The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

1Epidemiological transmission chains of Salmonella, Escherichia, or Yersinia have been reconstructed with the help of single-nucleotide polymorphisms (SNPs) from hundreds or even thousands of core genomes. However, the scale of these studies pales in comparison to the numbers of publicly available archives (e.g., NCBI Sequence Read Archive [SRA]) of short-read sequences of bacterial pathogens that have been deposited since the recent drop in price of high-throughput sequencing (https://www.genome.gov/sequencingcostsdata/). In October 2019, SRA contained genomic sequence reads from 430,417 Salmonella, Escherichia/Shigella, Clostridioides, Vibrio, and Yersinia. However, until very recently, relatively few draft genomic assemblies were publicly available, and even the current comparative genomic analyses in NCBI Pathogen Detection (https://www.ncbi.nlm.nih.gov/pathogens/) are restricted to relatively closely related genetic clusters. Since 2014, EnteroBase (https://enterobase.warwick.ac.uk) has attempted to address this gap for selected genera that include bacterial pathogens (Table 1). EnteroBase provides an integrated software platform (Fig. 1) that can be used by microbiologists with limited bioinformatic skills to upload short reads, assemble and genotype genomes, and immediately investigate their genomic relationships to all natural populations within those genera. These aspects have been illustrated by recent publications providing overviews of the population structures of Salmonella and Clostridioides, a description of the GrapeTree GUI, and a reconstruction of the genomic history of the Salmonella enterica Para C Lineage. However, EnteroBase also provides multiple additional features, which have hitherto largely been promulgated by word of mouth. Here, we provide a high-level overview of the functionality of EnteroBase, followed by exemplary case studies of S. enterica serovar Agama, Yersinia pestis, and all of Escherichia.

2The EnteroBase back end consists of multiple, cascading automated pipelines (Supplemental Fig. S1) that implement the multiple functions that it provides (Supplemental Fig. S2A). Many of these EnteroBase pipelines are also available within EToKi (EnteroBase ToolKit) (Supplemental Code), a publicly available repository (https://github.com/zheminzhou/EToKi) of useful modules (Supplemental Fig. S2B–E) that facilitate genomic assemblies (EToKi modules prepare and assemble), MLST (MLSType), calling nonrepetitive SNPs against a reference genome (EToKi modules align and phylo), or predicting serotypes of Escherichia coli from genome assemblies (EBEis).

3EnteroBase performs daily scans of SRA via its Entrez APIs for novel Illumina short-read sequences for each of the bacterial genera that it supports. It uploads the new reads and assembles them (EBAssembly [Supplemental Fig. S2B]) into annotated draft genomes, which are published if they pass quality control (Supplemental Table S1). EnteroBase fetches the metadata associated with the records and attempts to transcribe it automatically into EnteroBase metadata format (Supplemental Table S2; Supplemental Fig. S3). During the conversion, geographic metadata are translated into structured format using the Nominatim engine offered by OpenStreetMap (OpenStreetMap contributors 2017; Planet dump retrieved from https://planet.osm.org) and the host/source metadata are assigned to predefined categories (Supplemental Table S4). Until recently, metadata was parsed using a pretrained Native Bayesian classifier implemented in the Natural Language Toolkit (NLTK) for Python with an estimated accuracy of 60%. Since November 2019, a new metaparser is being used, with an estimated accuracy of 93% (Supplemental Material), and all old data will soon be re-parsed. Registered users can upload their own Illumina short reads and metadata into EnteroBase; these are then processed with the same pipelines.

4The annotated genomes are used to call alleles for multilocus sequence typing (MLST) (MLSType [Supplemental Fig. S2C]) and their sequence types (STs) are assigned to population groupings as described below. Salmonella serovars are predicted from the legacy MLST eBurstGroups (eBGs), which are strongly associated with individual serovars, or by two external programs—SISTR1 and SeqSero2—which evaluate genomic sequences. Escherichia serotypes are predicted from the genome assemblies by the EnteroBase module EBEis (Supplemental Fig. S2E). Clermont haplogroups are predicted for Escherichia by two external programs—ClermonTyping and EZClermont—and fimH type by a third (FimTyper). By default, all registered users have full access to strain metadata and the genome assemblies, predicted genotypes, and predicted phenotypes, but a delay in the release date of up to 12 mo can be imposed by users when uploading short-read sequences.

