# CRISPRi Screening Identifies Essential E. coli Virulence Factors for Placental Barrier Breach in a Maternal–Fetal Infection Model

**Authors:** Xiaochen Cai, Xiao Liang, Peicen Zou, Ruiqi Xiao, Yajuan Wang

PMC · DOI: 10.3390/ijms27041661 · International Journal of Molecular Sciences · 2026-02-09

## TL;DR

This study identifies key E. coli virulence factors that help the bacteria cross the placental barrier, causing neonatal sepsis.

## Contribution

The study uses CRISPRi screening to systematically identify and validate E. coli genes essential for placental barrier breach in a maternal-fetal infection model.

## Key findings

- Genes related to motility, iron acquisition, hemolysin secretion, and adherence/invasion are critical for E. coli placental translocation.
- The hlyB gene is essential for uterine infection, and ibeA facilitates placental cell penetration by interacting with host receptors PSF/VIM.
- Host cells defend against ibeA+ E. coli infection via upregulation of ASPHD1 as part of a novel defense pathway.

## Abstract

Early-onset neonatal sepsis caused by Escherichia coli (E. coli) threatens neonates’ lives due to the pathogen’s high virulence and multidrug resistance. The mechanisms that enable its placental barrier breach are poorly understood. Using a clinically isolated ST95 ExPEC strain from a neonatal sepsis case, along with a pregnant rat model and an in vitro placental barrier model, we performed CRISPR interference screening. This screen targeted 264 virulence factor genes and identified virulence factors for motility, iron acquisition, hemolysin secretion, and adherence/invasion as critical. We demonstrated that hlyB is essential for uterine infection, and we elucidated a mechanism for ibeA that facilitates syncytial trophoblast cell layer penetration by interacting with the host receptor(s) PSF/VIM to enhance bacterial internalization. Host cells countered ibeA+ E. coli infection via a novel host defense pathway involving upregulation of ASPHD1. This study systematically mapped the virulence factors required for E. coli placental translocation and delineated key host–pathogen interactions.

## Linked entities

- **Genes:** hlyB (hemolysin B) [NCBI Gene 1789727], ibeA (putative intracellular survival FAD-dependent oxidoreductase IbeA) [NCBI Gene 89519310], ASPHD1 (aspartate beta-hydroxylase domain containing 1) [NCBI Gene 253982], IGFBP7 (insulin like growth factor binding protein 7) [NCBI Gene 3490], VIM (vimentin) [NCBI Gene 7431]
- **Diseases:** neonatal sepsis (MONDO:0700217)
- **Species:** Escherichia coli (taxon 562), Mus musculus (taxon 10090)

