Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil

2021 ◽  
Author(s):  
Diéssy Kipper ◽  
Renato H. Orsi ◽  
Laura M. Carroll ◽  
Andrea K. Mascitti ◽  
André F. Streck ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Health Concern ◽  
Recent Common Ancestor ◽  
Economic Losses ◽  
Multi Drug Resistance ◽  
Poultry Production ◽  
Production Chain ◽  
Genetic Characteristics ◽  
The World ◽  
Poultry Farms

Salmonella enterica Heidelberg is a serovar isolated from poultry-producing regions around the World. In Brazil, S. Heidelberg has been frequently detected in poultry flocks, slaughterhouses and chicken. The goal of the present study was to assess the population structure, recent temporal evolution and some important genetic characteristics of S. Heidelberg isolated from Brazilian poultry farms. Phylogenetic analysis of 68 S . Heidelberg genomes sequenced here and additional whole-genomes data from NCBI demonstrated that all isolates from the Brazilian poultry production chain clustered into a monophyletic group, here called S. Heidelberg Brazilian poultry lineage (SH-BPL). Bayesian analysis defined the time of the most recent common ancestor (tMRCA) as 2004 and the overall population size (N e ) constant until 2008, when a ∼10-fold N e increase was observed until circa 2013. SH-BPL presented at least two plasmids with replicons ColpVC ( n =68; 100%), IncX1 ( n =66; 97%), IncA/C2 ( n =65; 95.5%), ColRNAI ( n =43; 63.2%), IncI1 ( n =32; 47%), ColMG828, Col156, IncHI2A, IncHI2, IncQ1, IncX4, IncY and TrfA (each with n<4; <4% each). Antibiotic resistance genes were found, with high frequencies of fosA7 ( n =68; 100%), mdf A ( n =68; 100%), tet(34) ( n =68; 100%), sul2 ( n =64; 94.1%), blaCMY-2 ( n =56; 82.3%) and an overall multi-drug resistance (MDR) profile. Ten pathogenicity islands (SPI1-5, SPI9 and SPI11-14) and 139 virulence genes were also detected. SH-BPL profile was like other previous S. Heidelberg isolates from poultry around the world in the 1990s. In conclusion, the present study demonstrates the recent introduction (2004) and high level of dissemination of an MDR S. Heidelberg lineage in Brazilian poultry operations. IMPORTANCE S. Heidelberg is the most frequent serovar in several broiler farms from the main Brazilian poultry-producing regions. So avian-source foods (mainly chicken carcasses) commercialized in the country and exported to other continents are contaminated with this foodborne pathogen, generating several national and international economic losses. In addition, isolates of this serovar are usually resistant to antibiotics and can cause human invasive and septicemic infection, representing a public health concern. This study demonstrates the use of whole-genome sequencing (WGS) to obtain epidemiological information of one S. Heidelberg lineage highly spread among Brazilian poultry farms. This information will help to define biosecurity measures to control this important Salmonella serovar in Brazilian and worldwide poultry operations.

scholarly journals Molecular Characterization of Newcastle Disease Virus from Backyard Poultry Farms and Live Bird Markets in Kenya

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Irene N. Ogali ◽  
Lucy W. Wamuyu ◽  
Jacqueline K. Lichoti ◽  
Erick O. Mungube ◽  
Bernard Agwanda ◽  
...  
Keyword(s):  
Newcastle Disease ◽  
Cleavage Site ◽  
Economic Losses ◽  
Protein Cleavage ◽  
Genetic Characteristics ◽  
Backyard Poultry ◽  
Live Bird Markets ◽  
Cross Border ◽  
Poultry Farms ◽  
Live Bird

