Molecular characterization of NDM-1-producing Klebsiella pneumoniae ST29, ST347, ST1224, and ST2558 causing sepsis in neonates in a tertiary care hospital of North-East India

Mukherjee, Subhankar; Bhattacharjee, Anik; Naha, Sharmi; Majumdar, Tapan; Debbarma, Sanjib Kumar; Kaur, Harpreet; Basu, Sulagna

doi:10.1016/j.meegid.2019.01.024

Cited by 31 publications

(22 citation statements)

References 36 publications

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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%

“…Among the studies identified through the formal search described above, two did not report K-types and three included only a limited assessment, i.e. 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].…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Introductionmentioning

confidence: 99%

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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“…This funding is consistent with a previous study, which proved that NDM-1 positive strains harbored qnrS1 gene. 37 Studies showed that ESBL encoding genes and plasmid-mediated quinolone resistance genes can be cotransferred with the same mobile genetic elements. 24,38 Consistent with this, NDM-producing CRKP harbored bla SHV-187 , oqxA, and oqxB.…”

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confidence: 99%

Emergence of NDM-5-Producing Carbapenem-Resistant Klebsiella pneumoniae and SIM-Producing Hypervirulent Klebsiella pneumoniae Isolated from Aseptic Body Fluid in a Large Tertiary Hospital, 2017–2018: Genetic Traits of blaNDM-Like and blaSIM-Like Genes as Determined by NGS

Zhu

Kang

et al. 2020

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To characterize the clinical, resistance, and virulence features of carbapenemresistant Klebsiella pneumonaie (CRKP) and hypervirulent Klebsiella pneumoniae (hvKP) and also provide an effective selection of drug in CRKP and hvKP treatment. Materials and Methods: Twelve strains were collected and investigated these isolates for their antimicrobial susceptibility and molecular features. Resistance mechanisms, virulence-associated genes, multilocus sequence typing (MLST), and serotypes were detected by PCR and sequencing. Next general sequencing (NGS) was carried out to determine the features of carbapenem resistance and virulence. The synergistic activity of tigecycline-imipenem (TGC+IPM), tigecycline-meropenem (TGC+MEM), and tigecycline-aztreonam (TGC+ATM) combinations were performed by microdilution checkerboard method. Results: Eleven CRKP and one hvKP strains were collected. All strains showed highly sensitive rates to tigecycline (TGC) and amikacin (AMK). NDM (33.3%, 4/12) was the main resistance mechanism and MLST assigned 3 of them to ST11. CTX-M-producing (n = 1) and KPC-2-producing (n = 1) isolates belonged to ST147 and ST11, respectively. The MICs of ATM and quinolones in NDM-1 CRKP and NDM-5 CRKP strains were different. The serotype of the majority strains was KL22KL137 (58.3%, 7/12), hvKP stain belonged to K64. CRKP strains harbored plasmid-mediated quinolone resistance genes (oqxA, oqxB, qnrS, qnrB), β-lactams (bla CTX-M-3), aminoglycosides, type I and type III fimbriae genes, siderophore genes, and transporter and pumps. SIM-producing ST1764 K64 showed typical features of hvKP, showing hypermucoviscosity phenotype. The virulence genes, including rmpA2, alls and aerobactin genes, linked to hvKP, were found in ST1764 hvKP. hvKP was sensitive to quinolone; also, oqxA gene was detected. All TGC combinations showed highly synergistic effects and TGC+IPM was more effective treatment. Conclusion: We first identified the NDM-5-producing ST690 CRKP and SIM-producing ST1764 hvKP strains in Shanxi province. Tigecycline-carbapenem combinations were available treatments for CRKP.

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“…The insertion sequences and transposons play a role in the genetic variability. Accordingly, IS Aba 1/3 and IS Aba 125 have been reported to induce expression of several carbapenem resistance genes such as bla OXA-23-51-66 -like and bla NDM-1 in A. baumannii and K. pneumoniae [ 144 , 145 , 146 , 147 , 148 ]. Similarly, a novel Tn 4401 transposon variant (Tn 4401 h, a188-bp deletion) on conjugative plasmids has been associated with enhanced bla KPC expression and the degree of phenotypic resistance to carbapenemases in K. pneumoniae [ 149 ].…”

Section: Molecular Epidemiology Of Carbapenem Resistance (Cr) Genementioning

confidence: 99%

Molecular Epidemiology of Carbapenemases in Enterobacteriales from Humans, Animals, Food and the Environment

et al. 2020

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The Enterobacteriales order consists of seven families including Enterobacteriaceae, Erwiniaceae, Pectobacteriaceae, Yersiniaceae, Hafniaceae, Morganellaceae, and Budviciaceae and 60 genera encompassing over 250 species. The Enterobacteriaceae is currently considered as the most taxonomically diverse among all seven recognized families. The emergence of carbapenem resistance (CR) in Enterobacteriaceae caused by hydrolytic enzymes called carbapenemases has become a major concern worldwide. Carbapenem-resistant Enterobacteriaceae (CRE) isolates have been reported not only in nosocomial and community-acquired pathogens but also in food-producing animals, companion animals, and the environment. The reported carbapenemases in Enterobacteriaceae from different sources belong to the Ambler class A (blaKPC), class B (blaIMP, blaVIM, blaNDM), and class D (blaOXA-48) β-lactamases. The carbapenem encoding genes are often located on plasmids or associated with various mobile genetic elements (MGEs) like transposons and integrons, which contribute significantly to their spread. These genes are most of the time associated with other antimicrobial resistance genes such as other β-lactamases, as well as aminoglycosides and fluoroquinolones resistance genes leading to multidrug resistance phenotypes. Control strategies to prevent infections due to CRE and their dissemination in human, animal and food have become necessary. Several factors involved in the emergence of CRE have been described. This review mainly focuses on the molecular epidemiology of carbapenemases in members of Enterobacteriaceae family from humans, animals, food and the environment.

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Molecular characterization of NDM-1-producing Klebsiella pneumoniae ST29, ST347, ST1224, and ST2558 causing sepsis in neonates in a tertiary care hospital of North-East India

Cited by 31 publications

References 36 publications

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

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

Molecular Epidemiology of Carbapenemases in Enterobacteriales from Humans, Animals, Food and the Environment

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