Sequencing Analysis of Local Avian Coronavirus Isolated from Infected Broiler Chickens in Babylon Province, Iraq

Infectious coryza, caused by Avibacterium paragallinarum, is an acute respiratory disease of poultry that can result in substantial morbidity, mortality, and economic losses. In March 2017, the Turlock branch of the California Animal Health and Food Safety laboratory system encountered an unusual clinical and pathologic presentation of infectious coryza in 6 live, 29-d-old, commercial broiler chickens that were submitted for diagnostic investigation. Antemortem evaluation revealed severe neurologic signs, including disorientation, torticollis, and opisthotonos. Swollen head–like syndrome and sinusitis were also present. Histologically, severe sinusitis, cranial osteomyelitis, otitis media and interna, and meningoencephalitis were noted, explaining the clinical signs described. A. paragallinarum was readily isolated from the upper and lower respiratory tract, brain, and cranial bones. Infectious bronchitis virus (IBV) was also detected by PCR, and IBV was isolated in embryonated chicken eggs. Based on sequencing analysis, the IBV appeared 99% homologous to strain CA1737. A synergistic effect between A. paragallinarum and IBV, resulting in exacerbation of clinical signs and increased mortality, may have occurred in this case. A. paragallinarum should be considered among the possible causes of neurologic signs in chickens. Appropriate media should be used for bacterial isolation, and the role of additional contributing factors and/or complicating agents should be investigated in cases of infectious coryza.

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The Effect of Exogenous Bile Acids on Antioxidant Status and Gut Microbiota in Heat-Stressed Broiler Chickens

Frontiers in Nutrition ◽

10.3389/fnut.2021.747136 ◽

2021 ◽

Vol 8 ◽

Author(s):

Chang Yin ◽

Bing Xia ◽

Shanlong Tang ◽

Aizhi Cao ◽

Lei Liu ◽

...

Keyword(s):

Heat Stress ◽

Gut Microbiota ◽

Bile Acids ◽

Broiler Chickens ◽

Antioxidant Status ◽

Intestinal Morphology ◽

Lipid Absorption ◽

Rrna Gene ◽

Sequencing Analysis ◽

Crypt Depth

Bile acids are critical for lipid absorption, however, their new roles in maintaining or regulating systemic metabolism are irreplaceable. The negative impacts of heat stress (HS) on growth performance, lipid metabolism, and antioxidant status have been reported, but it remains unknown whether the bile acids (BA) composition of broiler chickens can be affected by HS. Therefore, this study aimed to investigate the modulating effects of the environment (HS) and whether dietary BA supplementation can benefit heat-stressed broiler chickens. A total of 216 Arbor Acres broilers were selected with a bodyweight approach average and treated with thermal neutral (TN), HS (32°C), or HS-BA (200 mg/kg BA supplementation) from 21 to 42 days. The results showed that an increase in average daily gain (P < 0.05) while GSH-Px activities (P < 0.05) in both serum and liver were restored to the normal range were observed in the HS-BA group. HS caused a drop in the primary BA (P = 0.084, 38.46%) and Tauro-conjugated BA (33.49%) in the ileum, meanwhile, the secondary BA in the liver and cecum were lower by 36.88 and 39.45% respectively. Notably, results were consistent that SBA levels were significantly increased in the serum (3-fold, P = 0.0003) and the ileum (24.89-fold, P < 0.0001). Among them, TUDCA levels (P < 0.01) were included. Besides, BA supplementation indeed increased significantly TUDCA (P = 0.0154) and THDCA (P = 0.0003) levels in the liver, while ileal TDCA (P = 0.0307), TLCA (P = 0.0453), HDCA (P = 0.0018), and THDCA (P = 0.0002) levels were also increased. Intestinal morphology of ileum was observed by hematoxylin and eosin (H&E) staining, birds fed with BA supplementation reduced (P = 0.0431) crypt depth, and the ratio of villous height to crypt depth trended higher (P = 0.0539) under the heat exposure. Quantitative RT-PCR showed that dietary supplementation with BA resulted in upregulation of FXR (P = 0.0369), ASBT (P = 0.0154), and Keap-1 (P = 0.0104) while downregulation of iNOS (P = 0.0399) expression in ileum. Moreover, 16S rRNA gene sequencing analysis and relevance networks revealed that HS-derived changes in gut microbiota and BA metabolites of broilers may affect their resistance to HS. Thus, BA supplementation can benefit broiler chickens during high ambient temperatures, serving as a new nutritional strategy against heat stress.

