Author: Nicole Stoesser

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Preprints

Impact of Delta on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK

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  • Site-wide: 287
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  • Site-wide: 220
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  • Site-wide: 1,476

Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom

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  • Site-wide: 524
  • In infectious diseases: 193
• Year to date:
  • Site-wide: 2,862
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  • Site-wide: 3,140

The impact of SARS-CoV-2 vaccines on antibody responses in the general population in the United Kingdom

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  • Site-wide: 725
  • In infectious diseases: 257
• Year to date:
  • Site-wide: 8,804
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  • Site-wide: 9,469

Virus detection and identification in minutes using single-particle imaging and deep learning

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  • Site-wide: 1,048
  • In infectious diseases: 340
• Year to date:
  • Site-wide: 4,753
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  • Site-wide: 8,478

Increased infections, but not viral burden, with a new SARS-CoV-2 variant

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  • Site-wide: 1,469
  • In infectious diseases: 442
• Year to date:
  • Site-wide: 9,674
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  • Site-wide: 13,393

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

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  • Site-wide: 1,512
  • In bioinformatics: 75
• Year to date:
  • Site-wide: 50,071
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  • Site-wide: 118,952

Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time

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  • Site-wide: 1,989
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• Year to date:
  • Site-wide: 4,013
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  • Site-wide: 11,769

Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing

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  • Site-wide: 3,698
  • In infectious diseases: 862
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  • Site-wide: 1,701
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  • Site-wide: 24,625

SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus

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  • Site-wide: 7,166
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  • Site-wide: 101,542

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

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  • Site-wide: 8,903
  • In bioinformatics: 892
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  • Site-wide: 58,762
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OMICRON-ASSOCIATED CHANGES IN SARS-COV-2 SYMPTOMS IN THE UNITED KINGDOM

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  • In epidemiology: 1,196
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  • Site-wide: 567
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SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 and correlates of protection in the UK general population

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  • Site-wide: 10,945
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  • Site-wide: 2,637
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  • Site-wide: 14,795

A haemagglutination test for rapid detection of antibodies to SARS-CoV-2

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  • Site-wide: 13,717
  • In infectious diseases: 1,983
• Year to date:
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  • Site-wide: 4,860

The duration, dynamics and determinants of SARS-CoV-2 antibody responses in individual healthcare workers

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  • Site-wide: 13,877
  • In infectious diseases: 1,805
• Year to date:
  • Site-wide: 68,791
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  • Site-wide: 42,709

Anti-spike antibody response to natural SARS-CoV-2 infection in the general population

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  • Site-wide: 13,973
  • In infectious diseases: 1,855
• Year to date:
  • Site-wide: 12,833
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  • Site-wide: 45,044

Stringent thresholds for SARS-CoV-2 IgG assays result in under-detection of cases reporting loss of taste/smell

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  • Site-wide: 18,248
  • In infectious diseases: 2,054
• Year to date:
  • Site-wide: 124,597
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  • Site-wide: 180,325

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies

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  • Site-wide: 20,341
  • In bioinformatics: 2,205
• Year to date:
  • Site-wide: 63,062
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  • Site-wide: 42,556

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

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  • Site-wide: 21,308
  • In microbiology: 1,149
• Year to date:
  • Site-wide: 177,817
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  • Site-wide: 172,894

Rapid turnaround multiplex sequencing of SARS-CoV-2: comparing tiling amplicon protocol performance

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  • Site-wide: 21,407
  • In infectious diseases: 3,494
• Year to date:
  • Site-wide: 1,084
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  • Site-wide: 3,543

Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli

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  • Site-wide: 22,915
  • In microbiology: 1,240
• Year to date:
  • Site-wide: 155,288
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  • Site-wide: 160,206

Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131

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  • In genomics: 2,816
• Year to date:
  • Site-wide: 128,053
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High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families

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  • Site-wide: 40,410
  • In microbiology: 2,216
• Year to date:
  • Site-wide: 174,095
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  • Site-wide: 130,356

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

• Downloaded 873 times
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  • Site-wide: 41,547
  • In microbiology: 2,410
• Year to date:
  • Site-wide: 93,292
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  • Site-wide: 98,461

Flanker: a tool for comparative genomics of gene flanking regions

• Downloaded 865 times
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  • Site-wide: 42,160
  • In bioinformatics: 4,461
• Year to date:
  • Site-wide: 47,984
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  • Site-wide: 32,703

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data

• Downloaded 864 times
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  • Site-wide: 42,188
  • In bioinformatics: 4,168
• Year to date:
  • Site-wide: 129,998
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  • Site-wide: 173,098

Increasing test specificity without impairing sensitivity - lessons learned from SARS-CoV-2 serology

• Downloaded 718 times
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  • Site-wide: 55,193
  • In infectious diseases: 3,726
• Year to date:
  • Site-wide: 32,165
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  • Site-wide: 47,208

Transmission dynamics and between-species interactions of multidrug-resistant Enterobacteriaceae

• Downloaded 678 times
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  • Site-wide: 59,931
  • In epidemiology: 2,715
• Year to date:
  • Site-wide: 147,873
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  • Site-wide: 94,251

Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

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  • Site-wide: 63,368
  • In microbiology: 3,646
• Year to date:
  • Site-wide: 119,239
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  • Site-wide: 140,489

Novel blaKPC-carrying species identified in the hospital environment

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  • Site-wide: 67,931
  • In microbiology: 3,918
• Year to date:
  • Site-wide: 170,426
• Since beginning of last month:
  • Site-wide: 119,556

