scholarly journals Whole genome sequence based capsular typing and antimicrobial resistance prediction of Group B streptococcal isolates from colonized pregnant women in Nigeria

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mienye Bob-Manuel ◽  
Lesley McGee ◽  
Jeremiah A Igunma ◽  
Mary A Alex-Wele ◽  
Orikomaba K Obunge ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Pregnant Women ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Group B Streptococcus ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Resistance Prediction ◽  
Group B ◽  
Capsular Typing

Abstract Background Streptococcus agalactiae (Group B Streptococcus, GBS) is one of the major bacterial pathogens responsible for neonatal sepsis. Whole genome sequencing has, in recent years, emerged as a reliable tool for capsular typing and antimicrobial resistance prediction. This study characterized vaginal and rectal isolates of Group B Streptococcus obtained from pregnant women in Port Harcourt, Nigeria using a whole-genome sequence-based approach. Results Capsular types Ia, Ib, II, III, IV and V were detected among the 43 isolates sequenced. Twelve sequence types (STs) were identified, with ST19 (n = 9, 27.3 %) and ST486 (n = 5, 15.2 %) the most frequent among non-duplicated isolates. Of the alpha-like proteins (alp) identified, Alp1 was the most prevalent in 11 (33.3 %) isolates. Macrolide and lincosamide resistance determinants were present in 15 (45.5 %) isolates; ermB was detected in 1 (3 %), ermTR in 7 (21.2 %) isolates, lnu gene was detected in 6 (18.2 %) and mef was identified in 3 (9.1 %) isolates. Resistance of GBS to erythromycin and clindamycin (predicted from presence of erm or mef genes) was found to be 30.3 % and 24.2 %, respectively. All isolates were predicted resistant to tetracycline with only the tetM gene identified. Fluoroquinolone-resistance conferring substitutions in gyrA + parC were detected in 9 (27.3 %) isolates and chloramphenicol resistance was predicted from presence of aac6’-aph2 gene in 11 (33.3 %). Conclusions The data available from the whole genome sequencing of these isolates offers a small but insightful description of common serotypes and resistance features within colonizing GBS in Nigeria.

scholarly journals Whole Genome Sequence based Capsular Typing and Antimicrobial Resistance Prediction of Group B Streptococcal Isolates from Colonized Pregnant Women in Nigeria

2021 ◽  
Author(s):  
Mienye Bob-Manuel ◽  
Lesley McGee ◽  
Jeremiah Igunma ◽  
Mary Alex-Wele ◽  
Orikomaba Obunge ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Pregnant Women ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Group B Streptococcus ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Resistance Prediction ◽  
Group B ◽  
Capsular Typing

Abstract Background: Streptococcus agalactiae (Group B Streptococcus, GBS) is one of the major bacterial pathogens responsible for neonatal sepsis. Whole genome sequencing has, in recent years, emerged as a reliable tool for capsular typing and antimicrobial resistance prediction. This study characterized vaginal and rectal isolates of Group B Streptococcus obtained from pregnant women in Port Harcourt, Nigeria using a whole-genome sequence-based approach.Results: Capsular types Ia, Ib, II, III, IV and V were detected among the 43 isolates sequenced. Twelve sequence types (STs) were identified, with ST19 (n=9, 27.3%) and ST486 (n=5, 15.2%) the most frequent among non-duplicated isolates. Of the alpha-like proteins (alp) identified, Alp1 was the most prevalent in 11 (33.3%) isolates. Macrolide and lincosamide resistance determinants were present in 15 (45.5%) isolates; ermB was detected in 1 (3%) and ermTR in 7 (21.2%) isolates. The lnu gene, was detected in 6 (18.2%) and mef was identified in 3 (9.1%) isolates. Resistance of GBS to erythromycin and clindamycin was found to be 30.3% and 24.2%, respectively. All isolates were resistant to tetracycline with only the tetM gene identified. Fluoroquinolone-resistance conferring substitutions in gyrA + parC were detected in 9 (27.3%) isolates and chloramphenicol resistance was predicted in 11 (33.3%).Conclusion: The data available from the whole genome sequencing of these isolates offers a small but insightful description of common serotypes and resistance features within colonizing GBS in Nigeria.

scholarly journals Capsular Typing Method for Streptococcus agalactiae Using Whole-Genome Sequence Data

2016 ◽  
Vol 54 (5) ◽  
pp. 1388-1390 ◽  
Author(s):  
Anna E. Sheppard ◽  
Alison Vaughan ◽  
Nicola Jones ◽  
Paul Turner ◽  
Claudia Turner ◽  
...  
Keyword(s):  
Sequence Data ◽  
Vaccine Coverage ◽  
Group B Streptococcus ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Typing Method ◽  
Potential Vaccine ◽  
Group B ◽  
Capsular Typing ◽  
Strong Agreement

Group B streptococcus (GBS) capsular serotypes are major determinants of virulence and affect potential vaccine coverage. Here we report a whole-genome-sequencing-based method for GBS serotype assignment. This method shows strong agreement (kappa of 0.92) with conventional methods and increased serotype assignment (100%) to all 10 capsular types.

