High-risk clones and novel sequence type ST4497 of Klebsiella pneumoniae clinical isolates producing different alleles of NDM-type and other carbapenemases from a single tertiary-care centre in Egypt

Gamal, Doaa; Egea, Pilar; Elías, Cristina; Fernández-Martínez, Marta; Causse, Manuel; Pérez‐Nadales, Elena; Salem, Dalia; Fam, Nevine; Diab, Manal; Aitta, Aisha Abu; El-Defrawy, Inas; Martı́nez-Martı́nez, Luis

doi:10.1016/j.ijantimicag.2020.106164

Cited by 7 publications

(3 citation statements)

References 29 publications

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“…ST11 is the dominant clone of carbapenemases-producing K. pneumoniae in Asia, especially in China, and ST11 clone was reported to account for up to 60% of carbapenem-resistant K. pneumoniae [ 9 , 29 , 30 ]. Recently, ST11 has been reported in several clinical infection cases from African countries, such as Egypt [ 31 , 32 ] and Tunisian [ 33 ]. And in ST11 carbapenem-resistant K. pneumoniae isolates, the most predominant carbapenemase genes are bla KPC-2 , bla NDM-1 and bla OXA-48 [ 10 , 34 ].…”

Section: Discussionmentioning

confidence: 99%

Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt

Yang

Ahmed

et al. 2022

BMC Genomics

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Background Carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) causes serious infections with significant morbidity and mortality. However, the epidemiology and transmission mechanisms of CR-hvKP and the corresponding carbapenem-resistant plasmids require further investigation. Herein, we have characterized an ST11 K. pneumoniae strain EBSI041 from the blood sample encoding both hypervirulence and carbapenem resistance phenotypes from a patient in Egypt. Results K. pneumoniae strain EBSI041 showed multidrug-resistance phenotypes, where it was highly resistant to almost all tested antibiotics including carbapenems. And hypervirulence phenotypes of EBSI041 was confirmed by the model of Galleria mellonella infection. Whole-genome sequencing analysis showed that the hybrid plasmid pEBSI041-1 carried a set of virulence factors rmpA, rmpA2, iucABCD and iutA, and six resistance genes aph(3′)-VI, armA, msr(E), mph(E), qnrS, and sul2. Besides, blaOXA-48 and blaSHV-12 were harboured in a novel conjugative IncL-type plasmid pEBSI041-2. The blaKPC-2-carrying plasmid pEBSI041-3, a non-conjugative plasmid lacking the conjugative transfer genes, could be transferred with the help of pEBSI041-2, and the two plasmids could fuse into a new plasmid during co-transfer. Moreover, the emergence of the p16HN-263_KPC-like plasmids is likely due to the integration of pEBSI041-3 and pEBSI041-4 via IS26-mediated rearrangement. Conclusion To the best of our knowledge, this is the first report on the complete genome sequence of KPC-2- and OXA-48-coproducing hypervirulent K. pneumoniae from Egypt. These results give new insights into the adaptation and evolution of K. pneumoniae during nosocomial infections.

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Section: Discussionmentioning

confidence: 99%

Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt

Yang

Ahmed

et al. 2022

BMC Genomics

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“…NDM variant was discovered in not only human but also food animals and environment ( van Duin and Doi, 2017 ; Liu et al, 2018 ). The highest distribution of NDM-positive species is observed in K. pneumoniae and Escherichia coli ( E. coli ) ( Gamal et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic and Phenotypic Characterization of the Novel Metallo-β-Lactamase NDM-29 From Escherichia coli

Zhu

Jia

et al. 2021

Front. Microbiol.

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Objectives: The New Delhi metallo-β-lactamase (NDM) can hydrolyze almost all clinically available β-lactam antibiotics and has widely spread all over the world. NDM-29, a novel carbapenemase, was discovered in an Escherichia coli (19NC225) isolated from a patient with biliary tract infection in 2019 in China.Methods: Conjugation, transformation, cloning test, fitness cost, PacBio Sequel, and Illumina sequencing were performed to analyze the genetic and phenotypic characterization of blaNDM–29.Results: The susceptibility testing results showed 19NC225 was resistant to cephalosporins, carbapenems, combinations of β-lactam and β-lactamase inhibitors, and levofloxacin. Conjugation and transformation were performed to verify the transferability of NDM-29-encoding plasmid, and cloning test was conducted to prove the function of blaNDM–29 to increase carbapenem resistance. Furthermore, fitness cost test confirmed that the presence of NDM-29 exerts no survival pressure on bacteria. PacBio Sequel and Illumina sequencing were performed to analyze the genetic characterization of 19NC225, which contains two plasmids (pNC225-TEM1B and pNC225-NDM-29). pNC225-NDM-29, exhibiting 99.96% identity and 100% coverage with pNDM-BTR (an IncN1 plasmid from an E. coli in urine specimen from Beijing in 2013), showed responsibility for the multidrug-resistant (MDR) phenotype. Compared with blaNDM–1, blaNDM–29, located on pNC225-NDM-29, carries a G388A (D130N) mutation. The region harboring blaNDM–29 is located in an ISKpn19-based transposon, and two Tn6292 remnants are symmetrically located upstream and downstream of the transposon. The sequence results also indicated several important virulence genes.Conclusion: The findings of the novel carbapenemase NDM-29 could pose a threat to the control of antimicrobial resistance and arouse attention about the mutation of bacteria.

