Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations.
Klebsiella pneumoniae
/ genetics
Humans
Klebsiella Infections
/ epidemiology
Longitudinal Studies
Bacterial Vaccines
/ immunology
Adult
Female
Hospitals
Child
Male
Child, Preschool
Infant
Middle Aged
Africa South of the Sahara
/ epidemiology
Cross Infection
/ microbiology
Adolescent
Genome, Bacterial
Drug Resistance, Multiple, Bacterial
/ genetics
Infant, Newborn
Malawi
/ epidemiology
Young Adult
AMR
Capsular polysaccharide
ESKAPE
Genome surveillance
Healthcare-associated
Malawi
Neonatal infection
Nosocomial infections
Sepsis
Surface antigens
Journal
Genome medicine
ISSN: 1756-994X
Titre abrégé: Genome Med
Pays: England
ID NLM: 101475844
Informations de publication
Date de publication:
06 May 2024
06 May 2024
Historique:
received:
10
10
2023
accepted:
30
04
2024
medline:
7
5
2024
pubmed:
7
5
2024
entrez:
6
5
2024
Statut:
epublish
Résumé
Infections caused by multidrug-resistant gram-negative bacteria present a severe threat to global public health. The WHO defines drug-resistant Klebsiella pneumoniae as a priority pathogen for which alternative treatments are needed given the limited treatment options and the rapid acquisition of novel resistance mechanisms by this species. Longitudinal descriptions of genomic epidemiology of Klebsiella pneumoniae can inform management strategies but data from sub-Saharan Africa are lacking. We present a longitudinal analysis of all invasive K. pneumoniae isolates from a single hospital in Blantyre, Malawi, southern Africa, from 1998 to 2020, combining clinical data with genome sequence analysis of the isolates. We show that after a dramatic increase in the number of infections from 2016 K. pneumoniae becomes hyperendemic, driven by an increase in neonatal infections. Genomic data show repeated waves of clonal expansion of different, often ward-restricted, lineages, suggestive of hospital-associated transmission. We describe temporal trends in resistance and surface antigens, of relevance for vaccine development. Our data highlight a clear need for new interventions to prevent rather than treat K. pneumoniae infections in our setting. Whilst one option may be a vaccine, the majority of cases could be avoided by an increased focus on and investment in infection prevention and control measures, which would reduce all healthcare-associated infections and not just one.
Sections du résumé
BACKGROUND
BACKGROUND
Infections caused by multidrug-resistant gram-negative bacteria present a severe threat to global public health. The WHO defines drug-resistant Klebsiella pneumoniae as a priority pathogen for which alternative treatments are needed given the limited treatment options and the rapid acquisition of novel resistance mechanisms by this species. Longitudinal descriptions of genomic epidemiology of Klebsiella pneumoniae can inform management strategies but data from sub-Saharan Africa are lacking.
METHODS
METHODS
We present a longitudinal analysis of all invasive K. pneumoniae isolates from a single hospital in Blantyre, Malawi, southern Africa, from 1998 to 2020, combining clinical data with genome sequence analysis of the isolates.
RESULTS
RESULTS
We show that after a dramatic increase in the number of infections from 2016 K. pneumoniae becomes hyperendemic, driven by an increase in neonatal infections. Genomic data show repeated waves of clonal expansion of different, often ward-restricted, lineages, suggestive of hospital-associated transmission. We describe temporal trends in resistance and surface antigens, of relevance for vaccine development.
CONCLUSIONS
CONCLUSIONS
Our data highlight a clear need for new interventions to prevent rather than treat K. pneumoniae infections in our setting. Whilst one option may be a vaccine, the majority of cases could be avoided by an increased focus on and investment in infection prevention and control measures, which would reduce all healthcare-associated infections and not just one.
