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OPEN Whole genomes from bacteria

Data Descriptor collected at diagnostic units
around the world 2020
Sidsel Nag et al.#

The Two Weeks in the World research project has resulted in a dataset of 3087 clinically
relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in
35 countries around the world during 2020. A relational database is available with metadata
and summary data from selected bioinformatic analysis, such as species prediction and
identification of acquired resistance genes.

Background & Summary

Acquiring resistance-conferring genes is one of a number of mechanisms that can cause bacterial pathogens to
become resistant to antimicrobial therapies1. Resistance genes can be located either chromosomally or on mobile
genetic elements, such as plasmids2. Mobile genetic elements, in turn, can be horizontally transferred within
bacterial communities and therefore play a key role in the geographic spread of antimicrobial resistance (AMR).
Surveillance and monitoring of antimicrobial resistance are of high priority in many national and supra-national
health organisations3–8. These efforts are highly motivated by a need to assess the size of the AMR problem, and
help provide policy guidance on how to best ensure effective treatment and limit the further spread and devel-
opment of AMR.
The presented dataset was collected and processed as part of a research project entitled “Two Weeks in the
World” (TWIW), led by the Technical University of Denmark (DTU). The main purpose of the research project
was to assess the species diversity and resistance gene abundance in clinically relevant pathogens across the
world, in 2020. Diagnostic units involved in diagnosing causative pathogens of clinical infections (i.e. patients
presenting with symptoms) from around the world, were invited to join the study. In total, 35 different countries
are represented through 59 different diagnostic units. Figure 1 depicts the countries represented in the study.
Summary descriptions of the dataset are depicted in Fig. 2.
Partners (i.e. diagnostic units) participated by sending either bacterial isolates or DNA extracted from bac-
terial isolates to Denmark (DTU). Here, isolates were cultured and DNA was extracted. All DNA (extracted by
partners or by DTU) was used for whole genome sequencing (WGS) on an Illumina-based platform. Minimal
metadata was required for all samples and “nice-to-know” metadata was provided by partners who were able to
do so. WGS data was used to perform bioinformatic species prediction of the bacterial pathogens, identification
of acquired resistance genes and inferring distance-based phylogeny. Figure 3 depicts an overview of the project
pipeline and framework.
The TWIW research project can be visited through the web app: https://twiw.genomicepidemiology.org.
The website allows browsing genomic insights such as phylogenetic trees.
The MySQL database is available as a “data dump“ via DTU Data https://doi.org/10.11583/DTU.217584569
and the raw sequencing data (fastq) is available on ENA (ERP141886)10. The MySQL database contains infor-
mation about ENA accession numbers for the sequencing data. Combined, these resources represent a complete
dataset of 3087 validated bacterial genomes of clinical relevance, collected across the globe in 2020. Everything
from sample origin, sequencing information, identified species, identified resistance genes, phylogenetic rela-
tionships is available and navigable through implemented relationships and table documentation in the MySQL
database.

#
A full list of authors and their affiliations appears at the end of the paper.

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Fig. 1 Country representation. The countries represented in the study are shown with colour coding according
to the WHO-defined regions they belong to.

Methods
Preparation of partners to collect samples. Partners registered for participation by contributing isolates
or DNA samples to the study. Material was sent to partners according to their registered participation format.
This included material for sample collection, metadata registration, DNA extraction and sample shipment to
Denmark. Specific protocols were provided, according to the registered participation format and a video for part-
ners sampling isolates was made available via the TWIW web application and YouTube.

Sample collection. Ethical considerations. Partners were in charge of navigating national guidelines and
regulations regarding ethical approval (such as institutional review boards, ethical review boards or other) of their
participation in the study. The Danish National Scientific Ethics Committee was consulted with regards to The
Technical University of Denmark leading the study, and based on their assessment of the study protocol, the com-
mittee concluded that the samples were not human and therefore the study did not require ethical approval. No
patient material was transferred with the samples, and no patient identifiers were shared with the project. Only
minimal metadata pertaining to the infection and bacterial isolates or their DNA were sampled.

