Global genotype distribution of human clinical isolates of New Delhi metallo-β-lactamase-producing Klebsiella pneumoniae; A systematic review

Safavi, Mahshid; Bostanshirin, Nazila; Hajikhani, Bahareh; Yaslianifard, Somayeh; Belkum, Alex van; Goudarzi, Mehdi; Hashemi, Ali; Darban-Sarokhalil, Davood; Dadashi, Masoud

doi:10.1016/j.jgar.2020.10.016

Cited by 34 publications

(24 citation statements)

References 36 publications

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“…In Europe, the common variants are bla NDM-1 and bla NDM-5. 16 Thus, our findings are consistent with available data on the distribution of NDM variants. Additional enzymes, like OXA-48 and CMY, have been also identified in the majority of cases.…”

Section: Discussionsupporting

confidence: 92%

“…Diverse range of STs is reported in different countries with a total of 86 unique STs reported globally for NDM-Kpn. 16 In fact, in our study, the heterogeneity was lower among strains isolated from patients coming from the same geographic area. Analysis by cgMLST revealed that NDM-Kpn isolated from 5 patients at H-3 were clonally related; in particular, strains from patients #3, #6 and #8 belonged to ST15 (CT-1), whereas isolates from patient #10 and #5 belonged to ST383, being part of CT-5.…”

Section: Discussionmentioning

confidence: 45%

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Importance of Surveillance of New Delhi Metallo-Beta-Lactamase Klebsiella pneumoniae: Molecular Characterization and Clonality of Strains Isolated in the Lazio Region, Italy

Spaziante¹,

Venditti²,

Butera³

et al. 2021

IDR

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Introduction: New Delhi metallo-β-lactamase producing Klebsiella pneumoniae (NDM-Kpn) strains have been causing healthcare-associated infections worldwide. The aim of this study was to describe the molecular mechanisms of antimicrobial resistance and to analyze the clonality of NDM-Kpn isolates collected between January 2019 and June 2020 from patients admitted to hospitals from the Lazio region, Italy. Methods: We performed a retrospective cohort study. Whole-genome sequencing (WGS) was performed on all NDM-Kpn strains; clonality and genetic relationships were further investigated. Results: During the surveillance period, 17 NDM-Kpn isolates were obtained from 17 patients admitted to seven different hospitals. Eight different sequence types (STs) were detected: ST147 (n = 4), ST383 (n = 4), ST15 (n = 3), ST11 (n = 2), ST17 (n = 1), ST29 (n = 1), ST307 (n = 1) and the newly identified ST4853 (n = 1). Genetic relationships were further investigated by the WGS-based core genome MLST (cgMLST) scheme, and 5 cluster types (CTs) were identified. Whereas a substantial overall heterogeneity among isolates was detected (8 different STs were identified out of 17 isolates), the strains within each cluster showed a very high level of genome similarity. Discussion: Our study highlights the key role of surveillance, which allowed taking a picture of a part of the NDM-Kpn strains circulating in Italy, adding further insight into their molecular features.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 45%

Importance of Surveillance of New Delhi Metallo-Beta-Lactamase Klebsiella pneumoniae: Molecular Characterization and Clonality of Strains Isolated in the Lazio Region, Italy

Spaziante¹,

Venditti²,

Butera³

et al. 2021

IDR

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“…These isolates comprise a set of diverse K. pneumoniae , represented by many STs in both animal species. Many of these STs, such as ST13, ST17, ST35, ST37 and ST290, have previously been identified in humans ( Marcade et al, 2013 ; Safavi et al, 2020 ; Raffelsberger et al, 2021 ). A recently published study from Norway screened 2,975 healthy persons for K. pneumoniae gut carriage ( Raffelsberger et al, 2021 ), and identified a diverse population of K. pneumoniae .…”

Section: Discussionmentioning

confidence: 99%

Exploring Klebsiella pneumoniae in Healthy Poultry Reveals High Genetic Diversity, Good Biofilm-Forming Abilities and Higher Prevalence in Turkeys Than Broilers

