Distinctive Mobile Genetic Elements Observed in the Clonal Expansion of Carbapenem-Resistant <i>Klebsiella pneumoniae</i> in India

Shankar, Chaitra; Jacob, Jobin John; Sugumar, Suganya Gopal; Natarajan, Lavanya; Rodrigues, Camilla; Mathur, Purva; Mukherjee, Dip Narayan; Sharma, Anita; Chitnis, DS; Bharagava, Anudita; Manesh, A Javad; Gunasekaran, Karthik; Veeraraghavan, Balaji

doi:10.1089/mdr.2020.0316

Cited by 16 publications

(15 citation statements)

References 33 publications

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“…Besides the virulence genes, p2096_hyb also carried genes encoding heavy metal tolerance such as merARCTP (mercury) and terBEDWXZ (tellurium) that were possibly inserted through the Tn 3 transposon, as shown in Figure 3A . Notably, a frameshift mutation was observed in rmpA2 among all the isolates, which we presumed to be associated with the negative string test results as has been previously described ( Yu et al., 2015 ; Shankar et al., 2021b ). The frameshift occurred due to the deletion of an adenine base at the 346th base in rmpA2 .…”

Section: Resultssupporting

confidence: 52%

Hybrid Plasmids Encoding Antimicrobial Resistance and Virulence Traits Among Hypervirulent Klebsiella pneumoniae ST2096 in India

Shankar

Vasudevan

Jacob

et al. 2022

Front. Cell. Infect. Microbiol.

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BackgroundHypervirulent variants ofKlebsiella pneumoniae(HvKp) were typically associated with a broadly antimicrobial susceptible clone of sequence type (ST) 23 at the time of its emergence. Concerningly, HvKp is now also emerging within multidrug-resistant (MDR) clones, including ST11, ST15, and ST147. MDR-HvKp either carry both the virulence and resistance plasmids or carry a large hybrid plasmid coding for both virulence and resistance determinants. Here, we aimed to genetically characterize a collection of MDR-HvKp ST2096 isolates haboring hybrid plasmids carrying both antimicrobial resistance (AMR) and virulence genes.MethodsNineK. pneumoniaeST2096 isolated over 1 year from the blood sample of hospitalized patients in southern India that were MDR and suspected to be HvKp were selected. All nine isolates were subjected to short-read whole-genome sequencing; a subset (n = 4) was additionally subjected to long-read sequencing to obtain complete genomes for characterization. Mucoviscosity assay was also performed for phenotypic assessment.ResultsAmong the nine isolates, seven were carbapenem-resistant, two of which carriedblaNDM-5on an IncFII plasmid and five carriedblaOXA-232on a ColKP3 plasmid. The organisms were confirmed as HvKp, with characteristic virulence genes (rmpA2,iutA, andiucABCD) carried on a large (~320 kbp) IncFIB–IncHI1B co-integrate. This hybrid plasmid also carried theaadA2,armA,blaOXA-1,msrE,mphE,sul1, anddfrA14AMR genes in addition to the heavy-metal resistance genes. The hybrid plasmid showed about 60% similarity to the IncHI1B virulence plasmid ofK. pneumoniaeSGH10 and ~70% sequence identity with the first identified IncHI1B pNDM-MAR plasmid. Notably, the hybrid plasmid carried its type IV-A3 CRISPR-Cas system which harbored spacer regions againsttraLof IncF plasmids, thereby preventing their acquisition.ConclusionThe convergence of virulence and AMR is clinically concerning inK. pneumoniae. Our data highlight the role of hybrid plasmids carrying both AMR and virulence genes inK. pneumoniaeST2096, suggesting that MDR-HvKp is not confined to selected clones; we highlight the continued emergence of such genotypes across the species. The convergence is occurring globally amidst several clones and is of great concern to public health.

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Section: Resultssupporting

confidence: 52%

Hybrid Plasmids Encoding Antimicrobial Resistance and Virulence Traits Among Hypervirulent Klebsiella pneumoniae ST2096 in India

Shankar

Vasudevan

Jacob

et al. 2022

Front. Cell. Infect. Microbiol.

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“…Notably, in the present study, CR-hvKp belonging to ST231 lacked rmpA and rmpA2 , while it encoded aerobactin. In the present study setting, ST231 CRKp is the endemic clone predominantly carrying bla OXA-232 on ColKP3 plasmid ( Shankar et al, 2021 ). As speculated, for better survival of this endemic clone, aerobactin has been acquired while excluding rmpA and rmpA2 .…”

Section: Discussionmentioning

confidence: 99%

“…In India, high rates of MDR and extensively drug-resistant (XDR) Kp are frequent causes of nosocomial infections, and they often carry NDM and OXA48-like carbapenemases alone or in combination ( Veeraraghavan et al, 2017 ; Shankar et al, 2021 ). The common clones of carbapenem-resistant Kp (CRKp) in India include ST231, the endemic clone, and other international high-risk clones such as ST11, ST14, ST15, and ST147 ( Shankar et al, 2021 ). Conventionally, these CRKp do not carry the virulence plasmid; instead, they are characterized by the presence of four to five plasmids that carry ARGs.…”

Section: Introductionmentioning

confidence: 99%

“…Although previous studies have reported the correlation of rmpA and rmpA2 as markers for hypervirulent and hypermucoviscous pathotypes, there is a dearth of comprehensive correlations between the constitutive virulence markers for hvKp, viz., rmpA , rmpA2 , and aerobactin , based on “genome-structure” perspectives. Our research group has extensively worked on genomics ( Jacob et al, 2019 ; Shankar et al, 2020a ; Vasudevan et al, 2020 ; Shankar et al, 2021 ) and in silico structural analysis ( Lavanya et al, 2013 ; Lavanya et al, 2014 ; Lavanya et al, 2015 ) to decipher the functional circuitry of various pathogenic proteins. The present study adopted a combination of whole-genome sequencing (WGS), genomic analysis, computational modeling, and structural dynamics studies, which have not been used previously to assess the concerned virulence markers as per our knowledge.…”

Section: Introductionmentioning

confidence: 99%

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Aerobactin Seems To Be a Promising Marker Compared With Unstable RmpA2 for the Identification of Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae: In Silico and In Vitro Evidence

Shankar

Basu

Lal

et al. 2021

Front. Cell. Infect. Microbiol.

