Biology subjects

Hanage, W. P.

Publications and source records attributed to Hanage, W. P..

14 recordsLinked to original sources

bioRxiv2025

SARS-CoV-2 Intra-host Variation Shows Evidence of Transmission and Convergent Evolution in a University Surveillance Cohort

Monitoring and understanding the transmission and evolution of SARS-CoV-2 remains a significant pub-lic health priority. Within-host genetic variation provides insight into viral evolution during infection and may help infer transmission events. In this study, we analyzed intrahost variation in SARS-CoV-2 genome sequences from Boston Universitys testing mandate. Focusing on intrahost single nucleotide variants (iSNVs), we inferred transmission events and assessed the selective forces shaping within-host viral evolution. To minimize false-positive iSNVs resulting from systematic biases, we implemented stringent data filtering and developed a heuristic to exclude contamination-derived artifacts arising from batched sequencing. We find that intrahost variation is limited and infrequently transmitted during acute infections, suggesting that shared iSNVs serve as highly specific but insensitive markers of transmission. We also observed incomplete purifying selection shaping within-host diversity, with the loci most affected changing among variants of concern. Finally, we identified a highly recurrent iSNV (G11083T) which may represent a site of positive selection. Our results highlight that within host variation provides insight towards within host pathogen evolution, in spite of a limited use towards genomic epidemiology. IMPACT STATEMENTSARS-CoV-2 is the most extensively sequenced pathogen to date, yet much of its genomic data remains underutilized. Intrahost variation, in particular, is less studied than consensus-level variation, partly because most datasets lack technical sequencing replicates to control false-positive signals. Using genomic data from a university testing mandate and applying rigorous filtering to systematically minimize false-positive iSNVs in a data-driven manner, we obtain insights into SARS-CoV-2 evolution and transmission from intrahost variation. Our work underscores the potential to use existing, large-scale datasets to better understand pathogen evolution in situ. DATA SUMMARYAll sequence data have been deposited in the Sequence Read Archive (SRA) of the national center for biotechnology information (NCBI), under the project accession number PRJNA892225. All code is open-access and available in GitHub at: https://github.com/Leacavalli/Sars-cov-2-Intrahost-Variation. Any additional supporting data has been provided within the article.

genomics↗

bioRxiv2025

Bronze Age Yersinia pestis genome from sheep sheds light on hosts and evolution of a prehistoric plague lineage

Most human pathogens are of zoonotic origin. Many emerged during prehistory, coinciding with domestication providing more opportunities for spillover from original host species. However, we lack direct evidence linking past animal reservoirs and human infections. Here we present a Yersinia pestis genome recovered from a 3rd millennium BCE domesticated sheep from the Eurasian Steppe belonging to the Late Neolithic Bronze Age (LNBA) lineage, until now exclusively identified in ancient humans across Eurasia. We show that this ancient lineage underwent ancestral gene decay paralleling extant lineages, but evolved under distinct selective pressures contributing to its lack of geographic differentiation. We collect evidence supporting a scenario where the LNBA lineage, unable to efficiently transmit via fleas, spread from an unidentified reservoir to humans via sheep and likely other domesticates. Collectively, our results connect prehistoric livestock with infectious disease in humans and showcase the power of moving paleomicrobiology into the zooarcheological record.

genetics↗

bioRxiv2022

Enterobacteriaceae isolated from patients share antibiotic resistance conferring plasmids recently acquired from those isolated from sinks in the same treatment room

Identifying how and where pathogens acquire antibiotic resistance is crucial to developing effective strategies to limit its spread. Many bacterial species carry and share plasmids harboring antibiotic resistant genes. Plasmids are mobile genetic elements whose horizontal transmission is difficult to assess through genomic comparison due to assembly issues when using short-read sequencing alone. In this study, we use hybrid assembly to fully assemble plasmids that are shared between different Enterobacteriaceae isolated from patients and sinks in the same hospital rooms. We isolated and sequenced pairs of carbapenem resistant Enterobacter hormaechei subsp. xiangfangensis and Klebsiella pneumoniae from patients and sinks within the same hospital room. The isolate pairs share plasmids that putatively confer antibiotic resistance, including carbapenem resistance. These plasmids differ by few mutations and structural changes, while the isolates carry unique plasmids. Together, this suggests that plasmids can act as vectors of antibiotic resistance spread from sink reservoirs to patients.

microbiology↗

bioRxiv2022

Beyond consensus sequence: a quantitative scheme for inferring transmission using deep sequencing in a bacterial transmission model

