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Christina Ahlstrom, Ph.D.

Christina is a Research Biologist for the Alaska Science Center.

My research aims to better understand wildlife and zoonotic diseases in Alaska and adjacent regions. I use molecular tools to investigate the genetic diversity and transmission pathways of pathogens in wildlife populations and the ecosystems they occupy. My main research topics include antimicrobial resistance in wild birds, avian influenza, and Giardia and Cryptosporidium parasites in Arctic Alaska. I strive to achieve a more comprehensive understanding of where pathogens are detected and their genetic relatedness among spatio-temporally diverse populations to help inform management actions aimed to interrupt transmission pathways.

Professional Experience

  • 2024 - Present   Research Biologist, USGS Alaska Science Center, Anchorage, Alaska

  • 2017 - 2023        Geneticist, USGS Alaska Science Center, Anchorage, Alaska

  • 2015 - 2017        Consultant Epidemiologist & Data Analyst, Epi-interactive, Wellington, New Zealand

  • 2017                    Molecular Epidemiology Consultant, Food and Agriculture Organisation, Rome, Italy

  • 2016                    Molecular Epidemiology Consultant, Food and Agriculture Organisation, Rome, Italy

  • 2005 - 2008      Seasonal Research Assistant, Quality Milk Production Services, Cornell University, Ithaca, NY

Education and Certifications

  • Ph.D.  2015    University of Calgary, Calgary, Alberta, Canada     Veterinary Medical Sciences

  • M.S.   2011    Colorado State University, Fort Collins, CO     Animal Science

  • B.S.   2008    University at Buffalo, Buffalo, NY     Biology

Science and Products

Northern Pintail pair on water, Copper River Delta, Alaska

Avian Influenza Research

Since 2006, the USGS Alaska Science Center has been part of the State and Federal interagency team for the detection and response to highly pathogenic (HPAI) viruses in North America. Avian influenza or "bird flu" is a viral disease that primarily infects domestic poultry and wild birds. Avian influenza viruses are naturally occurring in wild birds such as ducks, geese, swans, and gulls. These...
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Alaska Science Center
Avian Influenza Research

Avian Influenza Research

Since 2006, the USGS Alaska Science Center has been part of the State and Federal interagency team for the detection and response to highly pathogenic (HPAI) viruses in North America. Avian influenza or "bird flu" is a viral disease that primarily infects domestic poultry and wild birds. Avian influenza viruses are naturally occurring in wild birds such as ducks, geese, swans, and gulls. These...
Learn More
John Reed (USGS scientist) holding a gull marked with a satellite transmitter at the Soldotna landfill in June 2016

Antibiotic Resistant Bacteria in Migratory Birds

Migratory birds, and particularly those using habitats close to human settlements, may be infected with antibiotic resistant bacteria. The USGS is working with public health professionals to understand the role of birds in the maintenance and dispersal of antibiotic resistant bacteria. Additionally, the USGS is investigating how antibiotic resistant bacteria in birds may relate to public and...
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Alaska Science Center
Antibiotic Resistant Bacteria in Migratory Birds

Antibiotic Resistant Bacteria in Migratory Birds

Migratory birds, and particularly those using habitats close to human settlements, may be infected with antibiotic resistant bacteria. The USGS is working with public health professionals to understand the role of birds in the maintenance and dispersal of antibiotic resistant bacteria. Additionally, the USGS is investigating how antibiotic resistant bacteria in birds may relate to public and...
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Scientist swabbing hunter-harvested ducks in western Alaska

Q&A: Bird Flu - Ongoing Threat of Highly Pathogenic Avian Influenza (HPAI) in Alaska and North America

The USGS has cooperated with federal, state, and tribal partners to conduct research on Avian Influenza (AI) viruses and to assist with response to outbreaks of highly pathogenic AI (HPAI) since 2006. Read ahead for information about HPAI, the occurrence of HPAI among wildlife, USGS-led research and surveillance efforts, and potentially helpful online resources.
By
Alaska Science Center
Q&A: Bird Flu - Ongoing Threat of Highly Pathogenic Avian Influenza (HPAI) in Alaska and North America

Q&A: Bird Flu - Ongoing Threat of Highly Pathogenic Avian Influenza (HPAI) in Alaska and North America

The USGS has cooperated with federal, state, and tribal partners to conduct research on Avian Influenza (AI) viruses and to assist with response to outbreaks of highly pathogenic AI (HPAI) since 2006. Read ahead for information about HPAI, the occurrence of HPAI among wildlife, USGS-led research and surveillance efforts, and potentially helpful online resources.
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Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Antibiotic Resistant Bacteria Acquired by Wild Birds in Urban Settings and Dispersed via Migration

U.S. Geological Survey (USGS) scientists have developed a model that demonstrates how migratory wild birds in urban areas can acquire bacteria that are resistant to antibiotics, including those used in clinics, and potentially disperse these bacteria between continents via migration.
By
Ecosystems Mission Area, Environmental Health Program, Species Management Research Program, Alaska Science Center
Antibiotic Resistant Bacteria Acquired by Wild Birds in Urban Settings and Dispersed via Migration

Antibiotic Resistant Bacteria Acquired by Wild Birds in Urban Settings and Dispersed via Migration

U.S. Geological Survey (USGS) scientists have developed a model that demonstrates how migratory wild birds in urban areas can acquire bacteria that are resistant to antibiotics, including those used in clinics, and potentially disperse these bacteria between continents via migration.
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Filter Total Items: 16

Data on Exposure of Polar Bears Inhabiting Alaska to Highly Pathogenic H5 Clade 2.3.4.4b and N1 Avian Influenza Viruses Data on Exposure of Polar Bears Inhabiting Alaska to Highly Pathogenic H5 Clade 2.3.4.4b and N1 Avian Influenza Viruses

This dataset describes reactivity of sera collected from polar bears inhabiting Alaska to various influenza A antigens to assess prior exposure to H5 clade 2.3.4.4b highly pathogenic avian influenza viruses (HPAIVs).
By
Ecosystems Mission Area, Alaska Science Center, Molecular Ecology Laboratory

Data for Characterization of Antimicrobial Resistance Genes in Surface Waters in Two National Parks in Alaska Data for Characterization of Antimicrobial Resistance Genes in Surface Waters in Two National Parks in Alaska

This data set describes the assessment of surface waters in Denali National Park and Preserve and Wrangell St. Elias National Park and Preserve for antimicrobial resistance genes during four summer months (May - August).
By
Alaska Science Center, Molecular Ecology Laboratory

Data for Investigation of Egg Mortality in a Louisiana Population of Endangered Whooping Cranes Data for Investigation of Egg Mortality in a Louisiana Population of Endangered Whooping Cranes

This data set describes the genomic bacterial analysis of swabs and tissues collected from whooping cranes in Louisiana. The data includes targeted analysis from quantitative PCR for bacterial pathogens.
By
Alaska Science Center, Molecular Ecology Laboratory

Validation and Application of a Standardized Quantitative PCR Assay for the Assessment of Antimicrobial Resistance Genes Validation and Application of a Standardized Quantitative PCR Assay for the Assessment of Antimicrobial Resistance Genes

This data set describes results for two laboratory experiments to validate a quantitative PCR assay for the assessment of antimicrobial resistance genes in surface waters. Data are also provided for the application of the assay surface water samples collected from three national parks in Alaska.
By
Alaska Science Center, Molecular Ecology Laboratory

Data for Detection of Giardia and Cryptosporidium Parasites in Surface Water of a Subarctic City Data for Detection of Giardia and Cryptosporidium Parasites in Surface Water of a Subarctic City

This dataset describes the number and detection of Giardia cysts and Cryptosporidium oocysts in water samples collected from creeks and lakes in Anchorage, Alaska during 2021.
By
Alaska Science Center