Isolate selection. Partners collected samples according to their availability to do so, during 2020. Due to the
obstacles presented by the Covid-19 pandemic, ability to participate and carry out sampling was prioritised over
sampling during a specific time (original study design and planning targeted sampling during March 2020).
Approximately 60 samples were collected at each individual diagnostic unit over a week. Table S1 lists the
participating units with their study ID, country and city of origin, the month of collection, the amount of sam-
ples sent, whether the samples received were isolates or DNA and whether the unit made alterations to the sam-
pling protocol. The 60 samples were to be randomly selected at the diagnostic units over the course of a week.
Targeting sampling over all weekdays served the purpose of avoiding “logistical bias” from the internal logistics
of the diagnostic unit. Targeting random sampling served the purpose of not targeting specific species or sample
source types (i.e. urine samples, blood samples). Partners did “prospective random sampling” by estimating
how many samples to collect every day over the course of a week, in order to collect approximately 60 samples
over a week. Due to lack of diagnostic activities related to bacterial infections, a number of units prolonged the
sampling time where simply all samples were included in the study, until 60 samples were acquired or sampling
was halted due to other reasons.

Isolate sampling. Coal swabs were used to swab from the plates on which the pathogen was cultured — a video
illustrating the isolate sampling procedure can be viewed via this link. Parafilm was strapped around the lid of
the coal swab for extra sealing. Coal swabs were kept dark, at 4 °C or room temperature if 4 °C storage was not
available. Swabs were stored until shipment was possible for partners.

DNA sampling. For partners extracting DNA, material corresponding to the DNA extraction kit and meth-
odology used at DTU was provided to partners (DTU DNA extraction procedure is described under “DNA
extraction and library preparation”). Partners were asked to provide at least 50 µl of eluted DNA, or at least 80 µl
if the measured concentrations were <6 ng/µl.

Metadata registration. Metadata sheets were provided for all partners, together with labels with printed sample
names, unique to each sampling location. Labels were for application on the samples (coal swabs or tubes with DNA)

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Fig. 2 Summary description of samples in the dataset. (a) Number of genera identified in the dataset and
accounting for the 90 percent majority groups in the dataset, (b) major pathogen-source combinations
accounting for the majority of the dataset and (c) Area depiction of 9 major genera (black circles) and
represented species (grey circles) in the dataset.

Fig. 3 Project pipeline and framework – tasks in green were performed by DTU and tasks in yellow were
performed by partners. DNA extraction was performed by some partners, who could not dispatch swabs.

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Mandatory metadata “Nice-to-know” metadata

Geographical origin Age of patient
Date of sampling from patient Gender of patient
Date of sampling from lab Hospital- or community-acquired infection
Suspected pathogen Disease (reason for seeking health-care)
Sample source type AMR profile as assessed by partner
Antibiotic use history from 4 weeks prior to sampling

Table 1. Metadata variables.

and pertaining metadata sheets. Metadata sheets were for use in a laboratory setting, where metadata could not
be recorded electronically from other lab records. The collected metadata was subsequently submitted electron-
ically via Survey Monkey or in excel format for most partners. Few partners sent only the handwritten metadata
sheets. The metadata variables are listed in Table 1. Under no circumstances were internal patient identifiers
(ids) or other references to individuals shared for the project.

Sample shipment. Shipping isolates. Isolates were shipped as UN3373 – biological sample category B. All
coal swabs were put into absorptive pockets and into a zip lock bag labelled “UN3373”. The bag was placed in a
shipment box labelled UN3373, together with any metadata sheets (these were also submitted electronically for
the majority of samples). Shipment was performed by DHL, as “Medical Express” or ordinary parcel, depending
on the options for the departure location. A single parcel was shipped by World Courier, from Mozambique to
Denmark.

Shipping DNA. DNA samples were stored in Eppendorf tubes and sealed again with Parafilm. The tubes were
placed in an 84-compartment foldable freezer box and placed in a bubble-wrap envelope. All DNA samples were
shipped as ordinary parcels or letters, without cold chain.
Sample handling and processing. Logging of received samples. Upon arrival in Denmark, samples were
logged together with received metadata. Validation of the metadata was performed prior to database submission.
Validation of metadata is explained in detail under “Technical Validation”. Logging entailed entering sample
names (as written on the labels provided to partners), registration of unique sample id’s, original as well as vali-
dated metadata and processing information with regards to culturing and freezing of isolates. Once validated, all
information resulting from logging samples and their metadata was submitted to the MySQL database.

Culturing of received isolates. Isolates received on coal swabs were cultured on blood agar or chocolate agar, in
presence of CO2 if necessary, and sub-cultured until the expected (as submitted by sampling partner) species
were (presumedly) isolated (visual recognition by experienced laboratory professionals). In doubt of which
species to go forward with, multiple isolates were brought forward for DNA extraction and sequencing and the
correct isolate was decided upon after bioinformatic species prediction.

