A Selection of Presentations Featuring Oxford Nanopore Sequencing

Friday, 20 June, 2025

CIV-IDS-206. Emerging and re-emerging arboviruses: pathogenesis, diagnostics and vaccines

Time: 01:45 pm–03:45 pm PT | Location: 511ABC, LACC

• Development of a field-applicable pan-serotype whole genome sequencing protocol for Dengue virus
  M. Ulinici, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
• Developing a novel amplicon-based next generation sequencing approach to determine West Nile virus transmission dynamics during an outbreak
  S. Freed, Jr, University of Nebraska Medical Center, Omaha, NE, United States

Saturday, 21 June, 2025

AAR-IDS-303. Phage based therapeutics: progress/success?

Time: 08:15 am–10:15 am PT | Location: 502A, LACC

• A neonatal antibiotic resistant polymicrobial skin infection: a case report and laboratory investigation
  F. Vaskoudis, University of West London, London, United Kingdom

Sunday, 22 June, 2025

CPHM-IDS-401. Tools and applications for utilizing whole genome sequencing data for outbreak investigations

Time: 08:15 am–10:15 am PT | Location: 515B, LACC

• Identifying and interrupting intra-hospital norovirus GII transmission using whole-genome sequencing
  R. Potter, Children’s Hospital of Philadelphia, Philadelphia, PA, United States

CPHM-IDS-410. Assessing the clinical impact of next-generation sequencing: where are we now?

Time: 01:45 pm–03:45 pm PT | Location: 515B, LACC

• When all methods fail. Rapid whole genome sequencing directly from positive blood culture
  D. Navas, AdventHealth Orlando, Orlando, FL, United States

A selection of posters with rapid fire talks featuring Oxford Nanopore sequencing

Friday, 20 June, 2025

Time: 11:45 am–12:30 pm PT | Location: AAR Track Hub, Exhibit Hall

• AAR-RF-206. AAR Friday rapid fire
  Genomic insights into carbapenem resistant Acinetobacter baumannii from different clusters
  A. Uskudar Guclu, Baskent University Faculty of Medicine, Ankara, Turkey

Time: 11:45 am–12:30 pm PT | Location: AES Track Hub, Exhibit Hall

• AES-RF-205. AES Friday rapid fire: tiny microbes for tremendous tasks: using microbes as tools
  Integrating DNA watermarks into genetically engineered microorganisms to support agricultural-runoff threat assessments
  T. Cason, University of Colorado Boulder, Boulder, CO, United States

Time: 11:45 am–12:30 pm PT | Location: EEB Track Hub, Exhibit Hall

• EEB-RF-204. EEB Friday rapid fire
  Exploring the drivers of bacteriophage diversity to gain insights into climate change in the North
  A. Lehr, University of Alaska Fairbanks, Fairbanks, AK, United States

Time: 11:45 am–12:30 pm PT | Location: HMB Track Hub, Exhibit Hall

• HMB-RF-204. HMB Friday rapid fire
  Nanopore adaptive sequencing recovers full bacterial genomes from the mosquito microbiome
  J. Yuan, Connecticut Agricultural Experiment Station, New Haven, CT, United States

Saturday, 21 June, 2025

Time: 11:45 am–12:30 pm PT | Location: CPHM Track Hub, Exhibit Hall

• CPHM-RF-304. CPHM Saturday rapid fire
  Investigating the genetic origins of West Nile Virus (WNV) in Southern Nevada
  A. J. Tang, University of Nevada, Las Vegas, NV, United States

Sunday, 22 June, 2025

Time: 11:45 am–12:30 pm PT | Location: AES Track Hub, Exhibit Hall

• AES-RF-404. AES Sunday rapid fire: microbial pioneers: colonizing earth’s unique habitats
  Evaluation of psychrotrophic bacteria for biotechnological potential
  Q. Faber, Cold Regions Research and Engineering Laboratory, Hanover, NH, United States

A selection of posters featuring Oxford Nanopore sequencing

Friday, 20 June, 2025

Time: 10:00 am–05:00 pm PT | Location: Exhibit Hall

• AAR-P-201. AAR01 Friday surveillance of antimicrobial resistance in clinical isolates: molecular typing and molecular epidemiology
  Whole genome sequencing and characterization of the first macrolide-resistant Bordetella pertussis strain in Mexico: implications for public health and surveillance in Latin America
  A. Da Costa, American Society for Microbiology, Washington, DC, United States
• Detection of transferable antiphage defense mechanisms linked to antibiotic resistance genes with a one health approach
  M. F. Ferreira, Instituto de Higiene, Facultad de Medicina, Udelar, Montevideo, Uruguay
• From serotyping to genotyping. A rapid, accurate, and simplified protocol for Streptococcus pneumoniae typing by whole genome sequencing
  J. Alexander, Advent Health, Orlando, FL, United States
• Outbreak investigation of extensively drug resistant Acinetobacter baumannii of ST2 in the intensive care unit of a Lebanese hospital
  I. Bitar, Charles University, Plzen, Czech Republic

