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Veterinary Microbiology in Farm Animals
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Veterinary Microbiology in Farm Animals (Closed)

A topical collection in Animals (ISSN 2076-2615). This collection belongs to the section "Veterinary Clinical Studies".

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Editors

Prof. Dr. Beniamino T. Cenci-Goga

E-Mail Website
Collection Editor
Department of Veterinary Medicine, University of Perugia, Perugia, Italy
Interests: animal health; animal welfare; food hygiene; food microbiology
Special Issues, Collections and Topics in MDPI journals
Dr. Luca Grispoldi

E-Mail Website
Collection Editor
Department of Veterinary Medicine, University of Perugia, Perugia, Italy
Interests: Escherichia coli; meat; antibiotic resistance; antimicrobials; microbial molecular biology; bacteriology
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

Unlike medical microbiology, which focuses on just one species, veterinary microbiology covers the full range of vertebrates other than humans and some invertebrates, too.

Veterinary microbiology in farm animals is concerned with the etiology, pathogenesis, diagnosis and treatment of infection in the individual and with the epidemiology, prevention, and control of infections in the community. It includes microbial (bacterial, fungal, viral) diseases of animals that supply food or other products. It also deals with microbial diseases of wild animals (both feral and living in captivity) for their interrelation with farmed animals. 

We invite original research papers that address the microorganisms and the diseases which they cause, the international and public health significance of pathogens, especially in the context of one health, and the important role played by animals as reservoirs of zoonotic diseases, including aspects of control, host response, molecular biology, pathogenesis, prevention, and treatment of microbial diseases of animals and antimicrobial resistance.

Prof. Dr. Beniamino T. Cenci-Goga
Dr. Luca Grispoldi
Guest Editors

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbiology
  • one health
  • epidemiology
  • prevention
  • diagnosis

Published Papers (22 papers)

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2023

Jump to: 2022, 2021, 2020, 2019

16 pages, 2766 KiB  
Article
Exploring the Microbial Community Structure in the Chicken House Environment by Metagenomic Analysis
by Cheng Lou, Zhuo Chen, Yu Bai, Tongjie Chai, Yuling Guan and Bo Wu
Animals 2024, 14(1), 55; https://doi.org/10.3390/ani14010055 - 22 Dec 2023
Viewed by 697
Abstract
The environmental conditions of chicken houses play an important role in the growth and development of these animals. The chicken house is an essential place for the formation of microbial aerosols. Microbial aerosol pollution and transmission can affect human and animal health. In [...] Read more.
The environmental conditions of chicken houses play an important role in the growth and development of these animals. The chicken house is an essential place for the formation of microbial aerosols. Microbial aerosol pollution and transmission can affect human and animal health. In this work, we continuously monitored fine particulate matter (PM2.5) in the chicken house environment for four weeks and studied the microbial community structure in the aerosols of the chicken house environment through metagenomic sequencing. Our results found that bacteria, fungi, viruses, and archaea were the main components of PM2.5 in the chicken house environment, accounting for 89.80%, 1.08%, 2.06%, and 0.49%, respectively. Conditional pathogens are a type of bacteria that poses significant harm to animals themselves and to farm workers. We screened ten common conditional pathogens and found that Staphylococcus had the highest relative abundance, while Clostridium contained the most microbial species, up to 456. Basidiomycetes and Ascomycota in fungi showed dramatic changes in relative abundance, and other indexes showed no significant difference. Virulence factors (VF) are also a class of molecules produced by pathogenic microbes that can cause host diseases. The top five virulence factors were found in four groups: FbpABC, HitABC, colibactin, acinetobactin, and capsule, many of which are used for the iron uptake system. In the PM2.5 samples, eight avian viruses were the most significant discoveries, namely Fowl aviadovirus E, Fowl aviadovirus D, Avian leukosis virus, Avian endogenous retrovirus EAV-HP, Avian dependent parvovirus 1, Fowl adenovus, Fowl aviadovirus B, and Avian sarcoma virus. The above results significantly improve our understanding of the microbial composition of PM2.5 in chicken houses, filling a gap on virus composition; they also indicate a potential threat to poultry and to human health. This work provides an important theoretical basis for animal house environmental monitoring and protection. Full article
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2022

