Association of sequence types, antimicrobial resistance and virulence genes in Indian isolates of Klebsiella pneumoniae: A comparative genomics study

Sundaresan, Abhirami Krishnamoorthy; Vincent, Keerthana; Mohan, Ganesh Babu Malli; Ramakrishnan, Jayapradha

doi:10.1016/j.jgar.2022.05.006

Cited by 14 publications

(21 citation statements)

References 61 publications

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“…Some of the studies reported that serotypes and virulence are not directly correlated. For instance, in our previous report on comparative genome analysis, the hypervirulent associated rmpA and magA genes were present in non-K1/K2 strains as well (Sundaresan et al, 2022). In the present study, we identi ed 3 novel K-loci serotype and an O serotype among the studied strains.…”

Section: Discussionsupporting

confidence: 52%

“…K. pneumoniae exhibits high resistance to the broad spectrum of antibiotics including β-lactam drugs, uoroquinolones and aminoglycosides. Antibiotic inactivation by hydrolytic enzymes and antibiotic e ux are noti ed as predominant resistance mechanisms in K. pneumoniae (Sundaresan et al, 2022). Identi cation of strains that has both drug resistance and virulence is of the critical need for timely diagnosis and immediate appropriate antimicrobial therapy.…”

Section: Introductionmentioning

confidence: 99%

“…Our previous analysis with publicly available WGS of 153 K. pneumoniae Indian isolates majorly isolated from bloodstream infections provided unique genomic insights for identifying the strains that need more attention for immediate treatment and prevention of dissemination in clinical settings (Sundaresan et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

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Comparative Analysis of Complete Genome Sequences and Phenotypic Correlation of Klebsiella spp.

Sundaresan

Mohan

Murugavel

et al. 2022

Preprint

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In recent times K. pneumoniae, a common nosocomial pathogen, tends to evolve more virulent and multidrug-resistant. Urinary tract infections by antibiotic resistant and virulent K. pneumoniae are a growing concern due to the challenging treatment strategies. Hence understanding the genome and validating the genomic profile along with pan-genome analysis will facilitate surveillance of high risk-clones of K. pneumoniae to underpin management strategies toward early detection. Thus, the present study aimed to correlate genotypic and phenotypic antimicrobial resistance and pathogenicity associated with sequence types and virulence factors in Klebsiella spp. The complete genome profile of 3 K. pneumoniae and a K. variicola were analysed in the study which was assigned to ST200, ST45, ST147 and ST of K. variicola are not known. The accessory genome comprised 66% of genes consisting of shell and cloud genes in K. pneumoniae. The phenotypic antimicrobial resistance identified kp3 to have maximum resistance and the susceptibility of environment isolate K. variicola was less resistant to the tested antibiotics. The in vitro and genomic antimicrobial resistance profiling showed concordance with all the tested antibiotics against the 4 study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA, rmpA2 and magA. Though the genes encoding for major virulence factors; hypermucoviscosity, yersiniabactin and allantoin metabolism were absent, significant pathogenicity and mortality were observed for kp3 isolate in the Zebrafish infection model. In contrast, the isolates predicted with the aerobactin gene were observed with least mortality rate. In the present study virulome and in vivo study illustrate the discrepancies in the virulence. To the best of our knowledge, this is the first report on the presence of ste, stf, stc and sti major fimbrial operons of Salmonella enteric serotype Typhimurium in K. pneumoniae genome, that might contribute to the virulence of kp3. Our study highlights the further necessity of genomic and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high risk K. pneumoniae clones.

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Section: Discussionsupporting

confidence: 52%

Section: Introductionmentioning

confidence: 99%

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Comparative Analysis of Complete Genome Sequences and Phenotypic Correlation of Klebsiella spp.

Sundaresan

Mohan

Murugavel

et al. 2022

Preprint

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“…Recently, Kp genomic surveillance studies from India were reported mostly from South India [ 15 , 16 ]. To the best of our knowledge, in this report, Klebsiella genomes from Western India were included for the first time in a surveillance study.…”