Walrus Haulout Aerial Survey Data Near Point Lay, Alaska Walrus Haulout Aerial Survey Data Near Point Lay, Alaska

This dataset consists of the complete set of processed aerial imagery and survey data from walrus haulouts collected by unoccupied aerial system (UAS) surveys near Pt. Lay, Alaska, during the autumn 2024 and 2025. The data include georeferenced optical three band (red, green, blue) aerial images and orthoimages derived from those aerial images through the standardized structure from...
By
Alaska Science Center

Data for Genomic Characterization of Highly Pathogenic H5 Avian Influenza Viruses from Alaska in 2022 Data for Genomic Characterization of Highly Pathogenic H5 Avian Influenza Viruses from Alaska in 2022

This data set describes genomic sequence information from 2022 used to infer spatiotemporal trends pertaining to the introductions of highly pathogenic H5N1 avian influenza viruses into Alaska and spread among wild birds, backyard poultry, and mammals.
By
Alaska Science Center, Molecular Ecology Laboratory

Data for Infectivity of Wild-Bird Origin Influenza A Viruses in Minnesota Wetlands Across Seasons Data for Infectivity of Wild-Bird Origin Influenza A Viruses in Minnesota Wetlands Across Seasons

This data set represents an ecological and laboratory-based experiment to understand influenza virus viability in surface water. Data tables included in this release consist of 1) daily mean water temperature, 2) viability of viruses maintained in water, 3) influenza detection in duck samples, 4) viral titers of experimentally inoculated water samples, and 5) water chemistry.
By
Alaska Science Center, Molecular Ecology Laboratory

Molecular Detection and Characterization of Highly Pathogenic H5N1 Avian Influenza Viruses in Wild Birds Inhabiting Western Alaska Provides Evidence for Three Independent Viral Introductions Molecular Detection and Characterization of Highly Pathogenic H5N1 Avian Influenza Viruses in Wild Birds Inhabiting Western Alaska Provides Evidence for Three Independent Viral Introductions

This data set describes three independent viral introductions of Highly pathogenic H5N1 avian influenza viruses into Alaska.
By
Alaska Science Center

Antimicrobial resistance testing, and qPCR detection of antimicrobial resistance genes in surface water and gull (Larus spp.) feces on the Kenai Peninsula, Alaska, 2021 Antimicrobial resistance testing, and qPCR detection of antimicrobial resistance genes in surface water and gull (Larus spp.) feces on the Kenai Peninsula, Alaska, 2021

This data set includes information on collections of surface water and fecal samples from wild gulls (Larus spp.) at two locations on the Kenai Peninsula, Alaska, USA. Samples were screened for Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) and tested for resistance to multiple antibiotics.
By
Alaska Science Center

Tracking Data for Three Large-bodied Gull Species and Hybrids (Larus spp.) Tracking Data for Three Large-bodied Gull Species and Hybrids (Larus spp.)

This data release includes 2 child items with tracking data for three large-bodied gull species and hybrids (Larus species) utilizing coastal areas of Alaska. Child Item 1: "Argos and GPS Satellite Tracking Data for Three Large-Bodied Gull Species and Hybrids (Larus spp.) - Processed Data" -- Quality-controlled data collected from Argos and Argos-linked GPS satellite transmitters.
By
Alaska Science Center

Data for Continental-Scale Dispersal of Antimicrobial Resistant Bacteria by Alaska Landfill-Foraging Gulls Data for Continental-Scale Dispersal of Antimicrobial Resistant Bacteria by Alaska Landfill-Foraging Gulls

This data set includes information on collections of fecal samples from wild gulls (Larus spp.) at seven locations in Alaska, USA. Samples were screened for Escherichia coli (E. coli) and tested for resistance to multiple antibiotics.
By
Alaska Science Center
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.
Scientists sampling surface waters for antimicrobial resistant bacteria
Scientists sampling surface waters for antimicrobial resistant bacteria
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.

Scientists sampling surface waters for antimicrobial resistant bacteria

Scientists sampling surface waters for antimicrobial resistant bacteria

Antimicrobial resistance of clinical relevance may have important implications to human and animal health. In this photo, Laura Scott and Christina Ahlstrom (USGS – Alaska Science Center) are sampling surface waters for antimicrobial resistant bacteria at Exit Creek in Kenai Fjords National Park in Alaska.

By
Alaska Science Center
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.

Scientists sampling surface waters for antimicrobial resistant bacteria

Scientists sampling surface waters for antimicrobial resistant bacteria

Antimicrobial resistance of clinical relevance may have important implications to human and animal health. In this photo, Laura Scott and Christina Ahlstrom (USGS – Alaska Science Center) are sampling surface waters for antimicrobial resistant bacteria at Exit Creek in Kenai Fjords National Park in Alaska.

By
Alaska Science Center
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.
Scientists sampling surface waters
Scientists sampling surface waters
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.

Scientists sampling surface waters

Scientists sampling surface waters

Antimicrobial resistance of clinical relevance may have important implications to human and animal health. In this photo, Laura Scott and Christina Ahlstrom (USGS – Alaska Science Center) are sampling surface waters for antimicrobial resistant bacteria at Exit Creek in Kenai Fjords National Park in Alaska.

By
Alaska Science Center
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.

Scientists sampling surface waters

Scientists sampling surface waters

Antimicrobial resistance of clinical relevance may have important implications to human and animal health. In this photo, Laura Scott and Christina Ahlstrom (USGS – Alaska Science Center) are sampling surface waters for antimicrobial resistant bacteria at Exit Creek in Kenai Fjords National Park in Alaska.

By
Alaska Science Center
Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska
Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska
Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska
Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Photo of Herring and Glaucous gulls at the Bethel Landfill, Alaska.     

By
Alaska Science Center
Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Photo of Herring and Glaucous gulls at the Bethel Landfill, Alaska.     

By
Alaska Science Center
Filter Total Items: 22

Rapid expansion of genotype D1.1 A(H5N1) influenza viruses in wild birds across North America during the 2024 migratory season Rapid expansion of genotype D1.1 A(H5N1) influenza viruses in wild birds across North America during the 2024 migratory season

In late 2021, high pathogenicity avian influenza A(H5N1) clade 2.3.4.4b viruses entered North America and reassorted rapidly with local avian influenza viruses. In September 2024, we detected a new reassortant later classified as genotype D1.1. Using active and passive avian influenza surveillance across Canada and the USA, we tracked the emergence and rapid spread of D1.1 viruses in...
Authors
Walter N. Harrington, Anthony Signore, Lisa Kercher, Jolene A. Giacinti, Ahmed Kandeil, Christina A. Ahlstrom, Sarah N. Bevins, Beate Crossley, Tom P. Fabrizio, Trushar Jeevan, Julianna B. Lenoch, Jacqueline M. Nolting, Daniel Rejmanek, David E. Stallknecht, Trent Bollinger, Evan J. Buck, Deborah Carter, Bradley S. Cohen, Krista E. Dilione, Jamie C. Feddersen, John Franks, Dayna Goldsmith, Cory J. Highway, Chelsea Himsworth, Lydia P. Holmes, Claire M. Jardine, Mohammad Jawad Jahid, Paul K. Link, Lance Miller, Nicole M. Nemeth, Madison Owsiany, Margo J. Pybus, Laura C. Scott, Christopher Sharp, Lauren Smith, Nathan J. Steelman, Brian Stevens, Yohannes Berhane, Mia K. Torchetti, Andrew M. Ramey, Rebecca L. Poulson, Richard J. Webby
By
Alaska Science Center, Molecular Ecology Laboratory

