Global evolutionary epidemiology and resistome dynamics of Citrobacter species, Enterobacter hormaechei, Klebsiella variicola, and Proteeae clones

Sekyere, John Osei; Reta, Melese Abate

doi:10.1111/1462-2920.15387

Cited by 9 publications

(16 citation statements)

References 71 publications

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“…Therefore, plasmid‐borne ARGs such as mcr and carbapenemases are widespread due to their faster dissemination rate among bacteria species (Partridge et al ., 2018). Owing to the close connection between humans, animals and the environment (water, soil, air and communities/built environment), ARGS and virulence mechanisms can be disseminated between these three domains through bacterial hosts and plasmids (Osei Sekyere and Mensah, 2020; Osei Sekyere and Reta, 2020; Sekyere and Reta, 2020). Thus, antibiotics administration in livestock/food‐producing animals may select and spread antibiotic‐resistant GNB to humans and the environment through the food chain (Osei Sekyere and Mensah, 2020; Osei Sekyere and Reta, 2020; Sekyere and Reta, 2020) and their faeces/farm effluents respectively.…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics, epigenomics, virulome and mobilome of Gram‐negative bacteria co‐resistant to carbapenems and polymyxins: a One Health systematic review and meta‐analyses

Ramaloko

Sekyere

2022

Environmental Microbiology

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Gram-negative bacteria (GNB) continue to develop resistance against important antibiotics including lastresort ones such as carbapenems and polymyxins. An analysis of GNB with co-resistance to carbapenems and polymyxins from a One Health perspective is presented. Data of species name, country, source of isolation, resistance genes (ARGs), plasmid type, clones and mobile genetic elements (MGEs) were deduced from 129 articles from January 2016 to March 2021. Available genomes and plasmids were obtained from PATRIC and NCBI. Resistomes and methylomes were analysed using BAcWGSTdb and REBASE whilst Kaptive was used to predict capsule typing. Plasmids and other MEGs were identified using MGE Finder and ResFinder. Phylogenetic analyses were done using RAxML and annotated with MEGA 7. A total of 877 isolates, 32 genomes and 44 plasmid sequences were analysed. Most of these isolates were reported in Asian countries and were isolated from clinical, animal and environmental sources. Colistin resistance was mostly mediated by mgrB inactivation (37%; n = 322) and mcr-1 (36%; n = 312), while OXA-48/181 was the most reported carbapenemase. IncX and IncI were the most common plasmids hosting carbapenemases and mcr genes. The isolates were co-resistant to other antibiotics, with floR (chloramphenicol) and fosA3 (fosfomycin) being common; E. coli ST156 and K. pneumoniae ST258 strains were common globally. Virulence genes and capsular KL-types were also detected. Type I, II, III and IV restriction modification systems were detected, comprising various MTases and restriction enzymes. The escalation of highly resistant isolates drains the economy due to untreatable bacterial infections, which leads to increasing global mortality rates and healthcare costs.

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Section: Introductionmentioning

confidence: 99%

Phylogenomics, epigenomics, virulome and mobilome of Gram‐negative bacteria co‐resistant to carbapenems and polymyxins: a One Health systematic review and meta‐analyses

Ramaloko

Sekyere

2022

Environmental Microbiology

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“…A recent article focusing on the global evolutionary epidemiology and resistome dynamics of seldom isolated Enterobacteriaceae species has shown the wide distribution of multidrugresistant C. freundii, including ST22 strains with close evolutionary distance. 41 Overall, our data showed the first detection of NDM-1 and VIM-48 coproducing C. freundii strain isolated from the hospital environment in Tunisia and the second detection in the world of the bla VIM-48 gene. The presence of an extremely multidrug-resistant strain coharboring two MBL genes and containing various plasmid types in the hospital environment showed a higher risk of large-scale propagation of multiresistant bacteria constituting, therefore, a real danger to public health.…”

Section: Resultsmentioning

confidence: 52%

Whole Genome Sequencing of a Citrobacter freundii Strain Isolated from the Hospital Environment: An Extremely Multiresistant NDM-1 and VIM-48 Coproducing Isolate

