scholarly journals Genomic Characterization of a Nalidixic Acid-Resistant Salmonella Enteritidis Strain Causing Persistent Infections in Broiler Chickens

2021 ◽  
Vol 8 ◽  
Author(s):  
Grayson K. Walker ◽  
M. Mitsu Suyemoto ◽  
Dawn M. Hull ◽  
Sesny Gall ◽  
Fernando Jimenez ◽  
...  
Keyword(s):  
Nalidixic Acid ◽  
Broiler Chickens ◽  
Salmonella Enteritidis ◽  
Virulence Genes ◽  
Whole Genome Sequence ◽  
Virulence Plasmid ◽  
Whole Genome ◽  
Growing Period ◽  
Persistent Infections ◽  
Virulent Strains

Virulent strains of Salmonella enterica subsp. enterica serovar Enteritidis (SE) harbored by poultry can cause disease in poultry flocks and potentially result in human foodborne illness. Two broiler flocks grown a year apart on the same premises experienced mortality throughout the growing period due to septicemic disease caused by SE. Gross lesions predominantly consisted of polyserositis followed by yolk sacculitis, arthritis, osteomyelitis, and spondylitis. Tissues with lesions were cultured yielding 59 SE isolates. These were genotyped by Rep-PCR followed by whole-genome sequencing (WGS) of 15 isolates which were clonal. The strain, SE_TAU19, was further characterized for antimicrobial susceptibility and virulence in a broiler embryo lethality assay. SE_TAU19 was resistant to nalidixic acid and sulfadimethoxine and was virulent to embryos with 100% mortality of all challenged broiler embryos within 3.5 days. Screening the SE_TAU19 whole-genome sequence revealed seven antimicrobial resistance (AMR) genes, 120 virulence genes, and two IncF plasmid replicons corresponding to a single, serovar-specific pSEV virulence plasmid. The pef, spv, and rck virulence genes localized to the plasmid sequence assembly. We report phenotypic and genomic features of a virulent SE strain from persistently infected broiler flocks and present a workflow for SE characterization from isolate collection to genome assembly and sequence analysis. Further SE surveillance and investigation of SE virulence in broiler chickens is warranted.

scholarly journals Prevalence, virulence factor and antimicrobial resistance analysis of Salmonella Enteritidis from poultry and egg samples in Iran

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Hassan Bahramianfard ◽  
Abdollah Derakhshandeh ◽  
Zahra Naziri ◽  
Reza Khaltabadi Farahani
Keyword(s):  
Antimicrobial Resistance ◽  
Nalidixic Acid ◽  
Salmonella Enteritidis ◽  
Virulence Genes ◽  
Control Measures ◽  
Poultry Meat ◽  
Diffusion Method ◽  
Virulence Plasmid ◽  
Disk Diffusion Method ◽  
Zoonotic Risk

Abstract Background Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the most common serovars, associated with human salmonellosis. The food-borne outbreak of this bacterium is mainly related to the consumption of contaminated poultry meat and poultry products, including eggs. Therefore, rapid and accurate detection, besides investigation of virulence characteristics and antimicrobial resistance profiles of S. Enteritidis in poultry and poultry egg samples is essential. A total of 3125 samples (2250 poultry and 875 poultry egg samples), sent to the administrative centers of veterinary microbiology laboratories in six provinces of Iran, were examined for Salmonella contamination, according to the ISO 6579 guideline. Next, duplex PCR was conducted on 250 presumptive Salmonella isolates to detect invA gene for identification of the genus Salmonella and sdf gene for identification of S. Enteritidis. Subsequently, the S. Enteritidis isolates were examined for detection of important virulence genes (pagC, cdtB, msgA, spaN, tolC, lpfC, and spvC) and determination of antibiotic resistance patterns against nalidixic acid, trimethoprim-sulfamethoxazole, cephalothin, ceftazidime, colistin sulfate, and kanamycin by the disk diffusion method. Results Overall, 8.7 and 2.3% of poultry samples and 6.3 and 1.3% of eggs were contaminated with Salmonella species and S. Enteritidis, respectively. The invA and msgA genes (100%) and cdtB gene (6.3%) had the highest and the lowest prevalence rates in S. Enteritidis isolates. The spvC gene, which is mainly located on the Salmonella virulence plasmid, was detected in 50.8% of S. Enteritidis isolates. The S. Enteritidis isolates showed the highest and the lowest resistance to nalidixic acid (87.3%) and ceftazidime (11.1%), respectively. Unfortunately, 27.0% of S. Enteritidis isolates were multidrug-resistant (MDR). Conclusion The rate of contamination with Salmonella in the poultry and egg samples, besides the presence of antimicrobial resistant and MDR Salmonella isolates harboring the virulence genes in these samples, could significantly affect food safety and subsequently, human health. Therefore, continuous monitoring of animal-source foods, enhancement of poultry farm control measures, and limiting the use of antibiotics for prophylactic purposes in food producing animals, are essential for reducing the zoonotic risk of this foodborne pathogen for consumers and also choosing effective antibiotics for the treatment of salmonellosis.