5In September 2019, EnteroBase provided access to 364,690 genomes and their associated metadata and predictions (Table 1). To allow comparisons with historical data, EnteroBase also maintains additional legacy seven-gene MLST assignments (and metadata) that were obtained by classical Sanger sequencing from 18,478 strains.

6EnteroBase users can upload new entries, consisting of paired-end Illumina short reads plus their metadata. Short reads are deleted after genome assembly, or after automated, brokered uploading of the reads and metadata to the European Nucleotide Archive (ENA) upon user request.

7The search and graphical tools within EnteroBase can access all assembled genomes and their metadata, even if they are pre-release. However, ownership of uploaded data remains with the user and extends to all calculations performed by EnteroBase. Only owners and their buddies, administrators, or curators can edit the metadata; and only those individuals can download any data or calculations before their release date. To facilitate downloading of post-release data by the general community, downloads containing metadata and genotypes or genomic assemblies are automatically stripped of pre-release data for users who lack ownership privileges. Similarly, pre-release nodes within trees in the GrapeTree and Dendrogram graphical modules must be hidden before users without ownership privileges can download those trees.

8In general, metadata that were imported from SRA are not editable, except by administrators and curators. However, the administrators can assign editing rights to users with claims to ownership or to those who possess special insights.

9Each unique sequence variant of a gene in an MLST scheme is assigned a unique numerical designation. Seven-gene MLST STs consist of seven integers for the alleles of seven housekeeping gene fragments. rSTs consist of 51–53 integers for ribosomal protein gene alleles. cgMLST STs consist of 1553–3002 integers for the number of genes in the soft core genome for that genus (Table 1), which were chosen as described elsewhere. However, STs are arbitrary constructs, and natural populations can each encompass multiple, related ST variants. Therefore, seven-gene STs are grouped into ST complexes in Escherichia/Shigella by an eBurst approach and into their equivalent eBurst groups (eBGs) in Salmonella. EnteroBase implements similar population groups (reBGs) for rMLST in Salmonella, which are largely consistent with eBGs or their subpopulations. The EnteroBase Nomenclature Server (Supplemental Fig. S1) calculates these population assignments automatically for each novel ST on the basis of single-linkage clustering chains with maximal pairwise differences of one allele for seven-gene MLST and two alleles for rMLST. To prevent overlaps between ST complexes, growing chains are terminated when they extend too closely to other existing populations (two allele difference in seven-gene MLST and five in rMLST).

10cgMLST has introduced additional complexities over MLST and rMLST. Visual comparisons of cgSTs are tedious and rarely productive, because each consists of up to 3002 integers. Furthermore, almost all cgSTs contain some missing data because they are called from draft genomes consisting of multiple contigs. EnteroBase contains 100,000s of cgST numbers because almost every genome results in a unique cgST number, although many cgSTs differ from others only by missing data. EnteroBase supports working with so many cgSTs through Hierarchical Clustering (HierCC), a novel approach which supports analyses of population structures based on cgMLST at multiple levels of resolution. To identify the cutoff values in stepwise cgMLST allelic distances which would reliably resolve natural populations, we first calculated a matrix of pairwise allelic distances (excluding pairwise missing data) for all existing pairs of cgSTs, and one matrix for the HierCC cluster numbers at each level of allelic distance, that is, one matrix for HC0, HC1, HC2, …, HC3001. A genus-specific subset of the most reliable HierCC clusters is reported by EnteroBase.

11For Salmonella, 13 HierCC levels are reported, ranging from HC0 (indistinguishable except for missing data) to HC2850 (Fig. 2). Our experience with Salmonella indicates that HC2850 corresponds to subspecies, HC2000 to superlineages, and HC900 to cgMLST versions of eBGs. Long-term endemic persistence seems to be associated with HC100 or HC200; and epidemic outbreaks with HC2, HC5, or HC10. Eleven levels are reported for the other genera, ranging from HC0 up to HC2350 for Escherichia, HC2500 for Clostridioides, and HC1450 for Yersinia. Escherichia HC1100 corresponds to ST Complexes (see below) and the correspondences to population groupings in Clostridioides are described elsewhere. Further information on HierCC can be found in the EnteroBase documentation (https://enterobase.readthedocs.io/en/latest/features/clustering.html).

