Bacterial Landscape of Bloodstream Infections in Neutropenic Patients via High Throughput Sequencing.
BACKGROUND
Bloodstream infection (BSI) is a common and potentially life-threatening complication in patients with hematological malignancies and therapy-induced neutropenia. Administration of broad spectrum antibiotics has substantially decreased the mortality rate in febrile neutropenia, but bacterial infection is documented in only one-third or fewer of the cases. BSI is typically diagnosed by blood culture; however, this method can detect only culturable pathogens.


METHODS
In the present study, a total of 130 blood samples from hematological patients receiving dose-intensive antitumoural treatment were subjected to 16S rRNA PCR and 62 of them were cultured. PCR positive samples were processed to high throughput sequencing by amplifying the V1-V3 regions of the 16S rRNA gene to obtain a full spectrum of bacteria present in BSI.


RESULTS
Five phyla and 30 genera were identified with sequencing compared to 2 phyla and 4 genera with culture. The largest proportion of bacteria detected by sequencing belonged to Proteobacteria (55.2%), Firmicutes (33.4%) and Actinobacteria (8.6%), while Fusobacteria (0.4%) and Bacteroidetes (0.1%) were also detected. Ninety-eight percent of the bacteria identified by sequencing were opportunistic human pathogens and 65% belonged to the normal human microbiota.


CONCLUSIONS
The present study indicates that BSIs in neutropenic hosts contain a much broader diversity of bacteria, likely with host origin, than previously realized. The elevated ratio of Proteobacteria in BSI corroborates the results found in other systemic inflammatory diseases, such as inflammatory bowel disease or mucosal infections. This knowledge may become of value for tailoring antimicrobial drug administration.
Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Nobels väg 16, Stockholm, Sweden; Karolinska University Hospital, Department of Clinical Microbiology L2:02, Stockholm, Sweden.
Peter
P
Gyarmati
Karolinska Institutet, Department of Medicine, Division of Hematology, Stockholm, Sweden.
Christian
C
Kjellander
Karolinska Institutet, Department of Medicine, Solna, Infectious Diseases Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden.
Carl
C
Aust
Karolinska Institutet, Department of Infectious Diseases, Stockholm, Sweden.
Mats
M
Kalin
Karolinska Institutet, Department of Medicine, Solna, Infectious Diseases Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden.
Lars
L
Öhrmalm
Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Nobels väg 16, Stockholm, Sweden; Karolinska University Hospital, Department of Clinical Microbiology L2:02, Stockholm, Sweden.
Christian G
CG
Giske
D000328:Adult; D000368:Aged; D000970:Antineoplastic Agents / Q000009:adverse effects / Q000627:therapeutic use; D016470:Bacteremia / Q000382:microbiology*; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D015373:Bacterial Typing Techniques / Q000379:methods; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis; D005260:Female; D019337:Hematologic Neoplasms / Q000150:complications* / Q000188:drug therapy; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D008875:Middle Aged; D058889:Molecular Typing / Q000379:methods; D009503:Neutropenia / Q000150:complications* / Q000209:etiology / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D017422:Sequence Analysis, DNA / Q000379:methods*
D000970:Antineoplastic Agents; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S