTUs highly represented in the fecal microbiota and associated with Lactobacillus and Streptococcus genera, were absent from eggshells, suggesting a selection during the microbiota transfer and/or the potential role of environmental contamination. To the best of our knowledge, this is the first study using 16S rRNA sequencing to describe the contribution of the transfer from the fecal microbial ecosystem of laying breeder hens to the establishment of the microbiota on the surface of laid eggs, as well as the bacterial communities at both the broiler breeder feces and the eggshell levels.

Translating 'big data': better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry

Recent technological advances has led to the generation, storage, and sharing of colossal sets of information ('big data'), and the expansion of 'omics' in science. To date, genomics/metagenomics, transcriptomics, proteomics, and metabolomics are arguably the most ground breaking approaches in food and public safety. Here we review some of the recent studies of foodborne pathogens (Campylobacter spp., Salmonella spp., and Escherichia coli) in poultry using big data. Genomic/metagenomic approaches have reveal the importance of the gut microbiota in health and disease. They have also been used to identify, monitor, and understand the epidemiology of antibiotic-resistance mechanisms and provide concrete evidence about the role of poultry in human infections. Transcriptomics studies have increased our understanding of the pathophysiology and immunopathology of foodborne pathogens in poultry and have led to the identification of host-resistance mechanisms. Proteomic/metabolomic approaches have aided in identifying biomarkers and the rapid detection of low levels of foodborne pathogens. Overall, 'omics' approaches complement each other and may provide, at least in part, a solution to our current food-safety issues by facilitating the development of new rapid diagnostics, therapeutic drugs, and vaccines to control foodborne pathogens in poultry. However, at this time most 'omics' approaches still remain underutilized due to their high cost and the high level of technical skills required.

Effects of laying breeder hens dietary β-carotene, curcumin, allicin, and sodium butyrate supplementation on the growth performance, immunity, and jejunum morphology of their offspring chicks

This study evaluated the growth performance, immunity, and jejunum morphology of chicks hatched from laying breeder hens given dietary additive supplementation, as well as chicks receiving direct antibiotic supplementation in early life. Hy-line breeder hens were allotted to 2 groups with 3 replicates. A control group (CON) was fed a basal diet, and the treatment group (CCAB) received β-carotene, curcumin, allicin, and sodium butyrate in addition to basal diet for 5 wk. Breeder-hen eggs were collected and hatched. The chicks hatched from the CON group were assigned to 2 treatments: a chick control group (cCON) and a chick treatment group (Cipro) given ciprofloxacin lactate into drinking water; the cCON group, Cipro group, and the chicks hatched from the CCAB group (cCCAB) were fed the same diet for 4 wk. The results demonstrated that there were significant differences between the CON and CCAB groups in the serum levels of IgA, IgG, IgM (triple P < 0.01), lysozyme (P < 0.05), and β-defensin (P < 0.05). The body weights of the cCCAB group's chicks increased at 1, 7, and 28 D of age (P < 0.05, P < 0.05, P < 0.01, respectively), and those of the Cipro group's chicks increased at 7 and 21 D of age (P < 0.01, P < 0.05). The tibial lengths of the cCCAB group's chicks increased at 1, 7, 14, 21, and 28 D of age (P < 0.01, P < 0.05, triple P < 0.01), and the lengths in the Cipro group increased at 7 and 14 D of age (P < 0.01, P < 0.01). Intestinal development, including intestinal length, jejunum morphology, and IgA positive cells, helps to explain these results. The breeder eggs from the CCAB group had higher IgG (P < 0.05) and IgM (P < 0.05) levels in the egg whites and higher IgA, IgG, and IgM levels (triple P < 0.01) in the egg yolks. In conclusion, β-carotene, curcumin, allicin, and sodium butyrate supplementation of laying breeder hen diets produced more advantages in growth performance and intestinal development in offspring than in chicks directly supplemented with antibiotics.

Meta-analysis of the influence of phytobiotic (pepper) supplementation in broiler chicken performance