Dynamics of mcr-1 prevalence and mcr-1-positive Escherichia coli after the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing based molecular epidemiological study

• Downloaded 604 times
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  • Site-wide: 69,805
  • In microbiology: 4,066
• Year to date:
  • Site-wide: 131,577
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  • Site-wide: 120,406

Genomic epidemiology of a complex, multi-species plasmid-borne blaKPC carbapenemase outbreak in Enterobacterales in the UK, 2009-2014

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  • Site-wide: 73,399
  • In genomics: 4,752
• Year to date:
  • Site-wide: 141,228
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  • Site-wide: 159,219

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

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  • Site-wide: 75,791
  • In microbiology: 4,565
• Year to date:
  • Site-wide: 124,992
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  • Site-wide: 162,581

Panton-Valentine leukocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial genome-wide association study

• Downloaded 543 times
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  • Site-wide: 79,572
  • In microbiology: 4,734
• Year to date:
  • Site-wide: 167,486
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  • Site-wide: 150,581

Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction

• Downloaded 509 times
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  • Site-wide: 85,791
  • In genomics: None
• Year to date:
  • Site-wide: 4,842
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  • Site-wide: 1,164

Trends in Escherichia coli bloodstream infection, urinary tract infections and antibiotic susceptibilities in Oxfordshire, 1998-2016: an observational study

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  • Site-wide: 90,022
  • In epidemiology: 3,680
• Year to date:
  • Site-wide: 170,459
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  • Site-wide: 177,325

Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries

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  • Site-wide: 91,026
  • In genomics: 5,544
• Year to date:
  • Site-wide: 115,768
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  • Site-wide: 76,014

Molecular epidemiology of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire (UK) 2008-2018

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  • Site-wide: 97,470
  • In infectious diseases: 4,887
• Year to date:
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  • Site-wide: 65,002

Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399

• Downloaded 421 times
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  • Site-wide: 105,253
  • In evolutionary biology: 4,969
• Year to date:
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  • Site-wide: 111,812

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm

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  • Site-wide: 110,852
  • In microbiology: 7,221
• Year to date:
  • Site-wide: 119,718
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  • Site-wide: 128,460

Genomic network analysis of an environmental and livestock IncF plasmid population

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  • Site-wide: 111,656
  • In bioinformatics: 9,018
• Year to date:
  • Site-wide: 127,763
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  • Site-wide: 92,302

The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates

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  • Site-wide: 116,891
  • In microbiology: 7,455
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  • Site-wide: 184,977

Klebsiella quasipneumonaiae provides a window into carbapenemase gene transfer, plasmid rearrangements and nosocomial acquisition from the hospital environment

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  • Site-wide: 118,247
  • In microbiology: 7,528
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The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination

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  • Site-wide: 123,110
  • In infectious diseases: 5,926
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  • Site-wide: 41,294

Molecular epidemiology of paediatric bloodstream infections caused by Gram-negative bacteria in Oxfordshire, UK

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  • Site-wide: 126,492
  • In infectious diseases: 6,578
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Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia

• Downloaded 309 times
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  • Site-wide: 135,674
  • In microbiology: 9,066
• Year to date:
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The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study

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  • Site-wide: 137,625
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• Year to date:
  • Site-wide: 10,690
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  • Site-wide: 20,587

Transmission patterns of hyper-endemic multi-drug resistant Klebsiella pneumoniae in a Cambodian neonatal unit: a longitudinal study with whole genome sequencing

• Downloaded 297 times
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  • Site-wide: 139,266
  • In epidemiology: 5,502
• Year to date:
  • Site-wide: 155,646
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  • Site-wide: 177,327

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli

• Downloaded 291 times
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  • Site-wide: 141,121
  • In microbiology: 10,865
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  • Site-wide: 44,870
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  • Site-wide: 37,619

Plasmid overlap and evolution between Enterobacterales isolates from bloodstream infections and non-human compartments

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  • Site-wide: 149,259
  • In genomics: None
• Year to date:
  • Site-wide: 13,227
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  • Site-wide: 1,748

Antimicrobial resistance surveillance: can we estimate resistance in bloodstream infections from other types of specimen?

• Downloaded 240 times
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  • Site-wide: 156,114
  • In infectious diseases: 6,484
• Year to date:
  • Site-wide: 111,558
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  • Site-wide: 100,249

Mortality risks associated with empirical antibiotic activity in E. coli bacteraemia: an analysis of electronic health records

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  • Site-wide: 156,225
  • In infectious diseases: 6,932
• Year to date:
  • Site-wide: 15,209
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  • Site-wide: 43,225

Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections

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  • Site-wide: 158,521
  • In infectious diseases: 6,507
• Year to date:
  • Site-wide: 151,677
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  • Site-wide: 170,374

Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Enterobacterales in a hospital setting

• Downloaded 211 times
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  • Site-wide: 163,834
  • In epidemiology: 6,785
• Year to date:
  • Site-wide: 53,725
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  • Site-wide: 60,594

Changes in paediatric respiratory infections at a UK teaching hospital 2016-2021; impact of the SARS-CoV-2 pandemic.

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  • Site-wide: 171,428
  • In infectious diseases: 6,954
• Year to date:
  • Site-wide: 84,201
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Evaluation of metagenomic, 16S rRNA gene and ultra-plexed PCR-based sequencing approaches for profiling antimicrobial resistance gene and bacterial taxonomic composition of polymicrobial samples

• Downloaded 116 times
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  • Site-wide: 183,675
  • In genomics: None
• Year to date:
  • Site-wide: 39,715
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  • Site-wide: 6,633