Rye: genetic ancestry inference at biobank scale.

Biobank projects are generating genomic data for many thousands of individuals. Computational methods are needed to handle these massive data sets, including genetic ancestry (GA) inference tools. Current methods for GA inference do not scale to biobank-size genomic datasets. We present Rye-a new algorithm for GA inference at biobank scale. We compared the accuracy and runtime performance of Rye to the widely used RFMix, ADMIXTURE and iAdmix programs and applied it to a dataset of 488221 genome-wide variant samples from the UK Biobank. Rye infers GA based on principal component analysis of genomic variant samples from ancestral reference populations and query individuals. The algorithm's accuracy is powered by Metropolis-Hastings optimization and its speed is provided by non-negative least squares regression. Rye produces highly accurate GA estimates for three-way admixed populations-African, European and Native American-compared to RFMix and ADMIXTURE (${R}^2 = \ 0.998 - 1.00$), and shows 50× runtime improvement compared to ADMIXTURE on the UK Biobank dataset. Rye analysis of UK Biobank samples demonstrates how it can be used to infer GA at both continental and subcontinental levels. We discuss user consideration and options for the use of Rye; the program and its documentation are distributed on the GitHub repository: https://github.com/healthdisparities/rye.

Neurologic Manifestations of Long COVID Differ Based on Acute COVID-19 Severity.

OBJECTIVE: To characterize neurologic manifestations in post-hospitalization Neuro-PASC (PNP) and non-hospitalized Neuro-PASC (NNP) patients. METHODS: Prospective study of the first 100 consecutive PNP and 500 NNP patients evaluated at a Neuro-COVID-19 clinic between 5/2020 and 8/2021. RESULTS: PNP were older than NNP patients (mean 53.9 vs 44.9 y; p < 0.0001) with a higher prevalence of pre-existing comorbidities. An average 6.8 months from onset, the main neurologic symptoms were "brain fog" (81.2%), headache (70.3%), and dizziness (49.5%) with only anosmia, dysgeusia and myalgias being more frequent in the NNP compared to the PNP group (59 vs 39%, 57.6 vs 39% and 50.4 vs 33%, all p < 0.003). Moreover, 85.8% of patients experienced fatigue. PNP more frequently had an abnormal neurologic exam than NNP patients (62.2 vs 37%, p < 0.0001). Both groups had impaired quality of life in cognitive, fatigue, sleep, anxiety, and depression domains. PNP patients performed worse on processing speed, attention, and working memory tasks than NNP patients (T-score 41.5 vs 55, 42.5 vs 47 and 45.5 vs 49, all p < 0.001) and a US normative population. NNP patients had lower results in attention task only. Subjective impression of cognitive ability correlated with cognitive test results in NNP but not in PNP patients. INTERPRETATION: PNP and NNP patients both experience persistent neurologic symptoms affecting their quality of life. However, they harbor significant differences in demographics, comorbidities, neurologic symptoms and findings, as well as pattern of cognitive dysfunction. Such differences suggest distinct etiologies of Neuro-PASC in these populations warranting targeted interventions. ANN NEUROL 2023;94:146-159.

A randomized trial of blood donor iron repletion on red cell quality for transfusion and donor cognition and well-being.

Although altruistic regular blood donors are vital for the blood supply, many become iron deficient from donation-induced iron loss. The effects of blood donation-induced iron deficiency on red cell transfusion quality or donor cognition are unknown. In this double-blind, randomized trial, adult iron-deficient blood donors (n = 79; ferritin < 15 µg/L and zinc protoporphyrin >60 µMol/mol heme) who met donation qualifications were enrolled. A first standard blood donation was followed by the gold-standard measure for red cell storage quality: a 51-chromium posttransfusion red cell recovery study. Donors were then randomized to intravenous iron repletion (1 g low-molecular-weight iron dextran) or placebo. A second donation ∼5 months later was followed by another recovery study. Primary outcome was the within-subject change in posttransfusion recovery. The primary outcome measure of an ancillary study reported here was the National Institutes of Health Toolbox-derived uncorrected standard Cognition Fluid Composite Score. Overall, 983 donors were screened; 110 were iron-deficient, and of these, 39 were randomized to iron repletion and 40 to placebo. Red cell storage quality was unchanged by iron repletion: mean change in posttransfusion recovery was 1.6% (95% confidence interval -0.5 to 3.8) and -0.4% (-2.0 to 1.2) with and without iron, respectively. Iron repletion did not affect any cognition or well-being measures. These data provide evidence that current criteria for blood donation preserve red cell transfusion quality for the recipient and protect adult donors from measurable effects of blood donation-induced iron deficiency on cognition. This trial was registered at www.clinicaltrials.gov as NCT02889133 and NCT02990559.