Identifiants
pubmed: 38711148
doi: 10.1186/s13073-024-01342-3
pii: 10.1186/s13073-024-01342-3
doi:
Substances chimiques
Bacterial Vaccines
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
67Subventions
Organisme : Bill & Melinda Gates Foundation
ID : INV-005180
Pays : United States
Organisme : Wellcome Trust
ID : 217303/Z/19/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 206194
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 206454
Pays : United Kingdom
Informations de copyright
© 2024. The Author(s).
Références
Liu L, Oza S, Hogan D, Chu Y, Perin J, Zhu J, et al. Global, regional, and national causes of under-5 mortality in 2000–15: an updated systematic analysis with implications for the Sustainable Development Goals. Lancet Lond Engl. 2016;388(10063):3027–35.
doi: 10.1016/S0140-6736(16)31593-8
Sands K, Carvalho MJ, Portal E, Thomson K, Dyer C, Akpulu C, et al. Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries. Nat Microbiol. 2021;6(4):512–23.
pubmed: 33782558
pmcid: 8007471
doi: 10.1038/s41564-021-00870-7
Musicha P, Cornick JE, Bar-Zeev N, French N, Masesa C, Denis B, et al. Trends in antimicrobial resistance in bloodstream infection isolates at a large urban hospital in Malawi (1998–2016): a surveillance study. Lancet Infect Dis. 2017;17(10):1042–52.
pubmed: 28818544
pmcid: 5610140
doi: 10.1016/S1473-3099(17)30394-8
Salzberg NT, Sivalogan K, Bassat Q, Taylor AW, Adedini S, El Arifeen S, et al. Mortality surveillance methods to identify and characterize deaths in child health and mortality prevention surveillance network sites. Clin Infect Dis. 2019;69(Supplement_4):S262–73.
pubmed: 31598664
pmcid: 6785672
doi: 10.1093/cid/ciz599
Wyres KL, Lam MMC, Holt KE. Population genomics of Klebsiella pneumoniae. Nat Rev Microbiol. 2020;18:344–59.
pubmed: 32055025
doi: 10.1038/s41579-019-0315-1
Ellington MJ, Heinz E, Wailan AM, Dorman MJ, de Goffau M, Cain AK, et al. Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center. Genome Biol. 2019;20(1):184.
pubmed: 31477167
pmcid: 6717969
doi: 10.1186/s13059-019-1785-1
Lipworth S, Vihta KD, Chau K, Barker L, George S, Kavanagh J, et al. Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK. Genome Med. 2021;13(1):144.
pubmed: 34479643
pmcid: 8414751
doi: 10.1186/s13073-021-00947-2
Fostervold A, Hetland MAK, Bakksjø R, Bernhoff E, Holt KE, Samuelsen Ø, et al. A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001–15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307. J Antimicrob Chemother. 2022;77(3):665–74.
pubmed: 34935048
doi: 10.1093/jac/dkab463
Thorpe H, Booton R, Kallonen T, Gibbon MJ, Couto N, Passet V, et al. One Health or Three? Transmission modelling of Klebsiella isolates reveals ecological barriers to transmission between humans, animals and the environment. Microbiology. 2021. https://doi.org/10.1102/2021.08.05.455249 .
doi: 10.1102/2021.08.05.455249
Wyres KL, Nguyen TNT, Lam MMC, Judd LM, van Vinh CN, Dance DAB, et al. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiellapneumoniae from South and Southeast Asia. Genome Med. 2020;12(1):11.
pubmed: 31948471
pmcid: 6966826
doi: 10.1186/s13073-019-0706-y
Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15(3):R46.
pubmed: 24580807
pmcid: 4053813
doi: 10.1186/gb-2014-15-3-r46
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol J Comput Mol Cell Biol. 2012;19(5):455–77.
doi: 10.1089/cmb.2012.0021
Page AJ, De Silva N, Hunt M, Quail MA, Parkhill J, Harris SR, et al. Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microb Genomics. 2016;2(8):e000083.
doi: 10.1099/mgen.0.000083
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinforma Oxf Engl. 2014;30(14):2068–9.
doi: 10.1093/bioinformatics/btu153
Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019;37(5):540–6.