Jump to: 2023, 2021, 2020, 2019

12 pages, 1354 KiB  
Article
Role of Guinea Pigs (Cavia porcellus) Raised as Livestock in Ecuadorian Andes as Reservoirs of Zoonotic Yeasts
by Lenys Buela, Mercy Cuenca, Jéssica Sarmiento, Diana Peláez, Ana Yolanda Mendoza, Erika Judith Cabrera and Luis Andrés Yarzábal
Animals 2022, 12(24), 3449; https://doi.org/10.3390/ani12243449 - 07 Dec 2022
Cited by 3 | Viewed by 2836
Abstract
Guinea pigs (Cavia porcellus) have been reared for centuries in the Andean region for ceremonial purposes or as the main ingredient of traditional foods. The animals are kept in close proximity of households and interact closely with humans; this also occurs in [...] Read more.
Guinea pigs (Cavia porcellus) have been reared for centuries in the Andean region for ceremonial purposes or as the main ingredient of traditional foods. The animals are kept in close proximity of households and interact closely with humans; this also occurs in western countries, where guinea pigs are considered pets. Even though it is acknowledged that domestic animals carry pathogenic yeasts in their tissues and organs that can cause human diseases, almost nothing is known in the case of guinea pigs. In this work we used traditional microbiological approaches and molecular biology techniques to isolate, identify, and characterize potentially zoonotic yeasts colonizing the nasal duct of guinea pigs raised as livestock in Southern Ecuador (Cañar Province). Our results show that 44% of the 100 animals studied were colonized in their nasal mucosa by at least eleven yeast species, belonging to eight genera: Wickerhamomyces, Diutina, Meyerozyma, Candida, Pichia, Rhodotorula, Galactomyces, and Cryptococcus. Noticeably, several isolates were insensitive toward several antifungal drugs of therapeutic use, including fluconazole, voriconazole, itraconazole, and caspofungin. Together, our results emphasize the threat posed by these potentially zoonotic yeasts to the farmers, their families, the final consumers, and, in general, to public and animal health. Full article
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13 pages, 1723 KiB  
Article
Genetic Relationship between Salmonella Isolates Recovered from Calves and Broilers Chickens in Kafr El-Sheikh City Using ERIC PCR
by Rasha Gomaa Tawfik, Mahmoud F. Gawish, Mahmoud M. Abotaleb, Hassan S. Nada, Kareem Morsy, Mohamed M. A. Abumandour and Helmy Torky
Animals 2022, 12(23), 3428; https://doi.org/10.3390/ani12233428 - 05 Dec 2022
Cited by 1 | Viewed by 1392
Abstract
A prevalent bacterial intestinal infection with severe economic damage is salmonellosis. Our study was carried out to diagnose Salmonella from chickens and calves, to determine its resistance to antimicrobials’ phenotypic and genotypic characterization of integrons and β lactamase genes in the multidrug resistance [...] Read more.
A prevalent bacterial intestinal infection with severe economic damage is salmonellosis. Our study was carried out to diagnose Salmonella from chickens and calves, to determine its resistance to antimicrobials’ phenotypic and genotypic characterization of integrons and β lactamase genes in the multidrug resistance of different Salmonella serotypes, and to detect the genetic relationship between Salmonella isolates collected from different origins using an ERIC PCR. In total, 200 samples from diseased chicken and diarrheic calves were obtained from 50 various farms from Kafr El-sheikh, Egypt. Salmonella poultry isolates were characterized as S. Typhimurium (3/8), S. Enteritidis (3/8), and S. Kentucky (2/8), but Salmonella isolates from cattle were S. Enteritidis (1/2) and S. Kentucky (1/2). When antibiotic susceptibility testing was completed on all of the isolates, it showed that there was multidrug resistance present (MDR). A PCR was applied for identifying the accompanying class 1 integrons and ESBLs from MDR Salmonella isolates (two isolates of S. Kentucky were divided as one from calf and one from poultry). Our results detected blaTEM and class 1 integron, but were negative for bla IMP, bla VIM, and bla SHV. An ERIC PCR was conducted for understanding the clonal relation between various β-lactamase-producing MDR Salmonella isolates. The same four previously mentioned isolates were also tested. The two isolates of S. Enteritidis isolated from poultry and calves had 100% similarity despite indicating that there were interactions between broilers and calves living on the same farm that caused infection from the same Salmonella strains, while the other two isolates of S. Kentucky showed only 33% serovarities. Full article
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13 pages, 2745 KiB  
Article
In-Depth Analysis of an Obligate Anaerobe Paraclostridium bifermentans Isolated from Uterus of Bubalus bubalis
by Purva Gohil, Kajal Patel, Srushti Patel, Ramesh Pandit, Vishal Suthar, Srinivas Duggirala, Madhvi Joshi, Deepak Patil and Chaitanya Joshi
Animals 2022, 12(14), 1765; https://doi.org/10.3390/ani12141765 - 09 Jul 2022
Viewed by 1695
Abstract
Chronic non-specific contamination of the reproductive tract in animals is a major issue during early postpartum, natural coitus, or artificial insemination. Uterine infection is one of the major concerns reducing fertility, production loss, and early culling of the animals. Therefore, the aim of [...] Read more.
Chronic non-specific contamination of the reproductive tract in animals is a major issue during early postpartum, natural coitus, or artificial insemination. Uterine infection is one of the major concerns reducing fertility, production loss, and early culling of the animals. Therefore, the aim of this study was to identify any novel bacterium if present in the uterine environment of Bubalus bubalis causing infections. A strictly anaerobic bacterial strain designated as Paraclostridium bifermentans GBRC was isolated and characterized. Bacterium was found to be Gram positive moderate rod with motility. The optimum growth was observed at 40 ± 2 °C. The pathogenic characteristics of the GBRC strain, such as hemolysis, gelatin hydrolysis, and the production of volatile sulfur compounds, were similar to those seen in the epithelial layer invading pathogenic strains. Assembled genome size was 3.6 MB, with 78 contigs, and a G + C content of 28.10%. Furthermore, the whole genome sequence analysis confirmed the presence of genes encoding virulence factors and provided genomic insights on adaptation of the strain in the uterine environment. Based on the phenotypic and genetic differences with phylogenetic relatives, strain GBRC is proposed to represent a first reported species of the genus Paraclostridium with potential pathogenic character, from the buffalo uterine environment. This study analysis of the GBRC strain serves as a key reference point for the investigation of potential pathogenic strains that may cause endometritis and metritis in bovine. Full article
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2021