STing: accurate and ultrafast genomic profiling with exact sequence matches.

Genome-enabled approaches to molecular epidemiology have become essential to public health agencies and the microbial research community. We developed the algorithm STing to provide turn-key solutions for molecular typing and gene detection directly from next generation sequence data of microbial pathogens. Our implementation of STing uses an innovative k-mer search strategy that eliminates the computational overhead associated with the time-consuming steps of quality control, assembly, and alignment, required by more traditional methods. We compared STing to six of the most widely used programs for genome-based molecular typing and demonstrate its ease of use, accuracy, speed and efficiency. STing shows superior accuracy and performance for standard multilocus sequence typing schemes, along with larger genome-scale typing schemes, and it enables rapid automated detection of antimicrobial resistance and virulence factor genes. STing determines the sequence type of traditional 7-gene MLST with 100% accuracy in less than 10 seconds per isolate. We hope that the adoption of STing will help to democratize microbial genomics and thereby maximize its benefit for public health.

Native American admixture recapitulates population-specific migration and settlement of the continental United States.

European and African descendants settled the continental US during the 17th-19th centuries, coming into contact with established Native American populations. The resulting admixture among these groups yielded a significant reservoir of Native American ancestry in the modern US population. We analyzed the patterns of Native American admixture seen for the three largest genetic ancestry groups in the US population: African descendants, Western European descendants, and Spanish descendants. The three groups show distinct Native American ancestry profiles, which are indicative of their historical patterns of migration and settlement across the country. Native American ancestry in the modern African descendant population does not coincide with local geography, instead forming a single group with origins in the southeastern US, consistent with the Great Migration of the early 20th century. Western European descendants show Native American ancestry that tracks their geographic origins across the US, indicative of ongoing contact during westward expansion, and Native American ancestry can resolve Spanish descendant individuals into distinct local groups formed by more recent migration from Mexico and Puerto Rico. We found an anomalous pattern of Native American ancestry from the US southwest, which most likely corresponds to the Nuevomexicano descendants of early Spanish settlers to the region. We addressed a number of controversies surrounding this population, including the extent of Sephardic Jewish ancestry. Nuevomexicanos are less admixed than nearby Mexican-American individuals, with more European and less Native American and African ancestry, and while they do show demonstrable Sephardic Jewish ancestry, the fraction is no greater than seen for other New World Spanish descendant populations.

COVID-19 in children and young adults with moderate/severe inborn errors of immunity in a high burden area in pre-vaccine era.

BACKGROUND: Information regarding inborn error of immunity (IEI) as a risk factor for severe COVID-19 is scarce. We aimed to determine if paediatric patients with moderate/severe IEI got COVID-19 at the same level as the general population, and to describe COVID-19 expression. MATERIAL AND METHODS: We included patients with moderate/severe IEI aged 0-21 years old: cross-sectional study (June2020) to determine the prevalence of COVID-19; prospective study (January2020-January2021) including IEI patients with COVID-19. Assays used: nasopharyngeal swab SARS-CoV-2 PCR and SARS-CoV-2-specific immunoglobulins. RESULTS: Seven from sixty-five patients tested positive (prevalence: 10.7% (7%-13%)) after the first SARS-COV-2 wave and 13/15 patients diagnosed with COVID-19 had an asymptomatic/mild course. CONCLUSIONS: In our area, prevalence of COVID-19 in moderate/severe IEI paediatric patients after the first wave was slightly higher than in the general population. The majority of patients presented a benign course, suggesting a possible protective factor related with age despite IEI.

Delivery room ultrasound study to assess heart rate in newborns: DELIROUS study.