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PSIII-20 Antimicrobial resistance phenotype and genotype of generic Escherichia coli from encapsulated cinnamaldehyde and citral fed-broiler chicken

Journal of Animal Science ◽

10.1093/jas/skab235.626 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 341-341

Author(s):

Chongwu Yang ◽

Muhammad Attiq Rehman ◽

Xianhua Yin ◽

Catherine Carrillo ◽

Qi Wang ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Broiler Chickens ◽

Basal Diet ◽

Whole Genome ◽

Sequencing Analysis ◽

E Coli ◽

Close Relationship ◽

Amoxicillin Clavulanic Acid ◽

Dietary Treatments ◽

Relationship Of

Abstract This study investigated effects of in-feed encapsulated cinnamaldehyde (CIN) and citral (CIT) alone or in combination (CIN+CIT) on antimicrobial resistance (AMR) phenotypes and genotypes of E. coli isolated from feces of 6-, 16-, 23- and 27-days old broiler chickens. Five dietary treatments included the basal diet (NC), the basal diet supplemented with 55 ppm bacitracin (BAC), 100 ppm encapsulated CIN, CIT, or CIN+CIT. Antimicrobial susceptibility using a Sensititre method of 240 E. coli isolates showed that the most frequent resistances were against b-lactam, aminoglycoside, sulfonamide and tetracycline, however, the prevalence of AMR decreased (P < 0.05) when birds aged. The prevalence of resistance to amoxicillin-clavulanic acid, ceftiofur, ceftriaxone, cefoxitin, gentamicin, and sulfonamide was lower (P < 0.05) in isolates from CIN or CIN+CIT compared to those from NC or BAC. The whole-genome sequencing analysis of 227 of the 240 isolates detected 26 AMR genes (ARGs) and 19 plasmids but the prevalence of some ARGs and plasmid numbers were lower (P < 0.05) in E. coli isolated from CIN or CIN+CIT than NC or BAC. The most prevalent resistance genes included tet(A) (n = 108), aac3_Vla (n = 91), aadA1 (n = 86), blaCMY-2 (n = 78), sul1 (n = 77), aph3_lb (n = 58), aph6_ld (n = 58), and sul2 (n = 24). Interestingly, the number of most virulence genes (VGs) increased (P < 0.05) over time from 6 to 27 days of age. The prevalence of isolates of serotype O21:H16 was lower (P < 0.05) in CIN and CIN+CIT while colibacillosis-associated multi-locus sequence typing (ST117) was the most prevalent in isolates from day 23. A whole genome-based phylogenetic tree revealed a close relationship of 25 of 227 isolates to human or broiler extraintestinal pathogenic E. coli. This study indicates that AMR and virulence genotypes of E. coli could be modulated by encapsulated CIN or CIN+CIT feed supplementations and prompt further investigations on the involved mechanisms.

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16S rRNA Sequencing Analysis of the Gut Microbiota in Broiler Chickens Prophylactically Administered with Antimicrobial Agents

Antibiotics ◽

10.3390/antibiotics10020146 ◽

2021 ◽

Vol 10 (2) ◽

pp. 146 ◽

Cited By ~ 1

Author(s):

Matteo Cuccato ◽

Selene Rubiola ◽

Diana Giannuzzi ◽

Elena Grego ◽

Paola Pregel ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

Broiler Chickens ◽

Antimicrobial Agents ◽

Alpha Diversity ◽

Rrna Gene ◽

Sequencing Analysis ◽

Poultry Production ◽

Growth Promoters ◽

The Impact

In poultry production, gut microbiota (GM) plays a pivotal role and influences different host functions related to the efficiency of production performances. Antimicrobial (AM) use is one of the main factors affecting GM composition and functions. Although several studies have focused their attention on the role of AMs as growth promoters in the modulation of GM in broilers, the consequences of higher AM concentrations administered during prophylactic treatments need to be better elucidated. For this purpose, 16S rRNA gene sequencing was performed to evaluate the impact of different prophylactic AM protocols on the composition and diversity of the broiler GM. Diversity analysis has shown that AM treatment significantly affects alpha diversity in ileum and beta diversity in both ileum and caecum. In ileal samples, the Enterobacteriaceae family has been shown to be particularly affected by AM treatments. AMs have been demonstrated to affect GM composition in broiler. These findings indicate that withdrawal periods were not enough for the restoral of the original GM. Further studies are needed for a better elucidation of the negative effects caused by an altered GM in broilers.