Genomic surveillance provides a data source complementary to contact tracing to resolve putative transmission chains. However, the role of within-host diversity in transmission is understudied due to a lack of experimental and clinical datasets that capture within-host diversity in both donors and recipients. Here, we assess the utility of deep-sequenced genomic surveillance within a mouse transmission model where the gastrointestinal pathogen Citrobacter rodentium was controllably spread during co-housing of infected and naive animals. We observed that within-host variants were maintained over multiple transmission steps until fixation or elimination. We present a model for inferring the likelihood that a given pair of samples are linked by transmission, by comparing the allelic frequency at variant genomic loci. Our data affirm that within-host single nucleotide variants (iSNVs) can repeatedly pass from donor to recipient along the transmission chain, and the mere sharing of iSNVs between different transmission pairs offers limited confidence in identifying a transmission pair. Beyond the presence and absence of within-host variants, we show that differences arising in the relative abundance of iSNVs can infer transmission pairs with high precision. An important component of our approach is that the inference is based solely on sequence data, without incorporating epidemiological or demographic data for context. Our model, which substantially reduces the number of comparisons a contact tracer needs to consider, may enhance the accuracy of contact tracing and other epidemiological processes, including early detection of emerging transmission clusters.

genomics↗

bioRxiv2021

The role of interspecies recombinations in the evolution of antibiotic resistant pneumococci

AbstractThe evolutionary histories of the antibiotic-resistant Streptococcus pneumoniae lineages PMEN3 and PMEN9 were reconstructed using global collections of genomes. In PMEN3, one resistant clade spread worldwide, and underwent 25 serotype switches, enabling evasion of vaccine-induced immunity. In PMEN9, only 9 switches were detected, and multiple resistant lineages emerged independently and circulated locally. In Germany, PMEN9s expansion correlated significantly with the macrolide:penicillin consumption ratio. These isolates were penicillin sensitive but macrolide resistant, through a homologous recombination that integrated Tn1207.1 into a competence gene, preventing further diversification via transformation. Analysis of a species-wide dataset found 183 acquisitions of macrolide resistance, and multiple gains of the tetracycline-resistant transposon Tn916, through homologous recombination, often originating in other streptococcal species. Consequently, antibiotic selection preserves atypical recom- bination events that cause sequence divergence and structural variation throughout the S. pneumoniae chromosome. These events reveal the genetic exchanges between species normally counter-selected until perturbed by clinical interventions.

genomics↗

bioRxiv2020

Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures

Streptococcus pneumoniae can be split into multiple strains, each with a characteristic combination of core and accessory genome variation, able to co-circulate and compete within the same hosts. Previous analyses of epidemiological datasets suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), acting to maintain accessory loci at equilibrium frequencies. To test whether this model could explain how such multi-strain populations were generated, it was modified to incorporate recombination. The outputs of simulations featuring symmetrical recombination were compared with genomic data on locus frequencies and distributions between genotypes, pairwise genetic distances and tree shape. These demonstrated NFDS prevented the loss of variation through neutral drift, but generated unstructured populations of diverse isolates. Making recombination asymmetrical, favouring deletion of accessory loci over insertion, alongside multi-locus NFDS significantly improved the fit to genomic data. In a population at equilibrium, structuring into multiple strains was stable due to outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. As many bacteria inhibit the integration of insertions into their chromosomes, this combination of asymmetrical recombination and multi-locus NFDS may underlie the co-existence of strains within a single ecological niche.

evolutionary biology↗

bioRxiv2019

Choosing Your Battles: Which Resistance Genes Warrant Global Action?

The increasing accumulation of antibiotic resistance genes (ARGs) in pathogens poses a severe threat to the treatment of bacterial infections. However, not all ARGs do not pose the same threats to human health. Here, we present a framework to rank the risk of ARGs based on three factors: \"anthropogenic enrichment\", \"mobility\", and \"host pathogenicity\". The framework is informed by all available bacterial genomes (55,000), plasmids (16,000), integrons (3,000), and 850 metagenomes covering diverse global eco-habitats. The framework prioritizes 3% of all known ARGs in Rank I (the most at risk of dissemination amongst pathogens) and 0.3% of ARGs in Rank II (high potential emergence of new resistance in pathogens). We further validated the framework using a list of 38 ARG families previously identified as high risk by the World Health Organization and published literature, and found that 36 of them were properly identified as top risk (Rank I) in our approach. Furthermore, we identified 43 unreported Rank I ARG families that should be prioritized for public health interventions. Within the same gene family, homologous genes pose different risks, host range, and ecological distributions, indicating the need for high resolution surveillance into their sequence variants. Finally, to help strategize the policy interventions, we studied the impact of industrialization on high risk ARGs in 1,120 human gut microbiome metagenomes of 36 diverse global populations. Our findings suggest that current policies on controlling the clinical antimicrobial consumptions could effectively control Rank I, while greater antibiotic stewardship in veterinary settings could help control Rank II. Overall, our framework offered a straightforward evaluation of the risk posed by ARGs, and prioritized a shortlist of current and emerging threats for global action to fight ARGs.