pubmed: 30936562
doi: 10.1038/s41587-019-0072-8
Wick RR, Holt KE. Polypolish: Short-read polishing of long-read bacterial genome assemblies. Schneidman-Duhovny D, editor. PLoS Comput Biol. 2022;18(1):e1009802.
pubmed: 35073327
pmcid: 8812927
doi: 10.1371/journal.pcbi.1009802
Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895–903.
pubmed: 24777092
pmcid: 4068535
doi: 10.1128/AAC.02412-14
Lester R, Musicha P, Kawaza K, Langton J, Mango J, Mangochi H, et al. Effect of resistance to third-generation cephalosporins on morbidity and mortality from bloodstream infections in Blantyre, Malawi: a prospective cohort study. Lancet Microbe. 2022;3(12):e922–30.
pubmed: 36335953
pmcid: 9712123
doi: 10.1016/S2666-5247(22)00282-8
Cornick J, Musicha P, Peno C, Seager E, Iroh Tam PY, Bilima S, et al. Genomic investigation of a suspected Klebsiellapneumoniae outbreak in a neonatal care unit in sub-Saharan Africa. Microb Genomics. 2021;7(11):000703.
doi: 10.1099/mgen.0.000703
Musicha P, Msefula CL, Mather AE, Chaguza C, Cain AK, Peno C, et al. Genomic analysis of Klebsiellapneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. J Antimicrob Chemother. 2019;74(5):1223–32.
pubmed: 30778540
pmcid: 6477993
doi: 10.1093/jac/dkz032
Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genomics. 2017;3(10):e000131.
doi: 10.1099/mgen.0.000131
Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ, Tomita T, et al. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 2014;6(11):90.
pubmed: 25422674
pmcid: 4237778
doi: 10.1186/s13073-014-0090-6
Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M, Landraud L, et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother. 2014;58(1):212–20.
pubmed: 24145532
pmcid: 3910750
doi: 10.1128/AAC.01310-13
McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother. 2013;57(7):3348–57.
pubmed: 23650175
pmcid: 3697360
doi: 10.1128/AAC.00419-13
Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL, Holt KE. A genomic surveillance framework and genotyping tool for Klebsiellapneumoniae and its related species complex. Nat Commun. 2021;12(1):4188.
pubmed: 34234121
pmcid: 8263825
doi: 10.1038/s41467-021-24448-3
Lam MMC, Wick RR, Judd LM, Holt KE, Wyres KL. Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiellapneumoniae species complex. Microb Genomics. 2022;8:000800.
doi: 10.1099/mgen.0.000800
Wick RR, Heinz E, Holt KE, Wyres KL. Kaptive web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella Genomes. Diekema DJ, editor. J Clin Microbiol. 2018;56(6):e00197–18 /jcm/56/6/e00197-18.atom.
pubmed: 29618504
pmcid: 5971559
doi: 10.1128/JCM.00197-18
Follador R, Heinz E, Wyres KL, Ellington MJ, Kowarik M, Holt KE, et al. The diversity of Klebsiellapneumoniae surface polysaccharides. Microb Genomics. 2016;2(8):e000073.
doi: 10.1099/mgen.0.000073
Kelly SD, Ovchinnikova OG, Müller F, Steffen M, Braun M, Sweeney RP, et al. Identification of a second glycoform of the clinically prevalent O1 antigen from Klebsiellapneumoniae. Proc Natl Acad Sci U S A. 2023;120(29):e2301302120.
pubmed: 37428935
pmcid: 10629545
doi: 10.1073/pnas.2301302120
Torsten Seemann. snippy: fast bacterial variant calling from NGS reads. Available from: https://github.com/tseemann/snippy
Wu KM, Li LH, Yan JJ, Tsao N, Liao TL, Tsai HC, et al. Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis. J Bacteriol. 2009;191(14):4492–501.
pubmed: 19447910
pmcid: 2704730
doi: 10.1128/JB.00315-09
Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 2015;43(3):e15–e15.