scholarly journals Molecular Identification of Invasive Non-typeable Group B Streptococcus Isolates From Denmark (2015 to 2017)

2021 ◽  
Vol 11 ◽  
Author(s):  
Hans-Christian Slotved ◽  
Kurt Fuursted ◽  
Ioanna Drakaki Kavalari ◽  
Steen Hoffmann
Keyword(s):  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Virulence Factors ◽  
Group B Streptococcus ◽  
Clinical Manifestations ◽  
Whole Genome ◽  
Age Group ◽  
Group B ◽  
Species Specific ◽  
Genotype V

The number of invasive Streptococcus agalactiae (GBS) non-typeable (NT) isolates in Denmark received since 1999 has in general accounted for 10% of all invasive GBS isolates. We present data on 55 clinical NT isolates based on clinical manifestations, clonal relationship, antimicrobial resistance (AMR) determinants, and virulence factors. The GBS isolates included in this study were phenotypic-based NT obtained from 2015 to 2017, as well as 10 reference isolates. Whole genome sequencing (WGS) was performed on all isolates and the data were analyzed for the presence of both species specific genes, capsular genes (genotype), and other relevant genes. We furthermore compared different procedures for detection of serotype specific capsular genes. Overall we were able to genotype 54 of the 55 isolates. After retesting the isolates a phenotype was detected for 20 (36%) isolates, of which the initial phenotyping problem for 13 isolates was found to be due to a problem with serotype Ia specific antiserum. Thirty-five isolates remained phenotypic non-typeable with a majority of genotype V isolates which do not express a capsular gene. From all the Danish invasive GBS isolates from 2015 to 2017, the 35 NT isolates were all detected in the age group above 21 years with bacteremia. The 35 NT isolates belonged to six different well-known human pathogenic clonal complexes. The CDC recommended sequences for capsule genotyping were the most optimal for serotype prediction, because of the sequence simplicity and clear cutoff values. However we recommend to also use other capsular sequences for the NT isolates, if they cannot be genotyped by the CDC method.

scholarly journals SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Weili Cai ◽  
Schyler Nunziata ◽  
John Rascoe ◽  
Michael J. Stulberg
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Coverage ◽  
Metagenomic Sample ◽  
Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

Abstract 343: Bayesian Selection of Modifier Genes in Hypertrophic Cardiomyopathy Through Whole Genome Sequencing

2015 ◽  
Vol 117 (suppl_1) ◽  
Author(s):  
Matthew Wheeler ◽  
Daryl Waggott ◽  
Megan Grove ◽  
Frederick Dewey ◽  
Cuiping Pan ◽  
...  
Keyword(s):  
Hypertrophic Cardiomyopathy ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
A Priori ◽  
Copy Number Variants ◽  
Whole Genome Sequence ◽  
Monogenic Disease ◽  
Whole Genome ◽  
Genetic Modifiers ◽  
Structural Variants

Background: Technological advances have greatly reduced the cost of whole genome sequencing. For single individuals clinical application is apparent, while exome sequencing in tens of thousands of people has allowed a more global view of genetic variation that can inform interpretation of specific variants in individuals. We hypothesized that genome sequencing of patients with monogenic cardiomyopathy would facilitate discovery of genetic modifiers of phenotype. Methods and Results: We identified 48 individuals diagnosed with cardiomyopathy and with putative mutations in MYH7, the gene encoding beta myosin heavy chain. We carried out whole genome sequencing and applied a newly developed analytical pipeline optimized for discovery of genes modifying severity of clinical presentation and outcomes. Using a combination of external priors and rare variant burden tests we scored genes as potential modifiers. There were 96 genes that reached a modifier score of 6 out of 12 or better (9=2, 8=8, 7=17, 6=69). We identified NCKAP1, a gene that regulates actin filament dynamics, and CAMSAP1, a calmodulin regulate gene that regulates microtubule dynamics, as top scoring modifiers of hypertrophic cardiomyopathy phenotypes (score=9) while LDB2, RYR2, FBN1 and ATP1A2 had modifier scores of 8. Of the top scoring genes, 21 out of 96 were identified as candidates a priori. Our candidate prioritization scheme identified the previously described modifiers of cardiomyopathy phenotype, FHOD3 and MYBPC3, as top scoring genes. We identified structural variants in 21 clinically sequenced cardiomyopathy associated genes, 13 of which were at less than 10% frequency. Copy number variants in ILK and CSRP3 were nominally associated with ejection fraction (p=0.03), while 8 genes showed copy gains (GLA, FKTN, SGCD, TTN, SOS1, ANKRD1, VCL and NEBL). Structural variants were found in CSRP3, MYL3 and TNNC1, all of which have been implicated as causative for HCM. Conclusion: Evaluation of the whole genome sequence, even in the case of putatively monogenic disease, leads to important diagnostic and scientific insights not revealed by panel-based sequencing.

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