Publications
Preprints
Jaramillo Cartagena A*, Taylor KL*, Smith JT, Manson AL, Earl AM, Pierce VM, Bhattacharyya RP. The carbapenem inoculum effect provides insight into the molecular mechanisms underlying carbapenem resistance in Enterobacterales. bioRxiv 2023.05.23.541813, 2023 May 23.
Selected Publications: Research
Roach DJ, Sridhar S, Oliver E, Rao SR, Slater DM, Hwant W, Vater KH, Dinesh A, Qadri F, Chisti J, Pierce VM, Turbett SE, Bhattacharyya RP, Worby CJ, Earl AM, LaRocque RC, Harris JB. Clinical and genomic characterization of a cohort of patients with Klebsiella pneumoniae bloodstream infection. Clin Infect Dis. 2023 Aug 26, epub ahead of print, ciad507. PMID 37633257.
Ma P, Amemiya HM, He LL, Gandhi SJ, Nicol R, Bhattacharyya RP, Smillie CS, Hung DT. Bacterial droplet-based single-cell RNA-seq (bacDrop) reveals antibiotic-associated heterogeneous cellular states. Cell 2023 Jan 27, epub ahead of print. PMID 36708705, PMCID PMC10014032. (Preprint at bioRxiv 2022.08.01.502326). <pdf>
Ankomah PO, Siedner MJ, Bhattacharyya RP. Pre-existing population immunity and SARS-CoV-2 variant establishment and dominance dynamics in the United States: An ecological study. Open Forum Infect Dis 2022 Dec 20;9(12):ofac621. PMID: 36544861, PMCID PMC9764332. (Preprint at medRxiv 2022.07.01.22277157). <pdf>
Matzko ME*, Sephton-Clark PCS*, Young EL, Jhaveri TA, Martinsen MA, Mojica E, Boykin R, Pierce VM, Cuomo CA, Bhattacharyya RP. A novel rRNA hybridization-based approach to rapid, accurate Candida identification directly from blood culture. Med Mycol 2022 Sep 6;60(9):myac065. PMID: 36002024, PMCID PMC9989835. (Preprint at bioRxiv 2022.05.09.491195). <pdf | supp>
Carson DV, Patiño M, Elashal HE, Jaramillo Cartagena A, Zhang Y, Whitley ME, So L, Kayser-Browne AK, Earl AM, Bhattacharyya RP, Link AJ. Cloacaenodin, an antimicrobial lasso peptide with activity against Enterobacter. ACS Infect Dis 2023 Jan 13;9(1):111. PMID 36519726. <pdf>
LaSalle TJ, Gonye ALK, Freeman SS, Kaplonek P, Gushterova I, Kays KR, Manakongtreecheep K, Tantivit J, Rojas-Lopez M, Russo BC, Sharma N, Thomas MF, Lavin-Parsons KM, Lilly BM, Mckaig BN, Charland NC, Khanna HK, Lodenstein CL, Margolin JD, Blaum EM, Lirofonis PB, Sonny A, Bhattacharyya RP, Parry BA, Goldberg MB, Alter G, Filbin MR, Villani AC, Hacohen N, Sade-Feldman M. Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients. Cell Rep Med 2022 Oct 18;3(10):100779. PMID: 36208629, PMCID: PMC9510054 (Preprint at bioRxiv 2021.10.04.463121).
Martinsen MA, Jaramillo Cartagena A, Bhattacharyya RP. Core antibiotic-induced transcriptional signatures reflect susceptibility to all members of an antibiotic class. Antimicrobial Agents Chemother. 2021 May 18;65(6):e02296-20. PMID: 33846128, PMCID: PMC8315949. (Preprint at bioRxiv 2020.10.29.359208). <pdf | supp>
Lennon NJ*, Bhattacharyya RP*, Mina MJ, Rehm HL, Hung DT, Smole S, Woolley A, Lander ES, Gabriel S. Cross-sectional assessment of SARS-CoV-2 viral load by symptom status in Massachusetts congregate living facilities. J Infect Dis 2021 Jul 13:jiab367. PMID: 34255846, PMCID: PMC8420626. (Preprint at medRxiv 2020.07.20.20157792). <pdf>
Salamzade R, Manson AL, Walker BJ, Brennan-Krohn T, Worby CJ, Ma P, He LL, Shea TP, Qu J, Chapman SB, Howe W, Young SK, Wurster JI, Delaney ML, Kanjilal S, Onderdonk AB, Bittencourt CE, Gussin GM, Kim D, Peterson EM, Ferraro MJ, Hooper DC, Shenoy ES, Cuomo CA, Cosimi LA, Huang SS, Kirby JE, Bhattacharyya RP, Earl AM. Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance. Genome Med 2022 Apr 5;14(1):37. PMID: 35379360, PMCID: PMC8981930. <pdf>
Thakku SG, Ackerman CM, Myhrvold C, Bhattacharyya RP, Livny J, Ma P, Gomez GI, Sabeti PC, Blainey PC, Hung DT. Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays. PNAS Nexus 2022 Apr 15;1(1):pgac021. PMID: 35450424, PMICD: PMC9013781. <pdf>
Reyes M, Filbin MR, Bhattacharyya RP, Sonny A, Mehta A, Billman K, Kays KR, Pinilla-Vera M, Benson ME, Cosimi LA, Hung DT, Levy BD, Villani AC, Sade-Feldman M, Baron RM, Goldberg MB, Blainey PC, Hacohen N. Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro. SciTransl Med 2021 Jun 16;13(598):eabe9599. PubMed PMID: 34103408; PubMed Central PMCID: PMC8432955. (Preprint at bioRxiv 2020.09.02.280180). <pdf | supp>
Ma P, He LL, Pironti A, Laibinis HH, Ernst CM, Manson AL, Bhattacharyya RP, Earl AM, Livny J, Hung DT. Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics. eLife 2021 Apr 19;10:e67310. PMID: 33871353, PMCID: PMC8079144.