®
DNA extraction and library preparation. DNA was extracted using Qiagen DNeasy Blood & Tissue kit (Qiagen,
Venlo, Netherlands) according to manufacturer’s protocol. DNA concentrations were measured on Qubit using
Invitrogen’s Qubit dsDNA high-sensitivity (HS) assay kit (Carlsbad, CA, USA). DNA concentrations were diluted
to approximately 0.2 ng/µl for library preparation. Libraries were prepared according to the Illumina NexteraXT
DNA Library Prep Reference Guide (Illumina, Inc., San Diego, CA, USA) using standard normalisation.

Sequencing. All samples, except eight, were sequenced on an Illumina NextSeq 500 platform, paired-end
sequencing, medium output flowcell (NextSeq500/550 Mid Output Kit v2.5 300 cycles, Cat. nr 20024905).
Gram-negative samples were run 96 isolates in parallel, and Gram-positive samples were run 192 isolates in
parallel. Few flow cells were run with mixed Gram-negative and Gram-positive samples with approximately
100 samples on a single flow cell. Eight samples were sequenced on an Illumina MiSeq platform, paired-end
sequencing, 500 cycles (2 × 251) on a V3 flowcell.

Data processing and analytics. Sequencing data was downloaded from BaseSpace (Illumina’s customer cloud
platform) and transferred to the Danish National Supercomputer for Life Sciences11, a high-performance com-
puting cluster, where it was both stored and processed, and all downstream analytics took place.

Raw read quality control (QC). An in-house bioinformatics pipeline, called FoodQCPipeline v. 1.512, was used
at default settings to quality assess the raw sequence data, trim the raw reads according to predefined qual-
ity thresholds and perform de-novo assembly on the genomes. The quality assessment and trimming of raw
sequencing data is further described under “Technical Validation”. Given the ‘–spades’ option, FoodQCPipeline
performs de-novo assembly with SPAdes v. 3.11.013. After running the FoodQCPipeline, both trimmed fastq
data and fasta (draft assemblies) are available for downstream analyses. QC summary data was submitted to the
MySQL database after genome validation, which is explained in detail under “Technical Validation”.

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Species prediction with KmerFinder v. 3.0.2. KmerFinder14, was used as one of two species prediction pro-
grams. KmerFinder assesses species identity by matching k-mers from the query sequence to a kmer-based
database of reference strains. KmerFinder was run on the draft assemblies with default settings, the evaluation
was done on total query coverage, which is calculated as the number of unique k-mers shared between the query
and the template, divided by the number of unique k-mers in the query, with the first hit being accepted if it had
more than 80% total query coverage.

Species prediction with rMLST. The other species prediction software used, was rMLST15. In contrast to
KmerFinder, rMLST identifies species based only on ribosomal multi-locus sequence typing, which includes
the 53 genes that encode subunits of the bacterial ribosome. rMLST was run on assembled genomes through the
open access API at https://pubmlst.org/species-id/species-identification-via-api. The first hit was accepted if it
had more than 90% support.

Final species identification. The conclusion of the in silico identified species was based on either species or
genus level concordance between the top hits for KmerFinder and rMLST, or an acceptable hit from only one
of the two software. The point of using two different species prediction software was to allow for a sensitive
assessment of whether the genomes were contaminated (KmerFinder), while complementing with a more robust
but less sensitive species prediction software (rMLST). Species that could not be exactly identified are given as
NA, if the genome was validated. The genome validation is described under “Technical Validation”. As with QC
summary data, species prediction data was submitted to the MySQL database upon genome validation, and
concordance between the KmerFinder and rmlst is given.

Identification of resistance-conferring genes with ResFinder 4.1. In order to identify acquired resistance genes
in the validated bacterial genomes, ResFinder version 4.116 was run on the assemblies. All samples were run
with the ‘-s “other”’ option, meaning that the samples were not run as specific species. ResFinder has the option
to run the samples as specific species, in which case a secondary program, PointFinder, is run. This analysis is
omitted when running as ‘-s “other”’, and allows for complete cross-comparability of the output data resulting
from our in-house ResFinder summary script, which in this case only encompasses “acquired” resistance genes.
The ResFinder summary script produces different overviews of the ResFinder data, with both a class level and a
drug level overview of acquired resistance genes, as well as the query coverage, percent identity to reference and
position in the assembly of the hit. The ResFinder summary script is submitted as supplementary material, and
is available as Supplementary file 1

Phylogeny. Genetic distance-based phylogeny was inferred for sequencing runs that passed the technical valida-
tion (see below), using Evergreen COMPARE17–19 (commit b512e6e). The reference database was the complete bac-
terial chromosomal genomes from the refseq collection of National Center for Biotechnology Information (NCBI),
last fetched in April 2021, homology reduced to 98 percent sequence identity, using kma_index from KMA with
the settings for homology reduction -hr 0.769 and -ht 0.769. Consequently, the threshold for accepting a matching
reference was also lowered to 98% (76.90% k-mer identity), and the inclusion criterium for consensus sequence
completeness reduced to 80%. For displaying the phylogenies on the website, a custom script (Supplementary file 2)
was used to select the minimum amount of phylogenetic trees that in totality contained all possible samples.