The aim of the study is to use meta-analytical procedure to resolve uncertainty, identify knowledge gaps, and create new insights using published data on the phytobiotic effect of dietary pepper intervention on daily feed intake (DFI), average daily gain (ADG), and feed conversion ratio (FCR) in broiler chickens. The authors accessed AGORA, Scopus, ScienceDirect, and Google Scholar databases for primary studies published between 2011 and 2018 using combinations of different search terms. Fifteen studies were included to assess phytobiotic effect of pepper on DFI, FCR, and ADG in broiler chickens. Random-effects model (REM) was used to generate pooled effect estimates at 95% confidence intervals (CI). Analysis was performed using Open Meta-analyst for Ecology and Evolution (OpenMEE) software, while publication bias and source of heterogeneity were assessed using standard methods. Dietary pepper supplementation enhanced ADG (standardized mean difference (SMD) = 0.576, 95% CI 0.444 to 0.707, p < 0.001) and FCR (SMD = 0.325, 95% CI - 0.453 to - 0.196, p < 0.001) considering the presence of heterogeneity and publication bias. DFI (SMD = 0.052, 95%CI - 0.069 to 0.173, p = 0.403) was not significantly influenced by dietary pepper supplementation. Restricted subgroup analysis revealed that both black and red pepper increased ADG (p < 0.001). Broilers on black pepper intervention had better FCR (p = 0.002) than broilers on red pepper treatment. Higher (p < 0.05) DFI was obtained on broilers fed pepper-based diet at the rate of > 6 g/kg feed for 35 days. There was no association between DFI and explanatory variables (broiler strain used and number of broilers used), whereas study country influenced DFI (p < 0.001). Furthermore, there was an association between outcome of interests (ADG and FCR) and explanatory variables (supplementation level, study country, number of broilers used per treatment group, and broiler strain used). Broilers on dietary pepper intervention for 42 days had higher ADG (SMD = 62.2 g/bird/day, p < 0.001) than those on dietary pepper intervention for 56 days (SMD = 35.7 g/bird/day, p = 0.002). There is evidence of heterogeneity, and meta-regression analysis showed that study country, supplementation level, and broiler strain used explained most of the sources of heterogeneity. The results of the present study revealed the potential of dietary pepper intervention to improve production efficiency in broiler chickens. The current meta-analysis also set the steps for standardized experimental designs on the use of dietary pepper intervention in broiler feeding trials in the future.

Genome Analysis and Multiplex PCR Method for the Molecular Detection of Coresistance to Cephalosporins and Fosfomycin in Salmonella enterica Serovar Heidelberg

Heidelberg is among the top three Salmonella enterica serovars associated with human foodborne illness in Canada. Traditional culture and antimicrobial susceptibility testing techniques can be time-consuming to identify Salmonella Heidelberg resistant to cephalosporins and fosfomycin. Rapid and accurate detection of such antibiotic-resistant Salmonella Heidelberg isolates is essential to adopt appropriate control measures. In this study, 15 Salmonella Heidelberg strains isolated from feces of Canadian broiler chickens were characterized by whole genome sequencing. Salmonella Heidelberg genomes had an average coverage of greater than 80-fold, an average of 4,761 protein-coding genes, and all belonged to multilocus sequence type ST15. Genome sequences were compared with genomes in the National Center for Biotechnology Information Pathogen Detection database ( www.ncbi.nlm.nih.gov/pathogens/ ), including human outbreak isolates. The Canadian broiler isolates clustered with chicken isolates from the United States and an equine clinical isolate from Ontario, Canada. In agreement with their antimicrobial resistance phenotypes, several chromosomally encoded specific antimicrobial resistance genes including fosA7 and multidrug resistance efflux pump determinants were detected. An AmpC-like β-lactamase gene, bla_CMY-2, linked with a quaternary ammonium compound resistance gene, sugE, on a replicon type IncI1 plasmid was detected in all 15 broiler Salmonella Heidelberg isolates. Of the 205,031 published Salmonella genomes screened in silico, 4,954 (2.4%) contained bla_CMY-2, 8,143 (4.0%) contained fosA7, and 919 (0.4%) contained both resistance genes. The combination of both resistance genes (fosA7 and bla_CMY-2) was detected in 64% of the Heidelberg genomes and in a small proportion of various other serovars. A PCR method was developed to detect Salmonella Heidelberg in pure culture and chicken feces based on specific primers targeting genes conferring fosfomycin (fosA7) and third-generation cephalosporin (bla_CMY-2) resistance as well as the Salmonella-specific invA gene and the universal 16S rRNA genes. The PCR assay was specific and sensitive for bla_CMY-2 and fosA7 harboring Salmonella Heidelberg. However, some other Salmonella serovars containing these two resistance genes could also be detected by the developed PCR method.