Jump to: 2023, 2022, 2020, 2019

8 pages, 789 KiB  
Communication
Effect of Streptococcus uberis on Gamma Delta T Cell Phenotype in Bovine Mammary Gland
by Petr Slama, Terezie Zavadilova, Ales Pavlik, Pavel Horky, Sylvie Skalickova, Jiri Skladanka, Shubhadeep Roychoudhury, Simona Baldovska, Adriana Kolesarova, Roman Konecny, Vladimir Tancin and Monika Zouharova
Animals 2021, 11(12), 3594; https://doi.org/10.3390/ani11123594 - 19 Dec 2021
Viewed by 2356
Abstract
In this study, we focused analyzing γδ T cells during bovine mammary gland inflammation induced by Streptococcus uberis. A mammary gland cell suspension was obtained using lavage 24, 48, 72, and 168 h after intramammary-induced infection. The proportion of lymphocytes increased during [...] Read more.
In this study, we focused analyzing γδ T cells during bovine mammary gland inflammation induced by Streptococcus uberis. A mammary gland cell suspension was obtained using lavage 24, 48, 72, and 168 h after intramammary-induced infection. The proportion of lymphocytes increased during the entire week in which inflammation was present. The γδ T cells were also elevated during inflammation, reaching their peak at 72 h following induced inflammation. The percentage of apoptotic lymphocytes continually increased, with the highest proportion occurring 168 h after S. uberis infection. The results show that γδ T cells may be involved in the resolution of inflammation in bovine mammary glands, with the apoptosis of those cells potentially playing an important role. Full article
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11 pages, 1111 KiB  
Article
Evaluation of Postmortem Inspection Procedures to Diagnose Bovine Tuberculosis at Debre Birhan Municipal Abattoir
by Fanos Tadesse Woldemariyam, Tibebeu Markos, Dereje Shegu, Kassa Demissie Abdi and Jan Paeshuyse
Animals 2021, 11(9), 2620; https://doi.org/10.3390/ani11092620 - 07 Sep 2021
Cited by 6 | Viewed by 4708
Abstract
Routine meat inspection in the abattoir was used to examine carcass for subsequent approval for consumption. However, the chance of missing lesions results in approval of carcass and/or the offal with lesions of tuberculosis. A cross-sectional study was conducted at Debre Birhan Municipal [...] Read more.
Routine meat inspection in the abattoir was used to examine carcass for subsequent approval for consumption. However, the chance of missing lesions results in approval of carcass and/or the offal with lesions of tuberculosis. A cross-sectional study was conducted at Debre Birhan Municipal abattoir from October 2016 to May 2017. Lesion prevalence estimation and two meat inspection procedures’ efficacy evaluation was attempted. The breeds of the animals inspected were zebu breeds. Routine abattoir meat inspection involves visual inspection, palpation and incision of intact organs such as the liver and kidneys, as well as inspection, palpation and incision of tracheobronchial, mediastinal and prescapular lymph nodes. The detailed meat inspection involves inspection of each of the carcass. In this case, the seven lobes of the two lungs, lymph nodes and organs were also thoroughly examined. The cut surfaces were examined under bright light sources for the presence of an abscess, cheesy mass, and tubercles in detail. The study involved and compared both routine and detailed meat inspections at the abattoir. Chi-square test of independence and odds ratio were used to see the association of lesion and different risk factors. Based on detailed meat inspection, the overall lesion prevalence of bovine tuberculosis in the carcass of cattle slaughtered at Debre Birhan municipality abattoir was found to be 4.7% but only 0.5% of the carcass examined had detectable bovine tuberculosis lesions when routine abattoir meat inspection alone was used. The majority of the lesions were distributed to the lungs and associated lymph nodes. There was a significant association (p < 0.05) in TB infection rate and body condition score. In conclusion, this study has clearly indicated the prevalence of bovine tuberculosis lesions in the abattoir that are missed by routine abattoir meat inspection. In addition, it showed low sensitivity of the routine meat inspection procedure used. Hence, our study warrants immediate attention to strengthen the current meat inspection practices at Debre Birhan public abattoir. Full article
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2020