Validation and application of a standardized quantitative PCR assay for the assessment of antimicrobial resistance genes in surface water Validation and application of a standardized quantitative PCR assay for the assessment of antimicrobial resistance genes in surface water

Antimicrobial resistance can be an indicator of anthropogenic contamination in surface waters and is a potential public health threat. Methodological standardization for characterization of antimicrobial resistance in the environment is lacking. Quantitative PCR (qPCR) is used for rapid assessment of antibiotic resistance genes (ARGs) from environmental sources, including surface water...
Authors
Laura Celeste Scott, Christina A. Ahlstrom, Hanna Woksepp, Jonas Bonnedahl, Cherie Marie Mckeeman, Mark E. Miller, Dave Shirokauer, Andrew M. Ramey
By
Alaska Science Center, Molecular Ecology Laboratory

Observational, virological, and serological data provide insights into an outbreak of highly pathogenic avian influenza among wild birds on the Yukon-Kuskokwim Delta, Alaska in 2022 Observational, virological, and serological data provide insights into an outbreak of highly pathogenic avian influenza among wild birds on the Yukon-Kuskokwim Delta, Alaska in 2022

In 2021–22, clade 2.3.4.4b highly pathogenic avian influenza (HPAI) viruses were introduced by wild birds into North America, leading to geographically widespread disease. In response to HPAI outbreaks throughout late 2021 and early 2022, we recorded observations of sick and dead birds, estimated abundance of carcasses, collected swab and sera samples to detect viruses, and monitored...
Authors
Bryan Daniels, Erik E. Osnas, Megan Boldenow, Robert Gerlach, Christina A. Ahlstrom, Sarah Coburn, Michael J. Brook, Michael Brubaker, Julian Fischer, David N. Koons, Angela Matz, Marin Murphy, Daniel Rizzolo, Laura Celeste Scott, David R. Sinnett, Jordan M. Thompson, Juliana Lenoch, Mia Kim Torchetti, David E. Stallknecht, Rebecca L. Poulson, Andrew M. Ramey
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Alaska Science Center, Molecular Ecology Laboratory

Detection of Giardia and Cryptosporidium in surface water of a subarctic city Detection of Giardia and Cryptosporidium in surface water of a subarctic city

Giardia and Cryptosporidium spp. are globally distributed protozoan parasites that can cause gastrointestinal disease in humans and animals. These zoonotic parasites and their ecological relationships have been understudied in Alaska and elsewhere, despite being identified as priority zoonotic pathogens. We aimed to detect and characterize Giardia and Cryptosporidium spp. in waterbodies...
Authors
Christina A. Ahlstrom, Michael P. Carey, Damian M. Menning, Jonathan A. O’Donnell, Andrew M. Ramey
By
Alaska Science Center, Molecular Ecology Laboratory

Genomic characterization of highly pathogenic H5 avian influenza viruses from Alaska during 2022 provides evidence for genotype-specific trends of spatiotemporal and interspecies dissemination Genomic characterization of highly pathogenic H5 avian influenza viruses from Alaska during 2022 provides evidence for genotype-specific trends of spatiotemporal and interspecies dissemination

The ongoing panzootic of highly pathogenic H5 clade 2.3.4.4b avian influenza (HPAI) spread to North America in late 2021, with detections of HPAI viruses in Alaska beginning in April 2022. HPAI viruses have since spread across the state, affecting many species of wild birds as well as domestic poultry and wild mammals. To better understand the dissemination of HPAI viruses...
Authors
Christina A. Ahlstrom, Mia Kim Torchetti, Julianna B. Lenoch, Kimberlee Beckmen, Megan Boldenow, Evan J Buck, Bryan Daniels, Krista Dilione, Robert Gerlach, Kristina Lantz, Angela Matz, Rebecca L. Poulson, Laura Celeste Scott, Gay Sheffield, David R. Sinnett, David E. Stallknecht, Raphaela Stimmelmayr, Eric B. Taylor, Alison R. Williams, Andrew M. Ramey
By
Alaska Science Center, Molecular Ecology Laboratory

Infectivity of wild-bird origin Influenza A viruses in Minnesota wetlands across seasons Infectivity of wild-bird origin Influenza A viruses in Minnesota wetlands across seasons

The environmental tenacity of influenza A viruses (IAVs) in the environment likely plays a role in their transmission; IAVs are able to remain infectious in aquatic habitats and may have the capacity to seed outbreaks when susceptible wild bird hosts utilize these same environments months or even seasons later. Here, we aimed to assess the persistence of low-pathogenicity IAVs from...
Authors
Rebecca L. Poulson, Andrew B. Reeves, Christina A. Ahlstrom, Laura Celeste Scott, Laura E. Hubbard, Alinde Fojtik, Deborah L. Carter, David E. Stallknecht, Andrew M. Ramey
By
Upper Midwest Water Science Center, Alaska Science Center

Molecular detection and characterization of highly pathogenic H5N1 clade 2.3.4.4b avian influenza viruses among hunter-harvested wild birds provides evidence for three independent introductions into Alaska Molecular detection and characterization of highly pathogenic H5N1 clade 2.3.4.4b avian influenza viruses among hunter-harvested wild birds provides evidence for three independent introductions into Alaska

We detected and characterized highly pathogenic avian influenza viruses among hunter-harvested wild waterfowl inhabiting western Alaska during September–October 2022 using a molecular sequencing pipeline applied to RNA extracts derived directly from original swab samples. Genomic characterization of 10 H5 clade 2.3.4.4b avian influenza viruses detected with high confidence provided...
Authors
Andrew M. Ramey, Laura Celeste Scott, Christina A. Ahlstrom, Evan James Buck, Alison Williams, Mia Kim Torchetti, David E. Stallknecht, Rebecca L. Poulson
By
Alaska Science Center, Eastern Ecological Science Center, Molecular Ecology Laboratory

Environmental antimicrobial resistance gene detection from wild bird habitats using two methods: A commercially available culture-independent qPCR assay and culture of indicator bacteria followed by whole-genome sequencing Environmental antimicrobial resistance gene detection from wild bird habitats using two methods: A commercially available culture-independent qPCR assay and culture of indicator bacteria followed by whole-genome sequencing

Objectives
Authors
Christina A. Ahlstrom, Laura Celeste Scott, Hanna Woksepp, Jonas Bonnedahl, Andrew M. Ramey
By
Alaska Science Center

Exchange of carbapenem-resistant Escherichia coli Sequence Type 38 intercontinentally and among wild bird, human, and environmental niches Exchange of carbapenem-resistant Escherichia coli Sequence Type 38 intercontinentally and among wild bird, human, and environmental niches

Carbapenem-resistant Enterobacteriaceae (CRE) are a global threat to human health and are increasingly being isolated from nonclinical settings. OXA-48-producing Escherichia coli sequence type 38 (ST38) is the most frequently reported CRE type in wild birds and has been detected in gulls or storks in North America, Europe, Asia, and Africa. The epidemiology and evolution of CRE in...
Authors
Christina A. Ahlstrom, Hanna Woksepp, Linus Sandegren, Andrew M. Ramey, Jonas Bonnedahl
By
Alaska Science Center

Antibiotic resistance in free-ranging wildlife Antibiotic resistance in free-ranging wildlife

In this chapter, we provide an overview of antimicrobial resistant (AMR) bacteria in wildlife through the presentation of general trends of occurrence among both captive and free-ranging wild animal populations, discussion of importance to human health and wildlife conservation, and identification of priority areas for future research and monitoring efforts. Once most commonly identified...
Authors
Andrew M. Ramey, Christina A. Ahlstrom
By
Ecosystems Mission Area, Alaska Science Center

Maintenance and dissemination of avian-origin influenza A virus within the northern Atlantic Flyway of North America Maintenance and dissemination of avian-origin influenza A virus within the northern Atlantic Flyway of North America