Biotechnological potential of bacteria isolated from cattle environments of desert soils in Sonora Mexico

The aim of this research was to study the hydrolytic potential of bacteria isolated from cattle environments of two desert soils in one of the driest and hottest zones in America. A total of 26 points were sampled, 144 strains were isolated, and 50 strains were selected for the characterization of esterase, lipase, protease, and amylase activities and for 16S rRNA identification. Strains of the Bacillus, Pseudomonas, Acinetobacter, Enterobacter, Providencia, Escherichia, and Pantoea genera were identified. Comparisons of the proteolytic activity of the secretome from 14 strains (Bacillus n = 7, Escherichia n = 2; Providencia, Pseudomonas, Enterobacter, Pantoea and Acinetobacter n = 1) were performed. Four strains of Bacillus showed the highest proteolytic activity. These strains were characterized through a comparative analysis of pH and temperature as well as the effects of salt concentration on protease activity. Maximum proteolytic activity occurred in the range of pH 7-9 and temperatures between 50 and 70 °C for B. subtilis WD01, B. tequilensis WS11, B. tequilensis WS13, and B. tequilensis WS14. At a 20% NaCl concentration, the proteolytic activity retained was 71.4%, 65%, and 79.8% for WD01, WS11, and WS13, respectively; the activity of strain WS14 increased with 45% NaCl. Protease production by B. tequilensis WS14 with wheat, fish, and bone flours as low-cost substrates showed no differences between bone and fish flours and showed a decrease in protease production with wheat flour. The proteolytic activity in flour extracts with 20% NaCl was 82%, 75.61% and 38.04% for fish, bone and wheat flours, respectively. Data obtained in this work allow us to propose that strains isolated from environments with extreme conditions have a biotechnological potential.

Chronic impacts of oxytetracycline on mesophilic anaerobic digestion of excess sludge: Inhibition of hydrolytic acidification and enrichment of antibiotic resistome

We evaluated the chronic impact of oxytetracycline (OTC) on performance and antibiotic resistance development during the mesophilic anaerobic digestion (AD) of antibiotic-containing biomass. Mesophilic AD was conducted in a completely stirred tank reactor by constantly feeding municipal excess sludge spiked with increasing concentrations of OTC (0-1000 mg L^-1) under a solid retention time of 20 days over a period of 265 days. Results showed that methane generation of mesophilic AD was inhibited when the OTC concentration in digested sludge was increased to around 18,000 mg kg^-1 (OTC dose, 1000 mg L^-1), due to the inhibition of fermenting and acidogenic bacteria. Metagenomic sequencing and high-throughput quantitative PCR analysis demonstrated that tetracycline resistance genes were the most dominant type (38.47-43.76%) in the resistome, with tetG, tetX, tetM, tetR, tetQ, tetO, and tetL as the dominant resistant subtypes throughout the whole experimental period. The relative abundance of these tet genes increased from 2.10 × 10^-1 before spiking OTC (OTC concentration in digested sludge, 8.97 mg kg^-1) to 2.83 × 10^-1 (p < 0.05) after spiking OTC at a dose of 40 mg L^-1 (OTC concentration in digested sludge, 528.52 mg kg^-1). Furthermore, mobile genetic elements, including integrons, transposons, and plasmids, were also enriched with the increase in OTC dose. Based on partial canonical correspondence analysis, the contributions of horizontal (mobile element alteration) and vertical (bacterial community shift) gene transfer to antibiotic resistome variation were 29.35% and 21.51%, respectively. Thus, considering the inhibition of hydrolytic acidification and enrichment of antibiotic resistome, mesophilic AD is not suggested to directly treat the biomass containing OTC concentration higher than 200 mg L^-1.

Use of antibiotics in broiler production: Global impacts and alternatives

Antibiotics are used to fight bacterial infections. However, a selective pressure gave rise to bacteria resistant to antibiotics. This leaves scientists worried about the danger to human and animal health. Some strategies can be borrowed to reduce the use of antibiotics in chicken farms. Much research has been carried out to look for natural agents with similar beneficial effects of growth promoters. The aim of these alternatives is to maintain a low mortality rate, a good level of animal yield while preserving environment and consumer health. Among these, the most popular are probiotics, prebiotics, enzymes, organic acids, immunostimulants, bacteriocins, bacteriophages, phytogenic feed additives, phytoncides, nanoparticles and essential oils.

The first report of Escherichia fergusonii isolated from non-human primates, in Africa

The aim of this study was to determine the resistance phenotypes of selected enteric bacteria isolated from non-human primates at a wildlife-human interface. Bacterial isolates from faecal samples of non-human primates at two wildlife rehabilitation centres in South Africa were screened for the presence of Escherichia coli. The biochemical characterisation of E. coli and E. coli-like bacteria revealed both adonitol positive and sorbitol negative strains – a unique characteristic of Escherichia fergusonii and Escherichia coli K99. Further tests were carried out to identify the isolates, namely growth on Simmons citrate agar supplemented with 2% adonitol and biochemical tests based on their ability to ferment cellobiose and d-arabitol. Antimicrobial sensitivity was determined with microbroth dilution tests employing microtitre plates with 21 different antimicrobial drugs. Molecular characterisation was done with a duplex polymerase chain reaction (PCR) assay that targeted the yliE and EFER_1569 genes. E. fergusonii strains were confirmed by the presence of a 233 bp segment of the yliE gene and a 432 bp segment of the EFER_1569 gene.