pubmed: 25414349
doi: 10.1093/nar/gku1196
Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641–50.
pubmed: 19377059
pmcid: 2693737
doi: 10.1093/molbev/msp077
Elliott AG, Ganesamoorthy D, Coin L, Cooper MA, Cao MD. Complete genome sequence of Klebsiellaquasipneumoniae subsp. similipneumoniae Strain ATCC 700603. Genome Announc. 2016;4(3):e00438–16.
pubmed: 27231369
pmcid: 4882950
doi: 10.1128/genomeA.00438-16
Pinto-Tomás AA, Anderson MA, Suen G, Stevenson DM, Chu FST, Cleland WW, et al. Symbiotic nitrogen fixation in the fungus gardens of leaf-cutter ants. Science. 2009;326(5956):1120–3.
pubmed: 19965433
doi: 10.1126/science.1173036
Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genomics. 2016;2(4):e000056.
doi: 10.1099/mgen.0.000056
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–74.
pubmed: 25371430
doi: 10.1093/molbev/msu300
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14(6):587–9.
pubmed: 28481363
pmcid: 5453245
doi: 10.1038/nmeth.4285
Pupko T, Pe’er I, Shamir R, Graur D. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol. 2000;17(6):890–6.
pubmed: 10833195
doi: 10.1093/oxfordjournals.molbev.a026369
Wailan AM, Coll F, Heinz E, Tonkin-Hill G, Corander J, Feasey NA, et al. rPinecone: define sub-lineages of a clonal expansion via a phylogenetic tree. Microb Genomics. 2019;5(4):e000264.
doi: 10.1099/mgen.0.000264
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49(W1):W293–6.
pubmed: 33885785
pmcid: 8265157
doi: 10.1093/nar/gkab301
Shen Z, Gao Q, Qin J, Liu Y, Li M. Emergence of an NDM-5-Producing Hypervirulent Klebsiellapneumoniae Sequence Type 35 Strain with Chromosomal Integration of an Integrative and Conjugative Element, ICE Kp1. Antimicrob Agents Chemother. 2019;64(1):e01675–e1719.
pubmed: 31611359
pmcid: 7187603
doi: 10.1128/AAC.01675-19
Cabanel N, Rosinski-Chupin I, Chiarelli A, Botin T, Tato M, Canton R, et al. Evolution of VIM-1-producing Klebsiellapneumoniae isolates from a hospital outbreak reveals the genetic bases of the loss of the urease-positive identification character. Beiko RG, editor. MSystems. 2021;6(3):e00244–21.
pubmed: 34060914
pmcid: 8269217
doi: 10.1128/mSystems.00244-21
Stoesser N, Giess A, Batty EM, Sheppard AE, Walker AS, Wilson DJ, et al. Genome sequencing of an extended series of NDM-producing Klebsiellapneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community- versus hospital-associated transmission in an endemic setting. Antimicrob Agents Chemother. 2014;58(12):7347–57.
pubmed: 25267672
pmcid: 4249533
doi: 10.1128/AAC.03900-14
Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, et al. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol. 2020;21(1):180.
pubmed: 32698896
pmcid: 7376924
doi: 10.1186/s13059-020-02090-4
Wickham H. Ggplot2: elegant graphics for data analysis. New York: Springer; 2009. p. 212 (Use R!).
doi: 10.1007/978-0-387-98141-3
Yu G, Lam TTY, Zhu H, Guan Y. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Mol Biol Evol. 2018;35(12):3041–3.
pubmed: 30351396
pmcid: 6278858
doi: 10.1093/molbev/msy194
R Core Team. A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.; 2021. Available from: https://www.R-project.org
World Health Organization, editor. Antimicrobial resistance: global report on surveillance. Geneva, Switzerland: World Health Organization; 2014. p. 232.
