Salika M. Shakir
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Salika M. Shakir, PhD, D(ABMM)

Languages spoken: English

Salika M. Shakir, PhD, D(ABMM) is the Medical Director of the Microbial Amplified Detection and AFB Laboratories and Assistant Professor of Pathology at the University of Utah, School of Medicine. After receiving a doctoral degree in Microbiology at the University of Oklahoma Health Sciences Center (OUHSC), she went on to pursue a research fellowship in Pediatric Infectious Diseases at OUHSC. She completed a fellowship training in Medical and Public Health Microbiology through the University of Utah and ARUP Laboratories, Salt Lake City, UT and is a diplomate of the American Board of Medical Microbiology. Her research and academic interests focus on the implementation of novel molecular assays for pathogen detection into the clinical laboratory and effective utilization of these new diagnostic tests. She has also successfully conducted several industry-sponsored clinical research projects for diagnostic assays/devices seeking FDA approval.

Specialties

  • Pathology, Clinical

Board Certification

American Board of Medical Microbiology

Salika M. Shakir, PhD, D(ABMM) is the Medical Director of the Microbial Amplified Detection and AFB Laboratories and Assistant Professor of Pathology at the University of Utah, School of Medicine. After receiving a doctoral degree in Microbiology at the University of Oklahoma Health Sciences Center (OUHSC), she went on to pursue a research fellowship in Pediatric Infectious Diseases at OUHSC. She completed a fellowship training in Medical and Public Health Microbiology through the University of Utah and ARUP Laboratories, Salt Lake City, UT and is a diplomate of the American Board of Medical Microbiology. Her research and academic interests focus on the implementation of novel molecular assays for pathogen detection into the clinical laboratory and effective utilization of these new diagnostic tests. She has also successfully conducted several industry-sponsored clinical research projects for diagnostic assays/devices seeking FDA approval.

Board Certification and Academic Information

Academic Departments Pathology -Assistant Professor (Clinical)
Board Certification
American Board of Medical Microbiology

Education history

Undergraduate Microbiology - Bangalore University B.S.
Doctoral Training University of Oklahoma Health Sciences Center Ph.D.
Postdoctoral Fellowship University of Oklahoma Health Sciences Center Postdoctoral Fellow
Fellowship Clinical Microbiology - University of Utah School of Medicine Fellow

Selected Publications

Journal Article

  1. Haas AL, Ma A, Pham J, Punam V, Malhotra U, Church EC, Narita M, Escuyer V, Shakir S (2025). Limitations of the MTB/RIF assay: An Xpert review of four clinical cases . Open forum infectious diseases, 12(4),
  2. English P, Morrison M, Mathison B, Enrico Elizabeth, Shean R, O'Fallon B, Rupp D, Knight K, Rangel A, Gilivary J, Vance A, Hatch H, Lin L, Ng D, Shakir S (2025). Use of a Convolutional Neural Network for Direct Detection of Acid-Fast Bacilli from Clinical Specimens. Microbiology spectrum, 5(13),
  3. Rajagopalan S, Das L, Kohlerschmidt DJ, Rourke AK, Shakir SM, Larsen MH, O'Donnell MR, Szymczak WA, Escuyer VE, Thwe PM, Jacobs WR J (2025). Luciferase reporter mycobacteriophage (TM4:: GeNL) enables rapid assessment of drug susceptibilities and inducible macrolide resistance in Mycobacterium abscessus complex. Journal of clinical microbiology,
  4. Yang T, Beach KE, Zhu C, Gan M, Wang W, Zhou H, Peng L, Wang S, Cai L, Li W, Davis JB, Cicchetti N, Slechta ES, Barker A, Shakir SM, Carey AF, Liu (2024). Genomic Analysis of Global Mycobacterium abscessus Isolates Reveals Ongoing Evolution of Drug Resistance–Associated Genes. The Journal of infectious diseases,
  5. Metersky ML, Losier AJ, Fraulino DA, Warnock TA, Varley CD, Le AM, Winthrop KL, McArdle JR, Shakir SM, Khare (2024). Mycobacterium nebraskense isolated from patients in Connecticut and Oregon, USA. Emerging infectious diseases, 31(3), 507¿515.
  6. Shakir SM, Otiso J, Keller G, Van Heule H, Osborn LJ, Cole N, Schuetz AN, Richter SS, Couturier M (2022). Multicenter Evaluation of a Gradient Diffusion Method for Antimicrobial Susceptibility Testing of Helicobacter pylori. Microbiology spectrum, 10(2),
  7. Shakir SM, Gill R, Salberg J, Slechta ES, Feldman M, Fritsche T, Clarridge J, Sharp SE, Fisher M (2021). Clinical Laboratory Perspective on Streptococcus halichoeri, an Unusual Nonhemolytic, Lancefield Group B Streptococcus Causing Human Infections. Emerging infectious diseases, 27(5), 1309¿1316.
  8. Shakir SM, Mansfield CR, Hays ED, Couturier MR, Hillyard D (2020). Evaluation of a Novel High-Definition PCR Multiplex Assay for Simultaneous Detection of Tick-Borne Pathogens in Human Clinical Specimens. Journal of clinical microbiology, 58(3),
  9. Hanson KE, Barker AP, Hillyard DR, Gilmore N, Barrett JW, Orlandi RR, Shakir S (2020). Self-Collected Anterior Nasal and Saliva Specimens versus Healthcare Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2. Journal of clinical microbiology, 58(11),
  10. Creager HM, Cabrera Barbara, Schnaubelt A, Cox JL, Cushman-Vokouna AM, Shakir SM, Tardif KD, Huang ML ,Jerome KR, Greninger AL, Drobysheva D, Spaulding U, Rogatcheva M, Bourzace KM, Hinrichs SH, Broadhurst MJ, Fey P (2020). Clinical evaluation of the BioFire® Respiratory Panel 2.1 and detection of SARS-CoV-2. Journal of clinical virology, 129(2020), 104538.
  11. Shakir SM, Goldbeck JM, Robison D, Eckerd AM, Chavez-Bueno S (2014). Genotypic and phenotypic characterization of invasive neonatal Escherichia coli clinical isolates. Am J Perinatol, 31(11), 975-82.
  12. Larabee JL, Shakir SM, Barua S, Ballard J (2013). Increased cAMP in monocytes augments Notch signaling mechanisms by elevating RBP-J and transducin-like enhancer of Split (TLE). The Journal of biological chemistry, 288(30), 21526-36.
  13. Larabee JL, Maldonado-Arocho FJ, Pacheco S, France B, DeGiusti K, Shakir SM, Bradley KA, Ballard J (2011). Glycogen synthase kinase 3 activation is important for anthrax edema toxin-induced dendritic cell maturation and anthrax toxin receptor 2 expression in macrophages. Infection and immunity, 79(8), 3302-8.
  14. Bryant-Hudson KM, Shakir SM, Ballard J (2011). Autoregulatory characteristics of a Bacillus anthracis serine/threonine kinase. Journal of bacteriology, 193(8), 1833-42.
  15. Larabee JL, Shakir SM, Hightower L, Ballard J (2011). Adenomatous polyposis coli protein associates with C/EBP beta and increases Bacillus anthracis edema toxin-stimulated gene expression in macrophages. The Journal of biological chemistry, 286(22), 19364-72.
  16. Shakir SM, Bryant KM, Larabee JL, Hamm EE, Lovchik J, Lyons CR, Ballard J (2010). Regulatory interactions of a virulence-associated serine/threonine phosphatase-kinase pair in Bacillus anthracis. Journal of bacteriology, 192(2), 400-9.
  17. Barua S, McKevitt M, DeGiusti K, Hamm EE, Larabee J, Shakir S, Bryant K, Koehler TM, Blanke SR, Dyer D, Gillaspy A, Ballard J (2009). The mechanism of Bacillus anthracis intracellular germination requires multiple and highly diverse genetic loci. Infection and immunity, 77(1), 23-31.
  18. McKevitt MT, Bryant KM, Shakir SM, Larabee JL, Blanke SR, Lovchik J, Lyons CR, Ballard J (2007). Effects of endogenous D-alanine synthesis and autoinhibition of Bacillus anthracis germination on in vitro and in vivo infections. Infection and immunity, 75(12), 5726-34.