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Antimicrobial Resistance Phenotype and Genotype of Generic Escherichia coli from Encapsulated Cinnamaldehyde and Citral Fed-Broiler Chicken

Journal of Food Protection ◽

10.4315/jfp-21-033 ◽

2021 ◽

Author(s):

Chongwu Yang ◽

Muhammad Attiq Rehman ◽

Xianhua Yin ◽

Catherine D Carrilloc ◽

Qi Wang ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Broiler Chickens ◽

Basal Diet ◽

Whole Genome ◽

Sequencing Analysis ◽

E Coli ◽

Close Relationship ◽

Diet Control ◽

Dietary Treatments ◽

Relationship Of

This study investigated the effects of in-feed encapsulated cinnamaldehyde (CIN) and citral (CIT) alone or in combination (CIN+CIT) on antimicrobial resistance (AMR) phenotypes and genotypes of E. coli isolated from feces of 6-, 16-, 23- and 27-days old broiler chickens. The five dietary treatments including the basal diet (control; NC), the basal diet supplemented with 55 ppm bacitracin (BAC), 100 ppm encapsulated CIN, CIT, or CIN+CIT. Antimicrobial susceptibility using a Sensititre method of 240 E. coli isolates showed that the most frequent resistances were against b-lactam, aminoglycoside, sulfonamide and tetracycline, however, the prevalence of AMR decreased (P < 0.05) when birds aged in general. The prevalence of resistance to amoxicillin-clavulanic acid, ceftiofur, ceftriaxone, cefoxitin, gentamicin, and sulfonamide was lower (P < 0.05) in isolates from CIN or CIN+CIT compared to those from NC or BAC. The whole-genome sequencing analysis of 227 of the 240 isolates detected 26 AMR genes (ARGs) and 19 plasmids but the prevalence of some ARGs and plasmid numbers were lower (P < 0.05) in E. coli isolated from CIN or CIN+CIT than NC or BAC. The most prevalent resistance genes included tet(A) (n=108), aac3_Vla (n=91), aadA1 (n=86), blaCMY-2 (n=78), sul1 (n=77), aph3_lb (n=58), aph6_ld (n=58), and sul2 (n=24). Interestingly, the number of most virulence genes (VGs) increased (P < 0.05) over time from 6 to 27 days of age. The prevalence of isolates of serotype O21:H16 was lower (P < 0.05) in CIN and CIN+CIT while colibacillosis-associated multi-locus sequence typing (ST117) was the most prevalent in isolates from day 23. A whole genome-based phylogenetic tree revealed a close relationship of 25 of 227 isolates to human or broiler extraintestinal pathogenic E. coli. This study indicates that AMR and virulence genotypes of E. coli could be modulated by encapsulated CIN or CIN+CIT feed supplementations and prompt further investigations on the involved mechanisms.

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Hydroxychloride Trace Minerals Have a Positive Effect on Growth Performance, Carcass Quality and Impact Ileal and Cecal Microbiota in Broiler Chickens

10.21203/rs.3.rs-65394/v1 ◽

2020 ◽

Author(s):

Sandra J.A. van Kuijk ◽

Yanming Han ◽

Ana Isabel Garcia-Ruiz ◽

Ana Rodiles

Keyword(s):

Body Weight ◽

Gut Microbiota ◽

Growth Performance ◽

High Throughput ◽

Broiler Chickens ◽

High Throughput Sequencing ◽

Trace Minerals ◽

Carcass Quality ◽

Sequencing Analysis ◽

Breast Meat

Abstract Background: The objective was to study the effect of hydroxychloride trace minerals (HTM) on growth performance, carcass quality and gut microbiota of broiler chickens in comparison to sulphate trace minerals (STM). In total 1440 male Ross 308 day-old chicks were divided over 12 replicate pens with 30 birds each per treatment. Four different treatments were tested according to a 2×2 factorial study design, where the animals received a three phase diet containing either inorganic Zn from sulphates or Zn from HTM in high (80 ppm Zn) or low Zn dosage (20 ppm Zn). In all treatments 15 ppm Cu was added from the same mineral source as the Zn. Body weight and feed intake were measured on day 0, 10, 27 and 34, while carcass and breast meat yields were measured at the end of the study (day 34). In addition, high-throughput sequencing analysis was performed in digesta samples from ileum and cecum to study the gut microbiome (day 34). Results: The results showed an improved (P<0.05) body weight of broiler chickens fed HTM, regardless of Zn level, on day 27, while on day 34 this effect remained as a tendency (P= 0.0542). In the overall study period, birds fed HTM had a higher (P<0.05) average daily gain and average daily feed intake when compared to birds fed STM. The mineral source did not affect the carcass characteristics, however, feeding 80 ppm Zn resulted in a significantly higher (P=0.0171) breast meat yield, regardless of source. High-throughput sequencing analysis of the microbiota revealed a higher microbial diversity in the ileum and cecum of HTM fed birds compared to STM fed birds. Taxonomical differences were mainly found in the cecum, specifically between the group fed high and low Zn levels from HTM. This is in line with the mineral contents observed in the cecal digesta. Comparing both groups fed 80 ppm Zn, the HTM group had more Streptococcaceae, Streptococcus, Clostridia, Weissella and Leuconostocaceae compared to the STM group. Conclusions: HTM improved growth performance of the birds; and the source and level of Zn modulated the gut microbiota communities in broilers differentially.