scholarly journals Whole Genome Sequence Analysis of Brucella melitensis Phylogeny and Virulence Factors

2021 ◽  
Vol 12 (3) ◽  
pp. 698-710
Author(s):  
Peter Rabinowitz ◽  
Bar Zilberman ◽  
Yair Motro ◽  
Marilyn C. Roberts ◽  
Alex Greninger ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Pathogenic Bacteria ◽  
Virulence Genes ◽  
Brucella Melitensis ◽  
Geographic Region ◽  
Clinical Severity ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Pan Genome ◽  
Wide Range

Brucellosis has a wide range of clinical severity in humans that remains poorly understood. Whole genome sequencing (WGS) analysis may be able to detect variation in virulence genes. We used Brucella melitensis sequences in the NCBI Sequence Read Archive (SRA) database to assemble 248 whole genomes, and additionally, assembled 27 B. melitensis genomes from samples of human patients in Southern Israel. We searched the 275 assembled genomes for the 43 B. melitensis virulence genes in the Virulence Factors of Pathogenic Bacteria Database (VFDB) and 10 other published putative virulence genes. We explored pan-genome variation across the genomes and in a pilot analysis, explored single nucleotide polymorphism (SNP) variation among the ten putative virulence genes. More than 99% of the genomes had sequences for all Brucella melitensis virulence genes included in the VFDB. The 10 other virulence genes of interest were present across all the genomes, but three of these genes had SNP variation associated with particular Brucella melitensis genotypes. SNP variation was also seen within the Israeli genomes obtained from a small geographic region. While the Brucella genome is highly conserved, this novel and large whole genome study of Brucella demonstrates the ability of whole genome and pan-genome analysis to screen multiple genomes and identify SNP variation in both known and novel virulence genes that could be associated with differential disease virulence. Further development of whole genome techniques and linkage with clinical metadata on disease outcomes could shed light on whether such variation in the Brucella genome plays a role in pathogenesis.

scholarly journals Whole Genome and Phenotypic Characterization of Novel QnrB19-positive Salmonella Nigeria serovars from Food Animals in Ilorin, North-central, Nigeria.

2021 ◽  
Author(s):  
Ibrahim Adisa Raufu ◽  
Olayiwola Akeem Ahmed ◽  
Abdulfatai Aremu ◽  
Jessica C Chen ◽  
James A Ameh ◽  
...  
Keyword(s):  
Virulence Genes ◽  
Antimicrobial Agents ◽  
Farm Animals ◽  
Whole Genome Sequence ◽  
Phenotypic Characterization ◽  
Whole Genome ◽  
Single Mutation ◽  
North Central ◽  
Phenotypic Resistance ◽  
Food Animals

