Emergence of ST147 Klebsiella pneumoniae carrying bla on IncA/C2 with ompK35 and ompK36 mutations in India

Shankar, Chaitra; Kumar, Sathish; Venkatesan, M.; Veeraraghavan, Balaji

doi:10.1016/j.jiph.2019.03.023

Cited by 22 publications

(20 citation statements)

References 18 publications

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“…Our results are more consistent with the existence of a limited number of genetically related endemic strains, which constitute a reservoir from which patients become infected, either within the hospital or the larger community. Two of these lineages, ST147 and ST11, are well recognized and globally pervasive CRKP strains [ 38–41 ]. It was surprising that the third and most prevalent MLST, ST348 (17% of isolates), has previously been reported only in Portugal and Italy as a cause of carbapenem-resistant infections in both humans and in horses [ 12 , 42 , 43 ], but it has otherwise not been described outside these 2 countries.…”

Section: Discussionmentioning

confidence: 99%

Whole Genome Sequencing of Peruvian Klebsiella pneumoniae Identifies Novel Plasmid Vectors Bearing Carbapenem Resistance Gene NDM-1

Roach

Waalkes

Abanto

et al. 2020

Open Forum Infectious Diseases

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Abstract Klebsiella pneumoniae is a bacterial pathogen with increasing rates of resistance to carbapenem antibiotics, but the population structure and genetic drivers of carbapenem resistant K. pneumoniae (CRKP) remain under-explored in developing countries. CRKP were recently introduced into Peru but have grown rapidly in prevalence, enabling study of this pathogen as it expands into an unaffected environment. Here, using whole genome sequencing, we show that three distinct lineages encompass nearly all CRKP identified in the hospital where it was first reported in Peru. The most prevalent lineage, ST348, has not been described outside of Europe, raising concern for global dissemination. We identified metallo-B-lactamase NDM-1 as the primary carbapenem resistance effector, which was harbored on a novel vector resulting from recombination between two different plasmids, pKP1-NDM-1 and pMS7884A. This study is the first of its kind performed in Peru, and furthers our understanding of the landscape of CRKP infections in Latin America.

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Section: Discussionmentioning

confidence: 99%

Whole Genome Sequencing of Peruvian Klebsiella pneumoniae Identifies Novel Plasmid Vectors Bearing Carbapenem Resistance Gene NDM-1

Roach

Waalkes

Abanto

et al. 2020

Open Forum Infectious Diseases

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“…Searching PubMed for reports of multi-locus sequence typing (MLST) or whole-genome sequence analysis of K. pneumoniae BSI (see "Methods" for search terms) yielded just nine studies reporting ST information for India, Nepal, Vietnam, Thailand, Laos, Cambodia and/or Hong Kong (the foci of this work). The majority of these (six of nine) were case reports or genome announcements from India, while an additional study from India described a screen of Enterobacteriaceae isolated from neonatal sepsis, including 12 K. pneumoniae [17][18][19][20][21][22][23][24]. Together, these works from India report ST information for a single ESBL-producing strain (ST2318) and 24 CP strains; five each of ST231 and ST347; two each of ST29, ST147, ST1224 and ST2558; and one each of ST11, ST43 and ST101.…”

Section: Introductionmentioning

confidence: 99%

“…PCR screening for a small number of types that are associated with enhanced virulence (K1 and K2 [17,24], or K1, K2, K5, K20, K54 and K57 [23]). Among the remaining three studies, two reported single K17 and K64 CP isolates in India [19,20], while the Nepalese outbreak study reported the KL14 capsule locus, encoding capsule type K14 (ST1559) and a novel locus that was later defined as KL112 (ST15) [7]. None of these studies reported O-types.…”

