Capsule types driving carbapenem-resistant Klebsiella pneumoniae in Pakistan are largely absent from the phage literature
- 1Pak-Austria Fachhochschule Institute of Applied Sciences and Technology
Abstract
Phage therapy is increasingly proposed for carbapenem-resistant Klebsiella pneumoniae, but most Klebsiella phages bind a single capsule type, so a phage is useful only where its capsule type circulates. We asked whether published phages cover the capsule types found in Pakistani patients. We typed 254 clinical K. pneumoniae genomes from Pakistan and curated the phage and depolymerase literature into 34 phage-capsule records covering 27 phages and 15 capsule types. Nearly half the cohort was unmatched: 121 of 254 isolates (47.6%), spanning 51 of 66 capsule types, belong to types for which no phage has been described, and 67 of those isolates carry a carbapenemase. Collapsing each BioProject to one isolate per type raises the unmatched fraction to 51.8%. To ask why, we typed 475 genomes sampled on identical criteria from India, Bangladesh and Nepal, China, Europe and the USA. Two capsule types separated sharply. KL81 accounted for 6.3% of South Asian genomes and none of 275 from China, Europe or the USA, and has no published phage; KL107 showed the reverse, 9.8% in those regions and absent from South Asia. Both survived collapsing (P = 0.0014 and P = 0.0002). Six further differences did not, and are attributable to clonal expansion within single studies. Phages are isolated against locally available hosts, so the capsule types entering the global phage collection track the regions doing the isolating. KL81 is a defined target for phage isolation in South Asia.
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BibTeX
@misc{ahmed2026capsule,
title = {{Capsule types driving carbapenem-resistant Klebsiella pneumoniae in Pakistan are largely absent from the phage literature}},
author = {T. Ahmed and A. H. Shah},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.29.755075},
url = {https://www.biorxiv.org/content/10.64898/2026.09.29.755075v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Capsule types driving carbapenem-resistant Klebsiella pneumoniae in Pakistan are largely absent from the phage literature
AU - T. Ahmed
AU - A. H. Shah
PY - 2026
DA - 2026/09/29
PB - bioRxiv
DO - 10.64898/2026.09.29.755075
UR - https://www.biorxiv.org/content/10.64898/2026.09.29.755075v1
AB - Phage therapy is increasingly proposed for carbapenem-resistant Klebsiella pneumoniae, but most Klebsiella phages bind a single capsule type, so a phage is useful only where its capsule type circulates. We asked whether published phages cover the capsule types found in Pakistani patients. We typed 254 clinical K. pneumoniae genomes from Pakistan and curated the phage and depolymerase literature into 34 phage-capsule records covering 27 phages and 15 capsule types. Nearly half the cohort was unmatched: 121 of 254 isolates (47.6%), spanning 51 of 66 capsule types, belong to types for which no phage has been described, and 67 of those isolates carry a carbapenemase. Collapsing each BioProject to one isolate per type raises the unmatched fraction to 51.8%. To ask why, we typed 475 genomes sampled on identical criteria from India, Bangladesh and Nepal, China, Europe and the USA. Two capsule types separated sharply. KL81 accounted for 6.3% of South Asian genomes and none of 275 from China, Europe or the USA, and has no published phage; KL107 showed the reverse, 9.8% in those regions and absent from South Asia. Both survived collapsing (P = 0.0014 and P = 0.0002). Six further differences did not, and are attributable to clonal expansion within single studies. Phages are isolated against locally available hosts, so the capsule types entering the global phage collection track the regions doing the isolating. KL81 is a defined target for phage isolation in South Asia.
ER -