For a list of all publications: Search Pubmed
Selected publications
2026
Seeram D, Park H, Abrams JA, Uhlemann AC, Freedberg DE. Vancomycin-resistant Enterococcus often spreads from hospitalized patients into the local environment and less often spreads from the environment into patients. J Infect Dis. 2026 Apr 28:jiag240. doi: 10.1093/infdis/jiag240. Online ahead of print. PMID: 42047567
Parker JK, Toursarkissian LP, Chang JR, Sanchez-Paiva S, O’Donnell AC, Badmus HO, Nunez MP, Uhlemann A-C, Davies BW. Prevalence and activity of class II microcins in Serratia marcescens strains by isolation source. Appl Environ Microbiol. 2026 Apr 22;92(4):e0025926. doi: 10.1128/aem.00259-26. Epub 2026 Mar 31. PMID: 41914898
2025
Nobel YR, Park H, Tillman AM, Seeram D, Moallem DH, Intara A, Nandakumar R, Annavajhala MK, Gomez-Simmonds A, Verna EC, Uhlemann AC. Fecal Microbiota and Bile Acid Profiles in Early-Stage Hepatocellular Carcinoma: A Matched Case-Control Study. Clin Transl Gastroenterol. 2025 Dec 1;16(12):e00928. doi: 10.14309/ctg.0000000000000928. PMID: 41036798
Annavajhala MK, Kelley AL, Wen L, Tagliavia M, Moscovitz SZ, Park H, Huang S, Zucker JE, Uhlemann AC. Hospital wastewater surveillance for SARS-CoV-2 identifies intra-hospital dynamics of viral transmission and evolution. Appl Environ Microbiol. 2025 Jul 23;91(7):e0050125. doi: 10.1128/aem.00501-25.
Shoucri S, Blair NJ, Seeram D, Gomez-Simmonds A, Shi Q, Lowy FD, Uhlemann AC. The Clinical and molecular characteristics of community-associated Staphylococcus aureus bacteremia in persons who inject drugs at a New York City tertiary care facility during the opioid epidemic. Open Forum Infect Dis. 2025 May 21;12(6):ofaf304. doi: 10.1093/ofid/ofaf304. eCollection 2025 Jun.
Austin GI, Brown Kav A, ElNaggar S, Park H, Biermann J, Uhlemann AC, Pe’er I, Korem T. Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models. Nat Microbiol. 2025. doi: 10.1038/s41564-025-01954-4.
Park H, Abrams JA, Uhlemann AC, Freedberg DE. Gut colonization with vancomycin-resistant Enterococcus shapes the gut microbiome in the intensive care unit. J Infect Dis. 2025 Apr 16:jiaf194. doi: 10.1093/infdis/jiaf194.
Nenad Macesic, Anne-Catrin Uhlemann, Peleg AY. Multidrug-resistant Gram-negative bacterial infections. The Lancet. 2025;405(10474):257-272. PMID: 39826970
Cascante Vega J, Yaari R, Robin T, Wen L, Zucker J, Uhlemann AC, Pei S, Shaman J. Estimating nosocomial transmission of micro-organisms in hospital settings using patient records and culture data. Epidemics. 2025 Jan 25;50:100817. doi: 10.1016/j.epidem.2025.100817. Online ahead of print.PMID: 39946776
2024
Gomez-Simmonds A, Annavajhala MK, Seeram D, Hokunson TW, Park H, Uhlemann AC. Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a ten-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of blaKPC. Genome Research. 2024. Oct 4:gr.279355.124. doi: 10.1101/gr.279355.124.
Balamohan A, Annavajhala MK, Boyar V, Chong A, Uhlemann AC, Rubin LG. Recurrent colonization with methicillin-susceptible Staphylococcus aureus after successful decolonization in a neonatal intensive care unit. Infect Control Hosp Epidemiol. 2024 Oct 16:1-3. doi: 10.1017/ice.2024.110.
2023
Park H, Uhlemann AC, Jacobs SS, Mowbray C, Jubelirer T, Kelly KM, Walters M, Ladas EJ. Title: Obesogenic microbial signatures and the development of obesity in childhood acute lymphoblastic leukemia. Leukemia Research. 2023;126:107017.