Jump to: 2023, 2022, 2021, 2019

17 pages, 276 KiB  
Review
Epidemiology and Classification of Mastitis
by Maros Cobirka, Vladimir Tancin and Petr Slama
Animals 2020, 10(12), 2212; https://doi.org/10.3390/ani10122212 - 26 Nov 2020
Cited by 104 | Viewed by 12189
Abstract
Farmers should focus on milk quality over quantity because milk that contains unsuitable components and/or antibiotic residues, or has a high somatic cell count, cannot be used in food production and thereby results in reduced milk yield. One of the main problems affecting [...] Read more.
Farmers should focus on milk quality over quantity because milk that contains unsuitable components and/or antibiotic residues, or has a high somatic cell count, cannot be used in food production and thereby results in reduced milk yield. One of the main problems affecting the ultimate milk yield of dairy cows is mastitis. This disease is the most serious economic and health problem associated with dairy cow herds and is a major reason for excessive culling. Therefore, many studies have addressed this problem to further our understanding of the agents causing mastitis and their classification and virulence factors. This review summarizes the current knowledge regarding mastitis prevalence, the characteristics of its main causative agents, and the effects of mastitis on dairy production. The review also intends to provide guidance for future studies by examining external effects influencing dairy production in cows under field conditions. Full article
7 pages, 220 KiB  
Communication
The Prevalence of Salmonella spp. in Two Arctic Fox (Alopex lagopus) Farms in Poland
by Jan Siemionek, Konrad Przywara and Anna Szczerba-Turek
Animals 2020, 10(9), 1688; https://doi.org/10.3390/ani10091688 - 18 Sep 2020
Viewed by 2273
Abstract
The objective of the study was to determine the occurrence of Salmonella spp. infections in two Arctic fox (Alopex lagopus) farms in Poland, and to analyse the correlations between animals that tested positive for Salmonella spp and breeding results. Faecal samples [...] Read more.
The objective of the study was to determine the occurrence of Salmonella spp. infections in two Arctic fox (Alopex lagopus) farms in Poland, and to analyse the correlations between animals that tested positive for Salmonella spp and breeding results. Faecal samples were taken from 1094 clinically healthy blue foxes from the basic stock of farms A and B. Salmonella spp. were detected in 18.06% (56/310) of the samples collected in farm A and in 15.94% (125/784) of the samples collected in farm B. All isolated strains belonged to S. enterica subsp. enterica serotypes Salmonella Saintpaul (S. Saintpaul), Salmonella Reading (S. Reading), and Salmonella Heidelberg (S. Heidelberg). All three serotypes are typically isolated from commercial poultry flocks. Salmonella spp. infections significantly increased the risk of female infertility, but further research is needed to confirm the results. This is the first report on the prevalence of S. Heidelberg, S. Saintpaul, and S. Reading in faecal samples collected from Arctic fox (Alopex lagopus) farms in Poland. Full article
10 pages, 1254 KiB  
Article
First Molecular Detection and Characterization of Hemotropic Mycoplasma Species in Cattle and Goats from Uganda
by Benedicto Byamukama, Maria Agnes Tumwebaze, Dickson Stuart Tayebwa, Joseph Byaruhanga, Martin Kamilo Angwe, Jixu Li, Eloiza May Galon, Mingming Liu, Yongchang Li, Shengwei Ji, Paul Frank Adjou Moumouni, Aaron Ringo, Seung-Hun Lee, Patrick Vudriko and Xuenan Xuan
Animals 2020, 10(9), 1624; https://doi.org/10.3390/ani10091624 - 10 Sep 2020
Cited by 8 | Viewed by 3258
Abstract
Hemoplasmas (hemotropic mycoplasmas) are small pleomorphic bacteria that parasitize the surface of red blood cells of several mammalian species including cattle, goats, and humans, causing infectious anemia. However, studies on hemoplasmas have been neglected and to date, there are no studies on bovine [...] Read more.
Hemoplasmas (hemotropic mycoplasmas) are small pleomorphic bacteria that parasitize the surface of red blood cells of several mammalian species including cattle, goats, and humans, causing infectious anemia. However, studies on hemoplasmas have been neglected and to date, there are no studies on bovine and caprine hemoplasmas in Uganda or the entire East African region. In this study, a polymerase chain reaction (PCR) assay targeting the 16S rRNA gene was used to investigate the presence of hemoplasma in 409 samples (cattle = 208; goats = 201) collected from Kasese district, western Uganda. Results showed that 32.2% (67/208) of cattle samples and 43.8% (88/201) of goat samples were positive for hemoplasmas. Sequencing analysis identified Candidatus Mycoplasma haemobos and Mycoplasma wenyonii in cattle, while Candidatus Mycoplasma erythrocervae and Mycoplasma ovis were identified in goats. Statistical analysis showed that goats were at a higher risk of infection with hemoplasmas compared with cattle. To the best of our knowledge, this is the first molecular evidence of hemoplasmas in bovine and caprine animals in Uganda and the entire east African region. Full article
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15 pages, 653 KiB  
Article
Identifying Active Salmonella Infections in Swine Nurseries Using Serology and Bacterial Culture and Evaluating Associated Risk Factors
by Saranya Nair, Abdolvahab Farzan, Zvonimir Poljak and Robert Friendship
Animals 2020, 10(9), 1517; https://doi.org/10.3390/ani10091517 - 27 Aug 2020
Cited by 2 | Viewed by 1900
Abstract
The objectives of this study were: to identify nursery cohorts with an active Salmonella infection using combined serological and bacteriological methods, and to try to identify risk factors associated with swine nurseries with active Salmonella spread. Twenty pigs from each of 50 cohorts [...] Read more.
The objectives of this study were: to identify nursery cohorts with an active Salmonella infection using combined serological and bacteriological methods, and to try to identify risk factors associated with swine nurseries with active Salmonella spread. Twenty pigs from each of 50 cohorts of weaned pigs from 44 different nursery barns were sampled about the time of weaning and near the end of the nursery stage. Information regarding farm management and biosecurity practices were collected using a questionnaire. Blood samples were obtained at both visits, while rectal swabs were collected at the second visit. An enzyme-linked immunosorbent assay (ELISA) was used to test sera for Salmonella antibodies and rectal samples were cultured for Salmonella. A nursery cohort was identified as having an active Salmonella infection if Salmonella was cultured from one or more of the 20 pigs or if serological evidence suggested exposure to Salmonella. The association between farm-level management covariates and active Salmonella infection was assessed in 46 cohorts using a logistic regression model. Nine of 46 (20%) cohorts produced Salmonella-free pigs. The remaining 37 (80%) cohorts were classified as having an active infection. Examination of risk factors failed to identify how negative and positive nurseries differed. Full article