Section: Introductionmentioning

confidence: 99%

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia

et al. 2020

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Background: Klebsiella pneumoniae is a leading cause of bloodstream infection (BSI). Strains producing extendedspectrum beta-lactamases (ESBLs) or carbapenemases are considered global priority pathogens for which new treatment and prevention strategies are urgently required, due to severely limited therapeutic options. South and Southeast Asia are major hubs for antimicrobial-resistant (AMR) K. pneumoniae and also for the characteristically antimicrobial-sensitive, community-acquired "hypervirulent" strains. The emergence of hypervirulent AMR strains and lack of data on exopolysaccharide diversity pose a challenge for K. pneumoniae BSI control strategies worldwide. Methods: We conducted a retrospective genomic epidemiology study of 365 BSI K. pneumoniae from seven major healthcare facilities across South and Southeast Asia, extracting clinically relevant information (AMR, virulence, K and O antigen loci) using Kleborate, a K. pneumoniae-specific genomic typing tool. Results: K. pneumoniae BSI isolates were highly diverse, comprising 120 multi-locus sequence types (STs) and 63 Kloci. ESBL and carbapenemase gene frequencies were 47% and 17%, respectively. The aerobactin synthesis locus (iuc), associated with hypervirulence, was detected in 28% of isolates. Importantly, 7% of isolates harboured iuc plus ESBL and/or carbapenemase genes. The latter represent genotypic AMR-virulence convergence, which is generally considered a rare phenomenon but was particularly common among South Asian BSI (17%). Of greatest concern, we identified seven novel plasmids carrying both iuc and AMR genes, raising the prospect of co-transfer of these phenotypes among K. pneumoniae.Conclusions: K. pneumoniae BSI in South and Southeast Asia are caused by different STs from those predominating in other regions, and with higher frequency of acquired virulence determinants. K. pneumoniae carrying both iuc and AMR genes were also detected at higher rates than have been reported elsewhere. The study demonstrates how genomics-based surveillance-reporting full molecular profiles including STs, AMR, virulence and serotype locus information-can help standardise comparisons between sites and identify regional differences in pathogen populations.

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“…Herein, we described the emergence of ST11 K. pneumoniae carrying bla NDM– 7 on IncX3 plasmid in China. Although NDM-7 production has been reported in diverse clones of K. pneumoniae , including ST138, ST273, ST278, ST437, and ST654 ( Shankar et al, 2019 ), our study is the first to report the presence of bla NDM– 7 in ST11 K. pneumoniae in China. This strain was isolated from a 4-year-old boy with no history of traveling abroad.…”

Section: Discussionmentioning

confidence: 66%

Genotypic and Phenotypic Characterization of blaNDM–7-Harboring IncX3 Plasmid in a ST11 Klebsiella pneumoniae Isolated From a Pediatric Patient in China

et al. 2020

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NDM-7, a variant of New Delhi metallo-beta-lactamases (NDM), has the highest carbapenem-hydrolyzing activity. NDM-7-producing enterobacteria have been reported in many countries. In this study, we reported NDM-7 production in ST11 Klebsiella pneumoniae isolated from a boy hospitalized in the pediatric intensive care unit of a teaching hospital in China. The isolate exhibited resistance to β-lactam antimicrobials, quinolones, and trimethoprim/sulfamethoxazole, and it harbored bla NDM– 7 , bla CTX–M– 15 , qnrA , qnrB , and qnrS . The serotype of the isolated K. pneumoniae was assigned as K1, and it contained three virulence genes, including kfuBC , uge , and fim . The bla NDM– 7 gene was located on a conjugative IncX3 plasmid designated as pB14NDM-7. This plasmid was fully sequenced and compared with the available bla NDM– 7 -harboring IncX3 plasmids. pB14NDM-7 contained a conserved genetic context of ISkox3-umuD-IS26-ΔTn125 -IS5- ΔTn125-IS3000-ΔTn2 . pB14NDM-7 showed 99% nucleotide identity and the same genetic context with three bla NDM– 7 -harboring IncX3 plasmids obtained from Escherichia coli in China. Our results indicate that IncX3 plasmid may contribute to the prevalence of bla NDM– 7 in China. The high prevalence of NDM variants worldwide highlights the critical need for careful monitoring and control of the rapid dissemination of bla NDM .

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Emergence of ST147 Klebsiella pneumoniae carrying bla on IncA/C2 with ompK35 and ompK36 mutations in India

Cited by 22 publications

References 18 publications

Whole Genome Sequencing of Peruvian Klebsiella pneumoniae Identifies Novel Plasmid Vectors Bearing Carbapenem Resistance Gene NDM-1

Whole Genome Sequencing of Peruvian Klebsiella pneumoniae Identifies Novel Plasmid Vectors Bearing Carbapenem Resistance Gene NDM-1

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia

Genotypic and Phenotypic Characterization of blaNDM–7-Harboring IncX3 Plasmid in a ST11 Klebsiella pneumoniae Isolated From a Pediatric Patient in China

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