Rodrigues C, Passet V, Rakotondrasoa A, Diallo TA, Criscuolo A, Brisse S. Description of Klebsiellaafricanensis sp. nov., Klebsiellavariicola subsp. tropicalensis subsp. nov. and Klebsiellavariicola subsp. variicola subsp. nov. Res Microbiol. 2019;170(3):165–70.
pubmed: 30817987
doi: 10.1016/j.resmic.2019.02.003
Gordon MA, Walsh AL, Chaponda M, Soko D, Mbvwinji M, Molyneux ME, et al. Bacteraemia and mortality among adult medical admissions in Malawi–predominance of non-typhi salmonellae and Streptococcus pneumoniae. J Infect. 2001;42(1):44–9.
pubmed: 11243753
doi: 10.1053/jinf.2000.0779
Ejaz H, Wang N, Wilksch JJ, Page AJ, Cao H, Gujaran S, et al. Phylogenetic analysis of Klebsiellapneumoniae from hospitalized children. Pakistan Emerg Infect Dis. 2017;23(11):1872–5.
pubmed: 29048298
doi: 10.3201/eid2311.170833
Chung The H, Karkey A, Pham Thanh D, Boinett CJ, Cain AK, Ellington M, et al. A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiellapneumoniae. EMBO Mol Med. 2015;7(3):227–39.
pubmed: 25712531
pmcid: 4364942
doi: 10.15252/emmm.201404767
Wyres KL, Hawkey J, Hetland MAK, Fostervold A, Wick RR, Judd LM, et al. Emergence and rapid global dissemination of CTX-M-15-associated Klebsiellapneumoniae strain ST307. J Antimicrob Chemother. 2019;74(3):577–81.
pubmed: 30517666
doi: 10.1093/jac/dky492
Gorrie CL, Da Silva AG, Ingle DJ, Higgs C, Seemann T, Stinear TP, et al. Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis. Lancet Microbe. 2021;2(11):e575–83.
pubmed: 35544081
doi: 10.1016/S2666-5247(21)00149-X
Mangochi H, Tolhurst R, Simpson V, Kawaza K, Chidziwisano K, Feasey NA, et al. A qualitative study exploring hand hygiene practices in a neonatal unit in Blantyre, Malawi: implications for controlling healthcare-associated infections. Wellcome Open Res. 2022;7:146.
pubmed: 37224320
doi: 10.12688/wellcomeopenres.17793.1
Graf FE, Goodman RN, Gallichan S, Forrest S, Picton-Barlow E, Fraser AJ, et al. Molecular mechanisms of re-emerging chloramphenicol susceptibility in extended-spectrum beta-lactamase producing Enterobacterales. Microbiology; 2023. http://biorxiv.org/lookup/doi/10.1101/2023.11.16.567242 .
Sojo-Dorado J, López-Hernández I, Rosso-Fernandez C, Morales IM, Palacios-Baena ZR, Hernández-Torres A, et al. Effectiveness of fosfomycin for the treatment of multidrug-resistant Escherichiacoli bacteremic urinary tract infections: a randomized clinical trial. JAMA Netw Open. 2022;5(1):e2137277.
pubmed: 35024838
pmcid: 8759008
doi: 10.1001/jamanetworkopen.2021.37277
McGovern PC, Wible M, El-Tahtawy A, Biswas P, Meyer RD. All-cause mortality imbalance in the tigecycline phase 3 and 4 clinical trials. Int J Antimicrob Agents. 2013;41(5):463–7.
pubmed: 23537581
doi: 10.1016/j.ijantimicag.2013.01.020
Veleba M, Schneiders T. Tigecycline resistance can occur independently of the ramA Gene in Klebsiellapneumoniae. Antimicrob Agents Chemother. 2012;56(8):4466–7.
pubmed: 22644034
pmcid: 3421586
doi: 10.1128/AAC.06224-11
Zhang R, Dong N, Huang Y, Zhou H, Xie M, Chan EWC, et al. Evolution of tigecycline- and colistin-resistant CRKP (carbapenem-resistant Klebsiellapneumoniae) in vivo and its persistence in the GI tract. Emerg Microbes Infect. 2018;7(1):127.