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11 pages, 1333 KiB  
Article
Prevalence of Bovine Tuberculosis in Slaughtered Cattle in Sicily, Southern Italy
by Jessica M. Abbate, Francesca Arfuso, Carmelo Iaria, Giuseppe Arestia and Giovanni Lanteri
Animals 2020, 10(9), 1473; https://doi.org/10.3390/ani10091473 - 21 Aug 2020
Cited by 14 | Viewed by 3286
Abstract
Post-mortem inspection in slaughterhouses plays a key role in the epidemiological surveillance of infectious diseases, including bTB. This study assessed the prevalence of bTB in cattle in Sicily during two different three-year periods (2010–2012; 2017–2019), using data from meat inspections and histopathological methods. [...] Read more.
Post-mortem inspection in slaughterhouses plays a key role in the epidemiological surveillance of infectious diseases, including bTB. This study assessed the prevalence of bTB in cattle in Sicily during two different three-year periods (2010–2012; 2017–2019), using data from meat inspections and histopathological methods. Out of 100,196 cattle, 5221 (5.21%) were diagnosed with tuberculous lesions. Higher prevalence of bTB was recorded during the triennium 2010–2012 (6.74%; n = 3692) compared to the triennium 2017–2019 (3.36%; n = 1529), with a decreasing trend in annual occurrence throughout the study period and a heterogenous proportion of infected cattle among the Sicilian provinces (p < 0.01). Lower rates of infection were recorded in animals aged <12 months and >84 months (p < 0.0001). Pearson’s chi square analysis revealed a higher localization of lesions in the thoracic cavity (p < 0.0001). Gathered findings show that even though bTB occurrence in cattle was greatly reduced over the years, the disease still remains widespread in Sicily, also posing severe implications for public health. Full article
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13 pages, 551 KiB  
Article
Genomic Analysis of Staphylococcus aureus Strains Originating from Hungarian Rabbit Farms Reinforce the Clonal Origin of Various Virulence Types
by Zoltán Német, Ervin Albert, Ádám Dán, Gyula Balka, Áron Szenes, Rita Sipos, Szabolcs Bódizs and Imre Biksi
Animals 2020, 10(7), 1128; https://doi.org/10.3390/ani10071128 - 02 Jul 2020
Cited by 4 | Viewed by 2904
Abstract
Staphylococcosis is one of the most important infectious diseases in rabbit medicine, especially in commercial farming. Previous studies revealed the existence of virulent variants adapted to rabbits. Typical and atypical, highly virulent as well as low virulent variants have been isolated and reported [...] Read more.
Staphylococcosis is one of the most important infectious diseases in rabbit medicine, especially in commercial farming. Previous studies revealed the existence of virulent variants adapted to rabbits. Typical and atypical, highly virulent as well as low virulent variants have been isolated and reported from industrial units in all major rabbit-meat-producing countries. Preceding the research focused on detecting defined nucleotide sequences, the genome of these organisms as a whole was rarely subjected to scientific investigations. The authors sequenced 51 Staphylococcus strains originating from industrial rabbit farms in Hungary. Another 12 draft genomes of rabbit isolates were constructed from read sequences available in digital repositories, and were compared based on whole-genome multilocus sequence typing. The clonal origin of highly virulent variants is confirmed, the strains from Hungary were closely related with the strains isolated in the UK, Italy, and Spain. Atypical highly virulent strains are the most prevalent in Hungary, they form a separate clonal cluster. The low virulent strains were genetically similar, but more heterogeneous than the highly virulent (HV) and aHV strains even by the traditional MLST typing scheme. Other “non-aureus” Staphylococcus species were also identified. Full article
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11 pages, 511 KiB  
Brief Report
Assessing Antibiotic Residues in Poultry Eggs from Backyard Production Systems in Chile, First Approach to a Non-Addressed Issue in Farm Animals
by Javiera Cornejo, Ekaterina Pokrant, Francisco Figueroa, Ricardo Riquelme, Pablo Galdames, Francisca Di Pillo, Pedro Jimenez-Bluhm and Christopher Hamilton-West
Animals 2020, 10(6), 1056; https://doi.org/10.3390/ani10061056 - 19 Jun 2020
Cited by 23 | Viewed by 4206
Abstract
Eggs are the main product generated from backyard poultry production systems (BPS) because they can quickly be consumed and sold to meet essential family needs. Nevertheless, antimicrobial residues can accumulate in this product. The objective of this study was to evaluate the presence [...] Read more.
Eggs are the main product generated from backyard poultry production systems (BPS) because they can quickly be consumed and sold to meet essential family needs. Nevertheless, antimicrobial residues can accumulate in this product. The objective of this study was to evaluate the presence of antimicrobial residues in eggs produced by poultry kept in BPS in central Chile. To assess this, eggs were obtained from 83 BPS and analysed to evaluate the presence of antibiotic residues (families: tetracyclines, beta-lactams, aminoglycosides and macrolides), using a Four-Plate Test screening method for the detection, based on a bacterial growth inhibition method. Results show a lack of biosecurity procedures at BPS level, making these systems susceptible to the dissemination of antimicrobial residues. These include intensive animal production units in the proximity, and the presence of shared watercourses with other farms. Furthermore, 66% of the surveyed owners are indicated as giving pharmacological treatments to their chickens. Eggs from 61 BPS were positive for at least one antimicrobial. Fifty-three BPS were positive for more than one antimicrobial, and one BPS was positive for all four antimicrobials tested. Consequently, there is a risk that poultry eggs produced in BPS in central Chile carry residues of different families of antimicrobials. Full article
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10 pages, 878 KiB  
Article
Effect of Lipopolysaccharide and Muramyl Dipeptide on Apoptosis of Bovine Mammary Gland Lymphocytes