Austin GI, Park H, Meydan Y, Seeram D, Sezin T, Lou YC, Firek BA, Morowitz MJ, Banfield JF, Christiano AM, Pe’er I, Uhlemann AC, Shenhav L, Korem T. Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data. Nat Biotechnol. 2023; 41(12):1820-1828. PMID: 36928429.
Ahmad M, Prensky H, Balestrieri J, ElNaggar S, Gomez-Simmonds A, Uhlemann AC, Traxler B, Singh A, Lopatkin AJ. Tradeoff between lag time and growth rate drives the plasmid acquisition cost. Nat Commun. 2023 Apr 24;14(1):2343. doi: 10.1038/s41467-023-38022-6.
2022
McConville TH, Austin ED, Geng W, Shi Q, Balasubramanian D, Kubin CJ, Torres VJ, Uhlemann A-C. In Vitro Cytotoxicity and Clinical Correlates of MRSA Bacteremia. Antimicrobial Agents and Chemotherapy. 2022;66(1):e01559-21.
Gomez-Simmonds A, Annavajhala MK, Tang N, Rozenberg FD, Ahmad M, Park H, Lopatkin AJ, Uhlemann AC. Population structure of blaKPC-harbouring IncN plasmids at a New York City medical centre and evidence for multi-species horizontal transmission. Journal of Antimicrobial Chemotherapy. 2022;77(7):1873-1882.
Gomez-Simmonds A, Annavajhala MK, Nunez MP, Macesic N, Park H, Uhlemann A-C. Intestinal Dysbiosis and Risk of Posttransplant Clostridioides difficile Infection in a Longitudinal Cohort of Liver Transplant Recipients. mSphere 2022;7(5):e00361-22.
Iketani S, Mohri H, Culbertson B, Hong SJ, Duan Y, Luck MI, Annavajhala MK, Guo Y, Sheng Z, Uhlemann AC, Goff SP, Sabo Y, Yang H, Chavez A, Ho DD. Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir. Nature. 2023 Jan;613(7944):558-564. doi: 10.1038/s41586-022-05514-2.
Annavajhala MK, Kelly NE, Geng W, Ferguson SA, Giddins MJ, Grohs EC, Hill-Ricciuti A, Green DA, Saiman L, Uhlemann AC. Genomic and Epidemiological Features of Two Dominant Methicillin-Susceptible Staphylococcus aureus Clones from a Neonatal Intensive Care Unit Surveillance Effort. mSphere. 2022 Dec 21;7(6):e0040922. doi:10.1128/msphere.00409-22.
Satlin MJ, Chen L, Gomez-Simmonds A, Marino J, Weston G, Bhowmick T, Seo SK, Sperber SJ, Kim AC, Eilertson B, Derti S, Jenkins SG, Levi MH, Weinstein MP, Tang YW, Hong T, Juretschko S, Hoffman KL, Walsh TJ, Westblade LF, Uhlemann AC, Kreiswirth BN. Impact of a Rapid Molecular Test for Klebsiella pneumoniae Carbapenemase and Ceftazidime-Avibactam Use on Outcomes After Bacteremia Caused by Carbapenem-Resistant Enterobacterales. Clin Infect Dis. 2022 Dec 19;75(12):2066-2075. doi: 10.1093/cid/ciac354.
Wong Fok Lung T, Charytonowicz D, Beaumont KG, Shah SS, Sridhar SH, Gorrie CL, Mu A, Hofstaedter CE, Varisco D, McConville TH, Drikic M, Fowler B, Urso A, Shi W, Fucich D, Annavajhala MK, Khan IN, Oussenko I, Francoeur N, Smith ML, Stockwell BR, Lewis IA, Hachani A, Upadhyay Baskota S, Uhlemann AC, Ahn D, Ernst RK, Howden BP, Sebra R, Prince A. Klebsiella pneumoniae induces host metabolic stress that promotes tolerance to pulmonary infection. Cell Metab. 2022 May 3;34(5):761-774.e9. doi: 10.1016/j.cmet.2022.03.009.