pubmed: 29985412
pmcid: 6037711
doi: 10.1038/s41426-018-0129-7
Roy S, Datta S, Viswanathan R, Singh AK, Basu S. Tigecycline susceptibility in Klebsiellapneumoniae and Escherichiacoli causing neonatal septicaemia (2007–10) and role of an efflux pump in tigecycline non-susceptibility. J Antimicrob Chemother. 2013;68(5):1036–42.
pubmed: 23335112
doi: 10.1093/jac/dks535
He T, Wang R, Liu D, Walsh TR, Zhang R, Lv Y, et al. Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans. Nat Microbiol. 2019;4(9):1450–6.
pubmed: 31133751
doi: 10.1038/s41564-019-0445-2
Huang Y, Rana AP, Wenzler E, Ozer EA, Krapp F, Bulitta JB, et al. Aminoglycoside-resistance gene signatures are predictive of aminoglycoside MICs for carbapenem-resistant Klebsiella pneumoniae. J Antimicrob Chemother. 2022;77(2):356–63.
pubmed: 34668007
doi: 10.1093/jac/dkab381
Orskov I, Fife-Asbury MA. New Klebsiella capsular antigen, K82, and the deletion of five of those previously assigned. Int J Syst Bacteriol. 1977;27(4):386–7.
doi: 10.1099/00207713-27-4-386
Edmunds PN. Further Klebsiella capsule types. J Infect Dis. 1954;94(1):65–71.
pubmed: 13143223
doi: 10.1093/infdis/94.1.65
Edwards PR, Fife MA. Capsule types of Klebsiella. J Infect Dis. 1952;91(1):92–104.
pubmed: 14946431
doi: 10.1093/infdis/91.1.92
Lewis JM, Mphasa M, Banda R, Beale MA, Heinz E, Mallewa J, et al. Colonization dynamics of extended-spectrum beta-lactamase-producing Enterobacterales in the gut of Malawian adults. Nat Microbiol. 2022;7(10):1593–604.
pubmed: 36065064
pmcid: 9519460
doi: 10.1038/s41564-022-01216-7
Lewis JM, Mphasa M, Banda R, Beale MA, Mallewa J, Heinz E, et al. Genomic and antigenic diversity of colonizing Klebsiellapneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi. Microb Genomics. 2022;8(3):000778.
doi: 10.1099/mgen.0.000778
Feasey NA, Houston A, Mukaka M, Komrower D, Mwalukomo T, Tenthani L, et al. A reduction in adult blood stream infection and case fatality at a large african hospital following antiretroviral therapy roll-out. Pett S, editor. PLoS One. 2014;9(3):e92226.
pubmed: 24643091
pmcid: 3958486
doi: 10.1371/journal.pone.0092226
Centeleghe I, Norville P, Hughes L, Maillard JY. Klebsiellapneumoniae survives on surfaces as a dry biofilm. Am J Infect Control. 2023;51(10):1157–62.
pubmed: 36907360
doi: 10.1016/j.ajic.2023.02.009
Lewis JM, Lester R, Mphasa M, Banda R, Edwards T, Thomson NR, et al. Emergence of carbapenemase-producing Enterobacteriaceae in Malawi. J Glob Antimicrob Resist. 2020;20:225–7.
pubmed: 31899349
doi: 10.1016/j.jgar.2019.12.017
Kumwenda GP, Sugawara Y, Abe R, Akeda Y, Kasambara W, Chizani K, et al. First Identification and genomic characterization of multidrug-resistant carbapenemase-producing Enterobacteriaceae clinical isolates in Malawi. Africa J Med Microbiol. 2019;68(12):1707–15.
pubmed: 31661049
doi: 10.1099/jmm.0.001087
Zhang F, Li Q, Bai J, Ding M, Yan X, Wang G, et al. Heteroresistance to Amikacin in Carbapenem-Resistant Klebsiella pneumoniae Strains. Front Microbiol. 2021;12:682239.