by Petr Slama, Eliska Kabourkova, Zbysek Sladek, Terezie Zavadilova, Lucie Kratochvilova, Kristina Kharkevich, Shubhadeep Roychoudhury, Ales Pavlik, Andrea Roztocilova, Michal Uhrincat, Vladimir Tancin, Kazuhiro Kimura, Roman Konecny, Yoshio Kiku, Atsushi Watanabe, Jong-Young Kwak and Monika Zouharova
Animals 2020, 10(6), 990; https://doi.org/10.3390/ani10060990 - 05 Jun 2020
Cited by 3 | Viewed by 2659
Abstract
The aim of this study was to evaluate whether apoptosis of lymphocytes is modulated by stimulation by lipopolysaccharide (LPS) of Escherichia coli or muramyl dipeptide (MDP). Cell populations were obtained by lavaging of the mammary glands 24, 48, 72, and 168 h following [...] Read more.
The aim of this study was to evaluate whether apoptosis of lymphocytes is modulated by stimulation by lipopolysaccharide (LPS) of Escherichia coli or muramyl dipeptide (MDP). Cell populations were obtained by lavaging of the mammary glands 24, 48, 72, and 168 h following intramammary induced inflammation. The portion of apoptotic lymphocytes peaked at 48 h after treatment with LPS or MDP. The analysis of CD44 expression of the same cell populations showed a higher percentage of CD44-positive lymphocytes 24- and 48-h following induction of inflammation by LPS or MDP. The results demonstrate that during both experimental infection of bovine mammary glands with LPS or MDP, apoptosis of lymphocytes was induced in the initial phase of the inflammatory response and CD44 was also overexpressed at the beginning of inflammation. These data suggest a connection of lymphocyte apoptosis with the expression of CD44 receptors. Full article
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15 pages, 3175 KiB  
Article
Metataxonomic and Histopathological Study of Rabbit Epizootic Enteropathy in Mexico
by Xiao-Haitzi Daniel Puón-Peláez, Neil Ross McEwan, José Guadalupe Gómez-Soto, Roberto Carlos Álvarez-Martínez and Andrea Margarita Olvera-Ramírez
Animals 2020, 10(6), 936; https://doi.org/10.3390/ani10060936 - 28 May 2020
Cited by 7 | Viewed by 5079
Abstract
Epizootic rabbit enteropathy (ERE) affects young rabbits and represents 32% of the enteropathies in rabbit production farms in Mexico. The etiology of this syndrome has not been clarified yet. A metataxonomic and histopathology study of ERE was carried out to compare the gastrointestinal [...] Read more.
Epizootic rabbit enteropathy (ERE) affects young rabbits and represents 32% of the enteropathies in rabbit production farms in Mexico. The etiology of this syndrome has not been clarified yet. A metataxonomic and histopathology study of ERE was carried out to compare the gastrointestinal microbiota and histopathological lesions of healthy and positive-ERE rabbits. The metataxonomic study was done using an Illumina MiSeq (MiSeq® system, Illumina, San Diego California, USA) massive segmentation platform, and a Divisive Amplicon Denoising Algorithm 2 (DADA2 algorithm) was used to obtain Shannon and Simpson diversity indices as well as the relative abundance of the identified communities. For the histopathological study, paraffin sections of the cecum, ileo-cecal valve, and colon were stained with eosin and hematoxylin. AxioVision 4.9 software (Carl Zeiss MicroImaging GmbH, Jena, Germany) was used to measure the crypt depths. Statistical analysis was done using PERMANOVA analysis for the metataxonomic study and ANOVA for the histopathology study. Histopathologic analysis showed smaller sizes of crypts in the colon of ERE rabbits. Differences were observed in the diversity and abundance of the gastrointestinal microbiota between the analyzed groups. The genus Clostridium and the species Cloacibacillus porcorum and Akkermansia muciniphila were associated with ERE. The results obtained from this study can provide information for future clarification of the etiology and proposals of effective treatments. Full article
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11 pages, 400 KiB  
Article
Mechanical Transmission of Lumpy Skin Disease Virus by Stomoxys spp. (Stomoxys calsitrans, Stomoxys sitiens, Stomoxys indica), Diptera: Muscidae
by Arman Issimov, Lespek Kutumbetov, Mukhit B. Orynbayev, Berik Khairullin, Balzhan Myrzakhmetova, Kulyaisan Sultankulova and Peter J. White
Animals 2020, 10(3), 477; https://doi.org/10.3390/ani10030477 - 12 Mar 2020
Cited by 27 | Viewed by 4421
Abstract
Samples collected for PCR from recipient animals tested positive in 5 out of 6 cases, while the virus was isolated from 4 of 6 animals. The clinical signs exhibited by recipient animals were mostly moderate in nature with only one severe case. To [...] Read more.
Samples collected for PCR from recipient animals tested positive in 5 out of 6 cases, while the virus was isolated from 4 of 6 animals. The clinical signs exhibited by recipient animals were mostly moderate in nature with only one severe case. To our knowledge, this is the first time that transmission of LSDV by three Stomoxys species has been demonstrated, and their role as mechanical vectors of LSDV is indicated. Full article
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13 pages, 3560 KiB  
Article
Effects of Dietary Non-Fibrous Carbohydrate (NFC) to Neutral Detergent Fiber (NDF) Ratio Change on Rumen Bacteria in Sheep Based on Three Generations of Full-Length Amplifiers Sequencing
by Xuanxuan Pu, Xuefeng Guo, Khuram Shahzad, Mengzhi Wang, Chenyu Jiang, Junfeng Liu, Xiuping Zhang, Sujiang Zhang and Long Cheng
Animals 2020, 10(2), 192; https://doi.org/10.3390/ani10020192 - 22 Jan 2020
Cited by 8 | Viewed by 2758
Abstract
The study was conducted to investigate the effects of dietary NFC/NDF ratio change on rumen bacteria in sheep. Twelve Karakul sheep were assigned randomly into four groups fed with four dietary NFC/NDF ratios of 0.54, 0.96, 1.37, and 1.90 and they were assigned [...] Read more.