Newcastle disease (ND) is a serious disease of poultry that causes significant economic losses. Despite rampant ND outbreaks that occur annually in Kenya, the information about the NDV circulating in Kenya is still scarce. We report the first countrywide study of NDV in Kenya. Our study is aimed at evaluating the genetic characteristics of Newcastle disease viruses obtained from backyard poultry in farms and live bird markets in different regions of Kenya. We sequenced and analyzed fusion (F) protein gene, including the cleavage site, of the obtained viruses. We aligned and compared study sequences with representative NDV of different genotypes from GenBank. The fusion protein cleavage site of all the study sequences had the motif 112RRQKRFV118 indicating their velogenic nature. Phylogenetic analysis revealed that the NDV from various sites in Kenya was highly similar genetically and that it clustered together with NDV of genotype V. The study samples were 96% similar to previous Ugandan and Kenyan viruses grouped in subgenotype Vd This study points to possible circulation of NDV of similar genetic characteristics between backyard poultry farms and live bird markets in Kenya. The study also suggests the possible spread of velogenic NDV between Kenya and Uganda possibly through cross-border live bird trade. Our study provides baseline information on the genetic characteristics of NDV circulating in the Kenyan poultry population. This highlights the need for the ND control programmes to place more stringent measures on cross-border trade of live bird markets and poultry products to prevent the introduction of new strains of NDV that would otherwise be more difficult to control.

scholarly journals Improving the management of poultry production: Mobile application development and validation

2020 ◽  
Vol 9 (10) ◽  
pp. e4019108806
Author(s):  
Raquel Baracat Tosi Rodrigues da Silva ◽  
Irenilza de Alencar Nääs ◽  
Arilson José de Oliveira Júnior ◽  
João Gilberto Mendes dos Reis ◽  
Nilsa Duarte da Silva Lima ◽  
...  
Keyword(s):  
Mobile Application ◽  
Poultry Production ◽  
Application Development ◽  
Production Chain ◽  
Good Practices ◽  
Broiler Production ◽  
Good Production ◽  
The World ◽  
Production Practices ◽  
Development And Validation

The broiler production chain is productive, and chicken meat has achieved high export rates to several countries in the world. This study aimed to develop a mobile application that helps the producer to audit the issues of good production practices. The application was developed for Android and programmed in Java. For its development, questions were used, with different weights according to their importance for production. These questions were removed from the items that make up the manuals of good practices used in Brazil. A test was carried out with users to determine the possibility of using the application in the field. After answering all the questions, the user gets a score ranging from 5 to 1 (excellent to bad). It also indicates which questions they did agree with good practices. The test with users showed that the application was easy to understand and enabled users to make decisions that would improve broiler production.

scholarly journals Effect of Avian Influenza H9N2 Subtype Virus Infection on Backyard Poultry Production

2021 ◽  
Vol 9 (1) ◽  
pp. 19-23
Keyword(s):  
Avian Influenza ◽  
Influenza Viruses ◽  
Economic Losses ◽  
Poultry Production ◽  
Poultry Industry ◽  
Backyard Poultry ◽  
H9n2 Subtype ◽  
Pathogenic Avian Influenza ◽  
The World ◽  
Avian Influenza H9n2

Avian influenza is a viral pandemic disease of humans and birds, including commercial and house poultry. Avian influenza is a major concern around the world, which causes serious economic losses in the poultry industry, mainly in home backyard poultry. The backyard poultry is the potential source of income for rural people and indirectly contributes to decreasing the poverty of household women. Besides, in many developing countries, villagers full fill a part of their food demand by the backyard poultry; however, this sector is directly affected by biosecurity risks, including high and low pathogenic avian influenza infections like avian influenza H9N2 subtype. Avian influenza H9N2 subtype has low pathogenic zoonotic importance but still causes serious threats to the poultry industry. The backyard poultry industry is directly affected by this infection due to direct contact with wild migratory birds locating in different regions of the world. Antigenic drift and shift are one of the major conflicts of this infection resulting from a few days to a few months up to many years and also the main reason for the uncontrollable mutation in this infection. All over the world, there is no serious action taken to prevent the H9N2 subtype infection in backyard poultry. This situation has become severe because of the widespread of highly pathogenic avian influenza viruses in the past few years.

scholarly journals Genomic Characterization of Salmonella Minnesota Clonal Lineages Associated with Poultry Production in Brazil

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2043
Author(s):  
Diéssy Kipper ◽  
Laura M. Carroll ◽  
Andrea K. Mascitti ◽  
André F. Streck ◽  
André S. K. Fonseca ◽  
...  
Keyword(s):  
Comparative Approach ◽  
Poultry Production ◽  
Effective Population ◽  
Production Chain ◽  
Antimicrobial Resistance Genes ◽  
Whole Genomes ◽  
Poultry Farms ◽  
Genetic Clusters ◽  
Genomic Characterization ◽  
Salmonella Serotype

