2022
Differential richness inference for 16S rRNA marker gene surveys
Kumar M, Slud E, Hehnly C, Zhang L, Broach J, Irizarry R, Schiff S, Paulson J. Differential richness inference for 16S rRNA marker gene surveys. Genome Biology 2022, 23: 166. PMID: 35915508, PMCID: PMC9344657, DOI: 10.1186/s13059-022-02722-x.Peer-Reviewed Original ResearchConceptsMarker gene surveysRRNA marker gene surveysGene surveysMicrobial assemblagesSpecies discoveryMicrobial taxaMicrobial communitiesMicrobiome surveysRichness estimationSequencing readsDiversity measuresTaxaGenus abundanceMicrobiome dataR packageAbundanceRichnessDiscoveryDiversityReadsAssemblagesObserved numberExperimental evidenceAccumulationInference
2021
Vaginal microbiome topic modeling of laboring Ugandan women with and without fever
Movassagh M, Bebell L, Burgoine K, Hehnly C, Zhang L, Moran K, Sheldon K, Sinnar S, Mbabazi-Kabachelor E, Kumbakumba E, Bazira J, Ochora M, Mulondo R, Nsubuga B, Weeks A, Gladstone M, Olupot-Olupot P, Ngonzi J, Roberts D, Meier F, Irizarry R, Broach J, Schiff S, Paulson J. Vaginal microbiome topic modeling of laboring Ugandan women with and without fever. Npj Biofilms And Microbiomes 2021, 7: 75. PMID: 34508087, PMCID: PMC8433417, DOI: 10.1038/s41522-021-00244-1.Peer-Reviewed Original ResearchConceptsIntrapartum feverClinical variablesHigh prevalenceVaginal microbiomeUgandan womenLonger labour durationMaternal clinical featuresYoung maternal ageDuration of pregnancyOnset of laborMicrobial communitiesVaginal microbial communitiesAfebrile mothersFebrile mothersPeripartum courseMaternal feverNeonatal outcomesLabor durationClinical featuresMaternal ageVaginal microbesFeverOutcome riskVeillonella genusMicrobiome influences
2020
The Problem of Microbial Dark Matter in Neonatal Sepsis - Volume 26, Number 11—November 2020 - Emerging Infectious Diseases journal - CDC
Sinnar S, Schiff S. The Problem of Microbial Dark Matter in Neonatal Sepsis - Volume 26, Number 11—November 2020 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2020, 26: 2543-2548. PMID: 33080169, PMCID: PMC7588532, DOI: 10.3201/eid2611.200004.Peer-Reviewed Original ResearchConceptsNeonatal sepsisCausative pathogenInfectious Diseases journal - CDCCulture recovery ratesAntimicrobial therapyBlood culturesTimely diagnosisAntimicrobial stewardshipWorldwide deathsMost blood culturesUnidentified pathogensTransmission patternsDeathPathogen discoveryWhole metagenomic sequencingPathogensEffective diagnosticsMetagenomic sequencingSepsisPatientsInfantsTherapyDiagnosisRecovery rate
2013
The Microbial Spectrum of Neonatal Sepsis in Uganda: Recovery of Culturable Bacteria in Mother-Infant Pairs
Kiwanuka J, Bazira J, Mwanga J, Tumusiime D, Nyesigire E, Lwanga N, Warf B, Kapur V, Poss M, Schiff S. The Microbial Spectrum of Neonatal Sepsis in Uganda: Recovery of Culturable Bacteria in Mother-Infant Pairs. PLOS ONE 2013, 8: e72775. PMID: 24013829, PMCID: PMC3754959, DOI: 10.1371/journal.pone.0072775.Peer-Reviewed Original ResearchConceptsNeonatal sepsisMother-infant pairsVaginal specimensConsecutive mother-infant pairsMicrobial spectrumSeptic newborn infantsCerebrospinal fluid culturesBacterial culture techniquesSensitive molecular approachesClinical criteriaNewborn infantsPutative causative agentFluid cultureInfant bloodMaternal bloodSepsisCerebrospinal fluidSpinal fluidInfantsBloodCausative agentMaternal transmissionEnvironmental sourcesIdentifiable bacteriaCulture techniques
1989
Delayed Cerebrospinal-Fluid Shunt Infection in Children
Schiff S, Oakes J. Delayed Cerebrospinal-Fluid Shunt Infection in Children. Pediatric Neurosurgery 1989, 15: 131-135. PMID: 2702349, DOI: 10.1159/000120458.Peer-Reviewed Original Research