Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi

被引:10
作者
Lewis, Joseph M. [1 ,2 ,3 ,4 ]
Mphasa, Madalitso [1 ]
Banda, Rachel [1 ]
Beale, Mathew A. [4 ]
Mallewa, Jane [5 ]
Heinz, Eva [2 ]
Thomson, Nicholas R. [4 ,6 ]
Feasey, Nicholas A. [1 ,2 ,5 ,6 ]
机构
[1] Kamuzu Univ Hlth Sci, Malawi Liverpool Wellcome Res Programme, Blantyre, Malawi
[2] Univ Liverpool Liverpool Sch Trop Med, Liverpool, Merseyside, England
[3] Univ Liverpool, Liverpool, Merseyside, England
[4] Wellcome Sanger Inst, Hinxton, England
[5] Kamuzu Univ Hlth Sci, Blantyre, Malawi
[6] London Sch Hyg & Trop Med, London, England
来源
MICROBIAL GENOMICS | 2022年 / 8卷 / 03期
基金
英国惠康基金;
关键词
whole-genome sequencing; Africa south of the Sahara; drug resistance; microbial; extended-spectrum beta-lactamase; ANTIMICROBIAL RESISTANCE; SURVEILLANCE; ALGORITHM; INFECTION; VIRULENCE; QUALITY;
D O I
10.1099/mgen.0.000778
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Members of the Klebsiella pneumoniae species complex, particularly K. pneumoniae subsp. pneumoniae are antimicrobial resistance (AMR) associated pathogens of global importance, and polyvalent vaccines targeting Klebsiella O-antigens are in development. Whole-genome sequencing has provided insight into O-antigen distribution in the K. pneumoniae species complex, as well as population structure and virulence determinants, but genomes from sub-Saharan Africa are underrepresented in global sequencing efforts. We therefore carried out a genomic analysis of extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae species complex isolates colonizing adults in Blantyre, Malawi. We placed these isolates in a global genomic context, and compared colonizing to invasive isolates from the main public hospital in Blantyre. In total, 203 isolates from stool and rectal swabs from adults were whole-genome sequenced and compared to a publicly available multicounty collection and previously sequenced Malawian and Kenyan isolates from blood or sterile sites. We inferred phylogenetic relationships and analysed the diversity of genetic loci linked to AMR, virulence, capsule and LPS O-antigen (O-types). We find that the diversity of Malawian K. pneumoniae subsp. pneumoniae isolates represents the species' population structure, but shows distinct local signatures concerning clonal expansions. Siderophore and hypermucoidy genes were more frequent in invasive versus colonizing isolates (present in 13 % vs 1 %) but still generally lacking in most invasive isolates. O-antigen population structure and distribution was similar in invasive and colonizing isolates, with O4 more common (14%) than in previously published studies (2-5 %). We conclude that host factors, pathogen opportunity or alternate virulence loci not linked to invasive disease elsewhere are likely to be the major determinants of invasive disease in Malawi. Distinct ST and O -type distributions in Malawi highlight the need to sample locations where the burden of invasive Klebsiella disease is greatest to robustly define secular trends in Klebsiella diversity to assist in the development of a useful vaccine. Colonizing and invasive isolates in Blantyre are similar, hence O-typing of colonizing Klebsiella isolates may be a rapid and cost-effective approach to describe global diversity and guide vaccine development.
引用
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页数:14
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共 52 条
[1]   CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database [J].
Alcock, Brian P. ;
Raphenya, Amogelang R. ;
Lau, Tammy T. Y. ;
Tsang, Kara K. ;
Bouchard, Megane ;
Edalatmand, Arman ;
Huynh, William ;
Nguyen, Anna-Lisa, V ;
Cheng, Annie A. ;
Liu, Sihan ;
Min, Sally Y. ;
Miroshnichenko, Anatoly ;
Tran, Hiu-Ki ;
Werfalli, Rafik E. ;
Nasir, Jalees A. ;
Oloni, Martins ;
Speicher, David J. ;
Florescu, Alexandra ;
Singh, Bhavya ;
Faltyn, Mateusz ;
Hernandez-Koutoucheva, Anastasia ;
Sharma, Arjun N. ;
Bordeleau, Emily ;
Pawlowski, Andrew C. ;
Zubyk, Haley L. ;
Dooley, Damion ;
Griffiths, Emma ;
Maguire, Finlay ;
Winsor, Geoff L. ;
Beiko, Robert G. ;
Brinkman, Fiona S. L. ;
Hsiao, William W. L. ;
Domselaar, Gary, V ;
McArthur, Andrew G. .
NUCLEIC ACIDS RESEARCH, 2020, 48 (D1) :D517-D525
[2]   Virulence genes, capsular and plasmid types of multidrug-resistant CTXM(-2,-8,-15) and KPC-2-producing Klebsiella pneumoniae isolates from four major hospitals in Brazil [J].
