Complexity of Genomic Epidemiology of Carbapenem-Resistant <i>Klebsiella pneumoniae</i> Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs

Saavedra, Sandra Yamile; Bernal, Johan Fabian; Montilla-Escudero, Efraín Andrés; Arévalo, Stefany Alejandra; Prada, Diego Andrés; Valencia, María Fernanda; Moreno, Jaime; Hidalgo, Andrea Melissa; Abrudan, Monica; Argimón, Silvia; Kekre, Mihir; Underwood, Anthony; Aanensen, David M.; Duarte, Carolina; Donado-Godoy, Pilar

doi:10.1101/2021.06.21.449250

Cited by 5 publications

(1 citation statement)

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“…To the best of our knowledge this study tends to be the first to report the present of bla VIM 2(16.7) producing E. coli in Abakaliki while isolate positive for the bla VIM gene has been found by other researchers [20,23,39,40,41] and in one study it was located on an Incl1 plasmid of a novel sequence type (ST 297) [42]. Since this gene are carried on plasmid there is a tendency of cross-species dissemination over time.…”

Section: Discussionmentioning

confidence: 50%

Detection of Carbapenemase-Producing Escherichia coli and Klebsiella pneumoniae Implicated in Urinary Tract Infection

Nomeh

Federica²,

Joseph³

et al. 2023

AJRID

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Background and Objectives: Carbapenemase-producing bacteria are super bugs that make Urinary Tract Infections (UTIs) difficult to treat with drug of last resort such as carbapenem and other antibiotic thus limiting the treatment options. Carbapenemase production is increasing in clinical isolates of E. coli and K. pneumoniae, their potential to spread widely among patients necessitates molecular detection of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae implicated in Urinary Tract Infection. Methodology: A total of twelve (12) non-repeated clinical isolate of Escherichia coli (E1, E2, E3, E4, E5, E6, E7) and Klebsiella pneumoniae (K8, K9, K10, K11, K12) were selected based on their in vitro phenotypic resistant to carbapenem antibiotics from patients diagnosed with urinary tract infection at Alex Ekwueme Federal University Teaching Hospital, Abakaliki (AE-FEUTHA) Ebonyi Sate Nigeria. Escherichia coli and Klebsiella pneumoniae were further confirmed using standard routine microbiological technique for isolation and identification of bacteria. Escherichia coli and Klebsiella pneumoniae strains were further screen for carbapenemase-producing gene by PCR specific primer. Result: PCR analysis with specific primer for carbapenemase gene revealed the presence and predominant of blaKPC in Escherichia coli and Klebsiella pneumoniae 12(100 %) followed by blaNDM 11(91.7 %), blaIMP 7(58.3 %) and blaVIM 2(16.7) as the least carbapenemase-producing gene in Escherichia coli and Klebsiella pneumoniae. blaKPC was predominant in Escherichia coli 7(58.3 %) followed by blaNDM 6(50.0 %) and blaIMP 5(41.7 %) while both blaOXA and blaVIM (16.7 %) were the least detected carbapenemase gene. Klebsiella pneumoniae harbor high proportion of blaNDM and blaKPC both recording 5(41.7 %) followed by blaOXA and blaIMP both recording 2(16.7 %) but blaVIM gene was not identified in Klebsiella pneumoniae. Conclusion: The current findings highlight the occurrence of carbapenemase-producing gene in Escherichia coli and Klebsiella pneumoniae implicated in UTI. Since these genes are carried on the bacteria plasmid there is a tendency of cross-species dissemination over time. The detection of carbapenemase-producing gene call for prompt epidemiological surveillance and preventive strategies to limit the spread of these carbapenemase resistant genetic determinant and the need for antibiotic susceptibility testing of available antibiotic agent.

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Section: Discussionmentioning

confidence: 50%

Detection of Carbapenemase-Producing Escherichia coli and Klebsiella pneumoniae Implicated in Urinary Tract Infection

Nomeh

Federica²,

Joseph³

et al. 2023

AJRID

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Train-the-Trainer as an Effective Approach to Building Global Networks of Experts in Genomic Surveillance of AMR

Abrudan

Matimba

Nikolic

et al. 2021

Preprint

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Advanced genomics and sequencing technologies are increasingly becoming critical for global health applications such as pathogen and antimicrobial resistance (AMR) surveillance. Limited resources challenge capacity development in low- and middle-income countries (LMICs), with few countries having genomics facilities and adequately trained staff. Training research and public health experts who are directly involved in the establishment of such facilities offers an effective, but limited, solution to a growing need. Instead, training them to impart their knowledge and skills to others provides a sustainable model for scaling up the much needed capacity and capability for genomic sequencing and analysis locally with global impact. We designed and developed a Train-the-Trainer course integrating pedagogical aspects with genomic and bioinformatics activities. The course was delivered to 18 participants from 12 countries in Africa, Asia, and Latin America. A combination of teaching strategies culminating in a group project created a foundation for continued development at home institutions. Upon follow-up after 6 months, at least 40% of trainees had initiated training programs and collaborations to build capacity at local, national, and regional level. This work provides a framework for implementing a training and capacity building program for the application of genomics tools and resources in AMR surveillance.

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High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study

Nagaraj

Ravikumar

Govindan

et al. 2021

Preprint

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Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a threat to public health in India due to its high dissemination, mortality, and limited treatment options. Its genomic variability is reflected in the diversity of sequence types, virulence factors, and antimicrobial resistance (AMR) mechanisms. This study aims to characterize the clonal relationships and genetic mechanisms of resistance and virulence in CRKP isolates in India. Materials and Methods: We characterized 344 retrospective K. pneumoniae clinical isolates collected from 8 centers across India collected in 2013-2019. Susceptibility to antibiotics was tested with VITEK 2. Capsular types, MLST, virulence genes, AMR determinants, plasmid replicon types, and a single-nucleotide polymorphism (SNP) phylogeny were inferred from their whole genome sequences. Results: Phylogenetic analysis of the 325 Klebsiella isolates that passed QC revealed 3 groups: K. pneumoniae sensu stricto (n=307), K. quasipneumoniae (n=17), and K. varicolla (n=1). Sequencing and capsular diversity analysis of the 307 K. pneumoniae sensu stricto isolates revealed 28 sequence types, 26 K-locus types, and 11 O-locus types, with ST231, KL51, and O1V2 being predominant. blaOXA-48-like and blaNDM-1/5 were present in 73.2% and 24.4% of isolates respectively. The major plasmid replicon types associated with carbapenase genes were IncF (51.0%), and Col group (35.0%). Conclusion: Our study documents for the first time the genetic diversity of K- and O-antigens circulating in India. The results demonstrate the practical applicability of genomic surveillance and its utility in tracking the population dynamics of CRKP. It alerts us to the urgency for longitudinal surveillance of these virulent and transmissible lineages.

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Complexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs

Cited by 5 publications

References 46 publications

Detection of Carbapenemase-Producing Escherichia coli and Klebsiella pneumoniae Implicated in Urinary Tract Infection

Detection of Carbapenemase-Producing Escherichia coli and Klebsiella pneumoniae Implicated in Urinary Tract Infection

Train-the-Trainer as an Effective Approach to Building Global Networks of Experts in Genomic Surveillance of AMR

High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study

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