12Most bacterial isolates/strains in EnteroBase are linked to one set of metadata and one set of genotyping data. However, EnteroBase includes strains for which legacy MLST data from classical Sanger sequencing exists in addition to MLST genotypes from genomic assemblies. Similarly, some users have uploaded the same reads to both EnteroBase and SRA, and both sets of data are present in EnteroBase. In other cases, genomes of the same strain have been sequenced by independent laboratories, or multiple laboratory variants have been sequenced that are essentially indistinguishable (e.g., S. enterica LT2 or E. coli K-12).

13EnteroBase deals with such duplicates by implementing the concept of an Uberstrain, which can be a parent to one or more identical substrains. Substrains remain invisible unless they are specified in the search dialog (Supplemental Fig. S4), in which case they are shown with a triangle in the Uberstrain column (Fig. 3A). Examples of the usage of this approach can be found in Supplemental Material.

14Often the utility of a tool first becomes clear through examples of its use. Here, we present three case studies that exemplify different aspects of EnteroBase. Case Study 1 shows how geographically separated laboratories can collaborate in private on an EnteroBase project until its completion, upon which EnteroBase publishes the results. This example focuses on geographical microvariation and transmission chains between various host species of a rare serovar of S. enterica. Case Study 2 shows how to combine modern genomes of Yersinia pestis with partially reconstructed genomes from ancient skeletons of plague victims. It also shows how EToKi can extract SNPs from metagenomic sequence reads. Case Study 3 provides a detailed overview of the genomic diversity of the genus Escherichia and defines the EcoRPlus set of representative genomes.

15S. enterica subspecies enterica encompasses more than 1586 defined serovars. These differ in the antigenic formulas of their lipopolysaccharide (O antigen) and/or two alternative flagellar antigens (H1, H2), which are abbreviated as O:H1:H2. Some serovars are commonly isolated from infections and the environment and have been extensively studied. Others are rare, poorly understood, and often polyphyletic, including Salmonella that colonize badgers.

16In late 2018, serovar Agama (antigenic formula: 4,12:i:1,6) was specified in the Serovar metadata field for only 134/156,347 (0.09%) genome assemblies in EnteroBase, and all 134 isolates were from humans. We were therefore interested to learn that the University of Liverpool possessed serovar Agama isolates that had been isolated in 2006–2007 from European badgers (Meles meles) in Woodchester Park, Gloucestershire, England. We sequenced the genomes of 72 such isolates and uploaded the short reads and strain metadata into EnteroBase. This data was used to analyze the population structure of a rare serovar within a single host species over a limited geographical area and to compare Agama genomes from multiple hosts and geographical sources.

17The browser interface to EnteroBase is implemented as a spreadsheet-like window called a “Workspace” that can page through thousands of entries, showing metadata at the left and experimental data at the right (https://enterobase.readthedocs.io/en/latest/features/using-workspaces.html). However, visual scanning of so many entries is inefficient. EnteroBase therefore offers powerful search functions (https://enterobase.readthedocs.io/en/latest/enterobase-tutorials/search-agama.html) for identifying isolates that share common phenotypes (metadata) and/or genotypes (experimental data).

18EnteroBase also predicts serovars from assembled Salmonella genomes and from MLST data. However, the software predictions are not failproof, and many entries lack metadata information or the metadata is erroneous. We therefore used the Search Strains dialog box to find entries containing “Agama” in the metadata Serovar field or by the Serovar predictions from SISTR1 (https://enterobase.readthedocs.io/en/latest/enterobase-tutorials/search-agama.html). Phylogenetic analyses of the cgMLST data from those entries indicated that Agama consisted of multiple microclusters.

19Almost all Agama isolates in EnteroBase were from England, which represents a highly skewed geographical sampling bias that might lead to phylogenetic distortions. We therefore formed the Agama Study Group, consisting of colleagues at national microbiological reference laboratories in England, Scotland, Ireland, France, Germany, and Austria. The participants were declared as “buddies” within EnteroBase (https://enterobase.readthedocs.io/en/latest/features/buddies.html) with explicit rights to access the Workspaces and phylogenetic trees in the Workspace\Load\Shared\Zhemin\Agama folder. After completion of this manuscript, that folder was made publicly available.

20We facilitated the analysis of the Agama data by creating a new user-defined Custom View (https://enterobase.readthedocs.io/en/latest/features/user-defined-content.html), which can aggregate various sources of experimental data as well as user-defined fields. The Custom View was saved in the Agama folder, and thereby shared with the study group. It too was initially private but became public together with the other workspaces and trees when the folder was made public.