et al. 2021

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Klebsiella pneumoniae is a well-studied human pathogen for which antimicrobial resistant and hypervirulent clones have emerged globally. K. pneumoniae is also present in a variety of environmental niches, but currently there is a lack of knowledge on the occurrence and characteristics of K. pneumoniae from non-human sources. Certain environmental niches, e.g., animals, may be associated with high K. pneumoniae abundance, and these can constitute a reservoir for further transmission of strains and genetic elements. The aim of this study was to explore and characterize K. pneumoniae from healthy broilers and turkeys. A total of 511 cecal samples (broiler n = 356, turkey n = 155), included in the Norwegian monitoring program for antimicrobial resistance (AMR) in the veterinary sector (NORM-VET) in 2018, were screened for K. pneumoniae by culturing on SCAI agar. K. pneumoniae was detected in 207 (40.5%) samples. Among the broiler samples, 25.8% were positive for K. pneumoniae, in contrast to turkey with 74.2% positive samples (p < 0.01). Antibiotic susceptibility testing was performed, in addition to investigating biofilm production. Whole genome sequencing was performed on 203 K. pneumoniae isolates, and analysis was performed utilizing comparative genomics tools. The genomes grouped into 66 sequence types (STs), with ST35, ST4710 and ST37 being the most prevalent at 13.8%, 7.4%, and 5.4%, respectively. The overall AMR occurrence was low, with only 11.3% of the isolates showing both pheno- and genotypic resistance. Genes encoding aerobactin, salmochelin or yersiniabactin were detected in 47 (23.2%) genomes. Fifteen hypervirulent genomes belonging to ST4710 and isolated from turkey were identified. These all encoded the siderophore virulence loci iuc5 and iro5 on an IncF plasmid. Isolates from both poultry species displayed good biofilm-forming abilities with an average of OD595 0.69 and 0.64. To conclude, the occurrence of K. pneumoniae in turkey was significantly higher than in broiler, indicating that turkey might be an important zoonotic reservoir for K. pneumoniae compared to broilers. Furthermore, our results show a highly diverse K. pneumoniae population in poultry, low levels of antimicrobial resistance, good biofilm-forming abilities and a novel hypervirulent ST4710 clone circulating in the turkey population.

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“…The successful clinical treatment and control of CRErelated infections has faced great challenges. bla NDM is an MBL carbapenemase type usually seen in Asia (Safavi et al, 2020). The prevalence of NDM-producing E. coli was reported to be 82.6, 12.9, 1.5, 1.0, and 2.0% in Asia, Europe, America, Africa, and Oceania, respectively (Dadashi et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Rapid Detection of New Delhi Metallo-β-Lactamase Gene Using Recombinase-Aided Amplification Directly on Clinical Samples From Children

et al. 2021

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New Delhi metallo-β-lactamase, a metallo-β-lactamase carbapenemase type, mediates resistance to most β-lactam antibiotics including penicillins, cephalosporins, and carbapenems. Therefore, it is important to detect blaNDM genes in children’s clinical samples as quickly as possible and analyze their characteristics. Here, a recombinase-aided amplification (RAA) assay, which operates in a single one-step reaction tube at 39°C in 5−15 min, was established to target blaNDM genes in children’s clinical samples. The analytical sensitivity of the RAA assay was 20 copies, and the various bacterial types without blaNDM genes did not amplify. This method was used to detect blaNDM genes in 112 children’s stool samples, 10 of which were tested positive by both RAA and standard PCR. To further investigate the characteristics of carbapenem-resistant bacteria carrying blaNDM in children, 15 carbapenem-resistant bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Citrobacter freundii, Klebsiella oxytoca, Acinetobacter junii, and Proteus mirabilis) were isolated from the 10 samples. Notably, more than one bacterial type was isolated from three samples. Most of these isolates were resistant to cephalosporins, cefoperazone-sulbactam, piperacillin-tazobactam, ticarcillin-clavulanic acid, aztreonam, co-trimoxazole, and carbapenems. blaNDM–1 and blaNDM–5 were the two main types in these samples. These data show that the RAA assay has potential to be a sensitive and rapid blaNDM gene screening test for clinical samples. The common existence of blaNDM and multi-drug resistance genes presents major challenges for pediatric treatment.

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Global genotype distribution of human clinical isolates of New Delhi metallo-β-lactamase-producing Klebsiella pneumoniae; A systematic review

Cited by 34 publications

References 36 publications

Importance of Surveillance of New Delhi Metallo-Beta-Lactamase Klebsiella pneumoniae: Molecular Characterization and Clonality of Strains Isolated in the Lazio Region, Italy

Importance of Surveillance of New Delhi Metallo-Beta-Lactamase Klebsiella pneumoniae: Molecular Characterization and Clonality of Strains Isolated in the Lazio Region, Italy

Exploring Klebsiella pneumoniae in Healthy Poultry Reveals High Genetic Diversity, Good Biofilm-Forming Abilities and Higher Prevalence in Turkeys Than Broilers

Rapid Detection of New Delhi Metallo-β-Lactamase Gene Using Recombinase-Aided Amplification Directly on Clinical Samples From Children

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