Data Records
The dataset consists of:

1. Raw sequence reads available at ENA: Accession ERP14188610

2. One MySQL database (available as MySQL data dump) for download at DTU Data, https://doi.org/
10.11583/DTU.21758456 (URL: https://doi.org/10.11583/DTU.21758456.v2)9
3. One web application for browsing the data and selected findings, available at TWIW web app (URL: http://
twiw.genomicepidemiology.org)

The Technical University of Denmark has acted as data brokers to the partners. Data brokering is the act of
submitting data on behalf of another institute. This was done to ascertain that the partners would be properly
referenced when the data is reused for other purposes in the future.
The MySQL database contains metadata and summary output data as well as information regarding the
generation of the analysis output.

Technical Validation
The technical validation of the dataset consists of:

1. Validation of the acquired metadata for the samples

2. Quality controlling the raw sequencing data
3. Genome validation in order for genomes to be accepted in the final dataset
4. Identification of the “correct” bacterial isolate, if several isolates were cultured from a single swab

Validation of acquired metadata for the samples. The vast majority of partners only provided man-
datory metadata (see Table 1). Metadata was submitted either via Survey Monkey, through e-mail as digital

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spreadsheets, or simply by sending the handwritten metadata sheets. If the information given could not be val-
idated, no validated data was registered, in which case it is omitted from down-stream analysis. The following
validations were applied to the metadata:

• Geographical origin of sample identifiable via openstreetmap.org

• Species and genus information separated, according to validated nomenclature
• Date according to specific date format (yyyy-mm-dd)
• Sample source type according to 3 validated lists: 1) type of sample, 2) anatomical origin and 3) other source
indicator
• Age according to specific format (age in years)
• Gender according to specific format (‘f ’, ‘m’, ‘o’)
• Hospital- or community acquired infection according to specific format (‘h’ or ‘c’)

Quality controlling the raw sequencing data. FoodQCPipeline trims the raw reads using bbduk 2 (part
of BBMap version 36.4920), according to three criteria: (1) the length of the read must be >50 bp, (2) phred score
per base must be >20 and (3) adapters must be filtered away. FoodQCPipeline uses FastQC v. 0.11.5 to generate
a quality control report for every sample.

Genome validation. The genome validation consists of two assessments: sequencing QC and genome con-
tamination. The process is depicted in Fig. 4.
Based on the quality control reports generated by FoodQCPipeline, samples were discarded at the prelim-
inary quality assessment, if the raw data did not live up to any of four criteria: (1) >100 mega bp after quality
trimming, (2) depth of coverage >20X, (3) N50 > 15,000 bp and (4) <500 contigs in the assembly (unless the
species prediction was a Pseudomonas spp., in which case up to 1098 contigs were accepted). If any of the four
criteria were not met, a QC alert would be given and the genome would fail validation.
Genome contamination was assessed by the following 3 criteria:

1. the 1st KmerFinder hit had >80% total query coverage

2. that the 2nd KmerFinder hit had < than 80% total query coverage
3. that the 1st rMLST hit had >90% support.

If any of these criteria were not met, a contamination alert was given for the sample and the genome valida-
tion failed. However, in the case of a KmerFinder-based contamination alert, the genome could be validated if
the rMLST 1st hit had >95% support.
All failed genomes were assessed manually afterwards, and in certain cases a genome could be manually val-
idated based on various assessments. Reasons for manual validations (and failures) are indicated in the dataset.

Identification of the correct bacterial isolate. When several bacterial isolates were cultured from a
swab, the trained laboratory professionals attempted to correctly identify the suspected species by visual recog-
nition. When in doubt, all isolates were brought forward for sequencing and bioinformatic analyses. In the case
where one of the samples was in agreement with the suspected pathogen, this isolate was kept in the final dataset
with the pertaining metadata. In the case where none of the isolates matched the suspected pathogen, they were
all (typically two) kept in the final dataset with pertaining metadata and were given an “A” and “B” suffix in the
sample name, but registered with unique ids.