## Full-text entities

- **Genes:** NONO (non-POU domain containing octamer binding) [NCBI Gene 4841] {aka MRXS34, NMT55, NRB54, P54, P54NRB, PPP1R114}, NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790] {aka CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1}, FBXL15 (F-box and leucine rich repeat protein 15) [NCBI Gene 79176] {aka FBXO37, Fbl15, JET}, EGF (epidermal growth factor) [NCBI Gene 1950] {aka HOMG4, URG}, OCLN (occludin) [NCBI Gene 403844], TJP1 (tight junction protein 1) [NCBI Gene 403752] {aka ZO-1, ZO1}, ALOX15P1 (arachidonate 15-lipoxygenase pseudogene 1) [NCBI Gene 100652883] {aka ALOX15P}, OCLN (occludin) [NCBI Gene 100506658] {aka BLCPMG, PPP1R115, PTORCH1}, H3C13 (H3 clustered histone 13) [NCBI Gene 483172], HlyA [NCBI Gene 7701379], TNFRSF13C (TNF receptor superfamily member 13C) [NCBI Gene 115650] {aka BAFF-R, BAFFR, BROMIX, CD268, CVID4, prolixin}, BNIP3P11 (BCL2 interacting protein 3 pseudogene 11) [NCBI Gene 106480286], SFPQ (splicing factor proline and glutamine rich) [NCBI Gene 6421] {aka POMP100, PPP1R140, PSF}, VIM (vimentin) [NCBI Gene 7431], NPFF (neuropeptide FF-amide peptide precursor) [NCBI Gene 8620] {aka FMRFAL}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, ASPHD1 (aspartate beta-hydroxylase domain containing 1) [NCBI Gene 253982], CTAGE6 (CTAGE family member 6) [NCBI Gene 340307] {aka CTAGE6P}, TJP1 (tight junction protein 1) [NCBI Gene 7082] {aka ZO-1}, VIM (vimentin) [NCBI Gene 477991], ASPH (aspartate beta-hydroxylase) [NCBI Gene 444] {aka AAH, BAH, CASQ2BP1, FDLAB, HAAH, JCTN}, SMC2 (structural maintenance of chromosomes 2) [NCBI Gene 10592] {aka CAP-E, CAPE, SMC-2, SMC2L1}, MTOR (mechanistic target of rapamycin kinase) [NCBI Gene 2475] {aka FRAP, FRAP1, FRAP2, RAFT1, RAPT1, SKS}, CNTNAP1 (contactin associated protein 1) [NCBI Gene 8506] {aka CASPR, CHN3, CNTNAP, NRXN4, P190}, FN1 (fibronectin 1) [NCBI Gene 2335] {aka CIG, ED-B, FINC, FN, FNZ, GFND}, FREM1 (FRAS1 related extracellular matrix 1) [NCBI Gene 158326] {aka BNAR, C9orf143, C9orf145, C9orf154, MOTA, TRIGNO2}, CREB1 (cAMP responsive element binding protein 1) [NCBI Gene 1385] {aka CREB, CREB-1}, HlyB [NCBI Gene 7701380], NUP62 (nucleoporin 62) [NCBI Gene 23636] {aka IBSN, SNDI, p62}, SFPQ (splicing factor proline and glutamine rich) [NCBI Gene 100688260]
- **Diseases:** microbial infection (MESH:D015163), Neonatal Sepsis (MESH:D000071074), choriocarcinoma (MESH:D002822), hemolysis (MESH:D006461), injury to (MESH:D014947), inflammation (MESH:D007249), SD (MESH:D012735), uterine (MESH:D014591), bacterial (MESH:D001424), sepsis (MESH:D018805), colon cancer (MESH:D015179), deaths (MESH:D003643), E. coli infection (MESH:D004927), cytotoxic (MESH:D064420), placental (MESH:D010922), bacteremia (MESH:D016470), ExPEC Infection (MESH:D007239)
- **Chemicals:** iron (MESH:D007501), kanamycin (MESH:D007612), Gentamicin (MESH:D005839), paraffin (MESH:D010232), Rapamycin (MESH:D020123), DPBS (MESH:C012939), LPS (MESH:D008070), CO2 (MESH:D002245), IPTG (MESH:D007544), wortmannin (MESH:D000077191), formalin (MESH:D005557), chloramphenicol (MESH:D002701), DMSO (MESH:D004121), eosin (MESH:D004801), hematoxylin (MESH:D006416), Doxorubicin (MESH:D004317), H2O2 (MESH:D006861), 3-MA (-), nocodazole (MESH:D015739), FAD (MESH:D005182), forskolin (MESH:D005576)
- **Species:** Escherichia coli (E. coli, species) [taxon 562], Escherichia coli K1 (strain) [taxon 1392869], Listeria monocytogenes (species) [taxon 1639], Streptococcus sp. 'group B' (species) [taxon 1319], Homo sapiens (human, species) [taxon 9606], Rattus norvegicus (brown rat, species) [taxon 10116]
- **Mutations:** C0018S, (I) for 1
- **Cell lines:** BeWo — Homo sapiens (Human), Gestational choriocarcinoma, Cancer cell line (CVCL_0044), ST95 — Homo sapiens (Human), Lung non-small cell carcinoma, Cancer cell line (CVCL_7025), TOP10 — Homo sapiens (Human), Chronic myelogenous leukemia, BCR-ABL1 positive, Cancer cell line (CVCL_TT29)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12940985/full.md

## References

33 references — full list in the complete paper: https://tomesphere.com/paper/PMC12940985/full.md

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Source: https://tomesphere.com/paper/PMC12940985