21Members of the Agama Study Group were requested to sequence genomes from all Agama strains in their collections, and to upload those short reads to EnteroBase, or to send their DNAs to University of Warwick for sequencing and uploading. The new entries were added to the “All Agama Strains” workspace. The final set of 345 isolates had been isolated in Europe, Africa, and Australia, with collection years ranging from 1956 to 2018 (Supplemental Table S3).

22We created a neighbor-joining GrapeTree of cgMLST allelic differences to reveal the genetic relationships within serovar Agama. Color coding the nodes of the tree by SISTR1 serovar predictions confirmed that most isolates were Agama (Fig. 3A). However, one microcluster (shaded in light orange) consisted of seven monophasic Agama isolates with a defective or partial fljB (H2) CDS, which prevented a serovar prediction. SISTR1 also could not predict the O antigens of three other related isolates (arrows in Fig. 3). Sixteen other isolates on long branches were assigned to other serovars by SISTR1 (Fig. 3A, gray shading). Comparable results were obtained with SeqSero2 or eBG serovar associations, and these 16 isolates represent erroneous Serovar assignments within the metadata. Three of these erroneous Agama had the same predicted antigenic formula (1,4,[5],12:i:-) as the monophasic Agama isolates (orange shading), but these represent monophasic Typhimurium.

23In contrast to serovar, coloring the tree nodes by HC2000 clusters (Fig. 3B) immediately revealed that all genomes that were called Agama by SISTR1 belonged to HC2000 cluster number 299 (HC2000_299), and all HC2000_299 were genetically related and clustered together in the tree (Fig. 3B). In contrast, the 16 other isolates on long branches (gray shading) belonged to other HC2000 clusters.

24These results show that Agama belongs to one superlineage, HC2000_299, which has been isolated globally from humans, badgers, companion animals, and the environment since at least 1956. The genetic relationships would not have been obvious with lower resolution MLST: Some Agama isolates belong to eBG167, others to eBG336, and 13 Agama MLST STs do not belong to any eBG.

25All isolates from badgers were in HierCC cluster HC400_299 (Fig. 3B, dashed box), which also included other isolates from humans and other animals. HC400_299 was investigated by maximum-likelihood trees of core, nonrepetitive SNPs called against a reference draft genome with the help of the EnteroBase Dendrogram GUI. One tree (Fig. 4A) encompassed 149 isolates from the British Isles which were in EnteroBase before establishing the Agama Study Group. A second tree (Fig. 4B) contained the final data set of 213 genomes, including isolates from additional badgers and multiple countries. A comparison of the two trees is highly instructive on the effects of sample bias.

26Almost all of the initial HC400_299 genomes fell into three clades designated HC100_299, HC100_2433, and HC100_67355. All badger isolates were from Woodchester Park (2006–2007) within the context of a long-term live capture–mark–recapture study. The Agama isolates from those badgers formed a monophyletic subclade within HC100_2433, whose basal nodes represented human isolates. This branch topology suggested that a single recent common ancestor of all badger isolates had been transmitted from humans or their waste products.

27The badgers in Woodchester Park occupy adjacent social group territories, which each contain several setts (burrows). HC100_2433 contains multiple HC10 clusters of Agama from badgers (Supplemental Fig. S5A). To investigate whether these microclusters might mark transmission chains between setts and social groups, a Newick subtree of HC100_2433 plus geographical coordinates was transmitted from GrapeTree to Microreact, an external program which is specialized in depicting geographical associations. Badgers occasionally move between neighboring social groups. Transmissions associated with such moves are supported by the observation that five distinct HC10 clusters each contained isolates from two social groups in close proximity (Supplemental Fig. S5B).

28The 63 additional HC400_299 Agama genomes that were sequenced by the Agama Study Group provided important insights on the dissemination of Agama over a longer time frame and showed the problems that can result from sample bias. Seventeen Agama strains had been isolated from English badgers at multiple locations in southwest England between 1998 and 2016 (Supplemental Fig. S5B) and stored at APHA. Eleven of them were in HC100_2433. However, rather than being interspersed among the initial genomes from badgers, they defined novel microclusters, including HC10_171137 and HC10_171148, which were the most basal clades in HC100_2433 (Fig. 4B). The other six badger isolates were from additional geographical sources and interspersed among human isolates in HC100_299 (Fig. 4B), which had previously not included any badger isolates (Supplemental Fig. S5F). These results show that the diversity of Agama from English badgers is comparable to their diversity within English humans, and that it would be difficult to reliably infer the original host of these clades or the directionality of interhost transmissions. Further observations on microepidemiology of Agama transmissions between hosts and countries are presented in Supplemental Material.