microbiology↗

bioRxiv2019

Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae

The extent to which evolution is constrained by the rate at which horizontal gene transfer (HGT) allows DNA to move between genetic lineages is an open question, which we address in the context of antibiotic resistance in Streptococcus pneumoniae. We analyze microbiological, genomic and epidemiological data from the largest-to-date sequenced pneumococcal carriage study in 955 infants from a refugee camp on the Thailand-Myanmar border. Using a unified framework, we simultaneously test prior hypotheses on rates of HGT and a key evolutionary covariate (duration of carriage) as determinants of resistance frequencies. We conclude that in this setting, there is only weak evidence for the rate of HGT playing a role in the evolutionary dynamics of resistance. Instead, observed resistance frequencies are best explained as the outcome of selection acting on a pool of variants, irrespective of the rate at which resistance determinants move between genetic lineages.

evolutionary biology↗

bioRxiv2019

Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen

Identifying the forces that create and shape ecologically meaningful variation in bacteria remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show derived alleles less than 300bp apart in Neisseria gonorrhoeae exhibit more coupling linkage than repulsion linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles compared to synonymous alleles. While linkage is shaped by many evolutionary processes, extensive simulations show only two distinct forms of positive selection can drive an excess of coupling linkage between neighboring nonsynonymous alleles: directional selection on introgressed alleles or selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.

evolutionary biology↗

bioRxiv2018

Prediction of post-vaccine population structure of Streptococcus pneumoniae using accessory gene frequencies

Predicting how pathogen populations will change over time is challenging. Such has been the case with Streptococcus pneumoniae, an important human pathogen, and the pneumococcal conjugate vaccines (PCVs), which target only a fraction of the strains in the population. Here, we use the frequencies of accessory genes to predict changes in the pneumococcal population after vaccination, hypothesizing that these frequencies reflect negative frequency-dependent selection (NFDS) on the gene products. We find that the standardized predicted fitness of a strain estimated by an NFDS-based model at the time the vaccine is introduced enables to predict whether the strain increases or decreases in prevalence following vaccination. Further, we are able to forecast the equilibrium post-vaccine population composition and assess the invasion capacity of emerging lineages. Overall, we provide a method for predicting the impact of an intervention on pneumococcal populations with potential application to other bacterial pathogens in which NFDS is a driving force.

evolutionary biology↗

bioRxiv2018

Lineage calling can identify antibiotic resistant clones within minutes

Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empiric antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could impact patient treatment and outcomes. Here we present a method called genomic neighbor typing for inferring the phenotype of a bacterial sample by identifying its closest relatives in a database of genomes with metadata. We show that this technique can infer antibiotic susceptibility and resistance for both S. pneumoniae and N. gonorrhoeae. We implemented this with rapid k-mer matching, which, when used on Oxford Nanopore MinION data, can run in real time. This resulted in determination of resistance within ten minutes (sens/spec 91%/100% for S. pneumoniae and 81%/100% N. gonorrhoeae from isolates with a representative database) of sequencing starting, and for clinical metagenomic sputum samples (75%/100% for S. pneumoniae), within four hours of sample collection. This flexible approach has wide application to pathogen surveillance and may be used to greatly accelerate appropriate empirical antibiotic treatment.