Exclusion reasons. Through the process from receiving samples to validating the genomes for the final
dataset, reasons for samples to be excluded were:

• sample missing (some samples are registered as being received, because they were registered in the partner’s
metadata, however the sample was never received/recovered)
• alternative isolate (if several isolates were cultured from a swab and another isolate matched the suspected
pathogen)
• out of scope (if an isolate turned out to be something not bacteria (e.g. fungi))
• not viable
• not isolatable (typically due to insurmountable Proteus spp. contamination)
• contaminated with fungi (a bacterial pathogen was also present, but could not be isolated from the fungal
contamination)
• x-isolate (if several isolates were cultured from a swab but the suspected pathogen was assumed visually iden-
tified and brought forward, the remaining are x-isolates)
• lab material test (if a sample was registered multiple times, simply because it was used to test laboratory
material)
• not enough DNA (partners sending extracted DNA didn’t always send adequate amounts of DNA)
• contamination with no original isolate available (partners sending DNA may have sent DNA which was con-
taminated – in this case the original isolate could not be regrown and re-isolated)

A total 182 samples were excluded based on these reasons.

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Fig. 4 Schematic of the genome validation process employed in the qc_species_parser_v3.py.

Usage Notes
No unvalidated genomes have been submitted to ENA, and therefore it should be “safe” for data users to apply
these genomes in bioinformatic analyses. The MySQL database, however, contains information regarding all
received samples. Some samples could not be regrown in the laboratory in Denmark, and some DNA extracted
by partners was contaminated and could not be re-extracted in Denmark, because the original isolate was not
available. However, the metadata in the “sample” table in the mySQL still has information regarding what types
of samples were collected from which places, as well as the suspected genus and species of the samples - even
though the pertaining genomes do not exist on ENA.

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Code availability
The software used to generate the dataset is openly available either through their respective repositories
linked under “Methods”, or for custom scripts, in the code repository of the project: https://bitbucket.org/
genomicepidemiology/twiw_utilities/ as well as Supplementary files 1 and 2.

Received: 16 March 2023; Accepted: 23 August 2023;

Published: xx xx xxxx

References
1. Reygaert, W. C. An overview of the antimicrobial resistance mechanisms of bacteria. Aims Microbiology 4, 482–501, https://doi.
org/10.3934/microbiol.2018.3.482 (2018).
2. Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. Clinical
Microbiology Reviews 31, e00088–17, https://doi.org/10.1128/CMR.00088-17 (2018).
3. Antimicrobial resistance in g7 countries and beyond: policy brief. https://www.oecd.org/els/health-systems/Antimicrobial-
Resistance-in-G7-Countries-and-Beyond-Policy-Brief.pdf Last accessed April 2022 (2015).
4. Global action plan for antimicrobial resistance. https://www.who.int/publications/i/item/9789241509763 Last accessed April 2022
(2016).
5. Drug-resistant infections; a threat to our economic future. https://documents.worldbank.org/curated/en/323311493396993758/
pdf/114679-REVISED-v2-Drug-Resistant-Infections-Final-Report.pdf Last accessed April 2022 (2017).
6. Global antimicrobial resistance and use surveillance system (glass). Last accessed April https://www.who.int/initiatives/glass (2022).
7. European antimicrobial resistance surveillance network (ears-net). Last accessed April https://www.ecdc.europa.eu/en/about-us/
partnerships-and-networks/disease-and-laboratory-networks/ears-net (2022).
8. National antimicrobial resistance monitoring system for enteric bacteria (narm). Last accessed April https://www.cdc.gov/narms/
index.html (2022).
9. Nag, S. et al. TWIW database dump, DTU Data, https://doi.org/10.11583/DTU.21758456.v2 (2023).
10. Two weeks in the world 2020, ena accession erp141886 https://www.ebi.ac.uk/ena/browser/view/PRJEB56918 (2022).
11. Denmark’s national life science supercomputing center. Last accessed April https://computerome.dtu.dk (2022).
12. Foodqcpipeline v. 1.5. Last accessed April https://bitbucket.org/genomicepidemiology/foodqcpipeline/src/master/ (2022).
13. Bankevich, A. et al. Spades: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of
Computational Biology 19, 455–477, https://doi.org/10.1089/cmb.2012.0021 (2012).
14. Kmerfinder v. 3.0.2. Last accessed April https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/ (2022).
15. Jolley, K. A. et al. Ribosomal multilocus sequence typing: Universal characterization of bacteria from domain to strain. Microbiology
158, 1005–1015, https://doi.org/10.1099/mic.0.055459-0 (2012).
16. Resfinder v. 4.1. Last accessed April https://bitbucket.org/genomicepidemiology/resfinder/src/master/ (2022).
17. Evergreen. Last accessed April https://bitbucket.org/genomicepidemiology/evergreen/src/COMPARE/ (2022).
18. Szarvas, J. et al. Large scale automated phylogenomic analysis of bacterial isolates and the evergreen online platform.
Communications Biology 3, 137, https://doi.org/10.1038/s42003-020-0869-5 (2020).
19. Szarvas, J., Bartels, M. D., Westh, H. & Lund, O. Rapid open-source snp-based clustering offers an alternative to core genome mlst
for outbreak tracing in a hospital setting. Frontiers in Microbiology 12, 636608, https://doi.org/10.3389/fmicb.2021.636608 (2021).
20. Bbmap. Last accessed April https://jgi.doe.gov/data-and-tools/bbtools/ (2022).