Twenty-three E. coli-like bacteria were confirmed as E. fergusonii based on the confirmatory tests and they were in 100% agreement. Approximately 87% of them were resistant to polymyxins B and E (colistin) as well as the carbapenem group with occasional resistance to amikacin.

This is the first reported isolation and identification of E. fergusonii strains in non-human primates. The findings point to E. fergusonii as a possible emerging pathogen of zoonotic importance.

Extended-Spectrum-Beta-Lactamase- and Plasmid-Encoded Cephamycinase-Producing Enterobacteria in the Broiler Hatchery as a Potential Mode of Pseudo-Vertical Transmission

Antimicrobial resistance through extended-spectrum beta-lactamases (ESBLs) and transferable (plasmid-encoded) cephamycinases (pAmpCs) represents an increasing problem in human and veterinary medicine. The presence of ESBL-/pAmpC-producing commensal enterobacteria in farm animals, such as broiler chickens, is considered one possible source of food contamination and could therefore also be relevant for human colonization. Studies on transmission routes along the broiler production chain showed that 1-day-old hatchlings are already affected. In this study, ESBL-/pAmpC-positive broiler parent flocks and their corresponding eggs, as well as various environmental and air samples from the hatchery, were analyzed. The eggs were investigated concerning ESBL-/pAmpC-producing enterobacteria on the outer eggshell surface (before/after disinfection), the inner eggshell surface, and the egg content. Isolates were analyzed concerning their species, their phylogroup in the case of Escherichia coli strains, the respective resistance genes, and the phenotypical antibiotic resistance. Of the tested eggs, 0.9% (n = 560) were contaminated on their outer shell surface. Further analyses using pulsed-field gel electrophoresis showed a relationship of these strains to those isolated from the corresponding parent flocks, which demonstrates a pseudo-vertical transfer of ESBL-/pAmpC-producing enterobacteria into the hatchery. Resistant enterobacteria were also found in environmental samples from the hatchery, such as dust or surfaces which could pose as a possible contamination source for the hatchlings. All 1-day-old chicks tested negative directly after hatching. The results show a possible entry of ESBL-/pAmpC-producing enterobacteria from the parent flocks into the hatchery; however, the impact of the hatchery on colonization of the hatchlings seems to be low.

IMPORTANCE

ESBL-/pAmpC-producing enterobacteria occur frequently in broiler-fattening farms. Recent studies investigated the prevalence and possible transmission route of these bacteria in the broiler production chain. It seemed very likely that the hatcheries play an important role in transmission and/or contamination events. There are only few data on transmission investigations from a grandparent or parent flock to their offspring. However, reliable data on direct or indirect vertical transmission events in the hatchery are not available. Therefore, we conducted our study and intensively investigated the broiler hatching eggs from ESBL-/pAmpC-positive broiler parent flocks as well as the hatchlings and the environment of the hatchery.

Antibiotic resistance in conjunctival and enteric bacterial flora in raptors housed in a zoological garden

Antimicrobial resistance (AMR) in a wide range of infectious agents is a growing public health threat. Birds of prey are considered indicators of the presence of AMR bacteria in their ecosystem because of their predatory behaviour. Only few data are reported in the literature on AMR strains isolated from animals housed in zoos and none about AMR in raptors housed in zoological gardens. This study investigated the antibiotic sensitivity profile of the isolates obtained from the conjunctival and cloacal bacterial flora of 14 healthy birds of prey, 6 Accipitriformes, 3 Falconiformes and 5 Strigiformes, housed in an Italian zoological garden. Staphylococcus spp. was isolated from 50% of the conjunctival swabs, with S. xylosus as the most common species. From cloacal swabs, Escherichia coli was cultured from all animals, while Klebsiella spp. and Proteus spp. were isolated from a smaller number of birds. Worthy of note is the isolation of Escherichia fergusonii and Serratia odorifera, rarely isolated from raptors. Staphylococci were also isolated. All the isolates were multidrug resistant (MDR). To the author's knowledge, this is the first report regarding the presence of MDR strains within raptors housed in a zoological garden. Since resistance genes can be transferred to other pathogenic bacteria, this represents a potential hazard for the emergence of new MDR pathogens. In conclusion, the obtained data could be useful for ex-situ conservation programmes aimed to preserve the health of the endangered species housed in a zoo.

