Description of Citrobacter cronae sp. nov., isolated from human rectal swabs and stool samples

Oberhettinger, Philipp; Schüle, Leonard; Marschal, Matthias; Bezdan, Daniela; Ossowski, Stephan; Dörfel, Daniela; Vogel, Wichard; Rossen, John W. A.; Willmann, Matthias; Peter, Silke

doi:10.1099/ijsem.0.004100

Cited by 20 publications

(19 citation statements)

References 30 publications

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“…However, in March 2012, we detected the first Citrobacter freundii strain harboring the same carbapenemase-encoding bla IMP-8 gene ( 19 ), approximately 2.5 years after the first P. aeruginosa bla IMP-8 gene had been detected. Shortly after, the carbapenemase was detected in Citrobacter cronae ( 20 ). Since bla IMP-8 is rarely encountered in Europe and Germany ( 21 , 22 ) and has not yet been detected in rectal screening swabs from patients submitted to our hospital for the first time, we hypothesized that horizontal gene transfer had occurred within bacterial strains circulating in our hospital.…”

Section: Introductionmentioning

confidence: 99%

Tracking of Antibiotic Resistance Transfer and Rapid Plasmid Evolution in a Hospital Setting by Nanopore Sequencing

Peter

Bosio

Groß

et al. 2020

mSphere

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Infections with multidrug-resistant bacteria often leave limited or no treatment options. The transfer of antimicrobial resistance genes (ARG) carrying plasmids between bacterial species by horizontal gene transfer represents an important mode of expansion of ARGs. Here, we demonstrate the application of Nanopore sequencing in a hospital setting for monitoring transfer and rapid evolution of antibiotic resistance plasmids within and across multiple species. In 2009, we experienced an outbreak with extensively multidrug-resistant Pseudomonas aeruginosa harboring the carbapenemase-encoding blaIMP-8 gene. In 2012, the first Citrobacter freundii and Citrobacter cronae strains harboring the same gene were detected. Using Nanopore and Illumina sequencing, we conducted comparative analysis of all blaIMP-8 bacteria isolated in our hospital over a 6-year period (n = 54). We developed the computational platform plasmIDent for Nanopore-based characterization of clinical isolates and monitoring of ARG transfer, comprising de novo assembly of genomes and plasmids, plasmid circularization, ARG annotation, comparative genome analysis of multiple isolates, and visualization of results. Using plasmIDent, we identified a 40-kb plasmid carrying blaIMP-8 in P. aeruginosa and C. freundii, verifying the plasmid transfer. Within C. freundii, the plasmid underwent further evolution and plasmid fusion, resulting in a 164-kb megaplasmid, which was transferred to C. cronae. Multiple rearrangements of the multidrug resistance gene cassette were detected in P. aeruginosa, including deletions and translocations of complete ARGs. In summary, plasmid transfer, plasmid fusion, and rearrangement of the ARG cassette mediated the rapid evolution of opportunistic pathogens in our hospital. We demonstrated the feasibility of near-real-time monitoring of plasmid evolution and ARG transfer in clinical settings, enabling successful countermeasures to contain plasmid-mediated outbreaks. IMPORTANCE Infections with multidrug-resistant bacteria represent a major threat to global health. While the spread of multidrug-resistant bacterial clones is frequently studied in the hospital setting, surveillance of the transfer of mobile genetic elements between different bacterial species was difficult until recent advances in sequencing technologies. Nanopore sequencing technology was applied to track antimicrobial gene transfer in a long-term outbreak of multidrug-resistant Pseudomonas aeruginosa, Citrobacter freundii, and Citrobacter cronae in a German hospital over 6 years. We developed a novel computational pipeline, pathoLogic, which enables de novo assembly of genomes and plasmids, antimicrobial resistance gene annotation and visualization, and comparative analysis. Applying this approach, we detected plasmid transfer between different bacterial species as well as plasmid fusion and frequent rearrangements of the antimicrobial resistance gene cassette. This study demonstrated the feasibility of near-real-time tracking of plasmid-based antimicrobial resistance gene transfer in hospitals, enabling countermeasures to contain plasmid-mediated outbreaks.

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Section: Introductionmentioning

confidence: 99%

Tracking of Antibiotic Resistance Transfer and Rapid Plasmid Evolution in a Hospital Setting by Nanopore Sequencing

Peter

Bosio

Groß

et al. 2020

mSphere

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“…In clinical settings, Citrobacter spp. isolates represent up to 6% of all isolated Enterobacteriaceae from clinical specimens [ 28 ]. Members of the genus Citrobacter are reported to associate with nosocomial infections for a high mortality rate [ 29 ].…”

Section: Discussionmentioning

confidence: 99%

“…isolates can have chromosomal AmpC β-lactamases, as well as plasmid encoded carbapenemases, which results in ineffective of many antimicrobial agents for treatment [ 20 , 22 , 34 , 35 ]. C. cronae was identified as a new Citrobacter species from human stool samples very recently [ 28 ], the antimicrobial profiles of C. cronae are largely unknow. In this study, we first identified an AmpC β-lactamase encoding gene ( bla CMY-98 ) in C. cronae , which provides a glimpse of antimicrobial insight into this species.…”

