Detection of Five
            <i>mcr-9</i>
            -Carrying
            <i>Enterobacterales</i>
            Isolates in Four Czech Hospitals

Bitar, Ibrahim; Papagiannitsis, Costas C.; Kraftova, Lucie; Chudějová, Kateřina; Marchetti, Vittoria Mattioni; Hrabák, Jaroslav

doi:10.1128/msphere.01008-20

Cited by 27 publications

(39 citation statements)

References 27 publications

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“…In our three selected isolates, mcr-9 was demonstrated to be located on IncHI2/IncHI2A plasmids by the hybrid (Illumina-Oxford Nanopore) approach, together with other AMR genes conferring resistance to different antimicrobial classes, including the bla SHV −12 ESBL gene type detected in the two plasmids of pig origin, and different genes involved in heavy metals metabolism. Similarly, previous findings detected IncHI2-or IncHI2A-type plasmids in mcr-9 positive Enterobacteriaceae, often together with other resistance determinants (including HPCIAs) and to heavy metals mainly from human patients (Carroll et al, 2019;Chavda et al, 2019;Kieffer et al, 2019;Bitar et al, 2020;Faccone et al, 2020;Kananizadeh et al, 2020;Lin et al, 2020;Osei Sekyere et al, 2020;Soliman et al, 2020;Tsui et al, 2020;Umeda et al, 2020;Elbediwi et al, 2021;Marchetti et al, 2021;Sun et al, 2021), and also from animal (Börjesson et al, 2020;Yuan et al, 2019;Borowiak et al, 2020;Haenni et al, 2020;Leite et al, 2020), food (Borowiak et al, 2020;Sadek et al, 2020;Tyson et al, 2020), and environmental (Kamathewatta et al, 2020) sources. Few reports also described mcr-9 integrated into the chromosome of Citrobacter (Ribeiro et al, 2021) and Salmonella (Pan et al, 2020;Tyson et al, 2020) isolates, with a genetic context similar to the structure observed in mcr-9-harboring plasmid sequences, suggesting a possible mcr-9 transfer as a gene cassette between plasmids and chromosomes (Pan et al, 2020).…”

Section: Discussionsupporting

confidence: 76%

Emergence of IncHI2 Plasmids With Mobilized Colistin Resistance (mcr)-9 Gene in ESBL-Producing, Multidrug-Resistant Salmonella Typhimurium and Its Monophasic Variant ST34 From Food-Producing Animals in Italy

et al. 2021

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A collection of 177 genomes of Salmonella Typhimurium and its monophasic variant isolated in 2014–2019 from Italian poultry/livestock (n = 165) and foodstuff (n = 12), previously screened for antimicrobial susceptibility and assigned to ST34 and single-locus variants, were studied in-depth to check the presence of the novel mcr-9 gene and to investigate their genetic relatedness by whole genome sequencing (WGS). The study of accessory resistance genes revealed the presence of mcr-9.1 in 11 ST34 isolates, displaying elevated colistin minimum inhibitory concentration values up to 2 mg/L and also a multidrug-resistant (MDR) profile toward up to seven antimicrobial classes. Five of them were also extended-spectrum beta-lactamases producers (blaSHV–12 type), mediated by the corresponding antimicrobial resistance (AMR) accessory genes. All mcr-9-positive isolates harbored IncHI2-ST1 plasmids. From the results of the Mash analysis performed on all 177 genomes, the 11 mcr-9-positive isolates fell together in the same subcluster and were all closely related. This subcluster included also two mcr-9-negative isolates, and other eight mcr-9-negative ST34 isolates were present within the same parental branch. All the 21 isolates within this branch presented an IncHI2/2A plasmid and a similar MDR gene pattern. In three representative mcr-9-positive isolates, mcr-9 was demonstrated to be located on different IncHI2/IncHI2A large-size (∼277–297 kb) plasmids, using a combined Illumina–Oxford Nanopore WGS approach. These plasmids were also compared by BLAST analysis with publicly available IncHI2 plasmid sequences harboring mcr-9. In our plasmids, mcr-9 was located in a ∼30-kb region lacking different genetic elements of the typical core structure of mcr-9 cassettes. In this region were also identified different genes involved in heavy metal metabolism. Our results underline how genomics and WGS-based surveillance are increasingly indispensable to achieve better insights into the genetic environment and features of plasmid-mediated AMR, as in the case of such IncHI2 plasmids harboring other MDR genes beside mcr-9, that can be transferred horizontally also to other major Salmonella serovars spreading along the food chain.