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BackgroundThe incidence of hypervirulent (hv) carbapenem-resistant (CR) Klebsiella pneumoniae (Kp) is increasing globally among various clones and is also responsible for nosocomial infections. The CR-hvKp is formed by the uptake of a virulence plasmid by endemic high-risk clones or by the uptake of plasmids carrying antimicrobial resistance genes by the virulent clones. Here, we describe CR-hvKp from India belonging to high-risk clones that have acquired a virulence plasmid and are phenotypically unidentified due to lack of hypermucoviscosity.MethodsTwenty-seven CRKp isolates were identified to possess rmpA2 by whole-genome sequencing; and resistance and virulence determinants were characterized. By in silico protein modeling (and validation), protein backbone stability analysis, and coarse dynamics study, the fitness of RmpA, RmpA2, and aerobactin-associated proteins-IucA and IutA, were determined to establish a reliable marker for clinical identification of CR-hvKp.ResultsThe CR-hvKp belonged to multidrug-resistant (MDR) high-risk clones such as CG11, CG43, ST15, and ST231 and carried OXA-232 as the predominant carbapenemase followed by NDM. The virulence plasmid belonged to IncHI1B replicon type and carried frameshifted and truncated rmpA and rmpA2. This resulted in a lack of hypermucoviscous phenotype. However, functional aerobactin was expressed in all high-risk clones. In silico analysis portrayed that IucA and IutA were more stable than classical RmpA. Furthermore, IucA and IutA had lower conformational fluctuations in the functional domains than the non-functional RmpA2, which increases the fitness cost of the latter for its maintenance and expression among CR-hvKp. Hence, RmpA and RmpA2 are likely to be lost among CR-hvKp owing to the increased fitness cost while coding for essential antimicrobial resistance and virulence factors.ConclusionIncreasing incidence of convergence of AMR and virulence is observed among K. pneumoniae globally, which warrants the need for reliable markers for identifying CR-hvKp. The presence of non-functional RmpA2 among high-risk clones highlights the significance of molecular identification of CR-hvKp. The negative string test due to non-functional RmpA2 among CR-hvKp isolates challenges phenotypic screening and faster identification of this pathotype. This can potentially be counteracted by projecting aerobactin as a stable, constitutively expressed, and functional marker for rapidly evolving CR-hvKp.

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“… 2020 ; Kopotsa, Mbelle and Sekyere 2020 ; Shankar et al . 2021 ). Notably, a strong correlation was found between emerging polymyxin resistance in K. pneumoniae isolates and consumption of polymyxin in the hospital sector (ECDC – European Centre for Disease Prevention and Control, EFSA – European Food Safety Authority and EMA – European Medicines Agency 2017 ).…”

Section: Colistin Usage In Europementioning

confidence: 99%

Global colistin use: a review of the emergence of resistant Enterobacterales and the impact on their genetic basis

Binsker

Käsbohrer

Hammerl

2021

FEMS Microbiology Reviews

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The dramatic global rise of MDR and XDR Enterobacterales in human medicine forced clinicians to the reintroduction of colistin as last-resort drug. Meanwhile, colistin is used in the veterinary medicine since its discovery leading to a steadily increasing prevalence of resistant isolates in the livestock and meat-based food sector. Consequently, transmission of resistant isolates from animals to humans, acquisition via food, and exposure to colistin in the clinic are reasons for the increased prevalence of colistin-resistant Enterobacterales in humans in the last decades. Initially, resistance mechanisms were caused by mutations in chromosomal genes. However, since the discovery in 2015, the focus has shifted exclusively to mobile colistin resistances (mcr). This review will advance the understanding of chromosomal-mediated resistance mechanisms in Enterobacterales. We provide an overview about genes involved in colistin resistance and the current global situation of colistin-resistant Enterobacterales. A comparison of the global colistin use in veterinary and human medicine highlights the effort to reduce colistin sales in veterinary medicine under the One Health approach. In contrast, it uncovers the alarming rise in colistin consumption in human medicine due to the emergence of MDR Enterobacterales, which might be an important driver for the increasing emergence of chromosome-mediated colistin resistance.

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Distinctive Mobile Genetic Elements Observed in the Clonal Expansion of Carbapenem-Resistant Klebsiella pneumoniae in India

Cited by 16 publications

References 33 publications

Hybrid Plasmids Encoding Antimicrobial Resistance and Virulence Traits Among Hypervirulent Klebsiella pneumoniae ST2096 in India

Hybrid Plasmids Encoding Antimicrobial Resistance and Virulence Traits Among Hypervirulent Klebsiella pneumoniae ST2096 in India

Aerobactin Seems To Be a Promising Marker Compared With Unstable RmpA2 for the Identification of Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae: In Silico and In Vitro Evidence

Global colistin use: a review of the emergence of resistant Enterobacterales and the impact on their genetic basis

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