Section: Discussionmentioning

confidence: 99%

Comparative genomic characterization of multidrug-resistant Citrobacter spp. strains in Fennec fox imported to China

et al. 2021

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Background To investigate the antimicrobial profiles and genomic characteristics of MDR-Citrobacter spp. strains isolated from Fennec fox imported from Sudan to China. Methods Four Citrobacter spp. strains were isolated from stool samples. Individual fresh stool samples were collected and subsequently diluted in phosphate buffered saline as described previously. The diluted fecal samples were plated on MacConkey agar supplemented with 1 mg/l cefotaxime and incubated for 20 h at 37 °C. Matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI–TOF–MS) was used for identification. Antimicrobial susceptibility testing was performed using the broth microdilution method. Whole-genome sequencing was performed on an Illumina Novaseq-6000 platform. Acquired antimicrobial resistance genes and plasmid replicons were detected using ResFinder 4.1 and PlasmidFinder 1.3, respectively. Comparative genomic analysis of 277 Citrobacter genomes was also performed. Results Isolate FF141 was identified as Citrobacter cronae while isolate FF371, isolate FF414, and isolate FF423 were identified as Citrobacter braakii. Of these, three C. braakii isolates were further confirmed to be extended-spectrum β-lactamases (ESBL)-producer. All isolates are all multidrug resistance (MDR) with resistance to multiple antimicrobials. Plasmid of pKPC-CAV1321 belong to incompatibility (Inc) group. Comparative genomics analysis of Citrobacter isolates generated a large core-genome. Genetic diversity was observed in our bacterial collection, which clustered into five main clades. Human, environmental and animal Citrobacter isolates were distributed into five clusters. Conclusions To our knowledge, this is the first investigation of MDR-Citrobacter from Fennec Fox. Our phenotypic and genomic data further underscore the threat of increased ESBL prevalence in wildlife and emphasize that increased effort should be committed to monitoring the potentially rapid dissemination of ESBL-producers with one health perspective.

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“…isolates represent up to 6 % of all isolated Enterobacteriaceae from clinical specimens. [29] Members of the genus Citrobacter are reported to associate with nosocomial infections for a high mortality rate. [30] The Citrobacter genus is most closely related to Escherichia coli and Salmonella, and is divided into 11 different genomospecies.…”

Section: Discussionmentioning

confidence: 99%

“…isolates can have chromosomal AmpC β-lactamases, as well as plasmid encoded carbapenemases, which results in ineffective of many antimicrobial agents for treatment. [21,23,35,36] C. cronae was identi ed as a new Citrobacter species from human stool samples very recently, [29] the antimicrobial pro les of C. cronae are largely unknow. In this study, we rst identi ed an AmpC βlactamase encoding gene (bla CMY−98 ) in C. cronae, which provides a glimpse of antimicrobial insight into this species.…”

Section: Discussionmentioning

confidence: 99%

Comparative Genomic Characterization of Multidrug-resistant Citrobacter Spp. Strains in Fennec Fox Imported to China

Qin

Zhao

et al. 2021

Preprint

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Background: To investigate the antimicrobial profiles and genomic characteristics of MDR-Citrobacter spp. strains isolated from Fennec fox imported from Sudan to China.Methods: Citrobacter spp. strains were isolated from stool samples. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) was used for identification. Antimicrobial susceptibility testing was performed using the broth microdilution method. Whole-genome sequencing was performed on an Illumina Novaseq-6000 platform. Acquired antimicrobial resistance genes and plasmid replicons were detected using ResFinder 4.1 and PlasmidFinder 1.3, respectively. Comparative genomic analysis of 277 Citrobacter genomes was also investigated.Results: Isolate FF141 was identified as Citrobacter cronae, isolate FF371, isolate FF414, and isolate FF423 were identified as Citrobacter braakii. Of these, three C. braakii isolates were further confirmed to be ESBL-producer. All isolates are all MDR with resistance to multiple antimicrobials. Plasmids of incompatibility (Inc) group pKPC-CAV1321. Comparative genomics analysis of Citrobacter isolates generated a large core-genome. Genetic diversity was observed in our bacterial collection, which clustered into five main clades. Human, environmental and animal Citrobacter isolates were distributed into five clusters.Conclusions: To our knowledge, this is the first investigation of MDR-Citrobacter from Fennec Fox. Our phenotypic and genomic data further underscore the threat of increased ESBL prevalence in wildlife and emphasize that increased effort should be committed to monitoring the potentially rapid dissemination of ESBL-producers with one health perspective.

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Description of Citrobacter cronae sp. nov., isolated from human rectal swabs and stool samples

Cited by 20 publications

References 30 publications

Tracking of Antibiotic Resistance Transfer and Rapid Plasmid Evolution in a Hospital Setting by Nanopore Sequencing

Tracking of Antibiotic Resistance Transfer and Rapid Plasmid Evolution in a Hospital Setting by Nanopore Sequencing

Comparative genomic characterization of multidrug-resistant Citrobacter spp. strains in Fennec fox imported to China

Comparative Genomic Characterization of Multidrug-resistant Citrobacter Spp. Strains in Fennec Fox Imported to China

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