Wild waterbirds, the natural reservoirs for avian influenza viruses, undergo migratory movements each year, connecting breeding and wintering grounds within broad corridors known as flyways. In a continental or global view, the study of virus movements within and across flyways is important to understanding virus diversity, evolution, and movement. From 2015 to 2017, we sampled waterfowl...
Authors
Diann J. Prosser, Jiani Chen, Christina A. Ahlstrom, Andrew B. Reeves, Rebecca L. Poulson, Jeffery D. Sullivan, Daniel McAuley, Carl R. Callahan, Peter C. McGowan, Justin Bahl, David E. Stallknecht, Andrew M. Ramey
By
Ecosystems Mission Area, National Wildlife Health Center, Chesapeake Bay Activities, Eastern Ecological Science Center

Genomically diverse carbapenem resistant Enterobacteriaceae from wild birds provide insight into global patterns of spatiotemporal dissemination Genomically diverse carbapenem resistant Enterobacteriaceae from wild birds provide insight into global patterns of spatiotemporal dissemination

Carbapenem resistant Enterobacteriaceae (CRE) are a threat to public health globally, yet the role of the environment in the epidemiology of CRE remains elusive. Given that wild birds can acquire CRE, likely from foraging in anthropogenically impacted areas, and may aid in the maintenance and dissemination of CRE in the environment, a spatiotemporal comparison of isolates from different...
Authors
Christina A. Ahlstrom, Hanna Woksepp, Linus Sandegren, Mashkoor Mohsin, Badrul Hasan, Denys Muzyka, Jorge Hernandez, Filip Aguirre, Atalay Tok, Jan Soderman, Bjorn Olsen, Andrew M. Ramey, Jonas Bonnedahl
By
Ecosystems Mission Area, Alaska Science Center

Non-USGS Publications**

Muellner, U., G. Fournie, P. Muellner, C. A. Ahlstrom, and D. U. Pfeiffer. 2018. Epidemix - an Interactive Multi-Model Application for Teaching and Visualizing Infectious Disease Transmission. Epidemics 23:49-54. doi:10.1016/j.epidem.2017.12.003.
Ahlstrom, C. A., P. Muellner, G. Lammers, M. Jones, S. Octavia, R. Lan, and J. Heller. 2017. Shiga-toxin producing E. coli O157 shedding dynamics in an Australian beef herd. Frontiers in Veterinary Science 4:200. doi:10.3389/fvets.2017.00200.
Ahlstrom, C. A., C. S. Manuel, H. C. Den Bakker, M. Wiedmann, and K. K. Nightingale. 2017. Molecular Ecology of Listeria spp., Salmonella, Escherichia coli O157:H7, and non-O157 Shiga Toxin Producing Escherichia coli in Pristine Natural Environments in Northern Colorado. Journal of Applied Microbiology. doi:10.1111/jam.13657.
Ahlstrom, C. A., P. Muellner, S. Spencer, S. Hong, A. Saupe, A. Rovira, C. Hedberg, A. Perez, and J. Alvarez. 2017. Inferring source attribution from a multi-year multi-source dataset of Salmonella in Minnesota. Zoonoses and Public Health 64(8):589-598. doi:10.1111/zph.12351.
Bauman, C. A., A. Jones-Bitton, C. A. Ahlstrom, L. Mutharia, J. De Buck, J. Jansen, D. F. Kelton, and P. Menzies. 2017. Identification of Mycobacterium avium ssp. paratuberculosis strains isolated from dairy goats and dairy sheep in Ontario, Canada. Canadian Journal of Veterinary Research 81(4):304-307.
Hong, S., A. Rovira, P. Davies, C. A. Ahlstrom, P. Muellner, A. Rendahl, K. Olsen, J. B. Bender, S. Wells, A. Perez, and J. Alvarez. 2016. Serotypes and antimicrobial resistance in Salmonella enterica recovered from clinical samples from cattle and swine in Minnesota, 2006 to 2015. International Journal of Parasitology: Parasites and Wildlife 11(12):e0168016. doi:10.1371/journal.pone.0168016.
Muellner, P., U. Muellner, M. C. Gates, T. Pearce, C. A. Ahlstrom, D. O'Neill, D. Brodbelt, and N. J. Cave. 2016. Evidence in Practice – A Pilot Study Leveraging Companion Animal and Equine Health Data from Primary Care Veterinary Clinics in New Zealand. Frontiers in Veterinary Science 3:116. doi:10.3389/fvets.2016.00116.
Davidson, F., C. A. Ahlstrom, J. De Buck, H. G. Whitney, and K. Tahlan. 2016. Examination of Mycobacterium avium subspecies paratuberculosis mixed genotype infections in dairy animals using a whole genome sequencing approach. PeerJ 4:e2793. doi:10.7717/peerj.2793.
Ahlstrom, C. A., H. W. Barkema, and J. De Buck. 2016. Relative frequency of 4 major strain types of Mycobacterium avium ssp. paratuberculosis in Canadian dairy herds using a novel single nucleotide polymorphism-based polymerase chain reaction. Journal of Dairy Science 99(10):8297-8303. doi:10.3168/jds.2016-11397.
Ahlstrom, C. A., H. W. Barkema, K. Stevenson, R. N. Zadoks, R. Biek, R. Kao, H. Trewby, D. Haupstein, D. F. Kelton, G. Fecteau, O. Labrecque, G. P. Keefe, S. L. B. McKenna, K. Tahlan, and J. De Buck. 2016. Genome-wide diversity and phylogeography of Mycobacterium avium subsp. paratuberculosis in Canadian dairy cattle. PLoS One 11:e0149017. doi:10.1371/journal.pone.0149017.
Ahlstrom, C. A., H. W. Barkema, K. Stevenson, R. N. Zadoks, R. Biek, R. Kao, H. Trewby, S. Hendrick, D. Haupstein, D. F. Kelton, G. Fecteau, O. Labrecque, G. P. Keefe, S. L. B. McKenna, and J. De Buck. 2015. Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level. BMC Genomics 16:161. doi:10.1186/s12864-015-1387-6.
Den Bakker, H. C., S. Warchocki, E. M. Wright, A. F. Allred, C. A. Ahlstrom, C. S. Manuel, M. J. Stasiewicz, A. Burrell, S. Roof, L. Strawn, E. D. Fortes, K. K. Nightingale, D. Kephart, and M. Wiedmann. 2014. Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov., and Listeria grandensis sp. nov., from agricultural and natural environments. International Journal of Systematic and Evolutionary Microbiology 64:1882-1889. doi:10.1099/ijs.0.052720-0.
Ahlstrom, C. A., H. W. Barkema, and J. De Buck. 2014. Improved Short-Sequence-Repeat Genotyping of Mycobacterium avium subsp. paratuberculosis by Using Matrix-Assisted Laser Desorption Ionization—Time of Flight Mass Spectrometry. Applied and Environmental Microbiology 80:534-539. doi:10.1128/AEM.03212-13.
Zadoks, R. N., H. M. Griffiths, M. A. Munoz, C. A. Ahlstrom, G. J. Bennett, E. Thomas, and Y. H. Schukken. 2011. Sources of Klebsiella and Raoultella species on dairy farms: be careful where you walk. Journal of Dairy Science 94(2):1045-1051. doi:10.3168/jds.2010-3603.
Munoz, M. A., G. J. Bennett, C. A. Ahlstrom, H. M. Griffiths, Y. H. Schukken, and R. N. Zadoks. 2008. Cleanliness Scores as Indicator of Klebsiella Exposure in Dairy Cows. Journal of Dairy Science 91(10):3908-3916. doi:10.3168/jds.2008-1090.
Munoz, M. A., C. A. Ahlstrom, B. J. Rauch, and R. N. Zadoks. 2006. Fecal Shedding of Klebsiella pneumoniae by Dairy Cows. Journal of Dairy Science 89(9):3425-3430. doi:10.3168/jds.S0022-0302(06)72379-7.
Muellner, P., D. Hodges, C. A. Ahlstrom, M. Newman, R. Davidson, D. U. Pfeiffer, J. Marshall, and C. Morley. 2018. Creating a framework for the prioritization of biosecurity risks to the New Zealand dairy industry. Transboundary and Emerging Diseases 65(4):1067-1077. doi:10.1111/tbed.12848.