• AES-P-201. AES01 Friday agricultural systems microbiology
  Advancing livestock production through long-read metagenomic sequencing and integrated omics approaches
  B. A. Strickland, Cmbio, Germantown, MD, United States
• Isolation and characterization of novel xylooligosaccharide-utilizing probiotics for enhanced poultry health and sustainability
  X. Hu, University of Tennessee, Knoxville, TN, United States

• AES-P-309. AES09 Saturday marine and freshwater microbiology
  Metagenomic insights of antibiotic resistance genes (ARGs) in Laguna Lake using nanopore sequencing
  P. Vital, University of the Philippines Diliman, Quezon City, Philippines

• CPHM-P-302. CPHM03 Saturday diagnostic bacteriology
  Have you seen Kerstersia gyiorium on the bench? Reliable identification method and susceptibility profile
  H. Miraballes, AdventHealth Orlando-Microbiology, Altamonte Springs, FL, United States

• CPHM-P-309. CPHM12 Saturday molecular and genome sequencing for diagnostics and AMR detection
  Molecular characterization of the three genome segments of Crimean-Congo Hemorrhagic Fever Viruses (CCHFV) detected in 2020 in the Mopti Region, Mali
  I. Guindo, National Public Health Institute, NPHI-Mali, Bamako, Mali
• Development and validation of a 16S rRNA bioinformatic pipeline and curated reference database optimized for detection of bacterial pathogens from clinical specimens
  N. P. G. Gauthier, BugSeq Bioinformatics Inc., Vancouver, BC, Canada

• EEB-P-301. EEB01 Saturday microbial ecology
  A characterisation of the TupABC-MobAB complex in Vibrio spp. isolates from Hong Kong coastal waters
  A. N. H. Cheung, The ISF Academy, Pokfulam, Hong Kong

• EEB-P-302. EEB02 Saturday microbial evolution
  Variations in isaB and the Agr locus point to lineage-specific adaptations in Staphylococcus saprophyticus
  P. S. K. Leung, The ISF Academy, Pokfulam, Hong Kong

• EEB-P-303. EEB03 Saturday climate change: ecological interactions
  Non-linear response in microbiome structure and soil respiration along a gradient of soil water filled pore space
  J. Yuan, The Connecticut Agricultural Experiment Station, New Haven, CT, United States

• EEB-P-307. EEB07 Saturday microbiome ecology and evolution
  Oxford Nanopore sequencing enables strain-level metagenomics and reveals the structure and function of a mature compost microbiome
  C. He, Oxford Nanopore Technologies, Alameda, CA, United States

• HMB-P-304. HMB07 Saturday microbiome profiling
  Exploring the connection between obesity and the human gut virome through long-read sequencing
  G. Gulyás, University of Szeged Albert Szent-Györgyi Medical School, Szeged, Hungary

• MBP-P-301. MBP01 Saturday gene expression, regulation and signaling
  Decoding harmane biosynthesis in Delftia tsuruhatensis: RNAseq insights for novel malaria control strategies
  P. Sai, North Carolina State University, Raleigh, NC, United States

• MBP-P-304. MBP04 Saturday molecular and genome biology of microbes
  Epitranscriptomic dynamics in T5 phage-infected Escherichia coli: a dual perspective on RNA modifications
  L. Rivera Montero, Ludwig-Maximilians Universität, Munich, Germany

Sunday, 22 June, 2025

Time: 10:00 am–04:00 pm PT | Location: Exhibit Hall

• AAR-P-408. AAR08 Sunday new antimicrobial agents (in vitro and in vivo studies)
  Phenotypic and genotypic characterization of antimicrobial resistance (AMR) strains from the ATCC® collection: a key resource for diagnostics and therapeutic development
  B. Benton, ATCC, Manassas, VA, United States

• AES-P-402. AES02 Sunday food systems & food fermentations microbiology
  Factors to consider for probiotic safety: discovery of a safe, high GABA producing Lactiplantibacillus plantarum
  A. Aditya, Verb Biotics, Durham, NC, United States

• AES-P-404. AES04 Sunday wastewater and drinking water microbiology
  Monitoring influenza A virus in wastewater: combining RT-ddPCR and nanopore sequencing for enhanced surveillance
  A. A. Kalalah, Michigan State University, East Lansing, MI, United States

