scholarly journals Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis

2021 ◽  
Vol 17 (10) ◽  
pp. e1009992
Author(s):  
Sarah G. Earle ◽  
Mariya Lobanovska ◽  
Hayley Lavender ◽  
Changyan Tang ◽  
Rachel M. Exley ◽  
...  

Many invasive bacterial diseases are caused by organisms that are ordinarily harmless components of the human microbiome. Effective interventions against these microbes require an understanding of the processes whereby symbiotic or commensal relationships transition into pathology. Here, we describe bacterial genome-wide association studies (GWAS) of Neisseria meningitidis, a common commensal of the human respiratory tract that is nevertheless a leading cause of meningitis and sepsis. An initial GWAS discovered bacterial genetic variants, including single nucleotide polymorphisms (SNPs), associated with invasive meningococcal disease (IMD) versus carriage in several loci across the meningococcal genome, encoding antigens and other extracellular components, confirming the polygenic nature of the invasive phenotype. In particular, there was a significant peak of association around the fHbp locus, encoding factor H binding protein (fHbp), which promotes bacterial immune evasion of human complement by recruiting complement factor H (CFH) to the meningococcal surface. The association around fHbp with IMD was confirmed by a validation GWAS, and we found that the SNPs identified in the validation affected the 5’ region of fHbp mRNA, altering secondary RNA structures, thereby increasing fHbp expression and enhancing bacterial escape from complement-mediated killing. This finding is consistent with the known link between complement deficiencies and CFH variation with human susceptibility to IMD. These observations demonstrate the importance of human and bacterial genetic variation across the fHbp:CFH interface in determining IMD susceptibility, the transition from carriage to disease.

2017 ◽  
Vol 29 (2) ◽  
pp. 661-669 ◽  
Author(s):  
Perrine Jullien ◽  
Blandine Laurent ◽  
Guillaume Claisse ◽  
Ingrid Masson ◽  
Miriana Dinic ◽  
...  

Activation of complement through the alternative pathway has a key role in the pathogenesis of IgA nephropathy (IgAN). Large, international, genome-wide association studies have shown that deletion of complement factor H–related genes 1 and 3 (CFHR3,1Δ) is associated with a reduced risk of developing IgAN, although the prognostic value of these deletions in IgAN remains unknown. Here, we compared the renal outcomes of patients with IgAN according to their CFHR3,1Δ genotype. This retrospective, monocentric cohort study included 639 white patients with biopsy-proven IgAN since 1979 (mean age at diagnosis, 40.1 years; median follow-up, 132 months). We determined the number of CFHR3 and CFHR1 gene copies by quantitative PCR and collected clinical and biologic data by reviewing the patients’ medical records. In all, 30.5% of the patients were heterozygous and 4% were homozygous for CFHR3,1Δ. We did not detect an association between CFHR3,1Δ and age, eGFR, urinary protein excretion rate, or the presence of hypertension or hematuria at the time of diagnosis. The mean intensities of immune IgA, IgG, and C3 deposits were lower in the group with heterozygous or homozygous gene deletions than in those with no deletion. However, CFHR3,1Δ did not associate with progression to stage 3 CKD or renal death. In conclusion, the CFHR3,1Δ genotype did not associate with progression toward CKD stages 3 and 5 in our white population of patients with IgAN, although it did associate with a reduced level of glomerular immune deposits.


2019 ◽  
Author(s):  
Chandler Roe ◽  
Charles H.D. Williamson ◽  
Adam J. Vazquez ◽  
Kristen Kyger ◽  
Michael Valentine ◽  
...  

