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Volume 30, Number 8—August 2024
Research

Metagenomic Detection of Bacterial Zoonotic Pathogens among Febrile Patients, Tanzania, 2007–20091

Robert J. Rolfe, Sarah W. Sheldon, Luke C. Kingry, Jeannine M. Petersen, Venance P. Maro, Grace D. Kinabo, Wilbrod Saganda, Michael J. Maze, Jo E.B. Halliday, William L. Nicholson, Renee L. Galloway, Matthew P. Rubach, and John A. CrumpComments to Author 
Author affiliations: Duke University Department of Medicine Division of Infectious Diseases and International Health, Durham, North Carolina, USA (R.J. Rolfe, M.P. Rubach, J.A. Crump); Centers for Disease Control and Prevention, Fort Collins, Colorado, USA (S.W. Sheldon, L.C. Kingry, J.M. Petersen); Kilimanjaro Christian Medical Centre, Moshi, Tanzania (V.P. Maro, G.D. Kinabo, M.P. Rubach, J.A. Crump); Kilimanjaro Christian Medical University College, Moshi (V.P. Maro, G.D. Kinabo, J.A. Crump); Mawenzi Regional Referral Hospital, Moshi (W. Saganda); University of Otago Department of Medicine, Christchurch, New Zealand (M.J. Maze); University of Glasgow School of Biodiversity, One Health and Veterinary Medicine, Glasgow, Scotland, UK (J.E.B. Halliday); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (W.L. Nicholson, R.L. Galloway); Duke-National University of Singapore Programme in Emerging Infectious Diseases, Singapore (M.P. Rubach); Duke University Global Health Institute, Durham (M.P. Rubach, J.A. Crump); Centre for International Health, University of Otago, Dunedin, New Zealand (J.A. Crump)

Main Article

Table 2

Metagenomic sequencing results used for detection of bacterial zoonotic pathogens among febrile patients, Tanzania, 2007–2009*

Organism V1–V2 sufficient for species ID MiniKraken taxonomic prediction† BLASTn taxonomic prediction (% identity)‡ Sequence in database Read count % Abundance
Bartonella quintana Y B. quintana B. quintana AP019773.1 (100) Y 4,730 98.21
B. quintana
 Y
 B. quintana
 B. quintana AP019773.1 (100)
 Y
 3,568
 38.60
Coxiella burnetii
 Y
 C. burnetii
 C. burnetii CP014563.1 (100)
 Y
 1,795
 47.97
Leptospira borgpetersenii
 Y
 L. borgpetersenii
 L. borgpetersenii CP047520.1 (100)
 Y
 18,903
 94.41
L. kirschneri
 Y
 Leptospira spp.
 L. kirschneri CP092660.1 (100)
 N
 28,008
 99.32
Rickettsia conorii
 Y
 Rickettsia spp.
 R. conorii MG564258.1 (100)
 N
 159
 28.29
R. typhi Y Rickettsia typhi R. typhi LS992663.1 (100) Y 429 47.72
R. typhi Y Rickettsia typhi R. typhi LS992663.1 (100) Y 7,274 82.02
R. typhi
 Y
 Rickettsia typhi
 R. typhi LS992663.1 (100)
 Y
 9,527
 83.16
Candidatus Neoehrlichia spp. Y Anaplasmataceae, Ehrlichia ruminantium, Ehrlichia Uncultured Candidatus Neoehrlichia sp. SA1 OP208838.1 (100) N 40,238 98.56

*ID, identification; V1–V2, variable regions 1 and 2. †Johns Hopkins University Center for Computational Biology (https://ccb.jhu.edu/software/kraken). ‡National Center for Biotechnology Information taxonomy and accession nos. from BLASTn (https://blast.ncbi.nlm.nih.gov).

Main Article

1Preliminary results of this study were presented at the 72nd American Society of Tropical Medicine and Hygiene Annual Meeting; October 18­–22, 2023; Chicago, Illinois, USA.

Page created: June 15, 2024
Page updated: July 20, 2024
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