Abstract Background: Non-typhoidal Salmonella are major foodborne pathogens, posing serious challenges to public health and food safety worldwide. Salmonellosis in humans is commonly associated with the consumption of contaminated food, water, and direct contact with infected animals. This study aimed to characterize the distribution, diversity, virulence genotypes and antibiotic resistance of Salmonella enterica subsp. enterica serovar Nigeria, isolated from farm animals in north central Nigeria.Results: We recovered 9 different S. enterica ser. Nigeria isolates from our sampling, eight from pig and one from chicken. The antimicrobial susceptibility testing against 15 antimicrobial agents showed variable resistance profiles. Whole genome sequence (WGS) analysis revealed that all 9 isolates contained a single mutation parC (T57S) substitution in addition to qnrB19, expected to confer decreased susceptibility to ciprofloxacin and tet(A) expected to confer resistance to tetracycline. Furthermore, two plasmid targets were also detected in all the strains, Col(pHAD28) and IncQ1. MLST analysis showed that all 9 isolates exhibited only one sequence type, (ST-4911) irrespective of the source of isolation. A SNP-based phylogeny indicates that the 9 isolates are highly related and lack other close relatives in the pathogen detection database.Forty core (housekeeping) and accessory virulence genes were identified from different virulence loci including Salmonella Pathogenicity Islands, virulence associated plasmids (pSV), chromosomes and fimbriae. Conclusion: This study provided valuable information on the resistance determinants, virulence genes, phenotypic resistance profiles, plasmids and multilocus sequence typing (MLST) of Salmonella Nigeria from food animals by WGS. Highlighting the significance of poultry and pig to the spread and emergence of Salmonella Nigeria in this region of Nigeria, therefore, there is the need for consumer's education and enlightenments on the importance of proper handling and preparation of food, this will reduce the potential risk of transmission of this pathogen.

scholarly journals Whole-Genome Sequence of Streptococcus tigurinus Strain osk_001, Isolated from Postmortem Material

2017 ◽  
Vol 5 (35) ◽  
Author(s):  
Hidenori Yoshizawa ◽  
Daisuke Motooka ◽  
Ryuichi Katada ◽  
Yuki Matsumoto ◽  
Shota Nakamura ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Novel Species ◽  
Infected Tissue ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Virulent Strains ◽  
Highly Virulent

ABSTRACT Streptococcus tigurinus was recently described as a novel species, and some strains are highly virulent. We detected S. tigurinus in infected tissue sampled by necropsy. In order to characterize and confirm the virulence of this species, whole-genome sequencing of the pure cultured bacterium was performed. We found that the strain has specific and unique genetic elements contained in highly virulent strains of S. tigurinus.

Distribution of Virulence Genes among Salmonella Serotypes Isolated from Pigs in Southern Vietnam

2018 ◽  
Vol 81 (9) ◽  
pp. 1459-1466 ◽  
Author(s):  
TRAN T. Q. LAN ◽  
MARIE-LOU GAUCHER ◽  
NGUYEN T. M. NHAN ◽  
ANN LETELLIER ◽  
SYLVAIN QUESSY
Keyword(s):  
Salmonella Typhimurium ◽  
Virulence Genes ◽  
Virulence Gene ◽  
Virulence Plasmid ◽  
Southern Vietnam ◽  
Virulent Strains ◽  
Culture Enrichment ◽  
Paratyphi B ◽  
Salmonella Serotypes ◽  
Pcr Assays

ABSTRACT This study was carried out to evaluate the prevalence of Salmonella serogroups and serotypes and their virulence gene carriage in pig fecal samples from farms and slaughterhouses in some southern provinces of Vietnam. The presence of Salmonella was assessed based on culture enrichment of the collected samples and biochemical and serological analyses; 27.7% (51) of 184 samples were posititve for Salmonella. Based on the availability of antisera, serogroups were determined for 61% (31) of 51 isolates. Twenty isolates belonging to Salmonella serotypes Typhimurium (10 isolates), Anatum (8 isolates), Senftenberg (7 isolates), Paratyphi B (3 isolates), Paratyphi A (1 isolate), Montevideo (1 isolate), and Saintpaul (1 isolate) were further characterized by a multiplex PCR protocol targeting Salmonella invasion A and virulence plasmid C genes (invA and spvC, respectively). Individual PCR assays were developed to detect genes for Salmonella enterotoxin (stn), Salmonella outer protein B (sopB), and Salmonella fimbriae (pef). Various carriage patterns were identified among tested isolates. The invA and sopB genes were found in all isolates, and the stn gene was found in 95% of the isolates. The spvC gene was found in only 5% of the Salmonella Typhimurium isolates. None of the isolates were positive for the pef gene. Among all isolates, the predominant genotypic virulence profile (virulotype) was characterized by the concomitant presence of invA, sopB, and stn in carrier strains. In contrast, two virulotypes comprising either invA, sopB, spvC, and stn or invA and sopB were identified for the Salmonella Typhimurium isolates. Virulotypes made up of multiple virulence genes were predominant in most Salmonella strains tested in this study, indicating that pigs might act as a reservoir for these virulent strains.

scholarly journals Whole Genome Sequencing of Staphylococci Isolated From Bovine Milk Samples

