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 and phenotypic characterization of a Cbm+serotypeestrain ofStreptococcus mutans

2018 ◽  
Vol 33 (3) ◽  
pp. 257-269 ◽  
Author(s):  
A. Avilés-Reyes ◽  
I. A. Freires ◽  
J.K. Kajfasz ◽  
D. Barbieri ◽  
J.H. Miller ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Phenotypic Characterization ◽  
Whole Genome

scholarly journals Complete Genome Sequence of the Campylobacter ureolyticus Clinical Isolate RIGS 9880

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
William G. Miller ◽  
Emma Yee ◽  
Stephen L. W. On ◽  
Leif P. Andersen ◽  
James L. Bono
Keyword(s):  
Periodontal Disease ◽  
Clinical Isolate ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Emerging Pathogen ◽  
Genital Infections ◽  
Food Animals

The emerging pathogen Campylobacter ureolyticus has been isolated from human and animal genital infections, human periodontal disease, domestic and food animals, and from cases of human gastroenteritis. We report the whole-genome sequence of the human clinical isolate RIGS 9880, which is the first closed genome for C. ureolyticus .

scholarly journals Clonal transmission and new mechanism of resistance to trimethoprim-sulfamethoxazole in Stenotrophomonas maltophilia strains isolated in a neonatology unit at Antananarivo, Madagascar, deciphered by whole genome sequence analysis

2019 ◽  
Author(s):  
Mamitina Alain Noah Rabenandrasana ◽  
Volasoa Andrianoelina ◽  
Melanie Bonneault ◽  
Perlinot Herindrainy ◽  
Benoit Garin ◽  
...  
Keyword(s):  
Stenotrophomonas Maltophilia ◽  
Antimicrobial Agents ◽  
Susceptibility Testing ◽  
Acquired Resistance ◽  
Multidrug Resistant ◽  
Resistance Mechanisms ◽  
Whole Genome Sequence ◽  
Resistant Organism ◽  
Whole Genome ◽  
Single Nucleotide

ABSTRACTStenotrophomonas maltophilia has been recognized as an emerging multidrug resistant organism in hospital settings due to its resistance to a broad range of antimicrobial agents. These include β-lactams and aminoglycosides, afforded by the existence of intrinsic and acquired resistance mechanisms. Trimethoprim/sulfamethoxazole (SXT) is recommended as one of the best treatment choices against S. maltophilia infections; however increasing resistance to SXT has complicated the treatment. From July 2014 to March 2015, individuals and surfaces from a neonatology ward in Antananarivo, Madagascar, were longitudinally followed to assess the transmission of bacteria resistant to antibiotics between neonates, individuals (parents and nurses) and ward environments. Four S. maltophilia strains were successively isolated from a water-tap (N=1), from feces obtained from a newborn (N=1), and nursing staff (N=2). Antimicrobial susceptibility testing and whole genome sequencing were performed on each isolate. Based on coregenome alignment, all strains were identical and belonged to the new sequence type ST-288. They were resistant to trimethoprim-sulfamethoxazole, carbapenems and intermediate to levofloxacin. Each isolate carried the aadB, strA, strB and sul1 genes located in a class I integron but variants of the dfrA gene were absent. We assessed by PROVEAN analysis the single nucleotide mutations found in folA, folC and folM genes and only the mutation in folA (A114T:GCC→ACC) has an effect on the activity of trimethoprim. Our findings demonstrated the prolonged presence of SXT-resistant S. maltophilia in a clinical setting with consecutive transfers from the environment to a newborn and staff based on the isolation dates. We also hypothesized that single nucleotide mutations in folA could be responsible for trimethoprim resistance.

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 Integrative Analysis of Whole Genome Sequencing and Phenotypic Resistance Toward Prediction of Trimethoprim-Sulfamethoxazole Resistance in Staphylococcus aureus

2021 ◽  
Vol 11 ◽  
Author(s):  
Dennis Nurjadi ◽  
Elfi Zizmann ◽  
Quan Chanthalangsy ◽  
Klaus Heeg ◽  
Sébastien Boutin
Keyword(s):  
Staphylococcus Aureus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Point Mutations ◽  
Genetic Lineage ◽  
Whole Genome ◽  
Single Mutation ◽  
Protein Sequence Analysis ◽  
Sequencing Data ◽  
Phenotypic Resistance

As whole genome sequencing is becoming more accessible and affordable for clinical microbiological diagnostics, the reliability of genotypic antimicrobial resistance (AMR) prediction from sequencing data is an important issue to address. Computational AMR prediction can be performed at multiple levels. The first-level approach, such as simple AMR search relies heavily on the quality of the information fed into the database. However, AMR due to mutations are often undetected, since this is not included in the database or poorly documented. Using co-trimoxazole (trimethoprim-sulfamethoxazole) resistance in Staphylococcus aureus, we compared single-level and multi-level analysis to investigate the strengths and weaknesses of both approaches. The results revealed that a single mutation in the AMR gene on the nucleotide level may produce false positive results, which could have been detected if protein sequence analysis would have been performed. For AMR predictions based on chromosomal mutations, such as the folP gene of S. aureus, natural genetic variations should be taken into account to differentiate between variants linked to genetic lineage (MLST) and not over-estimate the potential resistant variants. Our study showed that careful analysis of the whole genome data and additional criterion such as lineage-independent mutations may be useful for identification of mutations leading to phenotypic resistance. Furthermore, the creation of reliable database for point mutations is needed to fully automatized AMR prediction.

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 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 Molecular detection of dugbe orthonairovirus in cattle and their infesting ticks (Amblyomma and Rhipicephalus (Boophilus)) in Nigeria

2021 ◽  
Vol 15 (11) ◽  
pp. e0009905
Author(s):  
Oluwafemi Babatunde Daodu ◽  
Albert Eisenbarth ◽  
Ansgar Schulz ◽  
Julia Hartlaub ◽  
James Olukayode Olopade ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Local Government ◽  
Molecular Detection ◽  
Phylogenetic Analyses ◽  
Prototype Strain ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
High Similarity ◽  
North Central ◽  
Tick Burden

Dugbe orthonairovirus (DUGV), a tick-borne zoonotic arbovirus, was first isolated in 1964 in Nigeria. For over four decades, no active surveillance was conducted to monitor the spread and genetic variation of DUGV. This study detected and genetically characterized DUGV circulating in cattle and their infesting ticks (Amblyomma and Rhipicephalus (Boophilus)) in Kwara State, North-Central Nigeria. Blood and or ticks were collected from 1051 cattle at 31 sampling sites (abattoirs and farms) across 10 local government areas of the State. DUGV detection was carried out by RT-qPCR, and positive samples sequenced and phylogenetically analysed. A total of 11824 ticks, mostly A. variegatum (36.0%) and R. (B.) microplus (63.9%), were obtained with mean tick burden of 12 ticks/cattle. Thirty-four (32 A. variegatum and two R. (B.) microplus) of 4644 examined ticks were DUGV-positive, whereas all of the cattle sera tested negative for DUGV genome. Whole genome sequence (S, M and L segments) and phylogenetic analyses indicate that the positive samples shared up to 99.88% nucleotide identity with and clustered around the Nigerian DUGV prototype strain IbAr 1792. Hence, DUGV with high similarity to the previously characterised strain has been detected in Nigeria. To our knowledge, this is the first report of DUGV in North-Central Nigeria and the most recent information after its last surveillance in 1974.

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