Salmonella serotype Minnesota has been increasingly detected in Brazilian poultry farms and food products (chicken meat, eggs) in recent years. In addition, S. Minnesota isolates from poultry are generally resistant to several antibiotics and persistent in farm environments. The present study aimed to assess phylogenomic diversity of S. Minnesota isolates from the poultry production chain in Brazil. In total, 107 worldwide S. Minnesota whole genomes (including 12 from Brazil) were analyzed using a comparative approach. Phylogenetic analysis demonstrated two clades more related to poultry production in Brazil: S. Minnesota poultry lineages I and II (SM-PLI and SM-PLII). Phylodynamic analysis demonstrated that SM-PLI had a common ancestor in 1915, while SM–PLII originated circa 1971. SM-PLII encompassed a higher number of isolates and presented a recent increase in effective population size (mainly from 2009 to 2012). Plasmids IncA/C2 and ColRNA, antimicrobial resistance genes (aph(3′)-Ia, blaCMY-2, qnrB19, sul2, and tet(A)) and mainly a virulence genetic cluster (including the yersiniabactin operon) were detected in isolates from SM-PLI and/or SM-PLII. This study demonstrates the dissemination of two distinct S. Minnesota lineages with high resistance to antibiotics and important virulence genetic clusters in Brazilian poultry farms.

Prevalence, Risk Factors, and Antimicrobial Resistance Profiles of Salmonella from Commercial Broiler Farms in Two Important Poultry-Producing Regions of Colombia

2012 ◽  
Vol 75 (5) ◽  
pp. 874-883 ◽  
Author(s):  
P. DONADO-GODOY ◽  
I. GARDNER ◽  
B. A. BYRNE ◽  
M. LEON ◽  
E. PEREZ-GUTIERREZ ◽  
...  
Keyword(s):  
Risk Factors ◽  
Antimicrobial Resistance ◽  
Nalidixic Acid ◽  
Health Concern ◽  
Resistance Pattern ◽  
Resistant Bacteria ◽  
Poultry Production ◽  
Poultry Farms ◽  
Paratyphi B ◽  
Salmonella Heidelberg

Salmonella is one of the most common foodborne pathogens associated with diarrheal disease in humans. Food animals, especially poultry, are important direct and indirect sources of human salmonellosis, and antimicrobial resistance is an emerging problem of public health concern. The use of antimicrobials benefits producers but contributes to the emergence of antimicrobial resistant bacteria. As a step toward implementing the Colombian Integrated Program for Antimicrobial Resistance Surveillance, this study was conducted to establish the prevalence, distribution of serovars, antimicrobial resistance profiles, and risk factors for Salmonella on poultry farms in the two largest states of poultry production in Colombia. Salmonella was isolated from 41% of farms and 65% of the 315 chicken houses sampled. Salmonella Paratyphi B variant Java was the most prevalent serovar (76%), followed by Salmonella Heidelberg (23%). All Salmonella isolates were resistant to 2 to 15 of the antimicrobial drugs tested in this study. For Salmonella Paratyphi B variant Java, 34 drug resistance patterns were present. The predominant resistance pattern was ciprofloxacin, nitrofurantoin, tetracycline, trimethoprim-sulfamethoxazole, ceftiofur, streptomycin, enrofloxacin, and nalidixic acid; this pattern was detected in 15% of isolates. The resistance pattern of tetracycline, ceftiofur, and nalidixic acid was found in over 40% of the isolates of Salmonella Heidelberg. Of the biosecurity practices considered, two factors were significantly associated with reduction in Salmonella: cleaning of fixed equipment and composting of dead birds on the farm. Findings from the present study provide scientific evidence to inform implementation of official policies that support new biosecurity legislation in an effort to decrease the prevalence of Salmonella on Colombian poultry farms.

scholarly journals Contamination Pathways can Be Traced along the Poultry Processing Chain by Whole Genome Sequencing of Listeria innocua

2020 ◽  
Vol 8 (3) ◽  
pp. 414 ◽  
Author(s):  
Mayada Gwida ◽  
Stefanie Lüth ◽  
Maged El-Ashker ◽  
Amira Zakaria ◽  
Fatma El-Gohary ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Genetic Relatedness ◽  
Food Product ◽  
Listeria Innocua ◽  
Health Concern ◽  
Poultry Production ◽  
Virulence Determinants ◽  
Pathogenic Species ◽  
Production Chain ◽  
Production Stages