**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.

Science and Products

Northern Pintail pair on water, Copper River Delta, Alaska

Avian Influenza Research

Since 2006, the USGS Alaska Science Center has been part of the State and Federal interagency team for the detection and response to highly pathogenic (HPAI) viruses in North America. Avian influenza or "bird flu" is a viral disease that primarily infects domestic poultry and wild birds. Avian influenza viruses are naturally occurring in wild birds such as ducks, geese, swans, and gulls. These...
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Alaska Science Center
Avian Influenza Research

Avian Influenza Research

Since 2006, the USGS Alaska Science Center has been part of the State and Federal interagency team for the detection and response to highly pathogenic (HPAI) viruses in North America. Avian influenza or "bird flu" is a viral disease that primarily infects domestic poultry and wild birds. Avian influenza viruses are naturally occurring in wild birds such as ducks, geese, swans, and gulls. These...
Learn More
John Reed (USGS scientist) holding a gull marked with a satellite transmitter at the Soldotna landfill in June 2016

Antibiotic Resistant Bacteria in Migratory Birds

Migratory birds, and particularly those using habitats close to human settlements, may be infected with antibiotic resistant bacteria. The USGS is working with public health professionals to understand the role of birds in the maintenance and dispersal of antibiotic resistant bacteria. Additionally, the USGS is investigating how antibiotic resistant bacteria in birds may relate to public and...
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Alaska Science Center
Antibiotic Resistant Bacteria in Migratory Birds

Antibiotic Resistant Bacteria in Migratory Birds

Migratory birds, and particularly those using habitats close to human settlements, may be infected with antibiotic resistant bacteria. The USGS is working with public health professionals to understand the role of birds in the maintenance and dispersal of antibiotic resistant bacteria. Additionally, the USGS is investigating how antibiotic resistant bacteria in birds may relate to public and...
Learn More
Scientist swabbing hunter-harvested ducks in western Alaska

Q&A: Bird Flu - Ongoing Threat of Highly Pathogenic Avian Influenza (HPAI) in Alaska and North America

The USGS has cooperated with federal, state, and tribal partners to conduct research on Avian Influenza (AI) viruses and to assist with response to outbreaks of highly pathogenic AI (HPAI) since 2006. Read ahead for information about HPAI, the occurrence of HPAI among wildlife, USGS-led research and surveillance efforts, and potentially helpful online resources.
By
Alaska Science Center
Q&A: Bird Flu - Ongoing Threat of Highly Pathogenic Avian Influenza (HPAI) in Alaska and North America

Q&A: Bird Flu - Ongoing Threat of Highly Pathogenic Avian Influenza (HPAI) in Alaska and North America

The USGS has cooperated with federal, state, and tribal partners to conduct research on Avian Influenza (AI) viruses and to assist with response to outbreaks of highly pathogenic AI (HPAI) since 2006. Read ahead for information about HPAI, the occurrence of HPAI among wildlife, USGS-led research and surveillance efforts, and potentially helpful online resources.
Learn More
Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Antibiotic Resistant Bacteria Acquired by Wild Birds in Urban Settings and Dispersed via Migration

U.S. Geological Survey (USGS) scientists have developed a model that demonstrates how migratory wild birds in urban areas can acquire bacteria that are resistant to antibiotics, including those used in clinics, and potentially disperse these bacteria between continents via migration.
By
Ecosystems Mission Area, Environmental Health Program, Species Management Research Program, Alaska Science Center
Antibiotic Resistant Bacteria Acquired by Wild Birds in Urban Settings and Dispersed via Migration

Antibiotic Resistant Bacteria Acquired by Wild Birds in Urban Settings and Dispersed via Migration

U.S. Geological Survey (USGS) scientists have developed a model that demonstrates how migratory wild birds in urban areas can acquire bacteria that are resistant to antibiotics, including those used in clinics, and potentially disperse these bacteria between continents via migration.
Learn More
Filter Total Items: 16

Data on Exposure of Polar Bears Inhabiting Alaska to Highly Pathogenic H5 Clade 2.3.4.4b and N1 Avian Influenza Viruses Data on Exposure of Polar Bears Inhabiting Alaska to Highly Pathogenic H5 Clade 2.3.4.4b and N1 Avian Influenza Viruses

This dataset describes reactivity of sera collected from polar bears inhabiting Alaska to various influenza A antigens to assess prior exposure to H5 clade 2.3.4.4b highly pathogenic avian influenza viruses (HPAIVs).
By
Ecosystems Mission Area, Alaska Science Center, Molecular Ecology Laboratory

Data for Characterization of Antimicrobial Resistance Genes in Surface Waters in Two National Parks in Alaska Data for Characterization of Antimicrobial Resistance Genes in Surface Waters in Two National Parks in Alaska

This data set describes the assessment of surface waters in Denali National Park and Preserve and Wrangell St. Elias National Park and Preserve for antimicrobial resistance genes during four summer months (May - August).
By
Alaska Science Center, Molecular Ecology Laboratory

Data for Investigation of Egg Mortality in a Louisiana Population of Endangered Whooping Cranes Data for Investigation of Egg Mortality in a Louisiana Population of Endangered Whooping Cranes

This data set describes the genomic bacterial analysis of swabs and tissues collected from whooping cranes in Louisiana. The data includes targeted analysis from quantitative PCR for bacterial pathogens.
By
Alaska Science Center, Molecular Ecology Laboratory

Validation and Application of a Standardized Quantitative PCR Assay for the Assessment of Antimicrobial Resistance Genes Validation and Application of a Standardized Quantitative PCR Assay for the Assessment of Antimicrobial Resistance Genes

This data set describes results for two laboratory experiments to validate a quantitative PCR assay for the assessment of antimicrobial resistance genes in surface waters. Data are also provided for the application of the assay surface water samples collected from three national parks in Alaska.
By
Alaska Science Center, Molecular Ecology Laboratory

Data for Detection of Giardia and Cryptosporidium Parasites in Surface Water of a Subarctic City Data for Detection of Giardia and Cryptosporidium Parasites in Surface Water of a Subarctic City

This dataset describes the number and detection of Giardia cysts and Cryptosporidium oocysts in water samples collected from creeks and lakes in Anchorage, Alaska during 2021.
By
Alaska Science Center

Walrus Haulout Aerial Survey Data Near Point Lay, Alaska Walrus Haulout Aerial Survey Data Near Point Lay, Alaska

This dataset consists of the complete set of processed aerial imagery and survey data from walrus haulouts collected by unoccupied aerial system (UAS) surveys near Pt. Lay, Alaska, during the autumn 2024 and 2025. The data include georeferenced optical three band (red, green, blue) aerial images and orthoimages derived from those aerial images through the standardized structure from...
By
Alaska Science Center

Data for Genomic Characterization of Highly Pathogenic H5 Avian Influenza Viruses from Alaska in 2022 Data for Genomic Characterization of Highly Pathogenic H5 Avian Influenza Viruses from Alaska in 2022