Dziri

Kuşkucu

Arfaoui

et al. 2022

Microbial Drug Resistance

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Citrobacter freundii has acquired resistance to several antimicrobial drugs, including last-resort antibiotics affecting, therefore, clinical efficacy and causing high rates of mortality. In this study, we investigate the whole genome sequence of a carbapenem-resistant C. freundii strain isolated from the hospital environment in Tunisia. A total of 210 samples were taken using sterile swabs, from inanimate surfaces, medical devices, and care staff, during the period extended between March and April 2019. After the microbiological analysis of samples and antimicrobial susceptibility testing, only one strain identified as C. freundii showing resistance to carbapenems was selected for the whole genome sequencing. The genome analysis revealed a high-level resistance to most antibiotics. Interestingly, we have noted the coexistence of bla NDM-1 and bla VIM-48 metallo-b-lactamase (MBL) encoding genes conferring resistance to carbapenems. Other b-lactamases encoding genes have also been detected, including bla TEM-1 , bla CMY-48 , and bla OXA-1 . Moreover, genes conferring resistance to aminoglycoside [aac(3)-IId, ant(3 †)-Ia, aadA, aac(6¢)-Ib], macrolide [mph(A)], sulfonamide (sul1), trimethoprim (dfrA1), tetracycline [tet(D)], chloramphenicol [cat(B3)], rifamycin (arr-3), and quinolone (qnrB) have been revealed. The multi-locus sequence typing analysis showed that this isolate could not be assigned to an existing sequence type (ST), but it is almost identical to ST22. The plasmid investigation revealed the presence of five plasmids belonging to diverse incompatibility groups (IncFII, IncHI1A, IncHI1B, IncN, and IncX3). To the best of our knowledge, our findings report the first detection of NDM-1 and VIM-48 coproducing C. freundii in Tunisia and the second detection in the world of the bla VIM-48 .

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“…The publicly released data also enable analyses to better understand AMR trends and patterns. For example, a recent study used the Isolates Browser, which links AMRFinderPlus output with isolate metadata, to assess the global resistome and evolutionary epidemiology of multiple Enterobacterales species [22].…”

Section: Resultsmentioning

confidence: 99%

Curation of the AMRFinderPlus databases: applications, functionality and impact

et al. 2022

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Antimicrobial resistance (AMR) is a significant public health threat. Low-cost whole-genome sequencing, which is often used in surveillance programmes, provides an opportunity to assess AMR gene content in these genomes using in silico approaches. A variety of bioinformatic tools have been developed to identify these genomic elements. Most of those tools rely on reference databases of nucleotide or protein sequences and collections of models and rules for analysis. While the tools are critical for the identification of AMR genes, the databases themselves also provide significant utility for researchers, for applications ranging from sequence analysis to information about AMR phenotypes. Additionally, these databases can be evaluated by domain experts and others to ensure their accuracy. Here we describe how we curate the genes, point mutations and blast rules, and hidden Markov models used in NCBI’s AMRFinderPlus, along with the quality-control steps we take to ensure database quality. We also describe the web interfaces that display the full structure of the database and their newly developed cross-browser relationships. Then, using the Reference Gene Catalog as an example, we detail how the databases, rules and models are made publicly available, as well as how to access the software. In addition, as part of the Pathogen Detection system, we have analysed over 1 million publicly available genomes using AMRFinderPlus and its databases. We discuss how the computed analyses generated by those tools can be accessed through a web interface. Finally, we conclude with NCBI’s plans to make these databases accessible over the long-term.

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Global evolutionary epidemiology and resistome dynamics of Citrobacter species, Enterobacter hormaechei, Klebsiella variicola, and Proteeae clones

Cited by 9 publications

References 71 publications

Phylogenomics, epigenomics, virulome and mobilome of Gram‐negative bacteria co‐resistant to carbapenems and polymyxins: a One Health systematic review and meta‐analyses

Phylogenomics, epigenomics, virulome and mobilome of Gram‐negative bacteria co‐resistant to carbapenems and polymyxins: a One Health systematic review and meta‐analyses

Whole Genome Sequencing of a Citrobacter freundii Strain Isolated from the Hospital Environment: An Extremely Multiresistant NDM-1 and VIM-48 Coproducing Isolate

Curation of the AMRFinderPlus databases: applications, functionality and impact

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