scholarly journals Genomic Characterization of Streptococcus suis Serotype 24 Clonal Complex 221/234 From Human Patients

2021 ◽  
Vol 12 ◽  
Author(s):  
Anusak Kerdsin ◽  
Rujirat Hatrongjit ◽  
Thidathip Wongsurawat ◽  
Piroon Jenjaroenpun ◽  
Peechanika Chopjitt ◽  
...  
Keyword(s):  
Clonal Complex ◽  
Streptococcus Suis ◽  
Human Infection ◽  
Genomic Comparison ◽  
Chloramphenicol Resistance ◽  
Antimicrobial Resistance Genes ◽  
Invasive Infections ◽  
Genomic Characterization ◽  
Weakly Virulent

Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Although S. suis serotype 2 is prevalent among patient and swine infections, other serotypes are occasionally detected in humans. Of these, serotype 24 clonal complex (CC) 221/234 are recognized as emerging clones of human infection. Genomic exploration of three S. suis serotype 24 CC221/234 strains revealed antimicrobial resistance genes, pathotyping, virulence-associated gene (VAG) profiles, minimum core genome (MCG) typing, and comparison of the genomes. Based on these analyzes, all three serotype 24 strains were MCG7-3 and should be classified in the intermediate/weakly virulent (I/WV) group. All selected serotype 24 strains were susceptible to several antibiotics including β-lactam, fluoroquinolone, and chloramphenicol. Resistance to tetracycline, macrolide, and clindamycin was observed and attributed to the genes tet(O) and erm(B). Genomic comparison revealed the strains S12X, LSS66, LS0L, LS0E, 92–4,172, and IMT40201 that had phylogenetic affinity with serotype 24 CC221/234. Analysis of 80 virulence-associated genes (VAG) showed that all three serotype 24 strains lacked 24 genes consisting of adhesin P, epf, hyl, ihk, irr, mrp, nadR, neuB, NisK/R, ofs, permease (SSU0835), rgg, revS, salK/R, sao, sly, spyM3_0908, srtBCD, srtF, srtG, SSU05_0473, virA, virB4, and virD4. Eleven specific sequences were identified in the 3 serotype 24 genomes that differed from the genomes of the representative strains of epidemic (E; SC84), highly virulent (HV; P1/7), I/WV (89–1,591), and avirulent (T15 and 05HAS68).

scholarly journals Non-Penicillin-Susceptible Streptococcus suis Isolated from Humans

Pathogens ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1178
Author(s):  
Nichari Bamphensin ◽  
Peechanika Chopjitt ◽  
Rujirat Hatrongjit ◽  
Parichart Boueroy ◽  
Nahuel Fittipaldi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Streptococcus Suis ◽  
Amino Acid Substitutions ◽  
Continuous Control ◽  
Antimicrobial Resistance Genes ◽  
Genes Encoding ◽  
Invasive Infections ◽  
Almost All

Streptococcus suis is a pathogen that causes invasive infections in humans and pigs. In this study, 448 S. suis isolates recovered from human infections in Thailand were characterized with regard to their antimicrobial susceptibility and antimicrobial resistance genes, including, for non-penicillin-susceptible isolates, sequence analyses of five genes encoding penicillin-binding proteins (pbp1a, pbp1b, pbp2a, pbp2b, and pbp2x). All 448 isolates were susceptible to cefepime and ceftriaxone, whereas 99.6%, 91.7%, and 72.9% of the isolates were susceptible to levofloxacin, penicillin, and chloramphenicol, respectively. Almost all isolates were resistant to tetracycline (98.2%), clindamycin (94%), erythromycin (92.4%), and azithromycin (82.6%). Genes tet(O) and ermB were the predominant resistance genes detected among macrolide- and tetracycline-resistant isolates. A total of 37 out of 448 isolates (8.2%) showed intermediately resistance to penicillin. Most of these isolates (59.5%) belonged to serotype 2-ST233. Comparison of the predicted translated sequences of five PBP proteins of a penicillin-susceptible isolate (strain P1/7) to the respective PBP sequences of ten non-penicillin-susceptible isolates revealed multiple amino acid substitutions. Isolates of CC221/234 showed highly variable amino acid substitutions in all PBP proteins. An ST104 isolate had a higher number of amino acid substitutions in PBP2X. Isolates belonging to CC233/379 had numerous substitutions in PBP2B and PBP2X. ST25 isolates exhibited fewer amino acid substitutions than isolates of other STs in all five PBPs. The antimicrobial resistance of S. suis is increasing worldwide; therefore, restrictions on antimicrobial use, continuous control, and the surveillance of this bacterium throughout the pork supply chain are crucial for ensuring public health and must be a priority concern.