The study was conducted to investigate the effects of dietary NFC/NDF ratio change on rumen bacteria in sheep. Twelve Karakul sheep were assigned randomly into four groups fed with four dietary NFC/NDF ratios of 0.54, 0.96, 1.37, and 1.90 and they were assigned into groups 1, 2, 3, and 4, respectively. The experiment was divided into four periods: I (1–18 d), II (19–36 d), III (37–54 d), and IV (55–72 d). In each period, the first 15 d were used for adaption, and then rumen fluid was collected for 3 d from each sheep before morning feeding. The fluid was analyzed with three generations of full-length amplifiers sequencing. Results showed that the bacterial diversity of group 4 was decreased in period III and IV. At the phylum level, Bacteroidetes (37–60%) and Firmicutes (26–51%) were the most dominant bacteria over the four periods. The relative abundance of Bacteroidetes, Firmicutes, Tenericutes, and Spirochaete changed with dietary NFC/NDF ratio change over the four periods, but there was no difference among groups over the four periods (p > 0.05). At the genus level, unidentified-Lachnospiraceae was the dominant genus, and its relative abundance in group 3 was high during the period I and III (p < 0.05). The relative abundance of Mycoplasma in group 4 was high in the period I and II (p < 0.05). The relative abundance of Succiniclasticum was high in group 2 of period II (p < 0.05). At the species level, the relative abundance of Butyrivibrio-fibrisolvens was found to be high in group 3 during periods I and III (p < 0.05). The main semi-cellulose-degrading bacteria and starch-degrading bacteria were low, and there was no significant difference among groups over four periods (p > 0.05). Taken together, the dietary NFC/NDF ratio of 1.90 decreased the diversity of bacteria as a period changed from I to IV. While the main phylum bacteria didn’t change, their relative abundance changed with the dietary NFC/NDF ratio change over the four periods. The most prevalent genus was unidentified-Lachnospiraceae, and its relative abundance was higher in dietary NFC/NDF ratio of 1.37 than other groups. Similarly, the main cellulose-degrading species was higher in the treatment of dietary NFC/NDF ratio of 1.37 than other groups. Full article
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14 pages, 2661 KiB  
Article
Diversity and Composition of Rumen Bacteria, Fungi, and Protozoa in Goats and Sheep Living in the Same High-Altitude Pasture
by Suo Langda, Chenguang Zhang, Ke Zhang, Ba Gui, De Ji, Ciren Deji, Awang Cuoji, Xiaolong Wang and Yujiang Wu
Animals 2020, 10(2), 186; https://doi.org/10.3390/ani10020186 - 22 Jan 2020
Cited by 33 | Viewed by 5179
Abstract
Environmental adaptation of ruminants was highly related to microbiota in the rumen. To investigate the diversity and composition of bacteria, fungi, and protozoa in the rumen of high-altitude animals, amplicon gene sequencing was performed using rumen fluid samples derived from both Tibetan goats [...] Read more.
Environmental adaptation of ruminants was highly related to microbiota in the rumen. To investigate the diversity and composition of bacteria, fungi, and protozoa in the rumen of high-altitude animals, amplicon gene sequencing was performed using rumen fluid samples derived from both Tibetan goats and sheep at the same pasture in a highland (altitude > 4800 m). Between these two species, the ruminal bacteria and fungi were significantly different at multiple taxonomic levels. The alpha diversity of bacteria was significantly high in goats (p < 0.05). One hundred and sixty-four and 29 Operational Taxonomy Units (OTUs) with significant differences were detected in bacteria and fungi, respectively. The abundance of bacteria, fungi, and protozoa in the rumen was characterized at multiple taxonomic levels, and we determined that Firmicutes, Bacteroidetes, Neocallimastigomycota, and Ciliophora were the most abundant bacteria, fungi, and protozoa. The family Neocallimastigaceae and the genus Metadinium had cellulose degradation capacity in the rumen with high abundance, thereby, suggesting that fungi and protozoa played an essential role in rumen fermentation. In addition, by comparing microbiota in the rumen of goats and sheep it was found, that the fiber-degrading fungi genus (Cyllamyces) was increased in the rumen of sheep (p < 0.05) whereas VFA-producing bacteria (Saccharofermentans and Lachnospiraceae_XPB1014) were increased in the rumen of goats (p < 0.05). Interestingly, in the rumen, no differences in protozoa were observed between goats and sheep (p > 0.05). Furthermore, when compared to sheep, level of acetic acid, propionic acid, and total volatile fatty acid (TVFA) were significantly increased in the rumen of goats (p < 0.05). Taken together, these results suggested microbiota in the rumen drive goats to better adapt to high-altitude grazing conditions. Full article
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15 pages, 2615 KiB  
Article
Characterization of the Rumen Microbiota and Volatile Fatty Acid Profiles of Weaned Goat Kids under Shrub-Grassland Grazing and Indoor Feeding
by Jiazhong Guo, Pengfei Li, Shuai Liu, Bin Miao, Bo Zeng, Yahui Jiang, Li Li, Linjie Wang, Yu Chen and Hongping Zhang
Animals 2020, 10(2), 176; https://doi.org/10.3390/ani10020176 - 21 Jan 2020
Cited by 15 | Viewed by 4128
Abstract
In this study, we conducted comparative analyses to characterize the rumen microbiota and volatile fatty acid (VFA) profiles of weaned Nanjiang Yellow goat kids under shrub-grassland grazing (GR), shrub-grassland grazing and supplementary feeding (SF), and indoor feeding (IF) systems. We observed significant differences [...] Read more.
In this study, we conducted comparative analyses to characterize the rumen microbiota and volatile fatty acid (VFA) profiles of weaned Nanjiang Yellow goat kids under shrub-grassland grazing (GR), shrub-grassland grazing and supplementary feeding (SF), and indoor feeding (IF) systems. We observed significant differences (p < 0.05) in the concentrations of total VFA and the proportions of acetate and butyrate in the rumen fluid among the three groups, whereas the proportions of propionate and the acetate/propionate ratio did not differ substantially. Alpha diversity of the rumen bacterial and archaeal populations in the GR and SF kids was significantly higher (p < 0.05) than that in the IF goat kids, and significant differences (p < 0.05) in similarity were observed in the comparisons of GR vs. IF and SF vs. IF. The most predominant bacterial phyla were Bacteroidetes and Firmicutes across the three groups, and the archaeal community was mainly composed of Euryarchaeota. At the genus and species levels, the cellulose-degrading bacteria, including Lachnospiraceae, Ruminococcaceae and Butyrivibrio fibrisolvens, were abundant in the GR and SF groups. Furthermore, 27 bacterial and 11 unique archaeal taxa, such as Lachnospiraceae, Butyrivibrio fibrisolvens, and Methanobrevibacter ruminantium, were identified as biomarkers, and showed significantly different (p < 0.05) abundances among the three groups. Significant Spearman correlations (p < 0.05), between the abundances of several microbial biomarkers and the concentrations of VFAs, were further observed. In summary, our results demonstrated that the adaptation to grazing required more rumen bacterial populations due to complex forage types in shrub-grassland, although the rumen fermentation pattern did not change substantially among the three feeding systems. Some microbial taxa could be used as biomarkers for different feeding systems, particularly cellulose-degrading bacteria associated with grazing. Full article
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2019

