Distribution of capsule and O types in Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: A meta-analysis of genome-predicted serotype prevalence to inform potential vaccine coverage

Thomas D Stanton, Shaun P Keegan, Jabir A Abdulahi, Anne V Amulele, Matthew Bates, Eva Heinz, Yogesh Hooda, Weiming Hu, Kajal Jain, Samiah Kanwar, Rindidzani Magobo, Courtney P Olwagen, John M Tembo, Tolbert Sonda, Jonathan Strysko, Caroline C Tigoi, Sameen Ahmad Amin, Kyle Bittinger, Jennifer Cornick, Ebenezer Foster-Nyarko, Wilson Gumbi, Aneeta Hotwani, Naveed Iqbal, Steven M Jones, Furqan Kabir, Waqasuddin Khan, Chileshe L Musyani, Carolyn M McGann, Varsha Mittal, Ahmed M Moustafa, Patrick Musicha, James CL Mwansa, Moreka L Ndumba, Erkison E Odih, Donwilliams O Omuoyo, Oliver Pearse, Laura T Phillips, Paul J Planet, Aniqa Abdul Rasool, Charlene M C Rodrigues, Kirsty Sands, Arif M Tanmoy, Erin Theiller, Allan M Zuza, Sulagna Basu, Grace J Chan, Kenneth C Iregbu, Jean-Baptiste Mazarati, Semaria Solomon Alemayehu, Timothy R Walsh, Rabaab Zahra, Angela Dramowski, Sombo Fwoloshi, Appiah-Korang Labi, Lola Madrid, Noah Obeng-Nkrumah, David Ojok, Boaz D Wadugu, Andrew C Whitelaw, Adhisivam Bethou, Anudita Bhargava, Atul Jindal, Ruchi N Nanavati, Priyanka S Prasad, Apurba Sastry, Joveria Q Farooqi, Najia Ghanchi, Fyezah Jehan, Erum Khan, Ramesh K Agarwal, Alexander M Aiken, James A Berkley, Susan E Coffin, Nicholas A Feasey, Nelesh P Govender, Davidson H Hamer, Shabir A Madhi, Muhammad Imran Nisar, Samir K Saha, Senjuti Saha, Mari Jeeva Sankar, Kelly L Wyres and Kathryn E Holt

PLOS Medicine, 2026, vol. 23, issue 1, 1-26

Abstract: Background: Klebsiella pneumoniae causes ~20% of sepsis in neonates, with ~40% crude mortality. A vaccine administered to pregnant women, protecting against ≥70% of K. pneumoniae infections, could avert ~400,000 cases and ~80,000 deaths annually, mostly in Africa and South Asia. Vaccine formulations targeting the capsular polysaccharide (K) or lipopolysaccharide (O) antigens are in development. Global K. pneumoniae populations display extensive K and O diversity, necessitating a polyvalent vaccine targeted to the serotypes associated with neonatal disease in relevant geographical regions. We investigated the prevalence of K and O types associated with neonatal sepsis in Africa and South Asia to inform maternal vaccine design. Methods and findings: We analysed 1,930 K. pneumoniae neonate blood isolates from 13 surveillance studies across 35 sites in 13 countries. We used pathogen whole-genome sequencing to predict K and O serotypes and adjust for local transmission clusters, and Bayesian hierarchical meta-analysis to estimate K and O prevalence overall and per region, treating site as a random effect. Eighty-seven K loci were identified. KL2, KL102, KL25, KL15, and KL62 accounted for 49% of isolates. We estimate that 20 K loci, combining the eight most prevalent per region, could cover 72.9% of all infections (95% credible interval: [69.4%, 76.5%]) and ≥70% in each of Eastern, Western, and Southern Africa and South Asia. Preliminary findings from three sites suggested sufficient temporal stability of K loci to maintain 20-valent K vaccine coverage over 5–10 years, but more longitudinal data are needed to support this prediction. O types were far less diverse (n = 14 types). We estimate the top-5 (O1⍺β,2⍺, O1⍺β,2β, O2⍺, O2β, and O4) would cover 86.2% [82.6, 89.9%] of total infections (76%–92% per region), while the top-10 would cover ~99% of infections in all four regions. The main limitations of our study are the reliance on genome sequences to predict K and O serotypes (as serological typing is not available) and a lack of longitudinal data to explore stability of antigen prevalence over time. Conclusions: Neonatal sepsis is associated with diverse K and O types, with substantial geographic and temporal variation even after adjusting for localised transmission clusters. Despite this, a single 20-valent K vaccine could theoretically cover ≥70% of infections in all target regions. Locally-targeted vaccines could achieve higher coverage with lower valency, but are less feasible. In principle, very high coverage could be achieved with lower valency O-based vaccines, however, the protective efficacy against disease of antibodies targeting the O antigen remains uncertain. Further research is needed on cross-reactivity, antigen exposure, and stability of antigens over time, to better inform vaccine development. Why Was This Study Done?: What Did the Researchers Do and Find?: What Do These Findings Mean?: Thomas Stanton and colleagues use whole genome sequencing to evaluate the prevalence of Klebsiella pneumoniae K and O antigen types in 13 countries in Africa and South Asia to help inform vaccine design against neonatal sepsis.

Date: 2026
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pmed00:1004879

DOI: 10.1371/journal.pmed.1004879

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