29EnteroBase automatically scours sequence read archives for Illumina short reads from cultivated isolates, assembles their genomes, and publishes draft assemblies that pass quality control. In October 2019, EnteroBase had assembled more than 1300 genomes of Y. pestis, including genomes that had already been assigned to population groups, other recently sequenced genomes from central Asia, and numerous unpublished genomes from Madagascar and Brazil. EnteroBase does not upload assembled genomes, for which adequate, automated quality control measures would be difficult to implement. However, EnteroBase administrators can upload such genomes after ad hoc assessment of sequence quality, and EnteroBase contains standard complete genomes such as CO92 and other genomes used to derive the Y. pestis phylogeny.

30EnteroBase also does not automatically assemble genomes from metagenomes containing mixed reads from multiple taxa, but similar to complete genomes, administrators can upload reconstructed ancient genomes derived from SNP calls against a reference genome.

31The number of publications describing ancient Y. pestis genomes has increased over the last few years as ancient plague has been progressively deciphered. The metagenomic short reads used to reconstruct these genomes are routinely deposited in the public domain, but the reconstructed ancient genomes are not. This practice has made it difficult for non-bioinformaticians to evaluate the relationships between ancient and modern genomes from Y. pestis. However, EnteroBase now provides a solution to this problem.

32The EnteroBase EToKi calculation package (Supplemental Code) can reconstruct an ancient genome assembly by unmasking individual nucleotides in a fully masked reference genome based on reliable SNP calls from metagenomic data (Supplemental Fig. S6). We ran EToKi on 56 published ancient metagenomes containing Y. pestis, and the resulting assemblies and metadata were uploaded to EnteroBase. EnteroBase users can now include those ancient genomes together with other reconstructed genomes and modern genomic assemblies in a workspace of their choice and use the EnteroBase SNP dendrogram module to calculate and visualize a maximum-likelihood tree (of up to a current maximum of 200 genomes).

33Figure 5 presents a detailed overview of the genomic relationships of all known Y. pestis populations from pandemic plague over the last 5500 years, including hundreds of unpublished modern genomes. This tree was manually annotated using a User-defined Field and Custom View with population designations for reconstructed ancient genomes that are consistent with the literature on modern isolates. We also assigned consistent population designations to additional modern genomes from central Asia and elsewhere. An interactive version of this tree and all related metadata in EnteroBase is publicly available (http://enterobase.warwick.ac.uk/a/21977/g), thus enabling its detailed interrogation by a broad audience from multiple disciplines and providing a common language for scientific discourse.

34Escherichia coli has long been one of the primary workhorses of molecular biology. Most studies of Escherichia have concentrated on a few well-characterized strains of E. coli, but the genus Escherichia includes other species: E. fergusonii, E. albertii, E. marmotae, and E. ruysiae. E. coli itself includes the genus Shigella, which was assigned a distinctive genus name because it causes dysentery. Initial analyses of the phylogenetic structure of E. coli identified multiple deep branches, called haplogroups, and defined the EcoR collection, a classical group of 72 bacterial strains that represented the genetic diversity found with multilocus enzyme electrophoresis. The later isolation of environmental isolates from lakes revealed the existence of “cryptic clades” I–VI which were distinct from the main E. coli haplogroups and the other Escherichia species. Currently, bacterial isolates are routinely assigned to haplogroups or clades by PCR tests for the presence of variably present genes from the accessory genome or by programs that identify the presence of those genes in genomic sequences.

35Legacy MLST is an alternative scheme for subdividing Escherichia, which includes the assignment of STs to ST Complexes. Several ST Complexes are common causes of invasive disease in humans and animals, such as ST131, ST95 Complex, and ST11 Complex (O157:H7). The large number of Escherichia genomes in EnteroBase (Table 1) offered the opportunity to reinvestigate the population structure of Escherichia on the basis of the greater resolution provided by cgMLST and within the context of a much larger and more comprehensive sample. In 2018, EnteroBase contained 52,876 genomes. To render this sample amenable to calculating a maximum-likelihood (ML) tree of core SNPs, we selected a representative sample consisting of one genome from each of the 9479 Escherichia rSTs. In homage to the EcoR collection, we designate this as the EcoRPlus Collection.

