Emergence ofblaNDM-7–ProducingEnterobacteriaceaein Gabon, 2016

Moussounda, Mesmin; Diène, Seydina M.; Santos, Sandra Dos; Goudeau, Alain; François, Patrice; Mee-Marquet, Nathalie van der

doi:10.3201/eid2302.161182

Cited by 26 publications

(15 citation statements)

References 10 publications

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“…These K. pneumoniae isolates shared the same molecular and MDR characteristics with isolates from the present study (Data S2), suggesting that the same strain is now circulating in hospitals in the Tshwane area. Bla NDM-7 , the first to be found in K. pneumoniae ST17 in South Africa, was reported in K. pneumoniae ST147 and ST273 involved in nosocomial cases in Canada, Gabon, Philippines, USA and India [59][60][61][62][63].…”

Section: Discussionmentioning

confidence: 99%

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Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains

2020

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Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP in South Africa and globally were characterized. CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex PCR, genotyping by repetitive element palindromic (REP)-PCR, plasmid size, number, incompatibility and mobility analyses, and PacBio’s SMRT sequencing (n=6). There were 56 multidrug-resistant CRKP, having bla OXA-48-like and bla NDM-1/7 carbapenemases on self-transmissible IncF, A/C, IncL/M and IncX3 plasmids endowed with prophages, traT, resistance islands, and type I and II restriction modification systems (RMS). Plasmids and clades detected in this study were respectively related to globally established/disseminated plasmids clades/clones, evincing transboundary horizontal and vertical dissemination. Reduced susceptibility to colistin occurred in 23 strains. Common clones included ST307, ST607, ST17, ST39 and ST3559. IncFIIk virulent plasmid replicon was present in 56 strains. Whole-genome sequencing of six strains revealed least 41 virulence genes, extensive ompK36 mutations, and four different K- and O-loci types: KL2, KL25, KL27, KL102, O1, O2, O4 and O5. Types I, II and III RMS, conferring m6A (G A TC, G A TGNNNNNNTTG, CA A NNNNNNCATC motifs) and m4C (C C WGG) modifications on chromosomes and plasmids, were found. The nature of plasmid-mediated, clonal and multi-clonal dissemination of blaOXA-48-like and blaNDM-1 mirrors epidemiological trends observed for closely related plasmids and sequence types internationally. Worryingly, the presence of both bla OXA-48 and bla NDM-1 in the same isolates was observed. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity and resistance, threatening infection treatment. The influence of RMS on antimicrobial and bacteriophage therapy needs urgent investigation.

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Section: Discussionmentioning

confidence: 99%

“…pneumoniae ST17 in South Africa, was reported in K. pneumoniae ST147 and ST273 involved in nosocomial cases in Canada, Gabon, Philippines, USA and India [59–63].…”

Section: Discussionmentioning

confidence: 99%

Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains

2020

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“…Tanzania, as well as in North African countries, including Morocco, Algeria, Tunisia, Libya, and Egypt. Specifically, NDM-1 and OXA-48-like are the most commonly reported carbapenemases in Africa (2)(3)(4)(5)(6)(7).…”

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Spread of Plasmid-Encoded NDM-1 and GES-5 Carbapenemases among Extensively Drug-Resistant and Pandrug-Resistant Clinical Enterobacteriaceae in Durban, South Africa