This data set describes genomic sequence information from 2022 used to infer spatiotemporal trends pertaining to the introductions of highly pathogenic H5N1 avian influenza viruses into Alaska and spread among wild birds, backyard poultry, and mammals.
By
Alaska Science Center, Molecular Ecology Laboratory

Data for Infectivity of Wild-Bird Origin Influenza A Viruses in Minnesota Wetlands Across Seasons Data for Infectivity of Wild-Bird Origin Influenza A Viruses in Minnesota Wetlands Across Seasons

This data set represents an ecological and laboratory-based experiment to understand influenza virus viability in surface water. Data tables included in this release consist of 1) daily mean water temperature, 2) viability of viruses maintained in water, 3) influenza detection in duck samples, 4) viral titers of experimentally inoculated water samples, and 5) water chemistry.
By
Alaska Science Center, Molecular Ecology Laboratory

Molecular Detection and Characterization of Highly Pathogenic H5N1 Avian Influenza Viruses in Wild Birds Inhabiting Western Alaska Provides Evidence for Three Independent Viral Introductions Molecular Detection and Characterization of Highly Pathogenic H5N1 Avian Influenza Viruses in Wild Birds Inhabiting Western Alaska Provides Evidence for Three Independent Viral Introductions

This data set describes three independent viral introductions of Highly pathogenic H5N1 avian influenza viruses into Alaska.
By
Alaska Science Center

Antimicrobial resistance testing, and qPCR detection of antimicrobial resistance genes in surface water and gull (Larus spp.) feces on the Kenai Peninsula, Alaska, 2021 Antimicrobial resistance testing, and qPCR detection of antimicrobial resistance genes in surface water and gull (Larus spp.) feces on the Kenai Peninsula, Alaska, 2021

This data set includes information on collections of surface water and fecal samples from wild gulls (Larus spp.) at two locations on the Kenai Peninsula, Alaska, USA. Samples were screened for Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) and tested for resistance to multiple antibiotics.
By
Alaska Science Center

Tracking Data for Three Large-bodied Gull Species and Hybrids (Larus spp.) Tracking Data for Three Large-bodied Gull Species and Hybrids (Larus spp.)

This data release includes 2 child items with tracking data for three large-bodied gull species and hybrids (Larus species) utilizing coastal areas of Alaska. Child Item 1: "Argos and GPS Satellite Tracking Data for Three Large-Bodied Gull Species and Hybrids (Larus spp.) - Processed Data" -- Quality-controlled data collected from Argos and Argos-linked GPS satellite transmitters.
By
Alaska Science Center

Data for Continental-Scale Dispersal of Antimicrobial Resistant Bacteria by Alaska Landfill-Foraging Gulls Data for Continental-Scale Dispersal of Antimicrobial Resistant Bacteria by Alaska Landfill-Foraging Gulls

This data set includes information on collections of fecal samples from wild gulls (Larus spp.) at seven locations in Alaska, USA. Samples were screened for Escherichia coli (E. coli) and tested for resistance to multiple antibiotics.
By
Alaska Science Center
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.
Scientists sampling surface waters for antimicrobial resistant bacteria
Scientists sampling surface waters for antimicrobial resistant bacteria
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.

Scientists sampling surface waters for antimicrobial resistant bacteria

Scientists sampling surface waters for antimicrobial resistant bacteria

Antimicrobial resistance of clinical relevance may have important implications to human and animal health. In this photo, Laura Scott and Christina Ahlstrom (USGS – Alaska Science Center) are sampling surface waters for antimicrobial resistant bacteria at Exit Creek in Kenai Fjords National Park in Alaska.

By
Alaska Science Center
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.

Scientists sampling surface waters for antimicrobial resistant bacteria

Scientists sampling surface waters for antimicrobial resistant bacteria

Antimicrobial resistance of clinical relevance may have important implications to human and animal health. In this photo, Laura Scott and Christina Ahlstrom (USGS – Alaska Science Center) are sampling surface waters for antimicrobial resistant bacteria at Exit Creek in Kenai Fjords National Park in Alaska.

By
Alaska Science Center
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.
Scientists sampling surface waters
Scientists sampling surface waters
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.

Scientists sampling surface waters

Scientists sampling surface waters

Antimicrobial resistance of clinical relevance may have important implications to human and animal health. In this photo, Laura Scott and Christina Ahlstrom (USGS – Alaska Science Center) are sampling surface waters for antimicrobial resistant bacteria at Exit Creek in Kenai Fjords National Park in Alaska.

By
Alaska Science Center
Two female scientists with USGS hat on rocky creek bank with water sampling equipment. Trees, mountains, and glacier in back.

Scientists sampling surface waters

Scientists sampling surface waters

Antimicrobial resistance of clinical relevance may have important implications to human and animal health. In this photo, Laura Scott and Christina Ahlstrom (USGS – Alaska Science Center) are sampling surface waters for antimicrobial resistant bacteria at Exit Creek in Kenai Fjords National Park in Alaska.

By
Alaska Science Center
Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska
Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska
Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska
Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Photo of Herring and Glaucous gulls at the Bethel Landfill, Alaska.     

By
Alaska Science Center
Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Herring and Glaucous gulls at the Bethel Landfill, Bethel, Alaska

Photo of Herring and Glaucous gulls at the Bethel Landfill, Alaska.     

By
Alaska Science Center
Filter Total Items: 22

Rapid expansion of genotype D1.1 A(H5N1) influenza viruses in wild birds across North America during the 2024 migratory season Rapid expansion of genotype D1.1 A(H5N1) influenza viruses in wild birds across North America during the 2024 migratory season

In late 2021, high pathogenicity avian influenza A(H5N1) clade 2.3.4.4b viruses entered North America and reassorted rapidly with local avian influenza viruses. In September 2024, we detected a new reassortant later classified as genotype D1.1. Using active and passive avian influenza surveillance across Canada and the USA, we tracked the emergence and rapid spread of D1.1 viruses in...
Authors
Walter N. Harrington, Anthony Signore, Lisa Kercher, Jolene A. Giacinti, Ahmed Kandeil, Christina A. Ahlstrom, Sarah N. Bevins, Beate Crossley, Tom P. Fabrizio, Trushar Jeevan, Julianna B. Lenoch, Jacqueline M. Nolting, Daniel Rejmanek, David E. Stallknecht, Trent Bollinger, Evan J. Buck, Deborah Carter, Bradley S. Cohen, Krista E. Dilione, Jamie C. Feddersen, John Franks, Dayna Goldsmith, Cory J. Highway, Chelsea Himsworth, Lydia P. Holmes, Claire M. Jardine, Mohammad Jawad Jahid, Paul K. Link, Lance Miller, Nicole M. Nemeth, Madison Owsiany, Margo J. Pybus, Laura C. Scott, Christopher Sharp, Lauren Smith, Nathan J. Steelman, Brian Stevens, Yohannes Berhane, Mia K. Torchetti, Andrew M. Ramey, Rebecca L. Poulson, Richard J. Webby
By
Alaska Science Center, Molecular Ecology Laboratory

Validation and application of a standardized quantitative PCR assay for the assessment of antimicrobial resistance genes in surface water Validation and application of a standardized quantitative PCR assay for the assessment of antimicrobial resistance genes in surface water

Antimicrobial resistance can be an indicator of anthropogenic contamination in surface waters and is a potential public health threat. Methodological standardization for characterization of antimicrobial resistance in the environment is lacking. Quantitative PCR (qPCR) is used for rapid assessment of antibiotic resistance genes (ARGs) from environmental sources, including surface water...
Authors
Laura Celeste Scott, Christina A. Ahlstrom, Hanna Woksepp, Jonas Bonnedahl, Cherie Marie Mckeeman, Mark E. Miller, Dave Shirokauer, Andrew M. Ramey
By
Alaska Science Center, Molecular Ecology Laboratory

