cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/0qts9-t5j57
title: 411V mass spec

description: CF4Q 30µM CF4Q3µM CheA6µMCheW725 µM Vesicle in Kinase buffer .  [added 2015-09-21 10:47:53] CF4Q 411V30µM CF4Q3µM CheA6µMCheW725 µM Vesicle in Kinase buffer
description: <strong>Tilt Series Date:</strong> 2015-03-30</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Escherichia coli in vitro</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: 8.0 μm,  magnification: 34000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Lynmarie Thompson</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-03-30-14/rawdata/</p>MassSpec411V2015March0014.mrc,  Tilt Series (Pixel Size 0.32 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-03-30-14/rawdata/MassSpec411V2015March0014.mrc"
        > <i class="download icon"></i> Download </a></p>

        MassSpec411V2015March0014_full.rec,  Reconstruction (Pixel Size 1.28 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-03-30-14/3dimage_53533/MassSpec411V2015March0014_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/yn6tc-dzv76
title: B/r H266 / R1-16 conjugation

description: Grid box YWC238
description: <strong>Tilt Series Date:</strong> 2017-01-19</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain and sample prepared by Carrie Shaffer</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-01-19-45/rawdata/</p>20160119_YWC238_10045.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-01-19-45/rawdata/20160119_YWC238_10045.mrc"
        > <i class="download icon"></i> Download </a></p>

        20160119_YWC238_10045_full.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-01-19-45/3dimage_81349/20160119_YWC238_10045_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/3tkwv-3jv82
title: H. pylori 26695 WT

description: grid box YWC259
description: <strong>Tilt Series Date:</strong> 2017-07-06</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain and sample prepared by Carrie Shaffer</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-07-06-81/rawdata/</p>20170706_YWC259_10082.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-07-06-81/rawdata/20170706_YWC259_10082.mrc"
        > <i class="download icon"></i> Download </a></p>

        20170706_YWC259_10082.rec,  Reconstruction (Pixel Size 1.56 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-07-06-81/3dimage_85808/20170706_YWC259_10082.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.t23mvn
title: Occurrence Download

description: A dataset containing 885 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Luciobarbus sclateri)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 885 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046838-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/cv32n-tz091
title: Pseudomonas full length aer2

description: Pseudomonas full length aer2 on plasmid, no induction
description: <strong>Tilt Series Date:</strong> 2015-07-28</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -8.0 μm,  magnification: 34000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> Kylie Watts</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-07-28-27/rawdata/</p>Pseudofullaer2plasmidJuly0030.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-07-28-27/rawdata/Pseudofullaer2plasmidJuly0030.mrc"
        > <i class="download icon"></i> Download </a></p>

        Pseudofullaer2plasmidJuly0030.rec,  Reconstruction (Pixel Size 1.28 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-07-28-27/3dimage_59787/Pseudofullaer2plasmidJuly0030.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8rf8k-g7c23
title: NR1769/R1-16 conjugation

description: Grid box YWC241
description: <strong>Tilt Series Date:</strong> 2017-01-30</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 170.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain and sample prepared by Carrie Shaffer</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-01-30-56/rawdata/</p>20170130_YWC241_10056.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-01-30-56/rawdata/20170130_YWC241_10056.mrc"
        > <i class="download icon"></i> Download </a></p>

        20170130_YWC241_10056.rec,  Reconstruction (Pixel Size 1.56 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-01-30-56/3dimage_81710/20170130_YWC241_10056.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/33mnq-bn578
title: Dflg

description: This is a flagellum mutant from Sahand (ATP connected) grown in serum bottle. We saw with perfusion setup that the same mutant makes nanowires. So I went back and imaged the serum bottle version just to make sure that it doesnt have nanowires.
description: <strong>Tilt Series Date:</strong> 2015-08-20</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -8.0 μm,  magnification: 18000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Moh and Sahand</p>
<strong>Sample Preparation:</strong> same as before</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-08-20-31/3dimage_60979/</p>dflgwithnanowires_atlas10031_full.rec,  Reconstruction (Pixel Size 2.4 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-08-20-31/3dimage_60979/dflgwithnanowires_atlas10031_full.rec"
        > <i class="download icon"></i> Download </a></p>