2021
Nobel YR, Rozenberg F, Park H, Freedberg DE, Blaser MJ, Green PHR, Uhlemann AC, Lebwohl B. Lack of Effect of Gluten Challenge on Fecal Microbiome in Patients With Celiac Disease and Non-Celiac Gluten Sensitivity. Clin Transl Gastroenterol. 2021;12(12):e00441.
Annavajhala MK, Mohri H, Zucker JE, Sheng Z, Wang P, Gomez-Simmonds A, Ho DD, Uhlemann AC. A novel SARS-CoV-2 variant of concern, B.1.526, identified in New York. Nature. 2021; 597:703-708. PMC8481122.
Annavajhala MK, Mohri H, Wang P, Nair M, Zucker JE, Sheng Z, Gomez-Simmonds A, Kelley AL, Tagliavia M, Huang Y, Bedford T, Ho DD, Uhlemann A-C. Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Nature. 2021;597(7878):703-708.
2020
McConville TH, Annavajhala MK, Giddins MJ, Macesic N, Herrera CM, Rozenberg FD, Bhushan GL, Ahn D, Mancia F, Trent MS, Uhlemann A-C. CrrB Positively Regulates High-Level Polymyxin Resistance and Virulence in Klebsiella pneumoniae. Cell Reports. 2020;33(4).
Macesic N, Walk OJBDt, Pe’er I, Tatonetti NP, Peleg AY, Uhlemann A-C. Predicting Phenotypic Polymyxin Resistance in Klebsiella pneumoniae through Machine Learning Analysis of Genomic Data. mSystems. 2020;5(3):10.1128/msystems.00656-19.
Gomez-Simmonds A, Annavajhala MK, McConville TH, Dietz DE, Shoucri SM, Laracy JC, Rozenberg FD, Nelson B, Greendyke WG, Furuya EY, Whittier S, Uhlemann A-C. Carbapenemase-producing Enterobacterales causing secondary infections during the COVID-19 crisis at a New York City hospital. Journal of Antimicrobial Chemotherapy. 2020;76(2):380-384.
Annavajhala MK, Khan SD, Sullivan SB, Shah J, Pass L, Kister K, Kunen H, Chiang V, Monnot GC, Ricupero CL, Mazur RA, Gordon P, Jong Ad, Wadhwa S, Yin MT, Demmer RT, Uhlemann A-C. Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy. mSphere. 2020;5(1):10.1128/msphere.00798-19.
2019
Macesic N, Nelson B, Mcconville TH, Giddins MJ, Green DA, Stump S, Gomez-Simmonds A, Annavajhala MK, Uhlemann A-C. Emergence of Polymyxin Resistance in Clinical Klebsiella pneumoniae Through Diverse Genetic Adaptations: A Genomic, Retrospective Cohort Study. Clinical Infectious Diseases. 2019;70(10):2084-2091.
Macesic N, Khan S, Giddins MJ, Freedberg DE, Whittier S, Green DA, Furuya EY, Verna EC, Annavajhala MK, Gomez-Simmonds A, Uhlemann A-C. Escherichia coli Harboring mcr-1 in a Cluster of Liver Transplant Recipients: Detection through Active Surveillance and Whole-Genome Sequencing. Antimicrobial Agents and Chemotherapy. 2019;63(6):10.1128/aac.02680-18.
Annavajhala MK, Gomez-Simmonds A, Uhlemann A-C. Multidrug-Resistant Enterobacter cloacae Complex Emerging as a Global, Diversifying Threat. Frontiers in Microbiology. 2019;10.
Annavajhala MK, Gomez-Simmonds A, Macesic N, Sullivan SB, Kress A, Khan SD, Giddins MJ, Stump S, Kim GI, Narain R, Verna EC, Uhlemann A-C. Colonizing multidrug-resistant bacteria and the longitudinal evolution of the intestinal microbiome after liver transplantation. Nature Communications. 2019;10(1):4715.
2018
Macesic N, Gomez-Simmonds A, Sullivan SB, Giddins MJ, Ferguson SA, Korakavi G, Leeds D, Park S, Shim K, Sowash MG, Hofbauer M, Finkel R, Hu Y, West J, Toussaint NC, Greendyke WG, Miko BA, Pereira MR, Whittier S, Verna EC, Uhlemann A-C. Genomic Surveillance Reveals Diversity of Multidrug-Resistant Organism Colonization and Infection: A Prospective Cohort Study in Liver Transplant Recipients. Clinical Infectious Diseases. 2018;67(6):905-912.