scholarly journals Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products

Foods ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2637
Author(s):  
Jolien D’aes ◽  
Marie-Alice Fraiture ◽  
Bert Bogaerts ◽  
Sigrid C. J. De Keersmaecker ◽  
Nancy H. C. Roosens ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetically Modified ◽  
Added Value ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes ◽  
Long Read ◽  
Genomic Characterization

Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM Bacillus velezensis used to synthesize a food enzyme protease, for which genomic characterization remains currently incomplete, and it is unknown whether these contaminations have a common origin. In this study, GM B. velezensis isolates from multiple food enzyme products were characterized by short- and long-read whole-genome sequencing (WGS), demonstrating that they harbor a free recombinant pUB110-derived plasmid carrying antimicrobial resistance genes. Additionally, single-nucleotide polymorphism (SNP) and whole-genome based comparative analyses showed that the isolates likely originate from the same parental GM strain. This study highlights the added value of a hybrid WGS approach for accurate genomic characterization of GMM (e.g., genomic location of the transgenic construct), and of SNP-based phylogenomic analysis for source-tracking of GMM.

scholarly journals Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste

2020 ◽  
Author(s):  
Jacob B Jørgensen ◽  
Amaru M Djuurhus ◽  
Alexander B. Carstens ◽  
Witold Kot ◽  
Cindy E. Morris ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Organic Waste ◽  
New Genus ◽  
Open Reading Frames ◽  
Genomic Comparison ◽  
Double Stranded Dna ◽  
The Family ◽  
Genomic Characterization ◽  
Reading Frames

AbstractThree phages targeting Pseudomonas syringae GAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to the Autographivirinae subfamily of the family Podoviridae. The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera within Autographivirinae, suggesting that the newly isolated phages could represent a new genus.

scholarly journals BKC-2, a New BKC Variant Detected in MCR-9.1-producing Enterobacter hormaechei subsp. xiangfangensis

2020 ◽  
pp. AAC.01193-20
Author(s):  
Willames M. B. S. Martins ◽  
Evelin R. Martins ◽  
Letícia K. de Andrade ◽  
Refath Farzana ◽  
Timothy R. Walsh ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Tertiary Hospital ◽  
Multidrug Resistant ◽  
Colistin Resistance ◽  
Antimicrobial Resistance Genes ◽  
Genomic Characterization ◽  
Enterobacter Hormaechei

We performed the characterization of a multidrug-resistant (MDR) Enterobacter spp. isolate highlighting the genetic aspects of the antimicrobial resistance genes. An Enterobacter spp. isolate (Ec61) was recovered in 2014 from a transtracheal aspirate sample from a patient admitted to a Brazilian tertiary hospital and submitted to further microbiological and genomic characterization. Ec61 was identified as Enterobacter hormaechei subsp. xiangfangensis ST451, showed a MDR profile and the presence of genes codifying new β-lactamase variants, BKC-2 and ACT-84, and the mobile colistin resistance gene mcr-9.1.

scholarly journals Genomic Characterization of Multidrug-Resistant Salmonella Serovars Derby and Rissen From the Pig Value Chain in Vietnam

2021 ◽  
Vol 8 ◽  
Author(s):  
Belén González-Santamarina ◽  
Silvia García-Soto ◽  
Sinh Dang-Xuan ◽  
Mostafa Y. Abdel-Glil ◽  
Diana Meemken ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Value Chain ◽  
Multidrug Resistant ◽  
Human Infection ◽  
Whole Genome ◽  
Bioinformatics Analyses ◽  
Antimicrobial Resistance Genes ◽  
Genomic Characterization