Andrade, Leonardo Neves ;
Novais, Angela ;
Marcato Stegani, Lenita Maria ;
Ferreira, Joseane Cristina ;
Rodrigues, Carla ;
Costa Darini, Ana Lucia ;
Peixe, Luisa .
DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE, 2018, 91 (02) :164-168
[3]  
[Anonymous], J Clin Microbiol
[4]  
[Anonymous], 2018, Consolidated guidelines on the use of antiretroviral drugs for treating and preventing HIV infection:Recommendations for a public health approach, P155
[5]   SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing [J].
Bankevich, Anton ;
Nurk, Sergey ;
Antipov, Dmitry ;
Gurevich, Alexey A. ;
Dvorkin, Mikhail ;
Kulikov, Alexander S. ;
Lesin, Valery M. ;
Nikolenko, Sergey I. ;
Son Pham ;
Prjibelski, Andrey D. ;
Pyshkin, Alexey V. ;
Sirotkin, Alexander V. ;
Vyahhi, Nikolay ;
Tesler, Glenn ;
Alekseyev, Max A. ;
Pevzner, Pavel A. .
JOURNAL OF COMPUTATIONAL BIOLOGY, 2012, 19 (05) :455-477
[6]   The Diversity of Lipopolysaccharide (O) and Capsular Polysaccharide (K) Antigens of InvasiveKlebsiella pneumoniaein a Multi-Country Collection [J].
Choi, Myeongjin ;
Hegerle, Nicolas ;
Nkeze, Joseph ;
Sen, Shaichi ;
Jamindar, Sanchita ;
Nasrin, Shamima ;
Sen, Sunil ;
Permala-Booth, Jasnehta ;
Sinclair, James ;
Tapia, Milagritos D. ;
Johnson, J. Kristie ;
Mamadou, Sylla ;
Thaden, Joshua T. ;
Fowler, Vance G. ;
Aguilar, Ana ;
Teran, Enrique ;
Decre, Dominique ;
Morel, Florence ;
Krogfelt, Karen Angeliki ;
Brauner, Annelie ;
Protonotariou, Efthymia ;
Christaki, Eirini ;
Shindo, Yuichiro ;
Lin, Yi-Tsung ;
Kwa, Andrea L. ;
Shakoor, Sadia ;
Singh-Moodley, Ashika ;
Perovic, Olga ;
Jacobs, Jan ;
Lunguya, Octavie ;
Simon, Raphael ;
Cross, Alan S. ;
Tennant, Sharon M. .
FRONTIERS IN MICROBIOLOGY, 2020, 11
[7]   Progress towards the development of Klebsiella vaccines [J].
Choi, Myeongjin ;
Tennant, Sharon M. ;
Simon, Raphael ;
Cross, Alan S. .
EXPERT REVIEW OF VACCINES, 2019, 18 (07) :681-691
[8]  
Cornick J, 2020, BIORXIV 202020200806
[9]   Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread [J].
David, Sophia ;
Reuter, Sandra ;
Harris, Simon R. ;
Glasner, Corinna ;
Feltwell, Theresa ;
Argimon, Silvia ;
Abudahab, Khalil ;
Goater, Richard ;
Giani, Tommaso ;
Errico, Giulia ;
Aspbury, Marianne ;
Sjunnebo, Sara ;
Feil, Edward J. ;
Rossolini, Gian Maria ;
Aanensen, David M. ;
Grundmann, Hajo ;
Koraqi, Andi ;
Lacej, Denada ;
Apfalter, Petra ;
Hartl, Rainer ;
Glupczynski, Youri ;
Huang, Te-Din ;
Strateva, Tanya ;
Marteva-Proevska, Yuliya ;
Tambic Andrasevic, Arjana ;
Butic, Iva ;
Pieridou-Bagatzouni, Despo ;
Maikanti-Charalampous, Panagiota ;
Hrabak, Jaroslav ;
Zemlickova, Helena ;
Hammerum, Anette ;
Jakobsen, Lotte ;
Ivanova, Marina ;
Pavelkovich, Anastasia ;
Jalava, Jari ;
Osterblad, Monica ;
Dortet, Laurent ;
Vaux, Sophie ;
Kaase, Martin ;
Gatermann, Soeren G. ;
Vatopoulos, Alkiviadis ;
Tryfinopoulou, Kyriaki ;
Toth, Akos ;
Janvari, Laura ;
Boo, Teck Wee ;
McGrath, Elaine ;
Carmeli, Yehuda ;
Adler, Amos ;
Pantosti, Annalisa ;
Monaco, Monica .
NATURE MICROBIOLOGY, 2019, 4 (11) :1919-1929
[10]   Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates [J].
Diancourt, L ;
Passet, V ;
Verhoef, J ;
Grimont, PAD ;
Brisse, S .
JOURNAL OF CLINICAL MICROBIOLOGY, 2005, 43 (08) :4178-4182