Reyes M*, Filbin MR*, Bhattacharyya RP, Billman K, Eisenhaure T, Hung DT, Levy BD, Baron RM, Blainey PC, Goldberg MB, Hacohen N. An immune-cell signature of bacterial sepsis. Nat Med. 2020 Mar;26(3):333-340. doi: 10.1038/s41591-020-0752-4. Epub 2020 Feb 17. PubMed PMID: 32066974; PubMed Central PMCID: PMC7235950. <pdf>
Bhattacharyya RP, Bandyopadhyay N, Ma P, Son SS, Liu J, He LL, Wu L, Khafizov R, Boykin R, Cerqueira GC, Pironti A, Rudy RF, Patel MM, Yang R, Skerry J, Nazarian E, Musser KA, Taylor J, Pierce VM, Earl AM, Cosimi LA, Shoresh N, Beechem J, Livny J, Hung DT. Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination. Nat Med. 2019 Dec;25(12):1858-1864. doi: 10.1038/s41591-019-0650-9. Epub 2019 Nov 25. PubMed PMID: 31768064; PubMed Central PMCID: PMC6930013. <pdf | supp>
Wadsworth CB, Sater MRA, Bhattacharyya RP, Grad YH. Impact of Species Diversity on the Design of RNA-Based Diagnostics for Antibiotic Resistance in Neisseria gonorrhoeae. Antimicrob Agents Chemother. 2019 Aug;63(8). doi: 10.1128/AAC.00549-19. Print 2019 Aug. PubMed PMID: 31138575; PubMed Central PMCID: PMC6658776.
Bhattacharyya RP, Walker M, Boykin R, Son SS, Liu J, Hachey AC, Ma P, Wu L, Choi K, Cummins KC, Benson M, Skerry J, Ryu H, Wong SY, Goldberg MB, Han J, Pierce VM, Cosimi LA, Shoresh N, Livny J, Beechem J, Hung DT. Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA. Sci Rep. 2019 Mar 14;9(1):4516. doi: 10.1038/s41598-019-40792-3. PubMed PMID: 30872641; PubMed Central PMCID: PMC6418090. <pdf | supp>
Gootenberg JS*, Abudayyeh OO*, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017 Apr 28;356(6336):438-442. doi: 10.1126/science.aam9321. Epub 2017 Apr 13. PubMed PMID: 28408723; PubMed Central PMCID: PMC5526198.
Hou HW*, Bhattacharyya RP*, Hung DT, Han J. Direct detection and drug-resistance profiling of bacteremias using inertial microfluidics. Lab Chip. 2015 May 21;15(10):2297-307. doi: 10.1039/c5lc00311c. PubMed PMID: 25882432; PubMed Central PMCID: PMC4437799. <pdf>
Shishkin AA, Giannoukos G, Kucukural A, Ciulla D, Busby M, Surka C, Chen J, Bhattacharyya RP, Rudy RF, Patel MM, Novod N, Hung DT, Gnirke A, Garber M, Guttman M, Livny J. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods. 2015 Apr;12(4):323-5. doi: 10.1038/nmeth.3313. Epub 2015 Mar 2. PubMed PMID: 25730492; PubMed Central PMCID: PMC4712044. <pdf>
Bhattacharyya RP*, Reményi A*, Good MC, Bashor CJ, Falick AM, Lim WA. The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway. Science 2006 Feb 10;311:822. PMID: 16424299. <pdf | supp>
Selected Publications: Reviews/Perspectives
Bhattacharyya RP, Hanage WP. Challenges in inferring intrinsic severity of the SARS-CoV-2 omicron variant. N Engl J Med 2022 Feb 17;386(7):e14. PMID: 35108465. (Preprint at Harvard Center for Population and Development Studies working paper series, 2021 Dec). <pdf | supp>
Ward RA, Aghaeepour N, Bhattacharyya RP, Clish CB, Gaudillière B, Hacohen N, Mansour MK, Mudd PA, Pasupneti S, Presti RM, Rhee EP, Sen P, Spec A, Tam JM, Villani AC, Woolley AE, Hsu JL, Vyas JM. Harnessing the potential of multiomics studies for precision medicine in infectious disease. Open Forum Infect Dis 2021 Sep 25;8(11):ofab483. PMID: 34805429, PMCID: PMC8598922.