Pedersen

Sekyere

Govinden

et al. 2018

Antimicrob Agents Chemother

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Whole-genome sequence analyses revealed the presence of ( = 31), ( = 8), ( = 1), or ( = 1) in extensively drug-resistant and pandrug-resistant organisms isolated from in-patients in 10 private hospitals (2012 to 2013) in Durban, South Africa. Two novel NDM-1-encoding plasmids from were circularized by PacBio sequencing. In p19-10_01 [IncFIB(K); 223.434 bp], was part of a Tn-like structure (16.276 bp) delineated by IS The multireplicon plasmid p18-43_01 [IncR_1/IncFIB(pB171)/IncFII(Yp); 212.326 bp] shared an 80-kb region with p19-10_01, not including the -containing region. The two plasmids were used as references for tracing NDM-1-encoding plasmids in the other genome assemblies. The p19-10_01 sequence was detected in ( = 7) only, whereas p18-43_01 was tracked to ( = 4), ( = 1), ( = 11), spp. ( = 7), and ( = 1), revealing horizontal spread of this -bearing plasmid structure. Global phylogeny showed clustering of the (18/20) isolates together with closely related carbapenemase-negative ST101 isolates from other geographical origins. The South African isolates were divided into three phylogenetic subbranches, where each group had distinct resistance and replicon profiles, carrying either p19-10_01, p18-10_01, or pCHE-A1 (8,201 bp). The latter plasmid carried and within an integron mobilization unit. Our findings imply independent plasmid acquisition followed by local dissemination. Additionally, we detected carried by pPKPN4 in (ST14) and contained by a pNDM-MGR194-like genetic structure in (ST167), adding even more complexity to the multilayer molecular mechanisms behind nosocomial spread of carbapenem-resistant in Durban, South Africa.

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“…These K. pneumoniae isolates shared the same molecular and MDR characteristics with isolates from this present study (Data S2), suggesting that the same strain is now circulating in hospitals in the Tshwane area. Bla NDM-7, the first to be found in K. pneumoniae ST17 in S. Africa, was reported in K. pneumoniae ST147 and ST273 involved in nosocomial cases in Canada, Gabon, Philippines, US and India 46–50 .…”

Section: Discussionmentioning

confidence: 99%

Epigenomics, Genomics, Resistome, Mobilome, Virulome and Evolutionary Phylogenomics of Carbapenem-resistant Klebsiella pneumoniae clinical strains

Kopotsa

Mbelle

Sekyere

2020

Preprint

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Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP were characterised. Methods: CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex-PCR, genotyping by Repetitive Element Palindromic-Polymerase Chain Reaction (REP-PCR), plasmid size, number, incompatibility, and mobility analyses, and PacBios SMRT sequencing (n=6). Results & conclusion: There were 56 multidrug-resistant CRKP, having blaOXA-48-like and blaNDM-1/7 carbapenemases on self-transmissible IncF, A/C, IncL/M and IncX3 plasmids endowed with prophages, traT, resistance islands and type I and II restriction modification systems (RMS). These plasmids were of close evolutionary relationship to several plasmids globally whilst the strains also clustered with several global clades, evincing transboundary horizontal and vertical dissemination. Reduced susceptibility to colistin occurred in 23 strains. Common clones included ST307, ST607, ST17, ST39, and ST3559. IncFIIk virulent plasmid replicon was present in 56 strains. The six strains contained at least 41 virulence genes and four different K- and O-loci types: KL2, KL25, KL27, KL102, O1, O2, O4 and O5. Types I, II, and III RMS, conferring m6A (GATC, GATGNNNNNNTTG, CAANNNNNNCATC motifs) and m4C (CCWGG) modifications on chromosomes and plasmids, were found. There is plasmid-mediated, clonal, and multiclonal dissemination of blaOXA-48-like and blaNDM-1 in South Africa, mirroring international epidemiology of similar clones and plasmids. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity, and resistance, threatening infection treatment. RMS influence on antimicrobial and bacteriophage therapy needs urgent investigation.

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Emergence ofbla_NDM-7–ProducingEnterobacteriaceaein Gabon, 2016

Cited by 26 publications

References 10 publications

Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains

Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains

Spread of Plasmid-Encoded NDM-1 and GES-5 Carbapenemases among Extensively Drug-Resistant and Pandrug-Resistant Clinical Enterobacteriaceae in Durban, South Africa

Epigenomics, Genomics, Resistome, Mobilome, Virulome and Evolutionary Phylogenomics of Carbapenem-resistant Klebsiella pneumoniae clinical strains

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