During neonatal resuscitation in the delivery room, heart rate guides clinical intervention, and although different methods have been evaluated as auscultation, pulse oximetry, and electrocardiography, they have various limitations. This was a prospective observational study which aim was to evaluate the accuracy and speed of ultrasound for measuring neonatal heart rate compared with stethoscope, pulse oximetry, and electrocardiography. Simultaneous determinations of heart rate using stethoscope, ultrasound, pulse oximetry, and electrocardiography were performed. Fifty term newborns were included. There were no differences according to the turn on time of the ultrasound, pulse oximetry, and electrocardiography (p = 0.666), but the placement time and the detection time from birth were shorter for ultrasound (p < 0.001). A stronger positive correlation was detected between ultrasound and electrocardiography at 90 (Rho = 0.926), and 120 s (Rho = 0.920) with p < 0.001. The Bland-Altman analysis showed a bias of - 2.23 (p = 0.129) between ultrasound and electrocardiography at 90 s, and a bias of 0.44 (p = 0.092) at 120 s. Instead, the bias between auscultation and electrocardiography at 90 s was - 6.71 (p = 0.131), and at 120 s was of - 4.67 (p = 0.793).Conclusions: Ultrasound is a fast method to detect heart rate in the delivery room and has a good correlation with stethoscope and electrocardiography. What is Known: • During neonatal resuscitation in the delivery room, heart rate guides clinical intervention, and although different methods have been evaluated, they have various limitations. What is New: • Heart rate ultrasound is a good and fast method to detect HR in the delivery room with a good correlation with electrocardiography and stethoscope.

Population structure and pharmacogenomic risk stratification in the United States.

BACKGROUND: Pharmacogenomic (PGx) variants mediate how individuals respond to medication, and response differences among racial/ethnic groups have been attributed to patterns of PGx diversity. We hypothesized that genetic ancestry (GA) would provide higher resolution for stratifying PGx risk, since it serves as a more reliable surrogate for genetic diversity than self-identified race/ethnicity (SIRE), which includes a substantial social component. We analyzed a cohort of 8628 individuals from the United States (US), for whom we had both SIRE information and whole genome genotypes, with a focus on the three largest SIRE groups in the US: White, Black (African-American), and Hispanic (Latino). Our approach to the question of PGx risk stratification entailed the integration of two distinct methodologies: population genetics and evidence-based medicine. This integrated approach allowed us to consider the clinical implications for the observed patterns of PGx variation found within and between population groups. RESULTS: Whole genome genotypes were used to characterize individuals' continental ancestry fractions-European, African, and Native American-and individuals were grouped according to their GA profiles. SIRE and GA groups were found to be highly concordant. Continental ancestry predicts individuals' SIRE with > 96% accuracy, and accordingly, GA provides only a marginal increase in resolution for PGx risk stratification. In light of the concordance between SIRE and GA, taken together with the fact that information on SIRE is readily available to clinicians, we evaluated PGx variation between SIRE groups to explore the potential clinical utility of race and ethnicity. PGx variants are highly diverged compared to the genomic background; 82 variants show significant frequency differences among SIRE groups, and genome-wide patterns of PGx variation are almost entirely concordant with SIRE. The vast majority of PGx variation is found within rather than between groups, a well-established fact for almost all genetic variants, which is often taken to argue against the clinical utility of population stratification. Nevertheless, analysis of highly differentiated PGx variants illustrates how SIRE partitions PGx variation based on groups' characteristic ancestry patterns. These cases underscore the extent to which SIRE carries clinically valuable information for stratifying PGx risk among populations, albeit with less utility for predicting individual-level PGx alleles (genotypes), supporting the concept of population pharmacogenomics. CONCLUSIONS: Perhaps most interestingly, we show that individuals who identify as Black or Hispanic stand to gain far more from the consideration of race/ethnicity in treatment decisions than individuals from the majority White population.

Ancestry effects on type 2 diabetes genetic risk inference in Hispanic/Latino populations.