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.

Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens

BACKGROUND

Non-typhoidal Salmonella enterica serovars, associated with different foods including poultry products, are important causes of bacterial gastroenteritis worldwide. The colonization of the chicken gut by S. enterica could result in the contamination of the environment and food chain. The aim of this study was to compare the genomes of 25 S. enterica serovars isolated from broiler chicken farms to assess their intra- and inter-genetic variability, with a focus on virulence and antibiotic resistance characteristics.

METHODOLOGY/PRINCIPAL FINDING

The genomes of 25 S. enterica isolates covering five serovars (ten Typhimurium including three monophasic 4,[5],12:i:, four Enteritidis, three Hadar, four Heidelberg and four Kentucky) were sequenced. Most serovars were clustered in strongly supported phylogenetic clades, except for isolates of serovar Enteritidis that were scattered throughout the tree. Plasmids of varying sizes were detected in several isolates independently of serovars. Genes associated with the IncF plasmid and the IncI1 plasmid were identified in twelve and four isolates, respectively, while genes associated with the IncQ plasmid were found in one isolate. The presence of numerous genes associated with Salmonella pathogenicity islands (SPIs) was also confirmed. Components of the type III and IV secretion systems (T3SS and T4SS) varied in different isolates, which could explain in part, differences of their pathogenicity in humans and/or persistence in broilers. Conserved clusters of genes in the T3SS were detected that could be used in designing effective strategies (diagnostic, vaccination or treatments) to combat Salmonella. Antibiotic resistance genes (CMY, aadA, ampC, florR, sul1, sulI, tetAB, and srtA) and class I integrons were detected in resistant isolates while all isolates carried multidrug efflux pump systems regardless of their antibiotic susceptibility profile.

CONCLUSIONS/SIGNIFICANCE

This study showed that the predominant Salmonella serovars in broiler chickens harbor genes encoding adhesins, flagellar proteins, T3SS, iron acquisition systems, and antibiotic and metal resistance genes that may explain their pathogenicity, colonization ability and persistence in chicken. The existence of mobile genetic elements indicates that isolates from a given serovar could acquire and transfer genetic material. Conserved genes in the T3SS and T4SS that we have identified are promising candidates for identification of diagnostic, antimicrobial or vaccine targets for the control of Salmonella in broiler chickens.

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.

Escherichia fergusonii

Escherichia fergusonii was introduced in the genus Escherichia almost 65 years later than Escherichia coli after which the genus was named. From then (1985) onwards mainly case reports on E. fergusonii associated with disease in individuals of veterinary or human origin have been reported and only very few more extensive studies became available. This has resulted in very fragmented knowledge on this organism. The aim of this manuscript is to give an overview of what is known on E. fergusonii today and to stimulate more research on this organism so that better insight can be obtained in the role that E. fergusonii plays in human and animal infections.

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.

Investigation of antibiotic resistance in the genomic era of multidrug-resistant Gram-negative bacilli, especially Enterobacteriaceae, Pseudomonas and Acinetobacter

The increase and spread of multidrug-resistant (MDR) Gram-negative bacteria, including Enterobacteriaceae, Pseudomonas and Acinetobacter species, have become major concerns worldwide. Although the frequent misuse of antibiotic drugs has greatly contributed to worldwide antibiotic resistance by causing a large dispersal of resistance determinants, recent studies demonstrate that these resistance determinants could have emerged from ancient or environmental sources. Moreover, during the last 10 years, we have been witnessing the emergence and development of technologies for high-throughput sequencing, coinciding with an exponential increase in the number of bacterial genomes sequenced. These sequencing technologies allow a complete study of MDR bacterial genomes and are the best way to investigate the genetic determinants of antimicrobial resistance. Accordingly, studies using genome sequencing to decipher resistance determinants in Enterobacteriaceae, Pseudomonas and Acinetobacter species have demonstrated several advantages including, among others: an exhaustive identification of resistance determinants from any clinical, epidemiological or environmental MDR bacterium; identification of the acquisition mechanisms for resistance determinants exchanged between bacterial species through mobile genetic elements and elucidation and understanding, in record time (less than 1 week), of some critical or epidemic events caused by particular pathogenic bacteria. Therefore, it is clear today that the bacterial genome sequencing approach has revolutionized all fields of scientific research and represents a powerful tool to explore the world of microorganisms.