Nontyphoidal Salmonella (NTS) is the most reported cause of bacterial foodborne zoonoses in Vietnam, and contaminated pork is one of the main sources of human infection. In recent years, the prevalence of NTS carrying multiple antimicrobial resistance genes (ARGs) have been increased. The genomic characterization along the pig value chain and the identification of ARGs and plasmids have the potential to improve food safety by understanding the dissemination of ARGs from the farm to the table. We report an analysis of 13 S. Derby and 10 S. Rissen isolates, collected in 2013 at different stages in Vietnamese slaughterhouses and markets. VITEK 2 Compact System was used to characterize the phenotypical antimicrobial resistance of the isolates. In addition, whole-genome sequencing (WGS) was used to detect ARGs and plasmids conferring multidrug resistance. Whole genome single nucleotide polymorphism typing was used to determine the genetic diversity of the strains and the spread of ARGs along the pig value chain. Altogether, 86.9% (20/23) of the samples were resistant to at least one antibiotic. Resistance to ampicillin was most frequently detected (73.9%), followed by piperacillin and moxifloxacin (both 69.6%). At least one ARG was found in all strains, and 69.6% (16/23) were multidrug-resistant (MDR). The observed phenotype and genotype of antimicrobial resistance were not always concordant. Plasmid replicons were found in almost all strains [95.6% (22/23)], and the phylogenetic analysis detected nine clusters (S. Derby, n = 5; S. Rissen, n = 4). ARGs and plasmid content were almost identical within clusters. We found six MDR IncHI1s with identical plasmid sequence type in strains of different genetic clusters at the slaughterhouse and the market. In conclusion, high rates of multidrug resistance were observed in Salmonella strains from Vietnam in 2013. Genomic analysis revealed many resistance genes and plasmids, which have the potential to spread along the pig value chain from the slaughterhouse to the market. This study pointed out that bioinformatics analyses of WGS data are essential to detect, trace back, and control the MDR strains along the pig value chain. Further studies are necessary to assess the more recent MDR Salmonella strains spreading in Vietnam.

scholarly journals Genomic Characterization of an Emerging Enterobacteriaceae Species for the First Case of Human Infection in Cooperation with a Typical Pathogen

2020 ◽  
Author(s):  
Zhao Zhang ◽  
Daixi Li ◽  
xing shi ◽  
Yao Zhai ◽  
Yatao Guo ◽  
...  
Keyword(s):  
Continuous Monitoring ◽  
Novel Species ◽  
Human Infection ◽  
Klebsiella Pneumonia ◽  
Opportunistic Pathogens ◽  
Antibiotic Resistant ◽  
First Case ◽  
Infection Treatment ◽  
Genomic Characterization

Abstract Opportunistic pathogens are important for clinical practice as they often cause antibiotic resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a novel species of extended-spectrum β-lactamase-producing Enterobacteriaceae from a patient of biliary tract infection. The isolate grows very slowly but confers strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumonia. As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis, and anti-infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains respectively isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. As its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both wild environment and animal host, tens of genetic mobile elements, and a plasmid bearing blaCTX-M-3 gene, indicating its ability to disseminate antimicrobial resistant genes from wild to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18 which could serve as targets for novel antimicrobial strategies. These findings imply that AF18 and its species are not only infection-relevant but also potential disseminators in transferring antibiotic determinants, which highlights the need for continuous monitoring for this novel species and efforts to develop controlling strategies.

A cluster of invasive meningococcal disease revealed by the characterization of a novel serogroup B meningococcal clone

2015 ◽  
Vol 144 (1) ◽  
pp. 183-188 ◽  
Author(s):  
L. VALINSKY ◽  
J. JAFFE ◽  
N. KELLER ◽  
C. BLOCK ◽  
N. ABRAMSON ◽  
...  
Keyword(s):  
Clonal Complex ◽  
Disease Spread ◽  
Post Exposure Prophylaxis ◽  
Post Exposure ◽  
Health Measures ◽  
First Case ◽  
Invasive Infections ◽  
Exposure Prophylaxis ◽  
Close Contacts

SUMMARYThe incidence of invasive infections due toNeisseria meningitidisin Israel is about 1/100 000 population annually. Three cases of meningococcal meningitis were reported in employees at a single plant; the first case appeared in March 2013 and the second and third cases appeared in December, almost 9 months later.N. meningitidisserogroup B was isolated from cerebrospinal fluid samples. Multilocus sequence typing assigned the three meningococcal isolates to ST10418, a new sequence type and a member of the ST32 clonal complex. The clonality was confirmed by performance of pulsed-field gel electrophoresis. Post-exposure antibiotic prophylaxis was administered to close contacts of the first case. Upon the diagnosis of the additional two cases, post-exposure prophylaxis was administered to all the plant employees. This report demonstrates the importance of combining public health measures and advanced laboratory studies to confirm clonality and to prevent further disease spread in a closed setting.

Genomic characterization of γ-terpinene synthase from Thymus caespititius

Planta Medica ◽  
2011 ◽  
Vol 77 (12) ◽  
Author(s):  
AS Lima ◽  
B Lukas ◽  
J Novak ◽  
AC Figueiredo ◽  
LG Pedro ◽  
...  
Keyword(s):  
Genomic Characterization
Sign in / Sign up

Export Citation Format

Share Document