BACKGROUND: Hispanic/Latino (HL) populations bear a disproportionately high burden of type 2 diabetes (T2D). The ability to predict T2D genetic risk using polygenic risk scores (PRS) offers great promise for improved screening and prevention. However, there are a number of complications related to the accurate inference of genetic risk across HL populations with distinct ancestry profiles. We investigated how ancestry affects the inference of T2D genetic risk using PRS in diverse HL populations from Colombia and the United States (US). In Colombia, we compared T2D genetic risk for the Mestizo population of Antioquia to the Afro-Colombian population of Chocó, and in the US, we compared European-American versus Mexican-American populations. METHODS: Whole genome sequences and genotypes from the 1000 Genomes Project and the ChocoGen Research Project were used for genetic ancestry inference and for T2D polygenic risk score (PRS) calculation. Continental ancestry fractions for HL genomes were inferred via comparison with African, European, and Native American reference genomes, and PRS were calculated using T2D risk variants taken from multiple genome-wide association studies (GWAS) conducted on cohorts with diverse ancestries. A correction for ancestry bias in T2D risk inference based on the frequencies of ancestral versus derived alleles was developed and applied to PRS calculations in the HL populations studied here. RESULTS: T2D genetic risk in Colombian and US HL populations is positively correlated with African and Native American ancestry and negatively correlated with European ancestry. The Afro-Colombian population of Chocó has higher predicted T2D risk than Antioquia, and the Mexican-American population has higher predicted risk than the European-American population. The inferred relative risk of T2D is robust to differences in the ancestry of the GWAS cohorts used for variant discovery. For trans-ethnic GWAS, population-specific variants and variants with same direction effects across populations yield consistent results. Nevertheless, the control for bias in T2D risk prediction confirms that explicit consideration of genetic ancestry can yield more reliable cross-population genetic risk inferences. CONCLUSIONS: T2D associations that replicate across populations provide for more reliable risk inference, and modeling population-specific frequencies of ancestral and derived risk alleles can help control for biases in PRS estimation.

Diagnostic accuracy of the Ottawa Knee Rule in adult acute knee injuries: a systematic review and meta-analysis.

OBJECTIVES: This systematic review and meta-analysis aimed to evaluate the current evidence on the diagnostic accuracy of the Ottawa Knee Rule (OKR) for acute knee injuries in adults. METHODS: A literature search of Embase (Elsevier), MEDLINE (U.S. National Library of Medicine), PubMed and Scopus databases (1995 to date; English language) was performed and the relevant references were assessed. Original articles documenting OKR use by emergency physicians to assess adult acute knee injuries were included. Study methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. Results of eligible studies were pooled using random effects or fixed effects modelling to calculate the diagnostic performance of the OKR. The Higgins I2 test and Begg's association test were performed to assess between-study heterogeneity and publication bias respectively, with Spearman's correlation test for threshold effect. RESULTS: Eight studies, including 7385 patients, were enrolled and pooled using the random effects model. Sensitivity, specificity, negative likelihood ratio, positive likelihood ratio and diagnostic odds ratio were 0.99 (95% CI, 0.97 to 1.00), 0.49 (95% CI, 0.47 to 0.51), 0.07 (95% CI, 0.02 to 0.24), 1.86 (95% CI, 1.72 to 2.01) and 25.10 (95% CI, 7.18 to 87.70) respectively. Based on the QUADAS-2 criteria, most studies presented low risk of bias and concern regarding applicability. CONCLUSIONS: Application of the OKR can rule out knee fracture and thus avoid unnecessary radiography. These results also translate to improved efficiency, lower medical costs and reduced waiting times. KEY POINTS: • The Ottawa Knee Rule helps clinicians to rule out fracture in adults with an acute knee injury. • The rule allows a reduction in radiography requests, patient waiting time in the emergency department and healthcare costs.

Efficacy of Neurofeedback Interventions for Cognitive Rehabilitation Following Brain Injury: Systematic Review and Recommendations for Future Research.

OBJECTIVES: Interest in neurofeedback therapies (NFTs) has grown exponentially in recent years, encouraged both by escalating public interest and the financial support of health care funding agencies. Given NFTs' growing prevalence and anecdotally reported success in treating common effects of acquired brain injury (ABI), a systematic review of the efficacy of NFTs for the rehabilitation of ABI-related cognitive impairment is warranted. METHODS: Eligible studies included adult samples (18+ years) with ABI, the use of neurofeedback technology for therapeutic purposes (as opposed to assessment), the inclusion of a meaningful control group/condition, and clear cognitive-neuropsychological outcomes. Initial automated search identified n = 86 candidate articles, however, only n = 4 studies met the stated eligibility criteria. RESULTS: Results were inconsistent across studies and cognitive domains. Methodological and theoretical limitations precluded robust and coherent conclusions with respect to the cognitive rehabilitative properties of NFTs. We take the results of these systematic analyses as a reflection of the state of the literature at this time. These results offer a constructive platform to further discuss a number of methodological, theoretical, and ethical considerations relating to current and future NFT-ABI research and clinical intervention. CONCLUSIONS: Given the limited quantity and quality of the available research, there appears to be insufficient evidence to comment on the efficacy of NFTs within an ABI rehabilitation context at this time. It is imperative that future work increase the level of theoretical and methodological rigour if meaningful advancements are to be made understanding and evaluating NFT-ABI applications.