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Hydroxychloride trace minerals have a positive effect on growth performance, carcass quality and impact ileal and cecal microbiota in broiler chickens

Journal of Animal Science and Biotechnology ◽

10.1186/s40104-021-00553-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Sandra J. A. van Kuijk ◽

Yanming Han ◽

Ana Isabel Garcia-Ruiz ◽

Ana Rodiles

Keyword(s):

Body Weight ◽

Gut Microbiota ◽

Growth Performance ◽

High Throughput ◽

Broiler Chickens ◽

High Throughput Sequencing ◽

Trace Minerals ◽

Carcass Quality ◽

Sequencing Analysis ◽

Breast Meat

Abstract Background The objective was to study the effect of hydroxychloride trace minerals (HTM) on growth performance, carcass quality and gut microbiota of broiler chickens in comparison to sulphate trace minerals (STM). In total 1440 male Ross 308 day-old chicks were divided into 12 replicate pens with 30 birds each per treatment. Four different treatments were tested according to a 2 × 2 factorial study design, where the animals received a three phase diet containing either inorganic Zn from sulphates or Zn from HTM in high (80 mg/kg Zn) or low Zn dosage (20 mg/kg Zn). In all treatments 15 mg/kg Cu was added from the same mineral source as the Zn. Body weight and feed intake were measured on day 0, 10, 27 and 34, while carcass and breast meat yields were measured at the end of the study (day 34). In addition, high-throughput sequencing analysis was performed in digesta samples from ileum and cecum to study the gut microbiome (day 34). Results The results showed an improved (P < 0.05) body weight of broiler chickens fed HTM, regardless of Zn level, on day 27, while on day 34 this effect remained as a tendency (P = 0.0542). In the overall study period, birds fed HTM had a higher (P < 0.05) average daily gain and average daily feed intake when compared to birds fed STM. The mineral source did not affect the carcass characteristics, however, feeding 80 mg/kg Zn resulted in a significantly higher (P = 0.0171) breast meat yield, regardless of source. High-throughput sequencing analysis of the microbiota revealed a higher microbial diversity in the ileum and cecum of HTM fed birds compared to STM fed birds. Taxonomical differences were mainly found in the cecum, specifically between the group fed high and low Zn levels from HTM. This correlated with the mineral contents observed in the cecal digesta. Comparing both groups fed 80 mg/kg Zn, the HTM group had more Streptococcaceae, Streptococcus, Clostridia, Weissella and Leuconostocaceae compared to the STM group. Conclusions HTM improved growth performance of broiler chickens; and the source and level of Zn modulated the gut microbiota communities in broilers differentially.

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Hydroxychloride trace minerals have a positive effect on growth performance, carcass quality and impact ileal and cecal microbiota in broiler chickens

10.21203/rs.3.rs-65394/v2 ◽

2020 ◽

Author(s):

Sandra van Kuijk ◽

Yanming Han ◽

Ana Isabel Garcia-Ruiz ◽

Ana Rodiles

Keyword(s):