Acknowledgements
The authors would like to acknowledge Rolf Sommer Kaas and Thomas Nordahl Petersen for assisting in creating
the necessary in-house data management infrastructure to enable compliance with FAIR and Baptiste Avot with
assistance in data upload. A contribution also goes to Frederik Duus Møller for creating summary scripts for
KmerFinder and ResFinder, enabling easy extraction of summary output from these analyses as well as to Victor
Hyltoft for maintaining the TWIW web app. The authors would also like to acknowledge Ana Rita Bastos Rebelo
for guidance and advice in relation to the assessment of the genomes generated and how to validate these. The
authors would also like to thank Martin Koliba for technical support and expertise related to the development
of the data-sharing infrastructure and partner database and to Christina Aaby Svendsen, Jacob Dyring Jensen,
Michella Oppenheuser, Birthe S. Rosenkvist Lund, Hanne Nørgaard Nielsen & Hanne Mordhorst for assisting
in sample handling and processing in the laboratory. Lastly, the authors thank medical laboratory scientists and
other staff at participating sites that contributed to isolate and data collection.

Author contributions
All authors contributed to generating the dataset. Sidsel Nag, Gunhild Larsen, Frank Møller Aarestrup and Rene
Sjøgren Hendriksen were responsible for project design. Sidsel Nag was responsible for project management
and manuscript drafting. Judit Szarvas, Sidsel Nag and Laura Elmlund Kohl Birkedahl were responsible for
bioinformatic analyses. Gábor Máté Gulyás and Wojciech Jakub Ciok were responsible for building the data-
sharing infrastructure and partner database. Timmie Lagermann was responsible for curating and publishing
the final MySQL database and sequencing data. The authors responsible for the different international sub-
datasets, including sampling and registration of acquired metadata are as follows: Silva Tafaj: Albania, Susan
Bradbury, Peter Collignon and Denise Daley: Australia, Victorien Dougnon and Kafayath Fabiyi: Benin,
Boubacar Coulibaly, Réné Dembélé, Natama Magloire, Isidore Ouindgueta: Burkina Faso, Zenat Zebin Houssain
and Anowara Begoum: Bangladesh, Deyan Donchev: Bulgaria, Mathiew Diggle, LeeAnn Turnbull and Simon
Lévesque: Canada, Sigrid Pranghofer, Kirstine Kobberoe Søgaard: Switzerland, Paula Diaz Guevara: Colombia,
Panagiota Maikanti: Cyprus, Jana Amlerova and Pavel Drevinek: Czech Republic, Milica Dilas and Aachim
Kaasch: Germany, Henrik Torkil Westch: Denmark, Mohamed Azzedine Bachtarzi and Wahiba Amhis: Algeria,
Carolina Elisabeth Satán Salazar and José Eduardo Vilacis: Ecuador, Mária Angeles Dominguez Lúzon and
Dàmaris Berbel Palau: Spain, Claire Duployez and Maxime Paluche: France, Solomon Asante-Sefa: Ghana,
Mie Møller: Greenland, Margaret Ip: Hong Kong, Ivana Mareković: Croatia, Agnes Pál-Sonnevend: Hungary,
Clementina Elvezia Coccuza: Italy, Asta Dambrauskiene: Lithuania, Alexandre Macanze, Anelsio Cossa and
Inácio Mandomando: Mozambique, Philip Nwajiobi-Princewell, Iruka Okeke, Aderemi O. Kehinde, Ini Adebiyi,

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Ifeoluwa Akintayo, Oluwafemi Popoola and Anthony Onipede: Nigeria, Anita Blomfeldt and Nora Elisabeth
Nyquist: Norway, Kiri Bocker and James Ussher: New Zealand, Amjad Ali, Nimat Ullah and Habibullah Khan:
Pakistan, Natalie Weiler Gustafson: Paraguay, Ikhlas Jarrar: Palestine, Arif Al-Hamad: Saudi Arabia, Viravarn
Luvira and Wantana Paveenkittiporn: Thailand, Irmak Baran: Turkey, James Mwansa, Linda Sikakwa and Kaunda
Yamba: Zambia.