        dflgwithnanowires_atlas10031.mrc,  Tilt Series (Pixel Size 0.6 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-08-20-31/rawdata/dflgwithnanowires_atlas10031.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/0erya-e4v03
title: HeLa cells

description: Synchronized HeLa cells, looking for midbodies
description: <strong>Tilt Series Date:</strong> 2015-01-15</p>
<strong>Data Taken By:</strong> Rasika Ramdasi</p>
<strong>Species / Specimen:</strong> HeLa cells</p>
<strong>Strain:</strong> ATCC</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Undefined</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSF tomo</p>
<strong>Sample Preparation:</strong> Synchronized HeLa cells with siRNA NUP 153 and Thymidine 2mM</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2015-01-15-46/rawdata/</p>helayfp60006.mrc,  Tilt Series (Pixel Size 0.6 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2015-01-15-46/rawdata/helayfp60006.mrc"
        > <i class="download icon"></i> Download </a></p>

        helayfp60006_full.rec,  Reconstruction (Pixel Size 2.4 nm), 623.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2015-01-15-46/3dimage_51110/helayfp60006_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ngx1c-7jj05
title: Cos7 cells

description: looking for midbodies in Cos7 cells
description: <strong>Tilt Series Date:</strong> 2015-02-07</p>
<strong>Data Taken By:</strong> Rasika Ramdasi</p>
<strong>Species / Specimen:</strong> Cos7</p>
<strong>Strain:</strong> Cos7 cells</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSF tomo</p>
<strong>Sample Preparation:</strong> cells+ thymidine 2mM, 11 hour after release</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2015-02-07-5/rawdata/</p>cos7atlas10002.mrc,  Tilt Series (Pixel Size 0.48 nm), 1.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2015-02-07-5/rawdata/cos7atlas10002.mrc"
        > <i class="download icon"></i> Download </a></p>

        cos7atlas10002_part64_4.rec,  Reconstruction (Pixel Size 1.92 nm), 623.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2015-02-07-5/3dimage_51540/cos7atlas10002_part64_4.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/x7ksw-67d49
title: H. pylori 26695 WT

description: grid box YWC259
description: <strong>Tilt Series Date:</strong> 2017-07-06</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain and sample prepared by Carrie Shaffer</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-07-06-34/rawdata/</p>20170706_YWC259_10035.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-07-06-34/rawdata/20170706_YWC259_10035.mrc"
        > <i class="download icon"></i> Download </a></p>

        20170706_YWC259_10035.rec,  Reconstruction (Pixel Size 1.56 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-07-06-34/3dimage_85703/20170706_YWC259_10035.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.dcurgx
title: Occurrence Download

description: A dataset containing 2485 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Cocos nucifera",
 "Year 2019-2025"
 ]
}

 The dataset includes 2485 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046839-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qa5dxg
title: Occurrence Download

description: A dataset containing 437 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tribulus terrestris",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 437 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046840-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/se6nn-dxy05
title: pED208_6um

description: t4ss in E.colli with F pilus
description: <strong>Tilt Series Date:</strong> 2015-02-11</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> LB o/n 37C</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2015-02-11-14/rawdata/</p>pED_6um_Feb100002.mrc,  Tilt Series (Pixel Size 0.5 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2015-02-11-14/rawdata/pED_6um_Feb100002.mrc"
        > <i class="download icon"></i> Download </a></p>

        pED_6um_Feb100002_part121_11.rec,  Reconstruction (Pixel Size 2.0 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2015-02-11-14/3dimage_51734/pED_6um_Feb100002_part121_11.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.9gvnc6
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tribulus terrestris",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 19 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046843-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wvce93
title: Occurrence Download

description: A dataset containing 4669 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tribulus terrestris",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4669 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046841-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/are7w-yrk61
title: E.coli minicell/Pul T2SS

description: grid box YWC252strain PAP5359 (minCDE knockout)Cells were grown on plate before freezing
description: <strong>Tilt Series Date:</strong> 2017-05-15</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain provided by Ingrid Guilvout in Olivera Francetic lab</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-05-15-43/rawdata/</p>20170515_YWC252b_10047.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-05-15-43/rawdata/20170515_YWC252b_10047.mrc"
        > <i class="download icon"></i> Download </a></p>