• AES-P-407. AES07 Sunday source tracking: non-clinical microbial & AMR detection and monitoring
  Evaluation of low biomass shotgun nanopore metagenomic sequencing for environmental microbial community profiling
  Q. Dai, Duke University, Durham, NC, United States
• A comparison of antimicrobial resistance in alpaca (Lama pacos) faecal isolates from six sites in China
  E. J. S. Dong, The ISF Academy, Pokfulam, Hong Kong

• AES-P-408. AES08 Sunday biotransformations: bioremediation, biodegradation, biofouling and biocorrosion
  Isolation and characterization of acid-tolerant mo-reducing bacteria from a disused tungsten mine in Hong Kong
  M. He, The ISF Academy, Pokfulam, Hong Kong

• CPHM-P-404. CPHM08 Sunday diagnostic public health microbiology
  Unmasking zoonotic tuberculosis: amplicon-based targeted metagenomics for Mycobacterium orygis diagnosis
  B. T. Hugh, University of Sydney, NSW, Sydney, Australia

• CPHM-P-406. CPHM12 Sunday molecular and genome sequencing for diagnostics and AMR detection
  Characterizing the defective and intact HIV-1 proviral milieu in the spleen and brain using near full-length NGS sequencing
  M. Collins, Drexel University, Philadelphia, PA, United States
• Host-pathogen dynamics in tracheal aspirates during chronic critical illness
  A. Gupta, University of Pittsburgh, Pittsburgh, PA, United States
• Genetic characterization of Francisella tularensis detected in Georgia
  G. Chanturia, National Center for Disease Control and Public Health (NCDC), Tbilisi, Georgia

• EEB-P-407. EEB07 Sunday microbiome ecology and evolution: diversity of host-microbe interactions
  Hidden palette: exploring the role of microbes on avian plumage coloration
  K. Sharma, The University at Buffalo (SUNY), Buffalo, NY, United States

• HMB-P-405. HMB07 Sunday microbiome profiling
  Unravelling gut microbiota disparities in term and preterm infants: insights into bacterial strain contributions and modulation
  E. Seo, Seoul National University, Seoul, Republic of Korea

• MBP-P-401. MBP01 Sunday gene expression, regulation and signaling
  Insights into the transcriptomic landscape of Caviid gammaherpesvirus 1 through long-read sequencing
  Á. Dörmo, University of Szeged Albert Szent-Györgyi Medical School, Szeged, Hungary

• MBP-P-404. MBP04 Sunday molecular and genome biology of microbes
  Understanding unannotated regions of the Leptospira transcriptome
  L. C. M. Salvador, University of Arizona, Tucson, AZ, United States

Friday, 20 June, 2025

Time: 10:00 am–05:00 pm PT | Location: Exhibit Hall

• AES-P-209. AES09 Friday marine and freshwater microbiology
  Microbiome variability in the Hudson River over short and long timescales
  I. Cohen, Brooklyn College, Brooklyn, NY, United States

• CIV-P-201. CIV01 Friday clinical studies of adult infectious diseases
  Analysis of genetic variability and prediction of T epitopes of the HPV16 E2 gene in a sample of asymptomatic women from Cajamarca, Peru
  J. del Valle Mendoza, Universidad Peruana de Ciencias Aplicada, Lima, Peru

• CPHM-P-202. CPHM03 Friday diagnostic bacteriology
  Improving flow in the blood culture laboratory: direct full length 16S rRNA gene sequencing from positive blood culture flasks
  D. S. Hansen, Herlev Gentofte Hospital, Herlev, Denmark

• CPHM-P-207. CPHM12 Friday molecular and genome sequencing for diagnostics and AMR detection
  Utilization of the ElysION automated sequencer to detect genetic markers predictive of hypervirulent Klebsiella pneumoniae
  S. Stevenson, University of Nebraska Medical Center, Omaha, NE, United States

• EEB-P-202. EEB02 Friday microbial evolution
  Nitrophenol degradation is not a defining feature of Arthrobacter nitrophenolicus
  R. Y. T. Shen, The ISF Academy, Pokfulam, Hong Kong