2021 ◽  
Vol 12 ◽  
Author(s):  
Marte Ekeland Fergestad ◽  
Fabrice Touzain ◽  
Sarne De Vliegher ◽  
Anneleen De Visscher ◽  
Damien Thiry ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Virulence Genes ◽  
Bovine Milk ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Bacterial Survival ◽  
Intramammary Infections ◽  
Antimicrobial Resistance Genes

Staphylococci are among the commonly isolated bacteria from intramammary infections in bovines, where Staphylococcus aureus is the most studied species. This species carries a variety of virulence genes, contributing to bacterial survival and spread. Less is known about non-aureus staphylococci (NAS) and their range of virulence genes and mechanisms, but they are the most frequently isolated bacteria from bovine milk. Staphylococci can also carry a range of antimicrobial resistance genes, complicating treatment of the infections they cause. We used Illumina sequencing to whole genome sequence 93 staphylococcal isolates selected from a collection of staphylococcal isolates; 45 S. aureus isolates and 48 NAS isolates from 16 different species, determining their content of antimicrobial resistance genes and virulence genes. Antimicrobial resistance genes were frequently observed in the NAS species as a group compared to S. aureus. However, the lincosamide resistance gene lnuA and penicillin resistance gene blaZ were frequently identified in NAS, as well as a small number of S. aureus. The erm genes conferring macrolide resistance were also identified in several NAS isolates and in a small number of S. aureus isolates. In most S. aureus isolates, no antimicrobial resistance genes were detected, but in five S. aureus isolates three to six resistance genes were identified and all five of these carried the mecA gene. Virulence genes were more frequently identified in S. aureus, which contained on average five times more virulence genes compared to NAS. Among the NAS species there were also differences in content of virulence genes, such as S. chromogenes with a higher average number of virulence genes. By determining the content of a large selection of virulence genes and antimicrobial resistance genes in S. aureus and 16 different NAS species our results contribute with knowledge regarding the genetic basis for virulence and antimicrobial resistance in bovine staphylococci, especially the less studied NAS. The results can create a broader basis for further research into the virulence mechanisms of this important group of bacteria in bovine intramammary infections.

scholarly journals Whole-Genome Sequence of Aeromonas hydrophila CVM861 Isolated from Diarrhetic Neonatal Swine

2020 ◽  
Vol 8 (11) ◽  
pp. 1648
Author(s):  
Toni L. Poole ◽  
Wayne D. Schlosser ◽  
Robin C. Anderson ◽  
Keri N. Norman ◽  
Ross C. Beier ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Aeromonas Hydrophila ◽  
Virulence Genes ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Human Pathogens ◽  
Accession Number ◽  
Beta Lactam ◽  
E Coli

Aeromonas hydrophila are ubiquitous in the environment and are highly distributed in aquatic habitats. They have long been known as fish pathogens but are opportunistic human pathogens. Aeromonas spp. have persisted through food-processing safeguards and have been isolated from fresh grocery vegetables, dairy, beef, pork, poultry products and packaged ready-to-eat meats, thus providing an avenue to foodborne illness. A beta-hemolytic, putative Escherichia coli strain collected from diarrheic neonatal pigs in Oklahoma was subsequently identified as A. hydrophila, and designated CVM861. Here we report the whole-genome sequence of A. hydrophila CVM861, SRA accession number, SRR12574563; BioSample number, SAMN1590692; Genbank accession number SRX9061579. The sequence data for CVM861 revealed four Aeromonas-specific virulence genes: lipase (lip), hemolysin (hlyA), cytonic enterotoxin (ast) and phospholipid-cholesterolacyltransferase (GCAT). There were no alignments to any virulence genes in VirulenceFinder. CVM861 contained an E. coli resistance plasmid identified as IncQ1_1__M28829. There were five aminoglycoside, three beta-lactam, and one each of macrolide, phenicol, sulfonamide, tetracycline and trimethoprim resistance genes, all with over 95% identity to genes in the ResFinder database. Additionally, there were 36 alignments to mobile genetic elements using MobileElementFinder. This shows that an aquatic pathogen, rarely considered in human disease, contributes to the resistome reservoir and may be capable of transferring resistance and virulence genes to other more prevalent foodborne strains such as E. coli or Salmonella in swine or other food production systems.

scholarly journals Mosaic antimicrobial resistance/virulence plasmid in hypervirulent ST2096 Klebsiella pneumoniae in India: The rise of a new superbug?