Early surfactant replacement guided by lung ultrasound in preterm newborns with RDS: the ULTRASURF randomised controlled trial.

This study aimed to investigate whether using lung ultrasound (LUS) scores in premature newborns with respiratory distress syndrome (RDS) allows for earlier surfactant therapy (within the first 3 h of life) than using FiO2 criteria. This was a randomised, non-blinded clinical trial conducted in a neonatal intensive care unit. The inclusion criteria were newborns with a gestational age of ≤ 32 weeks and RDS. Patients meeting the inclusion criteria were randomly assigned to two groups: the ultrasound group, administered surfactant based on LUS score and/or FiO2 threshold, and the control group, guided by FiO2 only. Fifty-six patients were included. The ultrasound group received surfactant earlier (1 h of life vs. 6 h, p < 0.001), with lower FiO2 (25% vs. 30%, p = 0.016) and lower CO2 (48 vs. 54, p = 0.011). After surfactant treatment, newborns in the ultrasound group presented a greater SpO2 (p = 0.001) and SpO2/FiO2 ratio (p = 0.012).Conclusions: LUS score allowed an earlier surfactant therapy, reduced oxygen exposure early in life and a better oxygenation after the treatment. This early surfactant replacement may lead to reduced oxygen exposure. What is Known: • Lung ultrasound scores predict the need for surfactant therapy in premature newborns. What is New: • This study shows that using lung ultrasound scores improves the timeliness of surfactant replacement compared with using FiO2 alone.

GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide.

Human populations from around the world show striking phenotypic variation across a wide variety of traits. Genome-wide association studies (GWAS) are used to uncover genetic variants that influence the expression of heritable human traits; accordingly, population-specific distributions of GWAS-implicated variants may shed light on the genetic basis of human phenotypic diversity. With this in mind, we developed the GlobAl Distribution of GEnetic Traits web server (GADGET http://gadget.biosci.gatech.edu). The GADGET web server provides users with a dynamic visual platform for exploring the relationship between worldwide genetic diversity and the genetic architecture underlying numerous human phenotypes. GADGET integrates trait-implicated single nucleotide polymorphisms (SNPs) from GWAS, with population genetic data from the 1000 Genomes Project, to calculate genome-wide polygenic trait scores (PTS) for 818 phenotypes in 2504 individual genomes. Population-specific distributions of PTS are shown for 26 human populations across 5 continental population groups, with traits ordered based on the extent of variation observed among populations. Users of GADGET can also upload custom trait SNP sets to visualize global PTS distributions for their own traits of interest.

A Nationwide Screen of Carbapenem-Resistant Klebsiella pneumoniae Reveals an Isolate with Enhanced Virulence and Clinically Undetected Colistin Heteroresistance.

The convergence of hypervirulence and multidrug resistance in Klebsiella pneumoniae is a significant concern. Here, we report the first screen for hypermucoviscosity, a trait associated with increased virulence, using a U.S. surveillance collection of carbapenem-resistant (CR) K. pneumoniae isolates. We identified one hypermucoviscous isolate, which carried a gene encoding the KPC-3 carbapenemase, among numerous resistance genes. The strain further exhibited colistin heteroresistance undetected by diagnostics. This convergence of diverse resistance mechanisms and increased virulence underscores the need for enhanced K. pneumoniae surveillance.

Benchmarking computational tools for polymorphic transposable element detection.

Transposable elements (TEs) are an important source of human genetic variation with demonstrable effects on phenotype. Recently, a number of computational methods for the detection of polymorphic TE (polyTE) insertion sites from next-generation sequence data have been developed. The use of such tools will become increasingly important as the pace of human genome sequencing accelerates. For this report, we performed a comparative benchmarking and validation analysis of polyTE detection tools in an effort to inform their selection and use by the TE research community. We analyzed a core set of seven tools with respect to ease of use and accessibility, polyTE detection performance and runtime parameters. An experimentally validated set of 893 human polyTE insertions was used for this purpose, along with a series of simulated data sets that allowed us to assess the impact of sequence coverage on tool performance. The recently developed tool MELT showed the best overall performance followed by Mobster and then RetroSeq. PolyTE detection tools can best detect Alu insertion events in the human genome with reduced reliability for L1 insertions and substantially lowered performance for SVA insertions. We also show evidence that different polyTE detection tools are complementary with respect to their ability to detect a complete set of insertion events. Accordingly, a combined approach, coupled with manual inspection of individual results, may yield the best overall performance. In addition to the benchmarking results, we also provide notes on tool installation and usage as well as suggestions for future polyTE detection algorithm development.

Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements.

Transposable element (TE) derived sequences are known to contribute to the regulation of the human genome. The majority of known TE-derived regulatory sequences correspond to relatively ancient insertions, which are fixed across human populations. The extent to which human genetic variation caused by recent TE activity leads to regulatory polymorphisms among populations has yet to be thoroughly explored. In this study, we searched for associations between polymorphic TE (polyTE) loci and human gene expression levels using an expression quantitative trait loci (eQTL) approach. We compared locus-specific polyTE insertion genotypes to B cell gene expression levels among 445 individuals from 5 human populations. Numerous human polyTE loci correspond to both cis and trans eQTL, and their regulatory effects are directly related to cell type-specific function in the immune system. PolyTE loci are associated with differences in expression between European and African population groups, and a single polyTE loci is indirectly associated with the expression of numerous genes via the regulation of the B cell-specific transcription factor PAX5. The polyTE-gene expression associations we found indicate that human TE genetic variation can have important phenotypic consequences. Our results reveal that TE-eQTL are involved in population-specific gene regulation as well as transcriptional network modification.

Genetic ancestry, admixture and health determinants in Latin America.

BACKGROUND: Modern Latin American populations were formed via genetic admixture among ancestral source populations from Africa, the Americas and Europe. We are interested in studying how combinations of genetic ancestry in admixed Latin American populations may impact genomic determinants of health and disease. For this study, we characterized the impact of ancestry and admixture on genetic variants that underlie health- and disease-related phenotypes in population genomic samples from Colombia, Mexico, Peru, and Puerto Rico. RESULTS: We analyzed a total of 347 admixed Latin American genomes along with 1102 putative ancestral source genomes from Africans, Europeans, and Native Americans. We characterized the genetic ancestry, relatedness, and admixture patterns for each of the admixed Latin American genomes, finding a spectrum of ancestry proportions within and between populations. We then identified single nucleotide polymorphisms (SNPs) with anomalous ancestry-enrichment patterns, i.e. SNPs that exist in any given Latin American population at a higher frequency than expected based on the population's genetic ancestry profile. For this set of ancestry-enriched SNPs, we inspected their phenotypic impact on disease, metabolism, and the immune system. All four of the Latin American populations show ancestry-enrichment for a number of shared pathways, yielding evidence of similar selection pressures on these populations during their evolution. For example, all four populations show ancestry-enriched SNPs in multiple genes from immune system pathways, such as the cytokine receptor interaction, T cell receptor signaling, and antigen presentation pathways. We also found SNPs with excess African or European ancestry that are associated with ancestry-specific gene expression patterns and play crucial roles in the immune system and infectious disease responses. Genes from both the innate and adaptive immune system were found to be regulated by ancestry-enriched SNPs with population-specific regulatory effects. CONCLUSIONS: Ancestry-enriched SNPs in Latin American populations have a substantial effect on health- and disease-related phenotypes. The concordant impact observed for same phenotypes across populations points to a process of adaptive introgression, whereby ancestry-enriched SNPs with specific functional utility appear to have been retained in modern populations by virtue of their effects on health and fitness.

stringMLST: a fast k-mer based tool for multilocus sequence typing.

Rapid and accurate identification of the sequence type (ST) of bacterial pathogens is critical for epidemiological surveillance and outbreak control. Cheaper and faster next-generation sequencing (NGS) technologies have taken preference over the traditional method of amplicon sequencing for multilocus sequence typing (MLST). But data generated by NGS platforms necessitate quality control, genome assembly and sequence similarity searching before an isolate's ST can be determined. These are computationally intensive and time consuming steps, which are not ideally suited for real-time molecular epidemiology. Here, we present stringMLST, an assembly- and alignment-free, lightweight, platform-independent program capable of rapidly typing bacterial isolates directly from raw sequence reads. The program implements a simple hash table data structure to find exact matches between short sequence strings (k-mers) and an MLST allele library. We show that stringMLST is more accurate, and order of magnitude faster, than its contemporary genome-based ST detection tools. AVAILABILITY AND IMPLEMENTATION: The source code and documentations are available at http://jordan.biology.gatech.edu/page/software/stringMLST CONTACT: lavanya.rishishwar@gatech.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline.

The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.