Observational, virological, and serological data provide insights into an outbreak of highly pathogenic avian influenza among wild birds on the Yukon-Kuskokwim Delta, Alaska in 2022 Observational, virological, and serological data provide insights into an outbreak of highly pathogenic avian influenza among wild birds on the Yukon-Kuskokwim Delta, Alaska in 2022

In 2021–22, clade 2.3.4.4b highly pathogenic avian influenza (HPAI) viruses were introduced by wild birds into North America, leading to geographically widespread disease. In response to HPAI outbreaks throughout late 2021 and early 2022, we recorded observations of sick and dead birds, estimated abundance of carcasses, collected swab and sera samples to detect viruses, and monitored...
Authors
Bryan Daniels, Erik E. Osnas, Megan Boldenow, Robert Gerlach, Christina A. Ahlstrom, Sarah Coburn, Michael J. Brook, Michael Brubaker, Julian Fischer, David N. Koons, Angela Matz, Marin Murphy, Daniel Rizzolo, Laura Celeste Scott, David R. Sinnett, Jordan M. Thompson, Juliana Lenoch, Mia Kim Torchetti, David E. Stallknecht, Rebecca L. Poulson, Andrew M. Ramey
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Alaska Science Center, Molecular Ecology Laboratory

Detection of Giardia and Cryptosporidium in surface water of a subarctic city Detection of Giardia and Cryptosporidium in surface water of a subarctic city

Giardia and Cryptosporidium spp. are globally distributed protozoan parasites that can cause gastrointestinal disease in humans and animals. These zoonotic parasites and their ecological relationships have been understudied in Alaska and elsewhere, despite being identified as priority zoonotic pathogens. We aimed to detect and characterize Giardia and Cryptosporidium spp. in waterbodies...
Authors
Christina A. Ahlstrom, Michael P. Carey, Damian M. Menning, Jonathan A. O’Donnell, Andrew M. Ramey
By
Alaska Science Center, Molecular Ecology Laboratory

Genomic characterization of highly pathogenic H5 avian influenza viruses from Alaska during 2022 provides evidence for genotype-specific trends of spatiotemporal and interspecies dissemination Genomic characterization of highly pathogenic H5 avian influenza viruses from Alaska during 2022 provides evidence for genotype-specific trends of spatiotemporal and interspecies dissemination

The ongoing panzootic of highly pathogenic H5 clade 2.3.4.4b avian influenza (HPAI) spread to North America in late 2021, with detections of HPAI viruses in Alaska beginning in April 2022. HPAI viruses have since spread across the state, affecting many species of wild birds as well as domestic poultry and wild mammals. To better understand the dissemination of HPAI viruses...
Authors
Christina A. Ahlstrom, Mia Kim Torchetti, Julianna B. Lenoch, Kimberlee Beckmen, Megan Boldenow, Evan J Buck, Bryan Daniels, Krista Dilione, Robert Gerlach, Kristina Lantz, Angela Matz, Rebecca L. Poulson, Laura Celeste Scott, Gay Sheffield, David R. Sinnett, David E. Stallknecht, Raphaela Stimmelmayr, Eric B. Taylor, Alison R. Williams, Andrew M. Ramey
By
Alaska Science Center, Molecular Ecology Laboratory

Infectivity of wild-bird origin Influenza A viruses in Minnesota wetlands across seasons Infectivity of wild-bird origin Influenza A viruses in Minnesota wetlands across seasons

The environmental tenacity of influenza A viruses (IAVs) in the environment likely plays a role in their transmission; IAVs are able to remain infectious in aquatic habitats and may have the capacity to seed outbreaks when susceptible wild bird hosts utilize these same environments months or even seasons later. Here, we aimed to assess the persistence of low-pathogenicity IAVs from...
Authors
Rebecca L. Poulson, Andrew B. Reeves, Christina A. Ahlstrom, Laura Celeste Scott, Laura E. Hubbard, Alinde Fojtik, Deborah L. Carter, David E. Stallknecht, Andrew M. Ramey
By
Upper Midwest Water Science Center, Alaska Science Center

Molecular detection and characterization of highly pathogenic H5N1 clade 2.3.4.4b avian influenza viruses among hunter-harvested wild birds provides evidence for three independent introductions into Alaska Molecular detection and characterization of highly pathogenic H5N1 clade 2.3.4.4b avian influenza viruses among hunter-harvested wild birds provides evidence for three independent introductions into Alaska

We detected and characterized highly pathogenic avian influenza viruses among hunter-harvested wild waterfowl inhabiting western Alaska during September–October 2022 using a molecular sequencing pipeline applied to RNA extracts derived directly from original swab samples. Genomic characterization of 10 H5 clade 2.3.4.4b avian influenza viruses detected with high confidence provided...
Authors
Andrew M. Ramey, Laura Celeste Scott, Christina A. Ahlstrom, Evan James Buck, Alison Williams, Mia Kim Torchetti, David E. Stallknecht, Rebecca L. Poulson
By
Alaska Science Center, Eastern Ecological Science Center, Molecular Ecology Laboratory

Environmental antimicrobial resistance gene detection from wild bird habitats using two methods: A commercially available culture-independent qPCR assay and culture of indicator bacteria followed by whole-genome sequencing Environmental antimicrobial resistance gene detection from wild bird habitats using two methods: A commercially available culture-independent qPCR assay and culture of indicator bacteria followed by whole-genome sequencing

Objectives
Authors
Christina A. Ahlstrom, Laura Celeste Scott, Hanna Woksepp, Jonas Bonnedahl, Andrew M. Ramey
By
Alaska Science Center

Exchange of carbapenem-resistant Escherichia coli Sequence Type 38 intercontinentally and among wild bird, human, and environmental niches Exchange of carbapenem-resistant Escherichia coli Sequence Type 38 intercontinentally and among wild bird, human, and environmental niches

Carbapenem-resistant Enterobacteriaceae (CRE) are a global threat to human health and are increasingly being isolated from nonclinical settings. OXA-48-producing Escherichia coli sequence type 38 (ST38) is the most frequently reported CRE type in wild birds and has been detected in gulls or storks in North America, Europe, Asia, and Africa. The epidemiology and evolution of CRE in...
Authors
Christina A. Ahlstrom, Hanna Woksepp, Linus Sandegren, Andrew M. Ramey, Jonas Bonnedahl
By
Alaska Science Center

Antibiotic resistance in free-ranging wildlife Antibiotic resistance in free-ranging wildlife

In this chapter, we provide an overview of antimicrobial resistant (AMR) bacteria in wildlife through the presentation of general trends of occurrence among both captive and free-ranging wild animal populations, discussion of importance to human health and wildlife conservation, and identification of priority areas for future research and monitoring efforts. Once most commonly identified...
Authors
Andrew M. Ramey, Christina A. Ahlstrom
By
Ecosystems Mission Area, Alaska Science Center

Maintenance and dissemination of avian-origin influenza A virus within the northern Atlantic Flyway of North America Maintenance and dissemination of avian-origin influenza A virus within the northern Atlantic Flyway of North America

Wild waterbirds, the natural reservoirs for avian influenza viruses, undergo migratory movements each year, connecting breeding and wintering grounds within broad corridors known as flyways. In a continental or global view, the study of virus movements within and across flyways is important to understanding virus diversity, evolution, and movement. From 2015 to 2017, we sampled waterfowl...
Authors
Diann J. Prosser, Jiani Chen, Christina A. Ahlstrom, Andrew B. Reeves, Rebecca L. Poulson, Jeffery D. Sullivan, Daniel McAuley, Carl R. Callahan, Peter C. McGowan, Justin Bahl, David E. Stallknecht, Andrew M. Ramey
By
Ecosystems Mission Area, National Wildlife Health Center, Chesapeake Bay Activities, Eastern Ecological Science Center

