Wasp

Cobas 6800

PALMS (Pandemic Applications Laboratory and Microbiology Service

Testing Platforms

As part of UCSD's ongoing response to the current and future pandemics, the PALMS laboratory will be opening in late 2021. This laboratory will specialize in developing tests to respond to current and future pandemics. It will also be involved in research and development for clinical microbiology assays. This laboratory has previously been known as Pride Lab West, but now has an official name. Dr. Pride serves to direct Clinical Microbiology at UCSD, and will also serve as the Director of this laboratory. 

Publications

Brucker Maldi Biotyper

1) Wu, T.F., Chen Y.C, Wang W.C., Fang Y.C., Fukuoka S., Pride D.T., and Pak, O.S. 2018. A rapid and low-cost pathogen detection platform by using a molecular agglutination assay. ACS Cent Sci. 4: 1485-1494. PMID 30555900.

2) Ahmad, W., Nguyen N.H., Boland B.S., Dulai P.S., Pride D.T., Bouland D., Sandborn W.J., and Singh S. Comparison of multiplex gastrointestinal pathogen panel and conventional stool testing for evaluation of diarrhea in patients with inflammatory bowel diseases. Dig. Dis. Sci. 64: 382-390. PMID 30361807.

3) Shin, J.H., and Pride, D.T. 2019. Comparison of three nucleic acid amplification tests and culture for detection of Group B Streptococcus from enrichment broth. J Clin Microbiol. 57: e01958. PMID 30944190.

4) Pride, D.T. 2019. Consider NAATs for detection of GBS in pregnant women. Medical Laboratory Observer. July 2019. MLO-Online.com.

5) Vasudevan, R., Shin J.H., Chopyk J., Peacock W.F., Torriani F.J., Maisel A.S., and Pride D.T. 2020. Aseptic barriers allow a clean contact for contaminated stethoscope diaphragms. Mayo Clin Proc Innov Qual Outcomes. 4(1): 21-30. PMID 32055768.

6) Kuo P, Realegeno S, Pride DT. Comparison of two nucleic acid amplification tests (NAATs) and two antigen tests for detection of SARS-CoV-2 from upper respiratory specimens. J Clin Virol Plus. 2021 Jun;1(1):100011. doi: 10.1016/j.jcvp.2021.100011. Epub 2021 Apr 3. PMID: 35261999; PMCID: PMC8019354. 

7) Realegeno, S., Hash S., Wong C., Liu R., Shepherd J., Schooley R.T., Lipson D., Fung F., Menon S., and Pride D.T. 2021. Molecular Mirror Technology facilitates high throughput, accurate SARS-CoV-2 testing. Microbiology Spectrum. 

8) Keehner J, Horton LE, Binkin NJ, Laurent LC; SEARCH Alliance; Pride D, Longhurst CA, Abeles SR, Torriani FJ. Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce. N Engl J Med. 2021 Sep 30;385(14):1330-1332. doi: 10.1056/NEJMc2112981. Epub 2021 Sep 1. PMID: 34469645; PMCID: PMC8451183.

9) Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, McHardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature. 2022 Sep;609(7925):101-108. doi: 10.1038/s41586-022-05049-6. Epub 2022 Jul 7. PMID: 35798029; PMCID: PMC9433318.

10) Chiu M, Kuo P, Lecrone K, Garcia A, Chen R, Quach NE, Tu XM, Pride DT. Comparison of the APAS Independence Automated Plate Reader System with the Manual Standard of Care for Processing Urine Culture Specimens. Microbiol Spectr. 2022 Oct 26;10(5):e0144222. doi: 10.1128/spectrum.01442-22. Epub 2022 Aug 16. PMID: 35972280; PMCID: PMC9603219.

11) Kuo P, LeCrone K, Chiu M, Realegeno S, Pride DT. Analysis of the FAST™ system for expedited identification and antimicrobial susceptibility testing of bloodborne pathogens. Diagn Microbiol Infect Dis. 2022 Dec;104(4):115783. doi: 10.1016/j.diagmicrobio.2022.115783. Epub 2022 Jul 30. PMID: 36031475.

12) Thwe PM, Faron ML, Pride DT, Cruz A, Gerstbrein D, Nahmod KA, Bigham L, Du X, Lu X, Moya S, Ren P. Multicenter Evaluation of the Cepheid Xpert GBS LB XC Test. J Clin Microbiol. 2022 Dec 21;60(12):e0135622. doi: 10.1128/jcm.01356-22. Epub 2022 Dec 6. PMID: 36472424; PMCID: PMC9769564.

13) Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell. 2023 Dec 21;186(26):5690-5704.e20. doi: 10.1016/j.cell.2023.11.024. Epub 2023 Dec 14. PMID: 38101407; PMCID: PMC10795731.

14) Keehner J, Abeles SR, Longhurst CA, Horton LE, Myers FE, Riggs-Rodriguez L, Ahmad M, Baxter S, Boussina A, Cantrell K, Cardenas P, De Hoff P, El-Kareh R, Holland J, Ikeda D, Kurashige K, Laurent LC; SEARCH Alliance; Lucas A, Pride D, Sathe S, Tran AR, Vasylyeva TI, Yeo G, Knight R, Wertheim JO, Torriani FJ. Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting. Clin Infect Dis. 2024 May 15;78(5):1204-1213. doi: 10.1093/cid/ciad738. PMID: 38227643; PMCID: PMC11093679.

15) Aralar A, Goshia T, Ramchandar N, Lawrence SM, Karmakar A, Sharma A, Sinha M, Pride DT, Kuo P, Lecrone K, Chiu M, Mestan KK, Sajti E, Vanderpool M, Lazar S, Crabtree M, Tesfai Y, Fraley SI. Universal Digital High-Resolution Melt Analysis for the Diagnosis of Bacteremia. J Mol Diagn. 2024 May;26(5):349-363. doi: 10.1016/j.jmoldx.2024.01.013. Epub 2024 Feb 21. PMID: 38395408; PMCID: PMC11090205.

16) Boussina A, Langouche L, Obirieze AC, Sinha M, Mack H, Leineweber W, Aralar A, Pride DT, Coleman TP, Fraley SI. Machine learning based DNA melt curve profiling enables automated novel genotype detection. BMC Bioinformatics. 2024 May 10;25(1):185. doi: 10.1186/s12859-024-05747-0. PMID: 38730317; PMCID: PMC11088152.

17) Press RD, Dressel D, McBean M, Tiong IS, Anderson MW, Pride D, Raman A, Doom RR, Kaldate R. Evaluation of a New Closed-System Automated RT-qPCR Assay for the Rapid Detection and Monitoring of Common Nucleophosmin Mutations in Patients with Acute Myeloid Leukemia. Int J Mol Sci. 2024 Jul 19;25(14):7912. doi: 10.3390/ijms25147912. PMID: 39063154; PMCID: PMC11277538.

18) Oles RE, Carrillo Terrazas M, Loomis LR, Hsu C-Y, Tribelhorn C, Belda-Ferre P, Ea AC, Bryant M, Young JA, Carrow HC, Sandborn WJ, Dulai PS, Sivagnanam M, Pride D, Knight R, Chu H. Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights. mSystems. 2024 Jul 23;9(7):e0051624. doi: 10.1128/msystems.00516-24. Epub 2024 Jun 27. PMID: 38934546; PMCID: PMC11265264.