Review

  1. Shakir SM, Shakir FA, Couturier M (2023). Updates to the Diagnosis and Clinical Management of Helicobacter pylori Infections. . Clinical Chemistry (Chicago), 69(8), 869-880.
  2. Kukull B, Shakir SM, Hanson K (2022). Performance of Non-nasopharyngeal Sample Types for Molecular Detection of SARS-CoV-2. Clinics in laboratory medicine, 42(2), 249-259.

Book Chapter

  1. Fisher MA, Shakir SM, Lopansri B (2022). Strain Typing Using Next-Generation Sequencing .

Case Report

  1. Montelongo-Jauregui D, Pham J, McFarland J, Shakir S (2025). The Brief Case: Complexity of Laboratory Diagnosis of Mycobacterium genavense: A Classic Case of an Unusual Pathogen. Journal of clinical microbiology, 63(4),
  2. Newstead S, Montelongo D, Shakir SM, Swaminathan (2025). Disseminated Mycobacterium kansasii and Mycobacterium avium complex co-infection in GATA2 mutated myelodysplastic syndrome: a case report. Therapeutic advances in infectious disease, 12,
  3. Pelt CE, Shakir SM, Cahill, MJ, Pupaibool, J, & Cahill, B (2024). Delayed Diagnosis of Mycobacterium bovis Bacillus Calmette-Guérin Periprosthetic Joint Infection Following Total Knee Arthroplasty. Arthroplasty today, 27(101350),
  4. Liu BM, Carlisle CP, Fisher MA, Shakir S (2021). The Brief Case: Capnocytophaga sputigena Bacteremia in a 94-Year-Old Male with Type 2 Diabetes Mellitus, Pancytopenia, and Bronchopneumonia. Journal of clinical microbiology, 59(7),
  5. Liu BM, Carlisle CP, Fisher MA, Shakir S (2021). Closing the Brief Case: Capnocytophaga sputigena Bacteremia in a 94-Year-Old Male with Type 2 Diabetes Mellitus, Pancytopenia, and Bronchopneumonia. Journal of clinical microbiology, 59(7),
  6. Shakir SM, Powers-Fletcher MV, Slechta ES, Fisher M (2017). Helicobacter canis bacteraemia and cellulitis in a patient with end-stage renal disease. JMM case reports, 4(11), e005126.

Letter

  1. Shakir SM, Barker AP, Hillyard DR, Gilmore N, Barrett JW, Orlandi RR, Hanson K (2020). Combined Self-collected Anterior Nasal and Oropharyngeal Specimens versus Provider-collected Nasopharyngeal Swabs for the Detection of SARS-CoV-2. Journal of clinical microbiology,

Other

  1. Shakir S (2025). Mycobacterium tuberculosis- Tuberculosis.
  2. Shakir S (2024). Human Papillomavirus.
  3. Shakir S (2021). Vaginitis - Bacterial Vaginosis, Vulvovaginal Candidiasis, and Trichomoniasis.
  4. Shakir S (2021). Group B Streptococcal Disease.
  5. Shakir S (2020). Sexually Transmitted Infections.
  6. Shakir S (2019). Respiratory Viruses.
  7. Shakir S (2019). Respiratory Syncytial Virus – RSV.