• EEB-P-205. EEB05 Friday comparative genomics: host-associated microbes
  Pathogenomes and resistance phenotypes of multi-drug resistant shiga toxin-producing Escherichia coli
  S. Eppinger, University of Texas at San Antonio, San Antonio, TX, United States
• Comparative genomic analysis of Corynebacterium xerosis yields clues about their role in the bovine respiratory tract
  S. Howe, University of Arkansas Division of Agriculture, Fayetteville, AR, United States
• Comparative genomics and virulence assessment of Pectobacterium brasiliense strains isolated from multiple hosts in Hawaii
  V. Stewart, University of Hawaii at Manoa, Honolulu, HI, United States
• Comparative genomics across diverse hosts: understanding the genomic variability of Aeromonas veronii in humans, fish, and medicinal leeches
  N. Vargas, University of Connecticut, Storrs, CT, United States

• HMB-P-202. HMB03 Friday basic science of pathogen during human infections
  From biomarkers to whole-genome insights: comprehensive analysis of virulence mechanisms and plasmids of carbapenem resistant hypervirulent Klebsiella pneumoniae
  C.-Y. Kao, National Yang Ming Chiao Tung University, Taipei, Taiwan

• MBP-P-202. MBP02 Friday stress responses and defenses
  Identification of genetic and epigenetic changes linked to salt tolerance in Escherichia coli: implication on antimicrobial resistance (AMR)
  P. Nagpal, Indian Institute of Technology Delhi, New Delhi, India

• MBP-P-204. MBP04 Friday molecular and genome biology of microbes
  Genetic and functional characterization of tumor-associated Lactobacilli
  L. D. Boatright, UT Health MD Anderson Graduate School of Biomedical Sciences, Houston, TX, United States

• MBP-P-205. MBP05 Friday metabolism, enzyme mechanics and physiology
  Thermodynamic- and sequencing-guided on-site media design and culturing from diverse ecosystems
  E. Miller, Two Frontiers Project, San Diego, CA, United States

• MBP-P-208. MBP08 Friday fundamental phage biology, phage defense, and mobile genetic elements
  Co-infection of bacteriophages (KHP30 and KHP40) with Helicobacter pylori
  M. Shiraishi, International University of Health and Welfare Graduate School, Narita, Japan

Saturday, 21 June, 2025

Time: 10:00 am–05:00 pm PT | Location: Exhibit Hall

• AAR-P-301. AAR01 Saturday surveillance of antimicrobial resistance in clinical isolates: molecular typing and molecular epidemiology
  First report of KPC-31 in Florida: redefining detection of KPC producing isolates with ESBL-like resistance pattern
  J. Alexander, Microbiology, Advent Health, Orlando, FL, United States

• AAR-P-304. AAR06 Saturday novel approaches: diagnostics/discovery and non-traditional therapies to combat drug-resistant infections
  Methylation scores reveal antibiotic resistance in Pseudomonas aeruginosa using a machine learning model
  S. Gan, University of Texas Southwestern Medical Center, Dallas, TX, United States

• AAR-P-307. AAR10 Saturday phage therapy: clinical applications and consideration
  Characterization of a novel Drulisvirus phage species against Klebsiella pneumoniae and in vivo assessment using the Galleria mellonella model
  G. Quispe-Villegas, Cayetano Heredia University, Lima, Peru

• AES-P-301. AES01 Saturday agricultural systems microbiology
  Isolation and characterisation of four novel Curtobacterium spp. with plant growth-promoting potential
  L. K. Y. Chow, The ISF Academy, Pokfulam, Hong Kong
• Isolation and characterisation of two seed endophytic bacteria displaying antifungal activity
  N. Cheung, The ISF Academy, Pokfulam, Hong Kong

• AES-P-302. AES02 Saturday food systems & food fermentations microbiology
  Evaluating real-time software-based host depletion for improved antimicrobial resistance surveillance
  D. C. Wrenn, University of Alaska Fairbanks, Fairbanks, AK, United States

• AES-P-303. AES03 Saturday engineered, built and urban environments microbiology
  Duckweed surfaces are selectively colonized by a subset of environmental bacteria
  I. Cohen, Brooklyn College, Brooklyn, NY, United States

• AES-P-305. AES05 Saturday industrial microbiology: bioproductions, bioconversions and fermentations
  Investigation of a unique pair of triacylglycerol lipases (EC 3.1.1.3) from Staphylococcus pseudintermedius
  J. J. S. Luan, The ISF Academy, Pokfulam, Hong Kong

• AES-P-307. AES07 Saturday source tracking: non-clinical microbial & AMR detection and monitoring
  Long-read sequencing reveals antimicrobial resistance and pathogenicity markers in Escherichia coli and Salmonella isolates from retail meats
  A. Ghorbani Tajani, University of Wyoming, Laramie, WY, United States
• Isolation and characterisation of 9 strains of Enterobacter mori from Hong Kong reveals 4 new ACT beta-lactamase variants
  A. Y. X. Huang, The ISF Academy, Pokfulam, Hong Kong