Bhattacharyya RP, Thakku SG, Hung DT. Harnessing CRISPR Effectors for Infectious Disease Diagnostics. ACS Infect Dis. 2018 Sep 14;4(9):1278-1282. doi: 10.1021/acsinfecdis.8b00170. Epub 2018 Aug 16. PubMed PMID: 30113801. <pdf>
Bhattacharyya RP, Reményi A, Yeh BJ, Lim WA. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem 2006;75:655. PMID: 16756506. <pdf>
Selected Publications: Clinical
Mohareb AM, Rosenberg JM, Bhattacharyya RP, Kotton CN, Chu JT, Jilg N, Hysell KM, Albin JS, Sen P, Bloom SM, Schiff AE, Zachary KC, Letourneau AR, Kim AY, Hurtado RM. Preventing infectious complications of immunomodulation in COVID-19 in foreign-born patients. J Immigr Minor Health 2021 Dec;23(6):1343. PMID: 34159495, PMCID: PMC8218971.
Chewcharat A, Chang YT, Sise ME, Bhattacharyya RP, Murray MB, Nigwekar SU. Phase-3 Randomized Controlled Trials on Exclusion of Participants With Kidney Disease in COVID-19. Kidney Int Rep. 2021 Jan;6(1):196-199. doi: 10.1016/j.ekir.2020.10.010. Epub 2020 Oct 21. PubMed PMID: 33106779; PubMed Central PMCID: PMC7577277.
Estiverne C, Strohbehn IA, Mithani Z, Hirsch JS, Wanchoo R, Goyal PG, Lee Dryden-Peterson S, Pearson JC, Kubiak DW, Letourneau AR, Bhattacharyya R, Jhaveri KD, Sise ME. Remdesivir in patients with estimated glomerular filtration rate < 30mL/min/1.73m2 or on renal replacement therapy. Kidney Int Rep. 2020 Nov 27;. doi: 10.1016/j.ekir.2020.11.025. [Epub ahead of print] PubMed PMID: 33263094; PubMed Central PMCID: PMC7694470.
Adamsick ML, Gandhi RG, Bidell MR, Elshaboury RH, Bhattacharyya RP, Kim AY, Nigwekar S, Rhee EP, Sise ME. Remdesivir in Patients with Acute or Chronic Kidney Disease and COVID-19. J Am Soc Nephrol. 2020 Jul;31(7):1384-1386. doi: 10.1681/ASN.2020050589. Epub 2020 Jun 8. Review. PubMed PMID: 32513665; PubMed Central PMCID: PMC7351006.
Bhattacharyya RP, Flores EJ, Azar MM. Case 30-2017. A 65-Year-Old Woman with Altered Mental Status, Bacteremia, and Acute Liver Failure. N Engl J Med. 2017 Sep 28;377(13):1274-1282. doi: 10.1056/NEJMcpc1706100. PubMed PMID: 28953442.
Wertheim BM, Aguirre AJ, Bhattacharyya RP, Chorba J, Jadhav AP, Kerry VB, Macklin EA, Motyckova G, Raju S, Lewandrowski K, Hunt DP, Wright DE. An Educational and Administrative Intervention to Promote Rational Laboratory Test Ordering on an Academic General Medicine Service. Am J Med. 2017 Jan;130(1):47-53. doi: 10.1016/j.amjmed.2016.08.021. Epub 2016 Sep 9. PubMed PMID: 27619354; PubMed Central PMCID: PMC6598201.
Baggett MV, Gonzalez RG, Bhattacharyya RP, Mahowald MA. CASE RECORDS of the MASSACHUSETTS GENERAL HOSPITAL. Case 4-2016. A 58-Year-Old Woman with a Skin Ulcer, Fever, and Lymphadenopathy. N Engl J Med. 2016 Feb 11;374(6):573-81. doi: 10.1056/NEJMcpc1508550. PubMed PMID: 26863359.