Key Publications

Most Recent

Microbiome Testing and Sequencing

Trym T Flygel, Evgeniya Sovershaeva, Shantelle Claassen-Weitz, Erik Hjerde, Kilaza S Mwaikono, Jon Ø Odland, Rashida A Ferrand, Grace Mchugh, Tore J Gutteberg, Mark P Nicol, Jorunn P Cavanagh, Trond Flægstad, Composition of Gut Microbiota of Children and Adolescents With Perinatal Human Immunodeficiency Virus Infection Taking Antiretroviral Therapy in Zimbabwe, The Journal of Infectious Diseases, Volume 221, Issue 3, 1 February 2020, Pages 483–492


Low Volume Sputum Samples

Molecular detection of Mycobacterium tuberculosis in poor-quality cough specimens 

Oral TB Screening

Tondani A Mboneni, Owen O Eales, Nontuthuko E Maningi, Jannie FM Hugo, P Bernard Fourie Detection by RT-PCR of Mycobacterium tuberculosis from Oral Swab Specimens using PrimeStore® Molecular Transport Medium. ECCMID 2019


von Mollendorf C, Hellferscee O, Valley-Omar Z, et al. Influenza Viral Shedding in a Prospective Cohort of HIV-Infected and Uninfected Children and Adults in 2 Provinces of South Africa, 2012-2014. J Infect Dis. 2018;218(8):1228–1237. 

Nepal Maternal/ Child Influenza Study

Alastair F. Murray, Janet A. Englund, Jane Kuypers, James M. Tielsch, Joanne Katz, Subarna K. Khatry, Steven C. Leclerq, and Helen Y. Chu Infant Pneumococcal Carriage During Influenza, RSV, and hMPV Respiratory Illness Within a Maternal Influenza Immunization Trial  J. of Inf. Disease 2019;220:956–60 


Uddin SMI, Englund JA, Kuypers JY, et al. Burden and Risk Factors for Coronavirus Infections in Infants in Rural Nepal. Clin Infect Dis. 2018;67(10):1507–1514

PrimeStore MTM General

Daum LT, Worthy SA, Yim KC, Nogueras N, Schuman RF, Choi YW, and Fischer GW. A Clinical Specimen Collection and Transport Medium for Molecular Diagnostic and Genomic Applications. Epidemiol. Infect (2011) 139 1764-1773.


Influenza and other Respiratory Viruses

Zar HJ, Barnett W, Stadler A, Gardner-Lubbe S, Myer L, and Nicol MP. Aetiology of Childhood Pneumoniia in a Well Vaccinated South African Birth Cohort: A Nested Case-Control Study of the Drakenstein Child Health Study. Lancet. Dx.doi.org/10.1016/ S2213-2600(16)00096-5. April 21, 2016.

Daum LT, Yim K, and Fischer GW. Quantitation of Influenza A Virus From Nasal and Lung Tissue of Cotton Rats Using Real-Time RT-PCR and Culture. 26th Annual Meeting of the European Society for Pediatric Infectious Diseases. May 13-16, 2008 Graz, Austria


Daum LT, Yim K, Fischer GW. Real-Time RT-PCR Detection of Influenza A Virus in Asymptomatic Culture-Negative Cotton Rats. The Pediatric Academic Societies (PAS) Annual Meeting. May 2-6th, 2008 Honolulu, HI.


Gramer MR, Susan E. Detmer, Kevin C. Juleen, Susan A. Worthy, Luke T. Daum. Effect of Swab Type, Collection Media, and Storage on the Detection of Influenza a Virus in Porcine Nasal Secretions. AAVLD Annual Conference Proceedings, November 2010 Minneapolis, MN.


Daum LT, Worthy SA, Sutter DE, and Fischer GW. Development of a Real Time Reverse- Transcription PCR (RRT-PCR) Assay for Detection of Influenza a H1N1 2009 From Clinical Respiratory Specimens. European Society for Pediatric Infectious Diseases. May 5-8, 2010 Nice, France.


Myhre KE, Daum LT, Fischer GW and Sutter DE. Symptomatology of Family Contacts of Influenza Positive and Negative Patients During Influenza Season. The Pediatric Academic Societies (PAS) Annual Meeting May 2-5, 2009 Baltimore, MD.


Rasmussen ZA, Baker JM, Jahan A, Aamir UB, Aziz F, Qureshi SM, Azam SI, Zaidi SSZ, Ahmed K, Viboud C, Knobler S. Detection of Respiratory Syncytial (RSV) and Influenza Viruses in Children with WHO Defined Pneumonia and Controls from Oshikhandass Village, Gilgit-Baltistan, Northern Pakistan From 2012-2014; Sensitivity and Specificity of Rapid Tests vs. PCR. ID Week 2014 Oct 07- 12th, Philadelphia, PA.


Schlaudecker EP, Heck JP, MacIntyre ET, Martinez R, Dodd CN, McNeal MM, Staat MA, Heck JE, and Steinhoff MC. Comparison of a New Transport Medium with Universal Transport Medium at a Tropical Field Site. Diagn Microbiol Infect Dis. October 2014, 80(2):107-110.


Meidany DRP, Perovic O and Lowman W. Microbial Aetiology of Community Acquired Pneumonia at a Tertiary Hospital. 4th Annual Federation of Infectious Diseases Societies of Southern Africa 2011 September 8-11 Durban, South Africa.


Daum LT, Sutter DE, Ottolini MG, Elwood R, and Fischer GW. Real-Time RT-PCR Detection of Influenza Virus Within Symptomatic and Asymptomatic Family Members. The 48th Annual IDSA/ICAAC.  October 25-28th, 2008 Washington D.C.