Competing interests
The authors declare no competing interests.

Additional information
Supplementary information The online version contains supplementary material available at https://doi.
org/10.1038/s41597-023-02502-7.
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© The Author(s) 2023

Sidsel Nag 1 ✉, Gunhild Larsen1, Judit Szarvas 1, Laura Elmlund Kohl Birkedahl1,

Gábor Máté Gulyás1, Wojchiech Jakub Ciok1, Timmie Mikkel Lagermann1, Silva Tafaj 2,
Susan Bradbury3, Peter Collignon3, Denise Daley4, Victorien Dougnon5, Kafayath Fabiyi5,
Boubacar Coulibaly6, René Dembélé7, Georgette Nikiema7, Natama Magloire8,
Isidore Juste Ouindgueta9, Zenat Zebin Hossain10, Anowara Begum10, Deyan Donchev 11,
Mathew Diggle12, LeeAnn Turnbull12, Simon Lévesque 13, Livia Berlinger14,
Kirstine Kobberoe Sogaard15, Paula Diaz Guevara16, Carolina Duarte Valderrama16,
Panagiota Maikanti17, Jana Amlerova18, Pavel Drevinek19, Jan Tkadlec19, Milica Dilas20,
Achim Kaasch20, Henrik Torkil Westh 21, Mohamed Azzedine Bachtarzi22, Wahiba Amhis22,
Carolina Elisabeth Satán Salazar23, JoséEduardo Villacis24, Mária Angeles Dominguez Lúzon25,
Dámaris Berbel Palau26, Claire Duployez27, Maxime Paluche28, Solomon Asante-
Sefa29, Mie Moller30, Margaret Ip 31, Ivana Mareković32, Agnes Pál-Sonnevend33,
Clementiza Elvezia Cocuzza34, Asta Dambrauskiene35, Alexandre Macanze36,
Anelsio Cossa36, Inácio Mandomando36, Philip Nwajiobi-Princewill37, Iruka N. Okeke 38,
Aderemi O. Kehinde39,40, Ini Adebiyi 38,40, Ifeoluwa Akintayo39, Oluwafemi Popoola39,40,
Anthony Onipede41, Anita Blomfeldt42, Nora Elisabeth Nyquist 42,
Kiri Bocker43, James Ussher 43, Amjad Ali44, Nimat Ullah 44, Habibullah Khan45,
Natalie Weiler Gustafson46, Ikhlas Jarrar47, Arif Al-Hamad48, Viravarn Luvira49,
Wantana Paveenkittiporn50, Irmak Baran51, James C. L. Mwansa52, Linda Sikakwa53,
Kaunda Yamba54, Rene Sjogren Hendriksen1 & Frank Moller Aarestrup1

1
National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark. 2Microbiology
Department, University Hospital “Shefqet Ndroqi”, Rruga Dr. Shefqet Ndroqi. Sauk, Tirana, 1044, Albania.
3
Microbiology Department, Canberra Hospital, Gilmore Cresent, Garran, 2605, Australian Capital Territory,
Australia. 4Department of Microbiology, PathWest Laboratory Medicine, Fiona Stanley Hospital, 9 Robin Warren
Drive, Murdoch, 6150, Western Australia, Australia. 5Research Unit in Applied Microbiology and Pharmacology
of Natural Substances, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01 PO Box, Abomey-
Calavi, 2009, Cotonou, Benin. 6Department of Laboratory, Nouna Health Research Centre, Rue Namory Keita,
Nouna, Burkina Faso. 7Training and Research Unit in Applied Sciences and Technologies/Biochemistry-microbiology,
University of Dedougou, Dedougou, 176, Boucle du Mouhoun, Burkina Faso. 8Clinical Research Unit of Nanoro,
National Institutes of Medical Research, Ouagadougou, 176, Burkina Faso. 9Department, University of Joseph KI-
ZERBO, Street, Ouagadouogou, Burkina Faso. 10Department of Microbiology, University of Dhaka, Dhaka, 1000,
Bangladesh. 11Clinical Laboratory of Microbiology and Virology, University Hospital “Lozenetz”, Str. Kozyak 1,

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www.nature.com/scientificdata/ www.nature.com/scientificdata

