Genomic insights into blaNDM-carrying carbapenem-resistant Klebsiella pneumoniae clinical isolates from a university hospital in Thailand

Chukamnerd, Arnon; Pomwised, Rattanaruji; Jeenkeawpiam, Kongpop; Sakunrang, Chanida; Chusri, Sarunyou; Surachat, Komwit

doi:10.1016/j.micres.2022.127136

Cited by 8 publications

(5 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In contrast, among the ST307 K. pneumoniae isolates (n = 3), M.Kpn34618Dcm was the sole common Mtase. Contrary to Chuckamnerd et al (2022) findings, there was no consistent pattern observed within the RMS in this study’s isolates 59 . However, it’s noteworthy that all Type II Mtases, including the type II restriction endonuclease (RE), shared the same recognition sequence.…”

Section: Discussioncontrasting

confidence: 99%

“…Among these, the Type II M.Kpn34618Dcm was the most predominant and was identified in all K. pneumoniae isolates. Previous research, as reported by Chuckamnerd et al 2022 and Ramaloko and Osei Sekyere (2022), has shown the common occurrence of this Mtase in K. pneumoniae 59,60 . Moreover, it is typically found alongside M.EcoRII, a pattern noted by Ramaloko and Osei Sekyere (2022).…”

Section: Discussionsupporting

confidence: 51%

See 1 more Smart Citation

Genomic, Epigenomic, and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms inKlebsiella pneumoniaeandEnterobacterspecies

Mmatli,

Mbelle,

Fourie

et al. 2023

Preprint

View full text Add to dashboard Cite

The emergence of colistin and carbapenem-resistantKlebsiella pneumoniaeisolates presents a significant global health threat. This study investigates the resistance mechanisms in sixK. pneumoniaeand fourEnterobactersp. isolates lacking carbapenemases ormcrgenes using genomics and transcriptomics. The ten isolates were classified into three categories: non-carbapenemase-producing, carbapenem-resistant strains (n = 4), non-mcr–producing colistin-resistant strains (n = 5), and one isolate susceptible to both antibiotics.The analysis included phenotypic characterization using MicroScan ID/AST, enzyme (MCR and Metallo β-lactamase) and efflux pump inhibition (EPI) assays. Whole-genome sequencing, RNA sequencing, and bioinformatics tools were employed in subsequent analysis. Most of theK. pneumoniaewere ST307 with KL102 and O1/O2V2 serotypes. MicroScan revealed multidrug resistance, and AMR analysis identified numerous ARGs inK. pneumoniae.Enterobacterspecies possessed fewer resistance genes; nevertheless, they encoded virulence factors and gene mutations, potentially impacting the AST profile.K. pneumoniaeARGs were mainly plasmid-borne, with IncFIB(K)/IncFII(K) in Kp_15 harbouring up to nineteen ARGs. Virulence factors included biofilm formation, capsule production, and type IV secretion. Epigenomic investigations revealed prevalent type I (M1.Ecl34977I) and type II (M.Kpn34618Dcm) restriction modification sites. Compared to international isolates, the study isolates phylogenetically clustered more closely with Chinese strains. Transcriptomics showed high efflux pump activity in carbapenem-resistant isolates, confirmed by EPI. Further, mutations were identified in outer membrane proteins. Colistin-resistant isolates exhibited high capsule production, efflux pump, and putative glycotransferase activity, potentially influencing their phenotypes.In conclusion, genomic and transcriptional analyses enhanced our understanding of adaptive mechanisms in clinical multidrug-resistant pathogens, posing significant public health challenges.

show abstract

Section: Discussioncontrasting

confidence: 99%

Section: Discussionsupporting

confidence: 51%

Genomic, Epigenomic, and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms inKlebsiella pneumoniaeandEnterobacterspecies

Mmatli,

Mbelle,

Fourie

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…ComX4 is a RiPP that is involved in surfactin synthesis by being a quorum-sensing player ( 57 ), and should be investigated for its role in the included K. pneumoniae genomes. Sactipeptide, bottromycin, and colicin BGCs were also recently reported in clinical isolates of Klebsiella in Thailand ( 58 ).…”

Section: Discussionmentioning

confidence: 81%

Biosynthetic gene cluster signature profiles of pathogenic Gram-negative bacteria isolated from Egyptian clinical settings