Foodborne infection with Listeria causes potentially life-threatening disease listeriosis. Listeria monocytogenes is widely recognized as the only species of public health concern, and the closely related species Listeria innocua is commonly used by the food industry as an indicator to identify environmental conditions that allow for presence, growth, and persistence of Listeria spp. in general. In our study, we analyze the occurrence of Listeria spp. in a farm-to-fork approach in a poultry production chain in Egypt and identify bacterial entry gates and transmission systems. Prevalence of Listeria innocua at the three production stages (farm, slaughterhouse, food products) ranged from 11% to 28%. The pathogenic species Listeria monocytogenes was not detected, and Listeria innocua strains under study did not show genetic virulence determinants. However, the close genetic relatedness of Listeria innocua isolates (maximum 63 SNP differences) indicated cross-contamination between all stages from farm to final food product. Based on these results, chicken can be seen as a natural source of Listeria. Last but not least, sanitary measures during production should be reassessed to prevent bacterial contamination from entering the food chain and to consequently prevent human listeriosis infections. For this purpose, surveillance must not be restricted to pathogenic species.

scholarly journals Epidemiology of Salmonella enterica Serovar Dublin in Cattle and Humans in Denmark, 1996 to 2016: a Retrospective Whole-Genome-Based Study

2019 ◽  
Vol 86 (3) ◽  
Author(s):  
Eglė Kudirkiene ◽  
Gitte Sørensen ◽  
Mia Torpdahl ◽  
Leonardo V. de Knegt ◽  
Liza R. Nielsen ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Salmonella Enterica ◽  
Population Analysis ◽  
Antibiotic Resistance Genes ◽  
Health Concern ◽  
Economic Losses ◽  
Whole Genome ◽  
Content Type ◽  
Geographical Regions ◽  
Cattle Herds

ABSTRACT Salmonella enterica serovar Dublin is a cattle-adapted S. enterica serovar causing both intestinal and systemic infection in its bovine host, and it is also a serious threat to human health. The present study aimed to determine the population structure of S. Dublin isolates obtained from Danish cattle herds and to investigate how cattle isolates relate to Danish human isolates, as well as to non-Danish human and bovine isolates. Phylogenetic analysis of 197 Danish cattle isolates from 1996 to 2016 identified three major clades corresponding to distinct geographical regions of cattle herds. Persistence of closely related isolates within the same herd and their circulation between epidemiologically linked herds for a period of more than 20 years were demonstrated. These findings suggest that a lack of internal biosecurity and, to some extent, also a lack of external biosecurity in the herds have played an important role in the long-term persistence of S. Dublin in Danish cattle herds in the period investigated. Global population analysis revealed that Danish cattle isolates clustered separately from bovine isolates from other countries, whereas human isolates were geographically spread. Resistance genes were not commonly demonstrated in Danish bovine isolates; only the isolates within one Danish clade were found to often harbor two plasmids of IncFII/IncFIB and IncN types, the latter plasmid carrying blaTEM-1, tetA, strA, and strB antibiotic resistance genes. IMPORTANCE S. Dublin causes economic losses in cattle production, and the bacterium is a public health concern. A surveillance and control program has been in place in Denmark since 2002 with the ultimate goal to eradicate S. Dublin from Danish cattle herds; however, a small proportion of herds have remained positive for many years. In this study, we demonstrate that herds with persistent infection often were infected with the same strain for many years, indicating that internal biosecurity has to be improved to curb the infection. Further, domestic cases of S. Dublin infection in humans were found to be caused both by Danish cattle isolates and by isolates acquired abroad. This study shows the strength of whole-genome sequencing to obtain detailed information on epidemiology of S. Dublin and allows us to suggest internal biosecurity as a main way to control this bacterium in Danish cattle herds.

scholarly journals The novel zoonotic COVID-19 pandemic: An expected global health concern

2020 ◽  
Vol 14 (03) ◽  
pp. 254-264 ◽  
Author(s):  
Carlo Contini ◽  
Mariachiara Di Nuzzo ◽  
Nicole Barp ◽  
Aurora Bonazza ◽  
Roberto De Giorgio ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Severe Acute Respiratory Syndrome ◽  
Southern China ◽  
Spillover Effect ◽  
Severe Pneumonia ◽  
Guangdong Province ◽  
Health Concern ◽  
Economic Losses ◽  
The Novel ◽  
The World