Body Weight ◽

Gut Microbiota ◽

Growth Performance ◽

High Throughput ◽

Broiler Chickens ◽

High Throughput Sequencing ◽

Trace Minerals ◽

Carcass Quality ◽

Sequencing Analysis ◽

Breast Meat

Abstract Background: The objective was to study the effect of hydroxychloride trace minerals (HTM) on growth performance, carcass quality and gut microbiota of broiler chickens in comparison to sulphate trace minerals (STM). In total 1440 male Ross 308 day-old chicks were divided into 12 replicate pens with 30 birds each per treatment. Four different treatments were tested according to a 2×2 factorial study design, where the animals received a three phase diet containing either inorganic Zn from sulphates or Zn from HTM in high (80 mg/kg Zn) or low Zn dosage (20 mg/kg Zn). In all treatments 15 mg/kg Cu was added from the same mineral source as the Zn. Body weight and feed intake were measured on day 0, 10, 27 and 34, while carcass and breast meat yields were measured at the end of the study (day 34). In addition, high-throughput sequencing analysis was performed in digesta samples from ileum and cecum to study the gut microbiome (day 34).Results: The results showed an improved (P<0.05) body weight of broiler chickens fed HTM, regardless of Zn level, on day 27, while on day 34 this effect remained as a tendency (P=0.0542). In the overall study period, birds fed HTM had a higher (P<0.05) average daily gain and average daily feed intake when compared to birds fed STM. The mineral source did not affect the carcass characteristics, however, feeding 80 mg/kg Zn resulted in a significantly higher (P=0.0171) breast meat yield, regardless of source. High-throughput sequencing analysis of the microbiota revealed a higher microbial diversity in the ileum and cecum of HTM fed birds compared to STM fed birds. Taxonomical differences were mainly found in the cecum, specifically between the group fed high and low Zn levels from HTM. This correlated with the mineral contents observed in the cecal digesta. Comparing both groups fed 80 mg/kg Zn, the HTM group had more Streptococcaceae, Streptococcus, Clostridia, Weissella and Leuconostocaceae compared to the STM group.Conclusions: HTM improved growth performance of broiler chickens ; and the source and level of Zn modulated the gut microbiota communities in broilers differentially.

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Molecular Characterization of a Type I Quantitative Factor V Deficiency in a Thrombosis Patient that Is “Pseudo Homozygous” for Activated Protein C Resistance

Thrombosis and Haemostasis ◽

10.1055/s-0038-1655948 ◽

1997 ◽

Vol 77 (02) ◽

pp. 252-257 ◽

Cited By ~ 32

Author(s):

Joan F Guasch ◽

Ruud P M Lensen ◽

Rogier M Bertina

Keyword(s):

Protein C ◽

Dna Analysis ◽

Activated Protein C ◽

Type I ◽

Factor V ◽

Sequencing Analysis ◽

Apc Resistance ◽

Quantitative Factor ◽

Factor V Deficiency ◽

Fv Leiden

SummaryResistance to activated protein C (APC), which is associated with the FV Leiden mutation in the large majority of the cases, is the most common genetic risk factor for thrombosis. Several laboratory tests have been developed to detect the APC-resistance phenotype. The result of the APC-resistance test (APC-sensitivity ratio, APC-SR) usually correlates well with the FV Leiden genotype, but recently some discrepancies have been reported. Some thrombosis patients that are heterozygous for FV Leiden show an APC-SR usually found only in homozygotes for the defect. Some of those patients proved to be compound heterozygotes for the FV Leiden mutation and for a type I quantitative factor V deficiency. We have investigated a thrombosis patient characterized by an APC-SR that would predict homozygosity for FV Leiden. DNA analysis showed that he was heterozygous for the mutation. Sequencing analysis of genomic DNA revealed that the patient also is heterozygous for a G5509→A substitution in exon 16 of the factor V gene. This mutation interferes with the correct splicing of intron 16 and leads to the presence of a null allele, which corresponds to the “non-FV Leiden” allele. The conjunction of these two defects in the patient apparently leads to the same phenotype as observed in homozygotes for the FV Leiden mutation.

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Kindler's Syndrome with Recurrent Neutropenia: Report of Two Cases from Saudi Arabia

Journal of Pediatric Genetics ◽

10.1055/s-0040-1721077 ◽

2020 ◽

Author(s):

Yousef Binamer ◽

Muzamil A. Chisti

Keyword(s):

Autosomal Recessive ◽

Common Mechanism ◽

Sequencing Analysis ◽

Loss Of Function ◽

Skin Atrophy ◽

Whole Exome ◽

Infancy And Childhood ◽

Genetics And Genomics ◽

New Feature ◽

Generation Sequencing

AbstractKindler syndrome (KS) is a rare photosensitivity disorder with autosomal recessive mode of inheritance. It is characterized by acral blistering in infancy and childhood, progressive poikiloderma, skin atrophy, abnormal photosensitivity, and gingival fragility. Besides these major features, many minor presentations have also been reported in the literature. We are reporting two cases with atypical features of the syndrome and a new feature of recurrent neutropenia. Whole exome sequencing analysis was done using next-generation sequencing which detected a homozygous loss-of-function (LOF) variant of FERMT1 in both patients. The variant is classified as a pathogenic variant as per the American College of Medical Genetics and Genomics guidelines. Homozygous LOF variants of FERMT1 are a common mechanism of KS and as such confirm the diagnosis of KS in our patients even though the presentation was atypical.

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