Abdelsalam,

Elhadidy,

Saif

et al. 2023

Microbiol Spectr

View full text Add to dashboard Cite

Biosynthetic gene clusters (BGCs) are a subset of consecutive genes present within a variety of organisms to produce specialized metabolites (SMs). These SMs are becoming a cornerstone to produce multiple medications including antibacterial and anticancer agents. Natural products (NPs) also play a pivotal role in enhancing the virulence of ESKAPE pathogens ( Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa , and Enterobacter spp.), which represent a global health threat. We aimed to sequence and computationally analyze the BGCs present in 66 strains pertaining to three different ESKAPE pathogenic species: 21 A. baumannii , 28 K. pneumoniae , and 17 P. aeruginosa strains recovered from clinical settings in Egypt. DNA was extracted using QIAamp DNA Mini kit and Illumina NextSeq 550 was used for whole-genome sequencing. The sequences were quality-filtered by fastp and assembled by Unicycler. BGCs were detected by antiSMASH, BAGEL, GECCO, and PRISM, and aligned using Clinker. The highest abundance of BGCs was detected in P. aeruginosa (590), then K. pneumoniae (146) and the least in A. baumannii strains (133). P. aeruginosa isolates shared mostly the non-ribosomal peptide synthase (NRPS) type, K. pneumoniae isolates shared the ribosomally synthesized and post-translationally modified peptide-like (RiPP-like) type, while A. baumannii isolates shared the siderophore type. Most of the isolates harbored non-ribosomal peptide (NRP) BGCs with few K. pneumoniae isolates encoding polyketide BGCs. Sactipeptides and bottromycin BGCs were the most frequently detected RiPP clusters. We hypothesize that each species’ BGC signature confers its virulence. Future experiments will link the detected clusters with their species and determine whether the encoded SMs are produced and cause their virulence. IMPORTANCE Our study analyzes the biosynthetic gene clusters (BGCs) present in 66 assemblies from clinical ESKAPE pathogen isolates pertaining to Acinetobacter baumannii , Klebsiella pneumoniae , and Pseudomonas aeruginosa strains. We report their sequencing and assembly followed by the analysis of their BGCs using several bioinformatics tools. We then focused on the most abundant BGC type in each species and we discussed their potential roles in the virulence of each species. This study is pivotal to further build on its experimental work that deciphers the role in virulence, possible antibacterial effects, and characterization of the encoded specialized metabolites (SMs). The study highlights the importance of studying the “harmful” BGCs and understanding the pathogenicity and virulence of those species, as well as possible benefits if the SMs were used as antibacterial agents. This could be the first study of its kind from Egypt and would shed light on BGCs from ESKAPE pathogens from Egypt.

show abstract

“…Klebsiella pneumoniae is an important human pathogen that causes nosocomial and community-acquired infectious diseases including septicemia and respiratory, urinary tract, skin and soft tissue and pneumonia infections ( 1 ). Over time, K. pneumoniae has acquired virulence factors and antibiotic resistance important for its pathogenesis ( 2 – 4 ). These genetic features of K. pneumoniae have been identified from multiple sources such as pulmonary infection and wounds, and have been associated with dysbiosis in the gut microbiome and changes in lung metabolome ( 5 , 6 ).…”

Section: Introductionmentioning

confidence: 99%

Klebsiella pneumoniae ST147 harboring bla _NDM-1 , multidrug resistance and hypervirulence plasmids

Ofosu-Appiah,

Acquah,

Mohammed

et al. 2024

Microbiol Spectr

View full text Add to dashboard Cite

The spread of hypervirulent (hv) and carbapenem-/multidrug-resistant Klebsiella pneumoniae is an emerging problem in healthcare settings. The New Delhi metallo-β-lactamase-1 ( bla NDM-1 ) is found in Enterobacteriaceae including K. pneumoniae. The bla NDM-1 is capable of hydrolyzing β-lactam antibiotics which are used for treatment of severe infections caused by multidrug-resistant Gram-negative bacteria. This is associated with the unacceptably high mortality rate in immunocompromised burn injury patients. This study reports on the characterization of bla NDM-1 gene and virulence factors in hv carbapenem-/multidrug-resistant K. pneumoniae ST147 in the burns unit of a tertiary teaching hospital during routine surveillance. Two K. pneumoniae strains were obtained from wounds of burn-infected patients from May 2020 to July 2021. The hypervirulence genes and genetic context of the bla NDM-1 gene and mobile genetic elements potentially involved in the transposition of the gene were analyzed. We identified a conserved genetic background and an IS 26 and open reading frame flanking the bla NDM-1 gene that could suggest its involvement in the mobilization of the gene. The plasmid harbored additional antibiotic resistance predicted regions that were responsible for resistance to almost all the routinely used antibiotics. To ensure the identification of potential outbreak strains during routine surveillance, investigations on resistance genes and their environment in relation to evolution are necessary for molecular epidemiology. IMPORTANCE Data obtained from this study will aid in the prompt identification of disease outbreaks including evolving resistance and virulence of the outbreak bacteria. This will help establish and implement antimicrobial stewardship programs and infection prevention protocols in fragile health systems in countries with limited resources. Integration of molecular surveillance and translation of whole-genome sequencing in routine diagnosis will provide valuable data for control of infection. This study reports for the first time a high-risk clone K. pneumoniae ST147 with hypervirulence and multidrug-resistance features in Ghana.

show abstract

Genomic insights into blaNDM-carrying carbapenem-resistant Klebsiella pneumoniae clinical isolates from a university hospital in Thailand

Cited by 8 publications

References 76 publications

Genomic, Epigenomic, and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms inKlebsiella pneumoniaeandEnterobacterspecies

Genomic, Epigenomic, and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms inKlebsiella pneumoniaeandEnterobacterspecies

Biosynthetic gene cluster signature profiles of pathogenic Gram-negative bacteria isolated from Egyptian clinical settings

Klebsiella pneumoniae ST147 harboring bla _NDM-1 , multidrug resistance and hypervirulence plasmids

Contact Info

Product

Resources

About

Genomic insights into blaNDM-carrying carbapenem-resistant Klebsiella pneumoniae clinical isolates from a university hospital in Thailand

Cited by 8 publications

References 76 publications

Genomic, Epigenomic, and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms inKlebsiella pneumoniaeandEnterobacterspecies

Genomic, Epigenomic, and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms inKlebsiella pneumoniaeandEnterobacterspecies

Biosynthetic gene cluster signature profiles of pathogenic Gram-negative bacteria isolated from Egyptian clinical settings

Klebsiella pneumoniae ST147 harboring bla NDM-1 , multidrug resistance and hypervirulence plasmids

Contact Info

Product

Resources

About

Klebsiella pneumoniae ST147 harboring bla _NDM-1 , multidrug resistance and hypervirulence plasmids