Section: Discussionmentioning

confidence: 99%

Diversity and Distribution of β-Lactamase Genes Circulating in Indian Isolates of Multidrug-Resistant Klebsiella pneumoniae

et al. 2023

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Klebsiella pneumoniae (Kp) has gained prominence in the last two decades due to its global spread as a multidrug-resistant (MDR) pathogen. Further, carbapenem-resistant Kp are emerging at an alarming rate. The objective of this study was (1) to evaluate the prevalence of β-lactamases, especially carbapenemases, in Kp isolates from India, and (2) determine the most prevalent sequence type (ST) and plasmids, and their association with β-lactamases. Clinical samples of K. pneumoniae (n = 65) were collected from various pathology labs, and drug susceptibility and minimum inhibitory concentrations (MIC) were detected. Whole genome sequencing (WGS) was performed for n = 22 resistant isolates, including multidrug-resistant (MDR) (n = 4), extensively drug-resistant (XDR) (n = 15), and pandrug-resistant (PDR) (n = 3) categories, and genomic analysis was performed using various bioinformatics tools. Additional Indian MDRKp genomes (n = 187) were retrieved using the Pathosystems Resource Integration Center (PATRIC) database. Detection of β-lactamase genes, location (on chromosome or plasmid), plasmid replicons, and ST of genomes was carried out using CARD, mlplasmids, PlasmidFinder, and PubMLST, respectively. All data were analyzed and summarized using the iTOL tool. ST231 was highest, followed by ST147, ST2096, and ST14, among Indian isolates. blaampH was detected as the most prevalent gene, followed by blaCTX-M-15 and blaTEM-1. Among carbapenemase genes, blaOXA-232 was prevalent and associated with ST231, ST2096, and ST14, which was followed by blaNDM-5, which was observed to be prevalent in ST147, ST395, and ST437. ST231 genomes were most commonly found to carry Col440I and ColKP3 plasmids. ST16 carried mainly ColKP3, and Col(BS512) was abundantly present in ST147 genomes. One Kp isolate with a novel MLST profile was identified, which carried blaCTX-M-15, blaOXA-1, and blaTEM-1. ST16 and ST14 are mostly dual-producers of carbapenem and ESBL genes and could be emerging high-risk clones in India.

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“…Recently, Kp genomic surveillance studies from India were reported mostly from South India [13,14]. To the best of our knowledge, in this report Klebsiella genomes from Western India were included for the first time in surveillance study.…”

Section: Discussionmentioning

confidence: 99%

Diversity and Distribution of <em>β</em>-lactamase Genes Circulating in Indian Isolates of Multi-drug Resistant <em>Klebsiella pneumoniae</em>

Shukla¹,

Desai²,

Bagchi³

et al. 2023

Preprint

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Klebsiella pneumoniae (Kp) has gained prominence in the last two decades due to its global spread as a multi-drug resistant (MDR) pathogen. Further, Carbapenem-Resistant Kp are emerging at an alarming rate. The objective of this study was (1) to evaluate the prevalence of β-lactamases, especially carbapenemases in Kp isolates from India, (2) determine the most prevalent sequence type (ST) & plasmids, and their association with β-lactamases. Clinical samples of K. pneumoniae (n=65) were collected from various pathology lab, drug susceptibility and minimum inhibitory concentrations (MIC) were detected. Whole genome sequencing (WGS) was done for (n=22) resistant isolates and WGS analysis was performed using various bioinformatics tools. Additional Indian MDR Kp genomes (n=187) were retrieved using Pathosystems Resource Integration Center (PATRIC) database. Detection of β-lactamase genes, location, plasmid replicons, and ST type of genomes were carried out using CARD, mlplasmids, PlasmidFinder, and PubMLST respectively. All data were analyzed and summarized using iTOL tool. ST231 was highest, followed by ST147, ST2096 & ST14 among Indian isolates. blaAmpH was detected as the most prevalent gene followed by blaCTX-M-15, blaTEM-1. Among carbapenemase genes, blaOXA-232 was prevalent and associated with ST231, ST2096 and ST14, which was followed by blaNDM-5 which was observed to prevalent in ST147, ST395 &ST437. ST231 genomes were most commonly found to carry Col440I and ColKP3 plasmids. ST16 carried mainly ColKP3, and Col (BS512) was abundantly present in ST147 genomes. One Kp isolate with novel MLST profile was identified, which carried blaCTX-M-15, blaOXA-1 and blaTEM-1. ST16 &ST14 from this study, which is mostly dual producer of carbapenem and ESBL genes, could be emerging high-risk clones in India.

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Association of sequence types, antimicrobial resistance and virulence genes in Indian isolates of Klebsiella pneumoniae: A comparative genomics study

Cited by 14 publications

References 61 publications

Comparative Analysis of Complete Genome Sequences and Phenotypic Correlation of Klebsiella spp.

Comparative Analysis of Complete Genome Sequences and Phenotypic Correlation of Klebsiella spp.

Diversity and Distribution of β-Lactamase Genes Circulating in Indian Isolates of Multidrug-Resistant Klebsiella pneumoniae

Diversity and Distribution of <em>β</em>-lactamase Genes Circulating in Indian Isolates of Multi-drug Resistant <em>Klebsiella pneumoniae</em>

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