36Homologous recombination is widespread within E. coli. We therefore anticipated that a phylogenetic tree of core genomic differences in EcoRPlus would be “fuzzy,” and that ST Complexes and other genetic populations would be only poorly delineated. Instead, considerable core genome population structure is visually apparent in a RapidNJ tree based on pairwise differences at cgMLST alleles between the EcoRPlus genomes (Fig. 6). The most predominant, discrete sets of node clusters were also largely uniform according to cgMLST HC1100 hierarchical clustering. Furthermore, assignments to HC1100 clustering were also largely congruent with ST Complexes based on legacy seven-gene MLST (Supplemental Fig. S7). With occasional exceptions (arrows), the tree topology was also consistent with Clermont typing (Supplemental Fig. S8; Supplemental Material).

37Figure 6 may represent the first detailed overview of the genetic diversity of the core genome of Escherichia. Real-time examination of its features (http://enterobase.warwick.ac.uk/a/15981) is feasible because the GrapeTree algorithm can handle large numbers of cgSTs. Nodes can be readily colored by metadata or experimental data (Supplemental Figs. S7, S8), and GrapeTree also readily supports analyses of subtrees in greater detail. However, although cgMLST allelic distances are reliable indicators of population structures, SNPs are preferable for examining genetic distances. We therefore calculated a ML tree of the 1,230,995 core SNPs within all 9479 genomes (Supplemental Fig. S9). This tree confirmed the clustering of the members of HC1100 groups within E. coli, and also showed that the other Escherichia species and cryptic clades II to VIII formed distinct long branches of comparable lengths (Supplemental Fig. S9 inset).

38EnteroBase was originally developed as a genome-based successor to the legacy MLST websites for Escherichia, Salmonella, Yersinia pseudotuberculosis, and Moraxella catarrhalis. Its underlying infrastructure is sufficiently generic that EnteroBase was readily extended to Clostridioides, Helicobacter, and Vibrio, and could in principle be extended to other taxa.

39EnteroBase was intended to provide a uniform and reliable pipeline that can assemble consistent draft genomes from the numerous short-read sequences in public databases and to link those assemblies with metadata and genotype predictions. It was designed to provide access to an unprecedentedly large global set of draft genomes to users at both extremes of the spectrum of informatics skills. A further goal was to provide analytical tools, such as GrapeTree, that could adequately deal with cgMLST from more than 100,000 genomes, and Dendrogram, which generates phylograms from nonrepetitive core SNPs called against a reference genome. Still another important goal was to support private analyses by groups of colleagues, with the option of subsequently making those analyses publicly available. Case Study 1 illustrates how EnteroBase can be used for all of these tasks, and more.

40EnteroBase has expanded beyond its original goals and is morphing in novel directions. It has implemented HierCC for cgMLST, which supports the automated recognition of population structures at multiple levels of resolution (Case Study 1), and may help with the annotation of clusters within phylogenetic trees (Case Study 2; see below). EnteroBase has also been extended to support analyses of metagenomic data from ancient genomes by implementing a subset of the functionality of SPARSE within the stand-alone EToKi package. Case Study 2 illustrates this capability for Y. pestis. Additional EnteroBase databases are under development for ancient and modern genomes of S. enterica and biofilms within dental calculus. EnteroBase has also shown its capacities for providing overviews of the core genome diversity of entire genera, with currently extant examples consisting of Salmonella and Escherichia (Case Study 3).

41EnteroBase is already being used by the community to identify genetically related groups of isolates, and HierCC has been used to mark international outbreaks of S. enterica serovar Poona and E. coli O26. Case Study 1 illustrates how to explore HierCC genomic relationships at multiple levels, ranging from HC2000 (superlineages) for intercontinental dispersion down to HC5-10 for detecting local transmission chains.

42Case Study 1 confirms that although S. enterica serovar Agama is rare, it has been isolated from multiple hosts and countries and is clearly not harmless for humans. The results also document that an enormous sample bias exists in current genomic databases because they largely represent isolates that are relevant to human disease from a limited number of geographic locations.

43Case Study 1 may also become a paradigm for identifying long-distance chains of transmission between humans or between humans and their companion or domesticated animals: Four Agama isolates in the HC5_140035 cluster from France (human) and Austria (frozen chives and a human blood culture) differed by no more than five of the 3002 cgMLST loci. These isolates also differed by no more than five nonrepetitive core SNPs. Similar discoveries of transmissions of E. coli between humans and wild birds are described below. We anticipate that large numbers of such previously silent transmission chains will be revealed as EnteroBase is used more extensively.