Gomez-Simmonds A, Stump S, Giddins MJ, Annavajhala MK, Uhlemann A-C. Clonal Background, Resistance Gene Profile, and Porin Gene Mutations Modulate In Vitro Susceptibility to Imipenem-Relebactam in Diverse Enterobacteriaceae. Antimicrobial Agents and Chemotherapy. 2018;62(8):10.1128/aac.00573-18.
Gomez-Simmonds A, Annavajhala MK, Wang Z, Macesic N, Hu Y, Giddins MJ, O’Malley A, Toussaint NC, Whittier S, Torres VJ, Uhlemann A-C. Genomic and Geographic Context for the Evolution of High-Risk Carbapenem-Resistant Enterobacter cloacae Complex Clones ST171 and ST78. mBio. 2018;9(3):10.1128/mbio.00542-18.
Giddins MJ, Macesic N, Annavajhala MK, Stump S, Khan S, McConville TH, Mehta M, Gomez-Simmonds A, Uhlemann AC. Successive Emergence of Ceftazidime-Avibactam Resistance through Distinct Genomic Adaptations in blaKPC-2-Harboring Klebsiella pneumoniae Sequence Type 307 Isolates. Antimicrob Agents Chemother. 2018 Feb 23;62(3). pii: e02101-17. doi: 10.1128/AAC.02101-17.
2017
Macesic N, Green D, Wang Z, Sullivan SB, Shim K, Park S, Whittier S, Furuya EY, Gomez-Simmonds A, Uhlemann AC. Detection of mcr-1-carrying Escherichia coli causing bloodstream infection in a New York City hospital: Avian origins, human concerns? Open Forum Infect Dis. 2017 May 20;4(3):ofx115. doi: 10.1093.
Sullivan SB, Austin ED, Stump S, Mathema B, Whittier S, Lowy FD, Uhlemann AC. Reduced vancomycin susceptibility of methicillin-susceptible Staphylococcus aureus has no significant impact on mortality but results in an increase in complicated infection. Antimicrob Agents Chemother. 2017; 61(7). pii: e00316-17.
Trivedi S, Uhlemann AC, Herman-Bausier P, Sullivan SB, Sowash MG, Flores E, Khan S, Dufrêne YF, Lowy FD. The Surface Protein SdrF mediates Staphylococcus epidermidis adherence to keratin. J Infect Dis. 2017 May 8. doi: 10.1093/infdis/jix213. In press.
Gomez-Simmonds A, Uhlemann AC. Clinical implications of genomic adaptation and evolution of carbapenem-resistant Klebsiella pneumoniae. J Infect Dis 2017; 15(suppl_1):S18-S27.
Cheng L, Nelson BC, Mehta M, Seval N, Park S, Giddins MJ, Shi Q, Whittier S, Gomez-Simmonds A, Uhlemann AC. Piperacillin-Tazobactam versus Other Antibacterial Agents for Treatment of Bloodstream Infections Due to AmpC β-Lactamase-Producing Enterobacteriaceae. Antimicrob Agents Chemother. 2017; 61(6). pii: e00276-17.
Uhlemann AC, McAdam PR, Sullivan SB, Knox JR, Khiabanian H, Rabadan R, Davies PR, Fitzgerald JR, Lowy FD. Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration. mBio. 2017; e01375016.
2016
Sullivan SB, Kamath S, McConville TH, Gray BT, Lowy FD, Gordon PG, Uhlemann AC. Staphylococcus epidermidis protection against Staphylococcus aureus colonization in people living with Human Immunodeficiency Virus in an inner-city outpatient population: A cross-sectional study. Open J Inf Dis. 2016; 3(4):ofw234.
Ahn D, Peñaloza H, Wang Z, Wickersham M, Parker D, Patel P, Koller A, Chen EI, Bueno SM, Uhlemann AC1,*, Prince A1. Acquired resistance to innate immune clearance promotes Klebsiella pneumoniae ST258 pulmonary infection. J Clin Invest Insight. 2016; e89704.