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Section: Discussionsupporting

confidence: 76%

Emergence of IncHI2 Plasmids With Mobilized Colistin Resistance (mcr)-9 Gene in ESBL-Producing, Multidrug-Resistant Salmonella Typhimurium and Its Monophasic Variant ST34 From Food-Producing Animals in Italy

et al. 2021

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“…Comparative analysis showed that the plasmids in E. cloacae SL 264 (pSL264), S. marcescens SL267 (pSL267) and K. aerogenes SL269 (pSL269) were completely identical. This plasmid, designated pSL264, was similar to other, previously identified plasmids, including pEB-1 in E. cloacae with 98.51% identity (KX230795) [24], pACM1 in Klebsiella oxytoca with 98.51% identity (KJ541681) [25], p51929_MCR_VIM in Citrobacter freundii with 98.51% identity (CP059429) [26], and pKp616_2 in K. pneumoniae with 98.52% identity (CP026497) [27]. However, the genetic environment surrounding bla IMP-1 in pSL264 was found to be unique.…”

Section: Structure Of the Plasmid Harboring Bla Imp-1supporting

confidence: 72%

A transferrable IncL/M plasmid harboring a gene encoding IMP-1 metallo-β-lactamase in clinical isolates of Enterobacteriaceae

et al. 2021

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Background The worldwide spread of carbapenemase-producing Enterobacteriaceae (CPE) has reduced the clinical utility of carbapenems. Plasmids often play an important role in the spread of genes encoding drug-resistance factors, especially in the horizontal transfer of these genes among species of Enterobacteriaceae. This study describes a patient infected with three species of CPE carrying an identical transferrable IncL/M plasmid. Methods Clinical isolates of CPE were collected at St. Luke’s International Hospital, Tokyo, Japan, from 2015 to 2019. Three species of CPE isolates, Enterobacter cloacae, Klebsiella aerogenes and Serratia marcescens, were isolated from a patient who developed severe gallstone pancreatitis associated with bloodstream infection, with all three isolates producing IMP-1 metallo-β-lactamase. The complete sequences of the plasmids of the three isolates were determined by both MiSeq and MinION. The medical chart of this patient was retrospectively reviewed conducted to obtain relevant clinical information. Results The three CPE species carried an IncL/M plasmid, pSL264, which was 81,133 bp in size and harbored blaIMP-1. The genetic environment surrounding blaIMP-1 consisted of int1-blaIMP-1-aac(6’)-IIc-qacL-qacEdelta1-sul1-istB-IS21. Conjugation experiments showed that S. marcescens could transmit the plasmid to E. cloacae and K. aerogenes. In contrast, pSL264 could not transfer from E. cloacae or K. aerogenes to S. marcescens. Conclusion The IncL/M plasmid pSL264 harboring blaIMP-1 was able to transfer among different species of Enterobacteriaceae in a patient receiving long-term antimicrobial treatment. The worldwide emergence and spread of IncL/M plasmids harboring carbapenemase-encoding genes among species of Enterobacteriaceae is becoming a serious public health hazard.

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“…The reports of VIM and MCR co-production in ECC isolates are increasing, as described elsewhere [30][31][32][33][34]. The presence of mcr-9-like genes bound by two insertion sequences as in p3849_IncHI2_mcr and as reported in Sadek et al 2020 andBitar et al 2020 will not express colistin resistance and such plasmids can circulate silently until detected.…”

Section: Discussionmentioning

confidence: 81%

“…The reports of VIM and MCR co-production in ECC isolates are increasing, as described elsewhere [30][31][32][33][34]. The presence of mcr-9-like genes bound by two insertion se-…”

Section: Discussionmentioning

confidence: 96%

Genomic Characterization of VIM and MCR Co-Producers: The First Two Clinical Cases, in Italy

et al. 2021

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Background: the co-production of carbapenemases and mcr-genes represents a worrisome event in the treatment of Enterobacteriaceae infections. The aim of the study was to characterize the genomic features of two clinical Enterobacter cloacae complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy. Methods: species identification and antibiotic susceptibility profiling were performed using MALDI-TOF and broth microdilution methods, respectively. Transferability of the blaVIM- and mcr- type genes was verified through conjugation experiment. Extracted DNA was sequenced using long reads sequencing technology on the Sequel I platform (PacBio). Results: the first isolate showed clinical resistance against ertapenem yet was colistin susceptible (EUCAST 2020 breakpoints). The mcr-9.2 gene was harbored on a conjugative IncHI2 plasmid, while the blaVIM-1 determinant was harbored on a conjugative IncN plasmid. The second isolate, resistant to both carbapenems and colistin, harbored: mcr-9 gene and its two component regulatory genes for increased expression on the chromosome, mcr-4.3 on non-conjugative (yet co-transferable) ColE plasmid, and blaVIM-1 on a non-conjugative IncA plasmid. Conclusions: to our knowledge, this is the first report of co-production of VIM and MCR in ECC isolates in Italy.

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Detection of Five mcr-9 -Carrying Enterobacterales Isolates in Four Czech Hospitals

Cited by 27 publications

References 27 publications

Emergence of IncHI2 Plasmids With Mobilized Colistin Resistance (mcr)-9 Gene in ESBL-Producing, Multidrug-Resistant Salmonella Typhimurium and Its Monophasic Variant ST34 From Food-Producing Animals in Italy

Emergence of IncHI2 Plasmids With Mobilized Colistin Resistance (mcr)-9 Gene in ESBL-Producing, Multidrug-Resistant Salmonella Typhimurium and Its Monophasic Variant ST34 From Food-Producing Animals in Italy

A transferrable IncL/M plasmid harboring a gene encoding IMP-1 metallo-β-lactamase in clinical isolates of Enterobacteriaceae

Genomic Characterization of VIM and MCR Co-Producers: The First Two Clinical Cases, in Italy

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