Genomically diverse carbapenem resistant Enterobacteriaceae from wild birds provide insight into global patterns of spatiotemporal dissemination Genomically diverse carbapenem resistant Enterobacteriaceae from wild birds provide insight into global patterns of spatiotemporal dissemination

Carbapenem resistant Enterobacteriaceae (CRE) are a threat to public health globally, yet the role of the environment in the epidemiology of CRE remains elusive. Given that wild birds can acquire CRE, likely from foraging in anthropogenically impacted areas, and may aid in the maintenance and dissemination of CRE in the environment, a spatiotemporal comparison of isolates from different...
Authors
Christina A. Ahlstrom, Hanna Woksepp, Linus Sandegren, Mashkoor Mohsin, Badrul Hasan, Denys Muzyka, Jorge Hernandez, Filip Aguirre, Atalay Tok, Jan Soderman, Bjorn Olsen, Andrew M. Ramey, Jonas Bonnedahl
By
Ecosystems Mission Area, Alaska Science Center

Non-USGS Publications**

Muellner, U., G. Fournie, P. Muellner, C. A. Ahlstrom, and D. U. Pfeiffer. 2018. Epidemix - an Interactive Multi-Model Application for Teaching and Visualizing Infectious Disease Transmission. Epidemics 23:49-54. doi:10.1016/j.epidem.2017.12.003.
Ahlstrom, C. A., P. Muellner, G. Lammers, M. Jones, S. Octavia, R. Lan, and J. Heller. 2017. Shiga-toxin producing E. coli O157 shedding dynamics in an Australian beef herd. Frontiers in Veterinary Science 4:200. doi:10.3389/fvets.2017.00200.
Ahlstrom, C. A., C. S. Manuel, H. C. Den Bakker, M. Wiedmann, and K. K. Nightingale. 2017. Molecular Ecology of Listeria spp., Salmonella, Escherichia coli O157:H7, and non-O157 Shiga Toxin Producing Escherichia coli in Pristine Natural Environments in Northern Colorado. Journal of Applied Microbiology. doi:10.1111/jam.13657.
Ahlstrom, C. A., P. Muellner, S. Spencer, S. Hong, A. Saupe, A. Rovira, C. Hedberg, A. Perez, and J. Alvarez. 2017. Inferring source attribution from a multi-year multi-source dataset of Salmonella in Minnesota. Zoonoses and Public Health 64(8):589-598. doi:10.1111/zph.12351.
Bauman, C. A., A. Jones-Bitton, C. A. Ahlstrom, L. Mutharia, J. De Buck, J. Jansen, D. F. Kelton, and P. Menzies. 2017. Identification of Mycobacterium avium ssp. paratuberculosis strains isolated from dairy goats and dairy sheep in Ontario, Canada. Canadian Journal of Veterinary Research 81(4):304-307.
Hong, S., A. Rovira, P. Davies, C. A. Ahlstrom, P. Muellner, A. Rendahl, K. Olsen, J. B. Bender, S. Wells, A. Perez, and J. Alvarez. 2016. Serotypes and antimicrobial resistance in Salmonella enterica recovered from clinical samples from cattle and swine in Minnesota, 2006 to 2015. International Journal of Parasitology: Parasites and Wildlife 11(12):e0168016. doi:10.1371/journal.pone.0168016.
Muellner, P., U. Muellner, M. C. Gates, T. Pearce, C. A. Ahlstrom, D. O'Neill, D. Brodbelt, and N. J. Cave. 2016. Evidence in Practice – A Pilot Study Leveraging Companion Animal and Equine Health Data from Primary Care Veterinary Clinics in New Zealand. Frontiers in Veterinary Science 3:116. doi:10.3389/fvets.2016.00116.
Davidson, F., C. A. Ahlstrom, J. De Buck, H. G. Whitney, and K. Tahlan. 2016. Examination of Mycobacterium avium subspecies paratuberculosis mixed genotype infections in dairy animals using a whole genome sequencing approach. PeerJ 4:e2793. doi:10.7717/peerj.2793.
Ahlstrom, C. A., H. W. Barkema, and J. De Buck. 2016. Relative frequency of 4 major strain types of Mycobacterium avium ssp. paratuberculosis in Canadian dairy herds using a novel single nucleotide polymorphism-based polymerase chain reaction. Journal of Dairy Science 99(10):8297-8303. doi:10.3168/jds.2016-11397.
Ahlstrom, C. A., H. W. Barkema, K. Stevenson, R. N. Zadoks, R. Biek, R. Kao, H. Trewby, D. Haupstein, D. F. Kelton, G. Fecteau, O. Labrecque, G. P. Keefe, S. L. B. McKenna, K. Tahlan, and J. De Buck. 2016. Genome-wide diversity and phylogeography of Mycobacterium avium subsp. paratuberculosis in Canadian dairy cattle. PLoS One 11:e0149017. doi:10.1371/journal.pone.0149017.
Ahlstrom, C. A., H. W. Barkema, K. Stevenson, R. N. Zadoks, R. Biek, R. Kao, H. Trewby, S. Hendrick, D. Haupstein, D. F. Kelton, G. Fecteau, O. Labrecque, G. P. Keefe, S. L. B. McKenna, and J. De Buck. 2015. Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level. BMC Genomics 16:161. doi:10.1186/s12864-015-1387-6.
Den Bakker, H. C., S. Warchocki, E. M. Wright, A. F. Allred, C. A. Ahlstrom, C. S. Manuel, M. J. Stasiewicz, A. Burrell, S. Roof, L. Strawn, E. D. Fortes, K. K. Nightingale, D. Kephart, and M. Wiedmann. 2014. Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov., and Listeria grandensis sp. nov., from agricultural and natural environments. International Journal of Systematic and Evolutionary Microbiology 64:1882-1889. doi:10.1099/ijs.0.052720-0.
Ahlstrom, C. A., H. W. Barkema, and J. De Buck. 2014. Improved Short-Sequence-Repeat Genotyping of Mycobacterium avium subsp. paratuberculosis by Using Matrix-Assisted Laser Desorption Ionization—Time of Flight Mass Spectrometry. Applied and Environmental Microbiology 80:534-539. doi:10.1128/AEM.03212-13.
Zadoks, R. N., H. M. Griffiths, M. A. Munoz, C. A. Ahlstrom, G. J. Bennett, E. Thomas, and Y. H. Schukken. 2011. Sources of Klebsiella and Raoultella species on dairy farms: be careful where you walk. Journal of Dairy Science 94(2):1045-1051. doi:10.3168/jds.2010-3603.
Munoz, M. A., G. J. Bennett, C. A. Ahlstrom, H. M. Griffiths, Y. H. Schukken, and R. N. Zadoks. 2008. Cleanliness Scores as Indicator of Klebsiella Exposure in Dairy Cows. Journal of Dairy Science 91(10):3908-3916. doi:10.3168/jds.2008-1090.
Munoz, M. A., C. A. Ahlstrom, B. J. Rauch, and R. N. Zadoks. 2006. Fecal Shedding of Klebsiella pneumoniae by Dairy Cows. Journal of Dairy Science 89(9):3425-3430. doi:10.3168/jds.S0022-0302(06)72379-7.
Muellner, P., D. Hodges, C. A. Ahlstrom, M. Newman, R. Davidson, D. U. Pfeiffer, J. Marshall, and C. Morley. 2018. Creating a framework for the prioritization of biosecurity risks to the New Zealand dairy industry. Transboundary and Emerging Diseases 65(4):1067-1077. doi:10.1111/tbed.12848.

**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.

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