18 years ago, in 2002, the world was astonished by the appearance of Severe Acute Respiratory Syndrome (SARS), supported by a zoonotic coronavirus, called SARS-CoV, from the Guangdong Province of southern China. After about 10 years, in 2012, another similar coronavirus triggered the Middle East Respiratory Syndrome (MERS-CoV) in Saudi Arabia. Both caused severe pneumonia killing 774 and 858 people with 8700 cases of confirmed infection for the former, and 2494 for the latter, causing significant economic losses. 8 years later, despite the MERS outbreak remaining in certain parts of the world, at the end of 2019, a new zoonotic coronavirus (SARS-CoV-2) and responsible of coronavirus Disease (COVID-19), arose from Wuhan, Hubei Province, China. It spread rapidly and to date has killed 3,242 persons with more than 81,000 cases of infection in China and causing over 126,000 global cases and 5,414 deaths in 166 other countries around the world, especially Italy. SARS-CoV-2 would seem to have come from a bat, but the intermediate reservoir continues to be unknown. Nonetheless, as for SARS-CoV and MERS CoV, the Spillover effect linked to animal-human promiscuity, human activities including deforestation, illegal bush-trafficking and bushmeat, cannot be excluded. Recently, however, evidence of inter-human only transmission of SARS-CoV-2 has been accumulated and thus, the outbreak seems to be spreading by human-to-human transmission throughout a large part of the world. Herein we will provide with an update on the main features of COVID-19 and suggest possible solutions how to halt the expansion of this novel pandemic.

scholarly journals Molecular characterization of Salmonella enterica from poultry farms in Ilorin, north-central Nigeria

2021 ◽  
Vol 19 (3) ◽  
pp. 197-207
Author(s):  
I.A. Raufu ◽  
O.A. Ahmed ◽  
A. Aremu ◽  
J.A. Ameh ◽  
A. Ambali
Keyword(s):  
Antimicrobial Resistance ◽  
Salmonella Enterica ◽  
Virulence Genes ◽  
Occurrence Rate ◽  
Poultry Production ◽  
Potential Health ◽  
North Central ◽  
Antimicrobial Resistance Genes ◽  
Poultry Farms ◽  
Sequence Types

Poultry salmonellosis caused by Salmonella enterica is one of the most important bacterial diseases posing serious challenges to poultry production and human health worldwide. This study investigated the occurrence, serotypes, multilocus sequence types (MLSTs), antimicrobial resistance, plasmids, and 12 selected virulence genes of non-typhoidal Salmonella from poultry layer farms using whole-genome sequencing (WGS) methods. Two hundred cloaca swab samples were aseptically collected from four commercial poultry farms (layers) and transferred in sterile universal bottles on ice to the laboratory for analysis. Presumptive Salmonella isolates were detected with selective media and conventional biochemical tests. Serovars were confirmed by serotyping using the slide agglutination and Seqsero methods. Seven samples were positive for Salmonella consisting of Salmonella Typhimurium (S. Typhimurium) (n = 4), S. Albany (n = 2), and S. Agama with an occurrence rate of 3.5 % (7/200). Overall, 3 isolates showed the parC mutation expected not to cause resistance. Similarly, one S. Typhimurium isolate carried plasmid replicons of IncFIB(S)/IncFII(S) type without antimicrobial resistance genes. Three sequence types (STs); 19 (S. Typhimurium), 5317 (S. Albany), and 467 (S. Agama) were obtained. Salmonella Agama harboured 12 virulence genes, while S. Typhimurium and S. Albany harboured 11 virulence genes each. This study highlights the importance of S. Typhimurium, S. Albany, and S. Agama as major pathogens associated with poultry farms in Ilorin, north-central Nigeria. It equally provided baseline information on the serovar distribution, STs, resistance and the virulence gene profiles of all the serovars. Therefore, chickens can serve as a potential source of Salmonella transmission to humans, and this constitutes a potential health risk to the human population. Hence, there is a need for a specific Salmonella control program to be instituted as part of a national food safety strategy.

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