bioinformatics↗

bioRxiv2018

Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci

Streptococcus pneumoniae serotype 3 remains a significant cause of morbidity and mortality worldwide, despite inclusion in the 13-valent pneumococcal conjugate vaccine (PCV13). Serotype 3 increased in carriage since the implementation of PCV13 in the United States, while invasive disease rates remain unchanged. We investigated the persistence of serotype 3 in carriage and disease, through genomic analyses of a global sample of 301 serotype 3 isolates of the Netherlands3-31 (PMEN31) clone CC180, combined with associated patient data and PCV utilization among countries of isolate collection. We assessed phenotypic variation between dominant clades in capsule charge (zeta potential), capsular polysaccharide shedding, and susceptibility to opsonophagocytic killing, which have previously been associated with carriage duration, invasiveness, and vaccine escape. We identify a recent shift in the CC180 population attributed to a lineage termed Clade II, which was estimated by Bayesian coalescent analysis to have first appeared in 1968 [95% HPD: 1939-1989] and increased in prevalence and effective population size thereafter. Clade II isolates are divergent from the pre-PCV13 serotype 3 population in non-capsular antigenic composition, competence, and antibiotic susceptibility, the last resulting from the acquisition of a Tn916-like conjugative transposon. Differences in recombination rates among clades correlated with variations in the ATP-binding subunit of Clp protease as well as amino acid substitutions in the comCDE operon. Opsonophagocytic killing assays elucidated the low observed efficacy of PCV13 against serotype 3. Variation in PCV13 use among sampled countries was not independently correlated with the CC180 population shift; therefore, genotypic and phenotypic differences in protein antigens and, in particular, antibiotic resistance may have contributed to the increase of Clade II. Our analysis emphasizes the need for routine, representative sampling of isolates from disperse geographic regions, including historically under-sampled areas. We also highlight the value of genomics in resolving antigenic and epidemiological variations within a serotype, which may have implications for future vaccine development.\n\nAuthor SummaryStreptococcus pneumoniae is a leading cause of bacterial pneumoniae, meningitis, and otitis media. Despite inclusion in the most recent pneumococcal conjugate vaccine, PCV13, serotype 3 remains epidemiologically important globally. We investigated the persistence of serotype 3 using whole-genome sequencing data form 301 isolates collected among 24 countries from 1993-2014. Through phylogenetic analysis, we identified three distinct lineages within a single clonal complex, CC180, and found one has recently emerged and grown in prevalence. We then compared genomic difference among lineages as well as variations in pneumococcal vaccine use among sampled countries. We found that the recently emerged lineage, termed Clade II, has a higher prevalence of antibiotic resistance compared to other lineages, diverse surface protein antigens, and a higher rate of recombination, a process by which bacteria can uptake and incorporate genetic material from its surroundings. Differences in vaccine use among sampled countries did not appear to be associated with the emergence of Clade II. We highlight the need to routine, representative sampling of bacterial isolates from diverse geographic areas and show the utility of genomic data in resolving epidemiological differences within a pathogen population.

evolutionary biology↗

bioRxiv2017

Weak epistasis may drive adaptation in recombining bacteria

The impact of epistasis on the evolution of multilocus traits depends on recombination. Population genetic theory has been largely developed for eukaryotes, many of which recombine so frequently that epistasis between polymorphisms has not been considered to play a large role in adaptation and has been compared to the fleeting influence of non-heritable effects. Many bacteria also recombine, some to the degree that their populations are described as panmictic or freely recombining. However, whether this recombination is sufficient to limit the ability of selection to act on epistatic contributions to fitness is unknown. We create a sensitive method to quantify homologous recombination in five bacterial pathogens and use these parameter estimates in a multilocus model of bacterial evolution with additive and epistatic effects. We find that even for highly recombining species (e.g. Streptococcus pneumoniae or Helicobacter pylori), selection may act on the cumulative effects of weak (as well as strong) interactions between distant mutations since homologous recombination typically transfers only short segments. Furthermore, whether selection acts more efficiently on physically proximal loci depends on the average recombination tract length. Epistasis may thus play an important role in the adaptive evolution of bacteria and, unlike in eukaryotes, does not need to be strong, involve near loci, or require specific metapopulation dynamics.

evolutionary biology↗

bioRxiv2017

Longitudinal samples of bacterial genomes potentially bias evolutionary analyses

Samples of bacteria collected over a period of time are attractive for several reasons, including the ability to estimate the molecular clock rate and to detect fluctuations in allele frequencies over time. However, longitudinal datasets are occasionally used in analyses that assume samples were collected contemporaneously. Using both simulations and genomic data from Neisseria gonorrhoeae, Streptococcus mutans, Campylobacter jejuni, and Helicobacter pylori, we show that longitudinal samples (spanning more than a decade in real data) may suffer from considerable bias that inflates estimates of recombination and the number of rare mutations in a sample of genomic sequences. While longitudinal data are frequently accounted for using the serial coalescent, many studies use other programs or metrics, such as Tajimas D, that are sensitive to these sampling biases and contain genomic data collected across many years. Notably, longitudinal samples from a population of constant size may exhibit evidence of exponential growth. We suggest that population genomic studies of bacteria should routinely account for temporal diversity in samples or provide evidence that longitudinal sampling bias does not affect conclusions.

genomics↗