pubmed: 35035381
pmcid: 8753984
doi: 10.3389/fmicb.2021.682239
Mankhomwa J, Tolhurst R, M’biya E, Chikowe I, Banda P, Mussa J, et al. A qualitative study of antibiotic use practices in intensive small-scale farming in urban and peri-urban blantyre, malawi: implications for antimicrobial resistance. Front Vet Sci. 2022;9:876513.
pubmed: 35685344
pmcid: 9171431
doi: 10.3389/fvets.2022.876513
Darlow CA, Farrington N, Johnson A, McEntee L, Unsworth J, Jimenez-Valverde A, et al. Flomoxef and fosfomycin in combination for the treatment of neonatal sepsis in the setting of highly prevalent antimicrobial resistance. J Antimicrob Chemother. 2022;77(5):1334–43.
pubmed: 35170719
pmcid: 9047679
doi: 10.1093/jac/dkac038
Lipworth S, Vihta KD, Chau KK, Kavanagh J, Davies T, George S, et al. Ten years of population-level genomic Escherichiacoli and Klebsiellapneumoniae serotype surveillance informs vaccine development for invasive infections. Clin Infect Dis. 2021;73(12):2276–82.
pubmed: 33411882
pmcid: 8677521
doi: 10.1093/cid/ciab006
Heinz E, Ejaz H, Bartholdson Scott J, Wang N, Gujaran S, Pickard D, et al. Resistance mechanisms and population structure of highly drug resistant Klebsiella in Pakistan during the introduction of the carbapenemase NDM-1. Sci Rep. 2019;9(1):2392.
pubmed: 30787414
pmcid: 6382945
doi: 10.1038/s41598-019-38943-7
Heinz E, Brindle R, Morgan-McCalla A, Peters K, Thomson NR. Caribbean multi-centre study of Klebsiellapneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors. Microb Genomics. 2019;5(5):e000266.
doi: 10.1099/mgen.0.000266
Wantuch PL, Knoot CJ, Robinson LS, Vinogradov E, Scott NE, Harding CM, et al. Capsular polysaccharide inhibits vaccine-induced O-antigen antibody binding and function across both classical and hypervirulent K2:O1 strains of Klebsiellapneumoniae. Hakansson AP, editor. PLoS Pathog. 2023;19(5):e1011367.
pubmed: 37146068
pmcid: 10191323
doi: 10.1371/journal.ppat.1011367
Loraine J, Heinz E, De Sousa Almeida J, Milevskyy O, Voravuthikunchai SP, Srimanote P, et al. Complement susceptibility in relation to genome sequence of recent Klebsiellapneumoniae isolates from thai hospitals. mSphere. 2018;3(6):e00537–18.
pubmed: 30404929
pmcid: 6222052
doi: 10.1128/mSphere.00537-18
Kol O, Wieruszeski JM, Strecker G, Fournet B, Zalisz R, Smets P. Structure of the O-specific polysaccharide chain of Klebsiella pneumoniae O1K2 (NCTC 5055) lipopolysaccharide. A complementary elucidation. Carbohydr Res. 1992;15(236):339–44.
doi: 10.1016/0008-6215(92)85028-X
Whitfield C, Richards JC, Perry MB, Clarke BR, MacLean LL. Expression of two structurally distinct D-galactan O antigens in the lipopolysaccharide of Klebsiella pneumoniae serotype O1. J Bacteriol. 1991;173(4):1420–31.
pubmed: 1704883
pmcid: 207279
doi: 10.1128/jb.173.4.1420-1431.1991
Kol O, Wieruszeski JM, Strecker G, Montreuil J, Fournet B, Zalisz R, et al. Structure of the O-specific polysaccharide chain from Klebsiella pneumoniae O1K2 (NCTC 5055) lipopolysaccharide. Carbohydr Res. 1991;18(217):117–25.
doi: 10.1016/0008-6215(91)84122-U