Klebsiella transmission on a Malawi neonatal nursery ward
A longitudinal cohort study of 928 samples from Chatinkha nursery in Malawi, investigating Klebsiella pneumoniae transmission and immunity to inform vaccine, antibiotic, and infection control strategies. machine-written summary
928 samples · 1,592 runs · MW · Infant / toddler · 2024 · 3.28 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,973 sample values (collection date, country, timepoint) |
| ✓ Abstract / description | 928 sample values (location site) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolvedhospital ward — not resolved
Schedule stated by the source: “Serial sampling labeled D1 through D12, suggesting repeated daily sampling of neonates on the nursery ward.”.
Study tracks Klebsiella transmission among neonates on Chatinkha nursery ward, Malawi; no individual family/sibling links given in metadata..
Genera, mean relative abundance over 828 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 928 | 100% | 928 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 928 | 100% | 928 | |||
| detailed_location | 928 | 100% | ||||
| location_site | 928 | 100% | 928 | |||
| timepoint_label | 117 | 13% | 117 |
- High ward-level and within-sample diversity of Klebsiella pneumoniae on a Malawian neonatal unit revealed by single colony whole genome sequencing and post-enrichment metagenomics curated
- Extended-Spectrum Beta-Lactamase Klebsiella pneumoniae on a Malawian neonatal unit is amplified by neonates and transmitted by maternal hands, cots and ward surfaces curated
Archive description
As treatment of KPn has become increasingly difficult, attention has turned to methods of prevention instead. One such strategy would be a KPn vaccine delivered to mothers to give their infants passive immunity in the first months of life, whilst they are most vulnerable. There is currently no vaccine against KPn, and it is not known which targets would offer protection. However, developing a vaccine based on surface exposed structures such as the O-antigen is most likely to be effective. A second potential method would be to identify infants most at risk of KPn infection and managing them with alternative first-line antibiotic therapy such as carbapenems, rather than waiting for the culture to become positive, as delay in starting therapy is dangerous. Lastly, we should identify the most important areas for targeting of infection prevention and control (IPC) measures based on the important modes of transmission. For each of these potential interventions (an O-antigen vaccine, empirical carbapenem therapy for high-risk infants and IPC strategies) whether they will work and how they should be deployed is uncertain due to a limited knowledge base. We see quality improvement in all three areas as being essential to improving outcomes and this study will improve the knowledge base in these three areas so that interventions aimed at prevention can be developed in an evidence-based manner.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “to give their infants passive immunity in”
- life stage study.description · “vaccine delivered to mothers to give their”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114246621 | collection_date | 2022-12-08 | R1 | 0.85 | biosample.attribute:collection_date | 2022-12-08 |
| SAMEA114246621 | country | MW | R1 | 0.90 | biosample_attr | Malawi |
| SAMEA114246621 | location_site | Chatinkha nursery | R4 | 0.40 | ena.study_title | Klebsiella_transmission_and_immunity_on_Chatinkha_nursery |
| SAMEA114246843 | timepoint_label | D10 | R1 | 0.70 | run.library_name | SQPP-6656-B:D10 |
Sequencing
1,592 runs over 928 samples · mean 2.53 Gbp per run (median 3.28 Gbp, total 4,020.72 Gbp; 1,592 runs with a base count) · layout PAIRED 1,592 · platform ILLUMINA 1,592 · models Illumina NovaSeq 6000 (1,592) · 89% of runs with a Sandpiper profile · first public 2024-09-24 – 2024-11-27
Authors (15)
Pearse O first · Zuza A · Lester R · Mangochi H · Siyabu P · Tewesa E · Edwards T · Thomson NR · Feasey NA · Kawaza K · Jewell C · Musicha P · Cornick J · Feasey N · Heinz E last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJEB63570.csv.gz (24.3 KB) · parquet (108.5 KB) — all 928 samples, every field with route and confidence · PRJEB63570_determinations.csv.gz (15.3 KB) — 2,901 evidence rows