2020 ◽  
Author(s):  
Chaitra Shankar ◽  
Karthick Vasudevan ◽  
Jobin John Jacob ◽  
Stephen Baker ◽  
Barney J Isaac ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Virulence Plasmid ◽  
Whole Genome ◽  
Drug Resistant ◽  
Virulence Determinants ◽  
Type Iv ◽  
Carbapenem Resistant ◽  
Oxford Nanopore ◽  
Hospitalised Patients

Hypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp is also emerging from clones ST11, ST15 and ST147, which are also multi-drug resistant (MDR). Here, we aimed to characterise nine novel MDR hvKp isolates harbouring mosaic plasmids simultaneously carrying antimicrobial resistance (AMR) and virulence genes. Nine HvKp isolates obtained from hospitalised patients in southern India were characterized for antimicrobial susceptibility and hypervirulence phenotypes. All nine hvKp isolates were subjected to whole genome sequencing (WGS) using Ilumina HiSeq2500 and a subset of four were sequenced using Oxford Nanopore MinION. Among the nine isolates, seven were carbapenem-resistant, two of which carried blaNDM-5 on an IncFII plasmid and five carried blaOXA-232 on a ColKP3 plasmid. The virulence determinants were encoded in a mosaic plasmid (~320 Kbp) that formed as a result of its insertion in a IncFIB-IncHI1B plasmid co-integrate. The mosaic plasmid carried AMR genes (aadA2, armA, blaOXA-1, msrE, mphE, sul1 and dfrA14) in addition to rmpA2, iutA and iucABCD virulence genes. Interestingly the mosaic plasmid carried its own type IV-A3 CRISPR-cas system that is likely able to target the acquisition of IncF plasmid with the help of a traL spacer. The convergence of virulence and AMR is the biggest threat among invasive K. pneumoniae infections. However, increasing reports of the presence of mosaic plasmid carrying both AMR and virulence genes suggests MDR-hvKp isolates are no longer confined to selected clones and the containment of such isolates is very challenging.

scholarly journals Virulence analysis of 81 of Pseudomonas aeruginosa genomes available in public sequence databases

2019 ◽  
Author(s):  
Marcin Brzozowski ◽  
Joanna Barbara Jursa-Kulesza ◽  
Danuta Kosik-Bogacka
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Virulence Genes ◽  
Opportunistic Infections ◽  
Pearson Correlation ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Secretion Systems ◽  
Wide Range ◽  
Genes Encoding ◽  
Sequence Databases

Abstract Background Pseudomonas aeruginosa is a pathogen capable of causing a wide range of severe opportunistic infections. Its genome contains numerous virulence genes encoding secretion systems of different types, structures responsible for adhesion and motility, toxins, proteases, siderophores, and others. The aim of this study is to analyse virulence, population structure, and distribution of highly divergent genes among 81 P. aeruginosa strains available in whole genome sequence databases. Results For this purpose, 260 virulence genes were searched in 81 different P. aeruginosa whole genomes that were available in databases. We identified most of the virulence genes as core and softcore genes. The most of the highly divergent sequences encoding pyoverdines, flagella and pilA were acknowledged as accessory, because of the differences in sequence among different alleles of those genes. Phylogenetic tree revealed the existence of three genetic groups of P. aeruginosa. Strains of the first clade were characterised as ExoS positive, whiles genomes of the second clade were ExoU positive. The member of third clade, PA7 strain was the only strain deprived of all T3SS genes. The analysis of pyoverdine locus facilitated finding a new pyoverdine type similar to pyoverdine type III. This newly described variant was present in 7 different strains. It contained a gene that was probably created by the fusion of pilD and pilI genes. In order to determine the coexistence of genes encoding exoenzymes, flagella and pyoverdines, Pearson correlation coefficients were calculated. There were significant correlations between genes encoding ExoS/ExoU-type strains and genes encoding type-A/type-B flagella. The correlation also occurred between Conclusion This study facilitates describing genetic differences of various P. aeruginosa strains based on Pseudomonas aeruginosa whole genome information from online databases. We conclude that most P. aeruginosa virulence genes are present in more than 95% of available genomes of the species. There are correlations of occurrence of different P. aeruginosa accessory virulence genes.

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