AbstractAntimicrobial resistance (AMR) in the nosocomial pathogen, Acinetobacter baumannii, is becoming a serious public health threat. While some mechanisms of AMR have been reported, understanding novel mechanisms of resistance is critical for identifying emerging resistance. One of the first steps in identifying novel AMR mechanisms is performing genotype/phenotype association studies. However, performing genotype/phenotype association studies is complicated by the plastic nature of the A. baumannii pan-genome. In this study, we compared the antibiograms of 12 antimicrobials associated with multiple drug families for 84 A. baumannii isolates, many isolated in Arizona, USA. in silico screening of these genomes for known AMR mechanisms failed to identify clear correlations for most drugs. We then performed a genome wide association study (GWAS) looking for associations between all possible 21-mers; this approach generally failed to identify mechanisms that explained the resistance phenotype. In order to decrease the genomic noise associated with population stratification, we compared four phylogenetically-related pairs of isolates with differing susceptibility profiles. RNA-Sequencing (RNA-Seq) was performed on paired isolates and differentially expressed genes were identified. In these isolate pairs, we identified four different potential mechanisms, highlighting the difficulty of broad AMR surveillance in this species. To verify and validate differential expression, amplicon sequencing was performed. These results suggest that a diagnostic platform based on gene expression rather than genomics alone may be beneficial in certain surveillance efforts. The implementation of such advanced diagnostics coupled with increased AMR surveillance will potentially improve A. baumannii infection treatment and patient outcomes.


PLoS Genetics ◽  
2018 ◽  
Vol 14 (11) ◽  
pp. e1007758 ◽  
Author(s):  
Magali Jaillard ◽  
Leandro Lima ◽  
Maud Tournoud ◽  
Pierre Mahé ◽  
Alex van Belkum ◽  
...  

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Kevin C. Ma ◽  
Tatum D. Mortimer ◽  
Marissa A. Duckett ◽  
Allison L. Hicks ◽  
Nicole E. Wheeler ◽  
...  

Abstract The emergence of resistance to azithromycin complicates treatment of Neisseria gonorrhoeae, the etiologic agent of gonorrhea. Substantial azithromycin resistance remains unexplained after accounting for known resistance mutations. Bacterial genome-wide association studies (GWAS) can identify novel resistance genes but must control for genetic confounders while maintaining power. Here, we show that compared to single-locus GWAS, conducting GWAS conditioned on known resistance mutations reduces the number of false positives and identifies a G70D mutation in the RplD 50S ribosomal protein L4 as significantly associated with increased azithromycin resistance (p-value = 1.08 × 10−11). We experimentally confirm our GWAS results and demonstrate that RplD G70D and other macrolide binding site mutations are prevalent (present in 5.42% of 4850 isolates) and widespread (identified in 21/65 countries across two decades). Overall, our findings demonstrate the utility of conditional associations for improving the performance of microbial GWAS and advance our understanding of the genetic basis of macrolide resistance.


2018 ◽  
Author(s):  
Magali Jaillard ◽  
Leandro Lima ◽  
Maud Tournoud ◽  
Pierre Mahé ◽  
Alex van Belkum ◽  
...  

AbstractMotivationGenome-wide association study (GWAS) methods applied to bacterial genomes have shown promising results for genetic marker discovery or fine-assessment of marker effect. Recently, alignment-free methods based on kmer composition have proven their ability to explore the accessory genome. However, they lead to redundant descriptions and results which are hard to interpret.MethodsHere, we introduce DBGWAS, an extended kmer-based GWAS method producing interpretable genetic variants associated with pheno-types. Relying on compacted De Bruijn graphs (cDBG), our method gathers cDBG nodes identified by the association model into subgraphs defined from their neighbourhood in the initial cDBG. DBGWAS is fast, alignment-free and only requires a set of contigs and phenotypes. It produces annotated subgraphs representing local polymorphisms as well as mobile genetic elements (MGE) and offers a graphical framework to interpret GWAS results.ResultsWe validated our method using antibiotic resistance phenotypes for three bacterial species. DBGWAS recovered known resistance determinants such as mutations in core genes in Mycobacterium tuberculosis and genes acquired by horizontal transfer in Staphylococcus aureus and Pseudomonas aeruginosa – along with their MGE context. It also enabled us to formulate new hypotheses involving genetic variants not yet described in the antibiotic resistance literature.ConclusionOur novel method proved its efficiency to retrieve any type of phenotype-associated genetic variant without prior knowledge. All experiments were computed in less than two hours and produced a compact set of meaningful subgraphs, thereby outperforming other GWAS approaches and facilitating the interpretation of the results.AvailabilityOpen-source tool available at https://gitlab.com/leoisl/dbgwas