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10 pages, 779 KiB  
Article
Prevalence of Salmonella by Serological and Direct Detection Methods in Piglets from Inconspicuous, Conspicuous, and Vaccinated Sow Herds
by Juhle-Marijke Buch, Christian Visscher, Anton Schulte zu Sundern, Josef Schulte-Wülwer, Ansgar Deermann and Carolin Holling
Animals 2020, 10(1), 29; https://doi.org/10.3390/ani10010029 - 21 Dec 2019
Cited by 3 | Viewed by 2316
Abstract
Due to the zoonotic potential of Salmonella, the high prevalence of Salmonella on pig farms deserves particular attention. Because there is limited precise data on piglet-producing farms, this survey evaluated the Salmonella status of 24 different pig farms that had previously been [...] Read more.
Due to the zoonotic potential of Salmonella, the high prevalence of Salmonella on pig farms deserves particular attention. Because there is limited precise data on piglet-producing farms, this survey evaluated the Salmonella status of 24 different pig farms that had previously been divided into 12 Salmonella-conspicuous (SC) and 12 Salmonella-inconspicuous (SI) farms on the basis of the serological status of their piglets (25 kg). The evaluation was based on 498 environmental samples and 2641 blood samples, as well as on a biosecurity screening. SC farms were subdivided into farms with sow vaccination against Salmonella (n = 3) and those without vaccination (n = 9). In accordance with the previous classification, both the highest Salmonella prevalence in the environment and the highest antibody titers of the examined piglets were determined on SC farms at both defined time points. Piglets from vaccinated sows showed the highest OD% values, before and after vaccination. On SC farms, most Salmonella-positive samples could be obtained in rearing areas (2017: 40.8%, 2019: 26.0%). The results of this study indicate that sow vaccination alone cannot influence Salmonella prevalence at the farm level. Above all, general infection pressure seems to play a major role for Salmonella prevalence in the environment and for high OD% values of related pigs. Full article
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17 pages, 4014 KiB  
Article
Maturation of the Goat Rumen Microbiota Involves Three Stages of Microbial Colonization
by Ke Zhang, Bibo Li, Mengmeng Guo, Gongwei Liu, Yuxin Yang, Xiaolong Wang, Yulin Chen and Enping Zhang
Animals 2019, 9(12), 1028; https://doi.org/10.3390/ani9121028 - 25 Nov 2019
Cited by 25 | Viewed by 4189
Abstract
With increasing age, the rumen microbiota of new-born ruminants become central in the translation of fibrous feed substances into essential nutrients. However, the colonization process of the microbial community (especially fungal community) remains poorly understood in ruminants at pre-weaning stages. In this study, [...] Read more.
With increasing age, the rumen microbiota of new-born ruminants become central in the translation of fibrous feed substances into essential nutrients. However, the colonization process of the microbial community (especially fungal community) remains poorly understood in ruminants at pre-weaning stages. In this study, the rumen bacterial and fungal colonization processes were investigated in goats at eight stages using amplicon sequencing. For bacteria, we found 36 common core genera at D0, D3, D14, D28, and D56, including mainly Bacillus, Alloprevotella, Bacteroides, Prevotella_1, Lactococcus, and Ruminococcaceae_NK4A214. Firmicutes was the dominant phylum among the total microbiota in newborn goat kids (prior to nursing), while Bacillus, Lactococcus, and Pseudomonas were predominant genera. Interestingly, the proportion of Bacillus was as high as 55% in newborn animals. After milk nursing, the predominant phylum changed to Bacteroidetes, while the proportion of Bacillus and Lactobacillus was very low. CowPi was used to predict the functional gene pathways and we found increases in the abundance of genes associated with amino acid related enzymes, DNA repair and recombination proteins, aminoacyl tRNA biosynthesis, and peptidases after D3. With regard to fungi, we found that there were 51 common genera at day 0 (D0), D3, D14, D28, and D56, including mainly Cryptococcus, Aspergillus, and Caecomyces. Aspergillus occupied approximately 47% at day 0, but then it decreased from day 3 to day 14. This study indicates that the core microbes of rumen emerged shortly after birth, but the abundance was very different from the core genus of the adult rumen. In addition, we also report a detailed scheme of the bacterial and fungal colonization process in rumens and propose three distinct stages during the rumen colonization process in pre-weaning goats, which will offer a reference for the development of milk substitutes for small ruminants. Full article
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13 pages, 1430 KiB  
Article
The Relationship between S. aureus and Branched-Chain Amino Acids Content in Composite Cow Milk
by L. Grispoldi, M. Karama, F. Ianni, A. La Mantia, L. Pucciarini, E. Camaioni, R. Sardella, P. Sechi, B. Natalini and B. T. Cenci-Goga
Animals 2019, 9(11), 981; https://doi.org/10.3390/ani9110981 - 16 Nov 2019
Cited by 12 | Viewed by 2811
Abstract
The early diagnosis of mastitis is an essential factor for the prompt detection of the animal for further actions. In fact, if not culled, infected cows must be segregated from the milking herd and milked last, or milked with separate milking units. Besides [...] Read more.
The early diagnosis of mastitis is an essential factor for the prompt detection of the animal for further actions. In fact, if not culled, infected cows must be segregated from the milking herd and milked last, or milked with separate milking units. Besides microbiological analysis, the somatic cell count (SCC) commonly used as predictor of intramammary infection, frequently lead to a misclassification of milk samples. To overcome these limitations, more specific biomarkers are continuously evaluated. The total amino acid content increases significantly in mastitic milk compared to normal milk. S. aureus requires branched-chain amino acids (BCAAs—isoleucine, leucine, and valine) for protein synthesis, branched-chain fatty acids synthesis, and environmental adaptation by responding to their availability via transcriptional regulators. The increase of BCAAs in composite milk has been postulated to be linked to mammary infection by S. aureus. The aim of this work is to demonstrate, by a direct ion-pairing reversed-phase method, based on the use of the evaporative light-scattering detector (IP-RP-HPLC-ELSD), applied to 65 composite cow milk samples, a correlation between the concentration of isoleucine and leucine, and S. aureus load. The correlation coefficient, r, was found to be 0.102 for SCC (p = 0.096), 0.622 for isoleucine (p < 0.0001), 0.586 for leucine (p < 0.0001), 0.013 for valine (p = 0.381), and 0.07 for tyrosine (p = 0.034), standing for a positive correlation between S. aureus and isoleucine and leucine concentration. The link between the content of BCAAs, isoleucine and leucine, and udder infection by S. aureus demonstrated with our study has an important clinical value for the rapid diagnosis of S. aureus mastitis in cows. Full article
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