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“…In contrast, several other types of carbapenemases, such as KPC, OXA-48, IMP, and VIM, have been found to be more common in other countries ( 11 , 12 ). The highest distribution of NDM-positive species is observed in K. pneumoniae and E. coli ( 13 ). Notably, one of the primary reasons for the rapid emergence and spread of NDM is its close association with E. coli carried by the vast majority of humans, in addition to its close association with different mobile genetic elements such as insertion sequences, ISCR elements, plasmids, other transposons, and integrons.…”

Section: Introductionmentioning

confidence: 99%

Whole genome-based genetic insights of bla _NDM producing clinical E. coli isolates in hospital settings of Pakistant

Abdullah,

Almusallam,

et al. 2023

Microbiol Spectr

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Carbapenem resistance among Enterobacterales has become a global health concern. Clinical Escherichia coli isolates producing the metallo β-lactamase NDM have been isolated from two hospitals in Faisalabad, Pakistan. These E. coli strains were characterized by MALDI-TOF, PCR, antimicrobial susceptibility testing, XbaI and S1 nuclease pulsed-field gel electrophoresis (PFGE), conjugation assay, DNA hybridization, whole genome sequencing, bioinformatic analysis, and Galleria mellonella experiments. Thirty-four bla NDM producing E. coli strains were identified among 52 nonduplicate carbapenem-resistant strains. More than 90% of the isolates were found to be multidrug resistant by antimicrobial susceptibility testing. S1 PFGE confirmed the presence of bla NDM gene on plasmids ranging from 40 kbps to 250 kbps, and conjugation assays demonstrated transfer frequencies of bla NDM harboring plasmids ranging from 1.59 × 10 −1 to 6.46 × 10 −8 per donor. Whole genome sequencing analysis revealed bla NDM-5 as the prominent NDM subtype with the highest prevalence of bla OXA-1 , bla CTX-M-15 , aadA2 , aac(6')-Ib-cr , and tet(A ) associated resistant determinants. E. coli sequence types: ST405, ST361, and ST167 were prominent, and plasmid Inc types: FII, FIA, FIB, FIC, X3, R, and Y, were observed among all isolates. The genetic environment of bla NDM region on IncF plasmids included partial IS Aba125 , the bleomycin ble gene, and a class I integron. The virulence genes terC, traT, gad, fyuA, irp2, capU, and sitA were frequently observed, and G. mellonella experiments showed that virulence correlated with the number of virulence determinants. A strong infection control management in the hospital is necessary to check the emergence of carbapenem resistance in Gram-negative bacteria. IMPORTANCE We describe a detailed analysis of highly resistant clinical E. coli isolates from two tertiary care centers in Pakistan including carbapenem resistance as well as common co-resistance mechanisms. South Asia has a huge problem with highly resistant E. coli . However, we find that though these isolates are very difficult to treat they are of low virulence. Thus the Western world has an increasing problem with virulent E. coli that are mostly of low antibiotic resistance, whereas, South Asia has an increasing problem with highly resistant E. coli that are of low virulence potential. These observations allow us to start to devise methodologies to limit both virulence and resistance and combat problems in developing nations as well as the Western world.

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High-risk clones and novel sequence type ST4497 of Klebsiella pneumoniae clinical isolates producing different alleles of NDM-type and other carbapenemases from a single tertiary-care centre in Egypt

Cited by 7 publications

References 29 publications

Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt

Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt

Genetic and Phenotypic Characterization of the Novel Metallo-β-Lactamase NDM-29 From Escherichia coli

Whole genome-based genetic insights of bla _NDM producing clinical E. coli isolates in hospital settings of Pakistant

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High-risk clones and novel sequence type ST4497 of Klebsiella pneumoniae clinical isolates producing different alleles of NDM-type and other carbapenemases from a single tertiary-care centre in Egypt

Cited by 7 publications

References 29 publications

Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt

Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt

Genetic and Phenotypic Characterization of the Novel Metallo-β-Lactamase NDM-29 From Escherichia coli

Whole genome-based genetic insights of bla NDM producing clinical E. coli isolates in hospital settings of Pakistant

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Whole genome-based genetic insights of bla _NDM producing clinical E. coli isolates in hospital settings of Pakistant