44Case Study 2 illustrates how EnteroBase can facilitate combining reconstructed genomes from metagenomic sequences with draft genomes from cultured strains. In this case, the metagenomes were from ancient tooth pulp that had been enriched for Y. pestis, and the bacterial isolates were modern Y. pestis from a variety of global sources since 1898. The resulting phylogenetic tree (Fig. 5) presents a unique overview of the core genomic diversity over 5000 years of evolution and pandemic spread of plague, which can now be evaluated and used by a broad audience. This tree will be updated at regular intervals as additional genomes or metagenomes become available.

45The manual population designations in Figure 5 are largely reflected by HC10 clusters. However, it is uncertain whether the current HierCC clusters would be stable with time because they were based on only 1300 Y. pestis genomes. EnteroBase will therefore maintain these manual annotations in parallel with automated HierCC assignments until a future date when a qualified choice is possible.

46Case Study 3 defines the EcoRPlus Collection of 9479 genomes, which represents the genetic diversity of 52,876 genomes. It is a worthy successor of EcoR, which contained 72 representatives of 2600 E. coli strains that had been tested by multilocus enzyme electrophoresis in the early 1980s. The genomic assemblies and known metadata of EcoRPlus are publicly available (http://enterobase.warwick.ac.uk/a/15931) and can serve as a reference set of genomes for future analyses with other methods.

47Visual examination of an NJ tree of cgMLST allelic diversity color coded by HierCC HC1100 immediately revealed several discrete E. coli populations that have each been the topics of multiple publications (Fig. 6). These included a primary cause of hemolytic uremic syndrome (O157:H7), a common cause of invasive disease in the elderly (the ST131 Complex), as well as multiple distinct clusters of Shigella that cause dysentery. However, it also contains multiple other discrete clusters of E. coli that are apparently also common causes of global disease in humans and animals, but which have not yet received comparable attention. The annotation of this tree would therefore be a laudable task for the entire scientific community interested in Escherichia. We also note that HierCC is apparently a one stop, complete replacement for haplogroups, Clermont Typing, and ST Complexes, some of whose deficiencies are also illustrated here.

48This case study also opened up new perspectives during the review phase of this paper, such as how EnteroBase could be used for the analysis of interhost transmission of antimicrobial resistance (AMR). Seagulls often carry E. coli that are resistant to multiple antibiotics and can transmit those bacteria to other seagulls, including at multiple sites in a small area of Alaska between which seagulls flew on a daily basis. We were therefore not surprised to find that some E. coli isolates from seagulls at those locations were associated within HC5 hierarchical clusters. We then searched for transmissions of HC5 clusters between seagulls and other hosts. EnteroBase contained 406 E. coli genomes from seagulls, distributed over 322 HC5 clusters. Of those clusters, four contained E. coli strains isolated from other hosts (Supplemental Table S5), including chickens, crows, swine, and humans. The dates of isolation of those isolates ranged over about 4 yr, and their geographical locations were separated by long distances: Alaska–New York; Alaska–Michigan; Tasmania–continental Australia. As indicated above, HC5 clusters in Salmonella are associated with recent transmission chains between badgers and across European borders. These additional observations suggest that E. coli from diverse ST Complexes which encode AMR have also been recently transmitted between humans and wild birds and domesticated animals.

49This user's guide provides an overview of what EnteroBase can do now. With time, we hope to include additional, currently missing features, such as community annotation of the properties of bacterial populations, predicting antimicrobial resistance/sensitivity, and distributing core pipelines to multiple mirror sites. However, EnteroBase is already able to help a broad community of users with a multitude of tasks for the selected genera it supports. More detailed instructions are available in the online documentation (https://enterobase.readthedocs.io/en/latest/), and questions can be addressed to the support team (enterobase@warwick.ac.uk).

50Supplemental Figure S5B provides a geographical overview of the area in Woodchester, Gloucestershire, in which badger setts and social groups were investigated in 2006–2007. This area has been subject to a multidecade investigation of badger mobility and patterns of infection with Mycobacterium bovis. According to the standard protocol for that study, badgers were subjected to routine capture using steel mesh box traps baited with peanuts, examination under anesthesia, and subsequent release. Fecal samples were cultivated at University of Liverpool after selective enrichment (Rappaport–Vassiliadis broth and semisolid agar), followed by cultivation on MacConkey agar. Lactose-negative colonies that swarmed on Rappaport–Vassiliadis agar but not on nutrient agar, and were catalase-positive and oxidase-negative, were serotyped by slide agglutination tests according to the Kauffmann and White scheme (Issenhuth-Jeanjean et al. 2014). Additional isolates from badgers from the geographical areas in England that are indicated in Supplemental Figure S5D–F were collected during routine investigations of animal disease at the APHA.