Austin ED, Sullivan SB, Whittier S, Lowy FD, Uhlemann AC. Peripheral intra-venous catheter placement is an under-recognized source of Staphylococcus aureus bloodstream infection. Open J Inf Dis 2016; 3(2):ofw072.
Arora S, Uhlemann AC, Lowy FD, Hook M. A novel MSCRAMM sub-family in coagulase negative staphylococcal species. Frontiers Microbiol. 2016; 7:540.
Gomez-Simmonds A, Hu Y, Sullivan SB, Wang Z, Whittier S, Uhlemann AC. Evidence from a New York City hospital of rising incidence of genetically diverse carbapenem-resistant Enterobacter cloacae and dominance of ST171, 2007 – 2014. J Antimicrob Chemother. 2016; 71(8):2351-3.
Vega MI, Dhingra SK, Henrich PP, Straimer J, Gnadig N, Uhlemann AC, Martin RE, Lehane AM, Fidock DA. Globally prevelent PfMDR1 mutations modulate Plasmodium falciparum susceptibility to artemisinin-based combination therapies. Nat Comm. 2016; 7:11553.
Knox JR, Sullivan SB, Urena J, Miller M, Vavagiakis P, Shi Q, Uhlemann AC, Lowy FD. Environmental contamination in the home and risk of recurrent Community-Associated Methicillin-Resistant Staphylococcus aureus. JAMA Int Med. 2016; 176(6):807-
Reviews and Commentaries
Pereira MR, Uhlemann AC. The widening threat of carbapenem-resistant infections after liver transplantation: the case of Acinetobacter baumannii. Liver Transpl. 2016; 22(5):579-81.
2015
Laabei M, Uhlemann AC, Lowy FD, Austin ED, Yokoyama M, Ouadi K, Feil E, Thorpe HA, Williams B, Perkins M, Peacock SJ, Clarke SR, Dordel J, Holden M, Votintseva AA, Bowden R, Crook DW, Young BC, Wilson DJ, Recker M, Massey RC. Evolutionary trade-offs underlie the multi-faceted virulence of Staphylococcus aureus. PLoS Biol. 2015; 13(9):e1002229.
Pereira MR, Scully BF, Pouch SM, Uhlemann AC, Goudie S, Emond JE, Verna EC. Risk factors and outcomes of carbapenem-resistant Klebsiella pneumoniae infections in liver transplant recipients. Liver Transpl. 2015; 21(12):1511-9.
Gomez-Simmonds A, Greenman M, Sullivan SB, Tanner JP, Sowash MG, Whittier S, Uhlemann AC. Population structure of Klebsiella pneumoniae causing bloodstream infections at a New York City tertiary care hospital: diversification of multidrug-resistant isolates. J Clin Microbiol. 2015; 53(7):2060-7.
Knox J, Van Rijen M, Uhlemann AC, Miller M, Hafer C, Vavagiakis P, Shi Q, Johnson PD, Coombs G, Kluytmans-Van Den Bergh M, Kluytmans J, Bennett CM, Lowy FD. Community-associated methicillin-resistant Staphylococcus aureus transmission in households of infected cases: a pooled analysis of primary data from three studies across international settings. Epidemiol Infect. 2015; 143(2):354-65.
2014
Benson MA, Ohneck EA, Ryan C, Alonzo F 3rd, Smith H, Narechania A, Kolokotronis SO, Satola SW, Uhlemann AC, Sebra R, Deikus G, Shopsin B, Planet PJ, Torres VJ. Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element. Mol Microbiol. 2014; 93(4):664-81.
Tanner J, Lin Y, Kornblum J, Herzig CT, Bystritsky R, Uhlemann AC, Lowy FD. Molecular characterization of methicillin-resistant Staphylococcus aureus clinical isolates obtained from the Rikers Island Jail System from 2009 to 2013. J Clin Microbiol. 2014; 52(8):3091-4.
Uhlemann AC1, Dordel J1, Knox JR, Raven K, Parkhill J, Holden MT, Peacock SJ, Lowy FD. Molecular tracing of the emergence, diversification and transmission of aureus sequence type 8/USA300 in a New York community. Proc Natl Acad Sci U S A. 2014; 111(18):6738-43.