        20170515_YWC252b_10047_part121_10.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29988471
title: Genomic heterogeneity and lineage-specific beta-lactamases in recurrent <i>Achromobacter</i> bloodstream infection patients

description: Recurrent <i>Achromobacter</i> infections pose significant clinical challenges due to antimicrobial resistance and within-host evolution. This study investigates the genetic and phenotypic changes among <i>Achromobacter</i> isolates using next-generation sequencing. We retrospectively analyzed 65 <i>Achromobacter</i> infection cases at a tertiary hospital in Taiwan from 2016 to 2023. Whole-genome sequencing of 12 isolates from patients with recurrent bloodstream infections was performed using Oxford Nanopore Technology. Resistance genes and beta-lactamases were identified, and genome similarity was assessed using average nucleotide identity (ANI) for phylogenetic analysis. Recurrent infections were significantly associated with bloodstream and urinary tract infections (p &lt; 0.01). Whole-genome sequencing improved species identification over matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS), leading to the discovery of a novel <i>Achromobacter</i> species and the first identification of <i>A. insuavis</i> as a bacteraemia pathogen. Beta-lactamases grouped according to phylogenetic clades, indicating lineage-specific resistance patterns. Missense mutations in genes such as <i>siaT</i>, <i>rapA</i>, <i>atzEa1</i>, <i>AL523_09115</i>, and <i>clpA</i> correlated with changes in antimicrobial resistance profiles, suggesting in vivo evolution during recurrent infections. This study enhances understanding of <i>Achromobacter</i> genomic heterogeneity and underscores the importance of whole-genome sequencing for accurate species identification and resistance detection. The findings highlight the need for larger-scale studies to monitor emerging variants and assess their clinical impact.
DOI: 10.6084/m9.figshare.29988471.v1
title: Genomic heterogeneity and lineage-specific beta-lactamases in recurrent <i>Achromobacter</i> bloodstream infection patients

description: Recurrent <i>Achromobacter</i> infections pose significant clinical challenges due to antimicrobial resistance and within-host evolution. This study investigates the genetic and phenotypic changes among <i>Achromobacter</i> isolates using next-generation sequencing. We retrospectively analyzed 65 <i>Achromobacter</i> infection cases at a tertiary hospital in Taiwan from 2016 to 2023. Whole-genome sequencing of 12 isolates from patients with recurrent bloodstream infections was performed using Oxford Nanopore Technology. Resistance genes and beta-lactamases were identified, and genome similarity was assessed using average nucleotide identity (ANI) for phylogenetic analysis. Recurrent infections were significantly associated with bloodstream and urinary tract infections (p &lt; 0.01). Whole-genome sequencing improved species identification over matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS), leading to the discovery of a novel <i>Achromobacter</i> species and the first identification of <i>A. insuavis</i> as a bacteraemia pathogen. Beta-lactamases grouped according to phylogenetic clades, indicating lineage-specific resistance patterns. Missense mutations in genes such as <i>siaT</i>, <i>rapA</i>, <i>atzEa1</i>, <i>AL523_09115</i>, and <i>clpA</i> correlated with changes in antimicrobial resistance profiles, suggesting in vivo evolution during recurrent infections. This study enhances understanding of <i>Achromobacter</i> genomic heterogeneity and underscores the importance of whole-genome sequencing for accurate species identification and resistance detection. The findings highlight the need for larger-scale studies to monitor emerging variants and assess their clinical impact.