Daum LT, Sutter DE, Worthy SA, Dotiwala AK, Koenig JA, Salinas EA, Chambers JP, Elwood RL, Ottolini MG, and Fischer GW. Detection and Molecular Characterization of Clinical Influenza A and B Viruses from Original Nasal Wash Specimens Preserved in PrimeStore® MTM. The 3rd European Conference of Influenza. September 14-17, 2008, Vilamoura Portugal.

Daum LT, Sutter DE, Worthy SA, Fischer GW. Genetic Analysis of Influenza A (H3N2) Viruses from Index Patients and Family Contacts. The 27th Annual Meeting of the European Society for Paediatric Infectious Diseases. June 9-13th, 2009 Brussels, Belgium.


Daum LT, Rodriguez JD, Worthy SA, and Fischer GW. Rapid Characterization of the Influenza A (H3N2) Hemagglutinin, Neuraminidase, and Matrix (HA, NA, MA) Genes Using Next-Generation Sequencing. The 25th European Congress of Clinical Microbiology and Infectious Diseases April 25- 28 th, 2009 Copenhagen, Denmark.


Fleige S, and Pfaffl MW. RNA Integrity and the Effect on the Real-Time qRT-PCR Performance.

Molecular Aspects of Medicine 27(2006)126-139.


Dube FS, Kaba M, Tow LA, Africa S, Lubbe S, Zar HJ and Nicol MP. Microbiology of the Nasopharynx in Children Hospitalized with Suspected Pulmonary Tuberculosis. 16th International Congress on Infectious Diseases April 2-5th, Cape Town, South Africa.


Omar SV, Peters RPH, Ismail NA, Dreyer AW, Said HM, Gwala T, Ismail N, and Fourie, PB. Laboratory Evaluation of a Specimen Transport Medium for Downstream Molecular Processing of Sputum Samples to Detect Mycobacterium Tuberculosis. Journal of Microbiological Methods 117 (2015) 57- 63.


Daum LT, Peters RPH, Fourie PB, Jonkman K, Worthy SA, Rodriguez JD, Ismail NA, Omar SV and Fischer GW. Molecular Detection of Mycobacterium Tuberculosis From Sputum Transported in PrimeStore® from Rural Settings. Int J Tuberc Lung Dis 19(5):552-557, 2015.

Maningi NE, Daum LT, Rodrigues JD, Mphahlele M, Peters R.P.H., Fischer GW, Chambers JP, and Fourie PB. Improved Detection by Next-Generation Sequencing of Pyrazinamide Resistance in Mycobacterium Tuberculosis Isolates. J Clin Microbiol, 53(12):1-5, 2015.


Daum LT, Rodriguez JD, Worthy SA, Omar SV, Ismail NA, Fourie PB, Dreyer AW, Hoosen AA, and Fischer GW. Analysis of Mycobacterium Tuberculosis MDR/XDR Genes Using Next-Generation Ion Torrent Sequencing from Genetically Diverse South African Clinical Isolates. Keystone Symposium Drug Resistance and Persistence in Tuberculosis May 13-18, 2012 Kampala, Uganda.


Daum LT, Omar SV, Ismail NA, Rodriguez JD, Worthy SA, Fourie BP, and Fischer GW. Next- Generation Ion Torrent Sequencing of Pyrazinamide Resistance in MDR/XDR South African Mycobacterium Tuberculosis Strains. American Society for Microbiology, May 18-21, 2013 Denver, CO.


Daum LT, Fischer GW, Sromek J, Khubbar M, Hunter P, Gradus MS, and Bhattacharyya S. Short Report: Characterization of Multi-Drug Resistant Mycobacterium Tuberculosis from Immigrants Residing in the USA Using Ion Torrent Full-Gene Sequencing. Epidemiol Infect, page 1-6, 2013.

Daum LT, Schuman RF, Sei CJ, Rikhi N, Mesadieu A, and Fischer. Real-time PCR PCR of Whole Blood Specimens Transported in PrimeStore MTM to Detect and Monitor MTB Bactermia. 17 ICID Hyderabad, India Mar 2-5, 2016.


Daum LT, Choi Y, Worthy SA, Rodriguez JD, Chambers JP, Fischer GW. A Molecular Transport Medium for Collection, Inactivation, Transport, and Detection of Mycobacterium Tuberculosis. Int J Tuberc Lung Dis 2014, 18(7):847-849.


Omar SV, Peters RPH, Ismail NA, Jonkman K, Dreyer AW, Said HM, Gwala T, Ismail N, and Fourie PB. Field Evaluation of a Novel Preservation Medium to Transport Sputum Specimens for Molecular Detection of Mycobacterium Tuberculosis in a Rural African Setting. 2016. TMIH, 21(6)776-782. Doi:10.1111/tmi.12701


Daum LT, Fourie PB, Peters RPH, Rodriguez JD, Worthy SA, Khubbar M, Bhattacharyya S, Gradus MS, Mboweni T, Marubini E, Helm C, Chambers J, and Fischer GW. Xpert MTB/RIF Detection of Mycobacterium Tuberculosis from Sputum Collected in Molecular Transport Medium. IJTLD, July/August, 2016.



Gous N, Scott L, and Stevens W. Can Dried Blood Spots or Whole Blood Liquid Transport Media Extend Access to HIV Viral Load Testing? African Society for Laboratory Medicine 2014 November 30th-December 4th, Cape Town, South Africa.


Daum LT, Bumah VV, Masson-Meyers DS, Khubbar M, Rodriguez JD, Fischer GW, Enwemeka CS, Gradus S, and Bhattacharyya S. Whole-Genome Sequence for Methicillin-Resistant Staphylococcus aureus Strain ATCC BAA-1680. GenomeA 3(2):1-2, 2015.