Sofia, 1407, Sofia, Bulgaria. 12Alberta Precision Laboratories, Alberta, Canada. 13Service de microbiologie, Centre
Integré Universitaire de Santé et de services sociaux de l’Estrie - Centre Hospitalier Universitaire de Sherbrooke,
3001 12è avenue Nord, Sherbrooke, J1H 5N4, Québec, Canada. 14Department, Bioanalytica AG, Luzern, 6006,
Switzerland. 15Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, Basel,
4031, Switzerland. 16Microbiology Group, Instituto Nacional de Salud, Avenida Calle 26·51-20 CAN, Bogotá, 111321,
Colombia. 17Charalampous, Microbiology Department, National Reference Laboratory for Antimicrobial Resistance
Surveillance, Nicosia General Hospital, 215, Paleos Dromos Lefkosia-Lemesos str., Strovolos, 2029, Nicosia, Cyprus.
18
Department of Microbiology, University Hospital in Plzen, Edvarda Benese 1128/13, Plzen, 305 99, Czech Republic.
19
Department of Medical Microbiology, Motol University Hospital, V Uvalu 84, Prague, 15006, Czech Republic.
20
Otto-von-Guericke University, Magdebourg, Germany. 21Klinisk Mikrobiologisk Afdeling, Hvidovre Hospital,
Kettegårds Allé, Hvidovre, 2650, Denmark. 22Laboratoire de Microbiologie Clinique, Centre Hospitalo-universitaire,
1 place du 1er Mai 1945, Algiers, 16000, Algeria. 23National Reference Center for Antimicrobial Resistance, National
Institute of Public Health Research “Dr. Leopoldo Izquieta Pérez”, Iquique N14-285, Quito, 170403, Pichicha,
Ecuador. 24Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del
Ecuador, Quinto, 1701-2184, Pichincha, Ecuador. 25Department of Pathology and Experimental Therapy, Universitat
de Barcelona, Barcelona, Spain. 26Microbiology Department, Hospital de Bellvitge, Barcelona, 10587, Spain.
27
Institute of Microbiology, Centre Hospitalier Universitaire de Lille, Rue du Pr. Jules Leclercq, Lille, 59037, France.
28
Bacteriology laboratory, Centre hospitalier de Valenciennes, Avenue Désandrouin, Valenciennes, 59300, France.
29
Sekondi Public Health Laboratory, Ghana Health Service, Effia Nkwanta Regional Hospital, Effia Nkwanta Regional
Hospital, Takoradi, Ghana. 30Dronning Ingrids Hospital, Nuuk, Greenland. 31Chinese University of Hong Kong, Shatin,
Hong Kong. 32Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Kišpatićeva 12,
Zagreb, 10000, Croatia. 33Medical Microbiology and Immunology, University of Pecs Medical School, Szigeti ut 12,
Pecs, 7631, Hungary. 34Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy. 35Laboratory
Medicine Department, Hospital of Lithuanian University of Health Sciences Kauno klinikos, Eiveniu Str. 2, Kaunas,
50161, Lithuania. 36Centro de Investigação em Saúde de Manhiça, Manhiça, Mozambique. 37National Hospital Abuja,
Abuja, Nigeria. 38Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria. 39College of Medicine,
University of Ibadan, Ibadan, Oyo State, Nigeria. 40University College of Ibadan, Ibadan, Oyo State, Nigeria.
41
Obafemi Awolowo University, Ile-Ife, Nigeria. 42Department of Microbiology and Infection Control, Akershus
University Hospital, Sykehusveien 25, Lørenskog, 1478, Norway. 43Southern Community Laboratories, University of
Otago, 472 George Street, Otago, 9016, Dunedin, New Zealand. 44Department of Industrial Biotechnology, Atta-ur-
Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), H-12, Islamabad,
44000, Pakistan. 45Molecular Diagnostic Section, Khyber Teaching Hospital (KTH), University Road, Peshawar,
25120, Pakistan. 46Departamento de Bacteriologia, Laboratorio Central de Salud Publico, Avenida Venezuela y Tte
Escurra, Asunción, CP, 1429, Paraguay. 47Basic Medical Sciences Department, Arab American University, AAUP st.,
Zababdeh, P240, Jenin, Palestine. 48Division of Clinical Microbiology, Qatif Central Hospital, 3213 Dharan-Jubail
Expressway, Al-Qatif, 32654-7376, Eastern Province, Saudi Arabia. 49Department of Clinical Tropical Medicine,
Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Bangkok, 10400, Thailand. 50Department of
Medical Sciences, National Institute of Health, Sariburi, Thailand. 51Medical Microbiology Department, Karadeniz
Technical University Farabi Hospital, Farabi Hastanesi, Trabzon, 61080, Ortahisar, Turkey. 52Lusaka Apex Medical
School, Lusaka, Zambia. 53Levy Mwanawasa Teaching Hospital, Lusaka, Zambia. 54University Teaching Hospital,
Lusaka, Zambia. ✉e-mail: [email protected]

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