51At University of Warwick, Salmonella were cultivated, and DNA was purified by automated procedures as described. Paired-end 150-bp genomic sequencing was performed in multiplexes of 96–192 samples on an Illumina NextSeq 500 using the High Output Kit v2.5 (FC-404-2002) according to the manufacturer's instructions. Other institutions used their own standard procedures. Metadata and features of all 344 genomes in Figure 4 are publicly available in EnteroBase in the workspace “Zhou et al. All Agama strains” (http://enterobase.warwick.ac.uk/a/21320).

52Metagenomic reads from ancient samples may contain a mixture of sequence reads from the species of interest as well as from genetically similar taxa that represent environmental contamination. To deal with this issue and remove such nonspecific reads after extraction with the EToKi prepare module, the EToKi assemble module can be used to align the extracted reads after comparisons with an ingroup of genomes related to the species of interest and with an outgroup of genomes from other species. In the case of Figure 5, the ingroup consisted of Y. pestis genomes CO92 (2001), Pestoides F, KIM10+ and 91001, and the outgroup consisted of Y. pseudotuberculosis genomes IP32953 and IP31758, Y. similis 228, and Y. enterocolitica 8081. Reads were excluded which had higher alignment scores to the outgroup genomes than to the ingroup genomes. Prior to mapping reads to the Y. pestis reference genome (CO92) (2001), a pseudogenome was created in which all nucleotides were masked to ensure that only nucleotides supported by metagenomic reads would be used for phylogenetic analysis. For the 13 ancient genomes whose publications included complete SNP lists, we unmasked the sites in the pseudogenomes that were included in the published SNP lists. For the other 43 genomes, EToKi was used as in Supplemental Figure S6 to map the filtered metagenomic reads onto the pseudogenome with minimap2, evaluate them with Pilon, and unmask sites in the pseudogenome that were covered by three or more reads and had a consensus base that was supported by ≥80% of the mapped reads. All 56 pseudogenomes were uploaded to EnteroBase together with their associated metadata.

53The Illumina sequence reads for 161 new genomes of S. enterica serovar Agama generated in this study have been submitted to the European Nucleotide Archive database (ENA; https://www.ebi.ac.uk/ena) under study accession numbers ERP114376, ERP114456, ERP114871, and ERP115055. The genomic properties, metadata, and accession codes for the 329 genomic assemblies in HC2000_299 are summarized in Supplemental Table S3 and in Online Table 1 (https://wrap.warwick.ac.uk/128112). The metadata, genomic assemblies, and annotations are also available from the publicly available workspace “Zhou et al. All Agama Strains” (http://enterobase.warwick.ac.uk/a/21320). The EToKi package and its documentation are accessible at https://github.com/zheminzhou/EToKi and as Supplemental Code. EnteroBase documentation is accessible at https://enterobase.readthedocs.io/en/latest/. An interactive version of Figure 3 is available at http://enterobase.warwick.ac.uk/a/24006. Trees presented in Figure 4A,B are available separately at http://enterobase.warwick.ac.uk/a/21773/d and http://enterobase.warwick.ac.uk/a/23882/d, respectively. An interactive version of Figure 5 is available at http://enterobase.warwick.ac.uk/a/21977/g. The MicroReact projects of Supplemental Figure S5A,B are available at https://microreact.org/project/t7qlSSslh/3e634888; Supplemental Figure S5C,D at https://microreact.org/project/9XUC7i-Fm/fed65ff5, and Supplemental Figure S5E,F at https://microreact.org/project/XaJm1cNjY/69748fe3. The tree shown in Figure 6 as well as Supplemental Figures S7, S8 are available at http://enterobase.warwick.ac.uk/a/15981.

54Derek Brown,3 Marie Chattaway,4 Tim Dallman,4 Richard Delahay,5 Christian Kornschober,6 Ariane Pietzka,6 Burkhard Malorny,7 Liljana Petrovska,8 Rob Davies,8 Andy Robertson,9 William Tyne,10 François-Xavier Weill,11 Marie Accou-Demartin,11 Nicola Williams,12