Author(s):  
Katie Saund ◽  
Evan S Snitkin

Bacterial genome-wide association studies (bGWAS) capture associations between genomic variation and phenotypic variation. Convergence based bGWAS methods identify genomic mutations that occur independently multiple times on the phylogenetic tree in the presence of phenotypic variation more often than is expected by chance. This work introduces hogwash, an open source R package that implements three algorithms for convergence based bGWAS. Hogwash additionally contains two burden testing approaches to perform gene- or pathway-analysis to improve power and increase convergence detection for related but weakly penetrant genotypes. To identify optimal use cases, we applied hogwash to data simulated with a variety of phylogenetic signals and convergence distributions. These simulated data are publicly available and contain the relevant metadata regarding convergence and phylogenetic signal for each phenotype and genotype. Hogwash is available for download from GitHub.


2020 ◽  
Vol 6 (11) ◽  
Author(s):  
Katie Saund ◽  
Evan S. Snitkin

Bacterial genome-wide association studies (bGWAS) capture associations between genomic variation and phenotypic variation. Convergence-based bGWAS methods identify genomic mutations that occur independently multiple times on the phylogenetic tree in the presence of phenotypic variation more often than is expected by chance. This work introduces hogwash, an open source R package that implements three algorithms for convergence-based bGWAS. Hogwash additionally contains two burden testing approaches to perform gene or pathway analysis to improve power and increase convergence detection for related but weakly penetrant genotypes. To identify optimal use cases, we applied hogwash to data simulated with a variety of phylogenetic signals and convergence distributions. These simulated data are publicly available and contain the relevant metadata regarding convergence and phylogenetic signal for each phenotype and genotype. Hogwash is available for download from GitHub.


Author(s):  
Kevin C Ma ◽  
Tatum D Mortimer ◽  
Marissa A Duckett ◽  
Allison L Hicks ◽  
Nicole E Wheeler ◽  
...  

AbstractThe emergence of resistance to azithromycin complicates treatment of N. gonorrhoeae, the etiologic agent of gonorrhea. Population genomic analyses of clinical isolates have demonstrated that some azithromycin resistance remains unexplained after accounting for the contributions of known resistance mutations in the 23S rRNA and the MtrCDE efflux pump. Bacterial genome-wide association studies (GWAS) offer a promising approach for identifying novel resistance genes but must adequately address the challenge of controlling for genetic confounders while maintaining power to detect variants with lower effect sizes. Compared to a standard univariate GWAS, conducting GWAS conditioned on known resistance mutations with high effect sizes substantially reduced the number of variants that reached genome-wide significance and identified a G70D mutation in the 50S ribosomal protein L4 (encoded by the gene rplD) as significantly associated with increased azithromycin minimum inhibitory concentrations (β = 1.03, 95% CI [0.76, 1.30]). The role and prevalence of these rplD mutations in conferring macrolide resistance in N. gonorrhoeae had been unclear. Here, we experimentally confirmed our GWAS results, identified other resistance-associated mutations in RplD, and showed that in total these RplD binding site mutations are prevalent (present in 5.42% of 4850 isolates) and geographically and temporally widespread (identified in 21/65 countries across two decades). Overall, our findings demonstrate the utility of conditional associations for improving the performance of microbial GWAS and advance our understanding of the genetic basis of macrolide resistance in a prevalent multidrug-resistant pathogen.


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