The dissemination of carbapenemase-producing Enterobacterales (CPE) is an important public health issue. The number of human CPE isolates has been steadily increasing during recent years, worldwide. Despite the fact that carbapenems are not licensed for use in veterinary medicine, increasing numbers of CPE from the veterinary sector have been reported. The transmission of CPE between pets/livestock and exposed humans as well as via food has been demonstrated. In this study, a detailed characterization of a carbapenem-resistant porcine Escherichia coli co-harbouring blaVIM-1, blaSHV-12 and blaACC-1 genes, along with other resistance genes, is provided

Grobbel, M.

Hammerl, J. A.

Irrgang, A.

Käsbohrer, A.

Malorny, B.

Meemken, Diana

Pauly, N.

Schwarz, Stefan

Tenhagen, B.-A.

English

Institutional Repository of the Freie Universität Berlin

J Antimicrob Chemother 2021; 76: 531–533doi:10.1093/jac/dkaa436Advance Access publication 11 November 2020Co-occurrence of the blaVIM-1 andblaSHV-12 genes on an IncHI2 plasmidof an Escherichia coli isolate recoveredfrom German livestockN. Pauly1*, J. A. Hammerl 1, S. Schwarz2, M. Grobbel1,D. Meemken3, B. Malorny1, B.-A. Tenhagen1,A. K€asbohrer1,4 and A. Irrgang 11Department Biological Safety, German Federal Institute for RiskAssessment, Berlin, Germany; 2Institute of Microbiology andEpizootics, Freie Universit€at Berlin, Berlin, Germany; 3Institute ofFood Safety and Food Hygiene, Freie Universit€at Berlin, Berlin,Germany; 4Unit for Veterinary Public Health and Epidemiology,University of Veterinary Medicine, Vienna, Austria*Corresponding author. E-mail: natalie_pauly@hotmail.comSir,The dissemination of carbapenemase-producing Enterobacterales(CPE) is an important public health issue. The number of humanCPE isolates has been steadily increasing during recent years,worldwide. Despite the fact that carbapenems are not licensed foruse in veterinary medicine, increasing numbers of CPE from theveterinary sector have been reported.1 The transmission of CPE be-tween pets/livestock and exposed humans as well as via food hasbeen demonstrated.2 In this study, a detailed characterization ofa carbapenem-resistant porcine Escherichia coli co-harbouringblaVIM-1, blaSHV-12 and blaACC-1 genes, along with other resistancegenes, is provided.Within the German annual monitoring of ESBL/AmpC b-lacta-mase-producing E. coli from animals and food in 2017–18, theisolate 17-AB02384 was recovered from the caecal content of afattening pig at slaughter. Based on EUCAST epidemiologicalcut-off values (https://www.eucast.org/mic_distributions_and_ecoffs/), the isolate showed a non-WT phenotype to carbapenemsand other antimicrobials [Table S1 (Table S1 is available asSupplementary data at JAC Online)]. Molecular analysis revealedthat E. coli 17-AB02384 belonged to the phylogenetic group A andthe multilocus sequence type (MLST) 7593.3 To our knowledge,this ST has not yet been described in E. coli from German livestockor food chain. However, ST7593 was reported for some NDM-5-producing isolates of retail meat samples in China.4Initial S1-PFGE plasmid profiling and subsequent DNA–DNA hy-bridization3 indicated that the blaVIM-1 gene was located on an ap-proximately 300 kb IncHI2 plasmid, designated pEC17-AB02384,which was transferable into the E. coli J53 by conjugation at atransfer rate of 2%10#4. For a detailed characterization, thewhole-genome sequence of E. coli 17-AB02384 was determinedby Illumina (CA, USA) short-read and PacBio (Menlo Park, USA)long-read sequencing, according to the manufacturers’ recom-mendations. Hybrid assembly of the plasmid sequence was carriedout using unicycler v.0.44. The resulting sequence of the plasmidpEC17-AB02384 was deposited at GenBank (NCBI) under the ac-cession number MT163739. MLST, resistance and virulence geneswere determined using online tools that were provided by theDanish Technical University (http://www.genomicepidemiology.org) . The annotation was carried out by RAST2 provided by PATRIC(www.patricbrc.org). Characteristics of the isolate and its plasmidare summarized in Table S2.Besides blaVIM-1, this plasmid harboured the ESBL gene blaSHV-12and the AmpC b-lactamase gene blaACC-1. Overall, pEC17-AB02384 showed similarity to the VIM-1-encoding plasmidspSE15-SA01028 (90% identity, CP026661.1) and pRH-R178 (93%identity, HG530658.1) from Salmonella enterica subsp. entericaand E. coli, respectively, which were both recovered from Germanpigs (Figure 1a).5 In contrast to these plasmids, pEC17-AB02384harboured three additional resistance gene-carrying segments.The 9773 bp segment 1 comprised the resistance genes sul1 andqnrA1 and was flanked by 124 bp inverted repeats. It was insertedinto the region upstream of the blaVIM-1-carrying class 1 multire-sistance integron in pEC17-AB02384 (Figure 1b). Downstream ofthe integrase gene intI1 of the blaVIM-1-carrying integron, the seg-ment 2 was integrated. It carried the macrolide resistance operonmph(A)-mrx-mphR, the trimethoprim resistance gene dfrA14 andanother intI1 gene. Immediately downstream of both intI1 genes,202 bp direct repeats were found (Figure 1b). It appears possiblethat a translocatable unit comprising the entire segment 2 wasinserted into plasmid pEC17-AB02384 by recombination with theintI1 gene of the blaVIM-1-carrying integron and its adjacent repeatregion. The 4979 bp segment 3 was inserted into segment 2 be-tween the Drec and the mph(A) gene. It carried the ESBL geneblaSHV-12 and was flanked by IS26 elements in opposite orienta-tion. However, no direct repeats were detected at the immediateboundaries of segment 3, suggesting that the IS26-boundedsegment 3 does not function as a transposon.To our knowledge, the co-occurrence of blaVIM-1 and blaSHV-12has not yet been described in plasmids from isolates of animalVC The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creati-vecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, providedthe original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com531Downloaded from https://academic.oup.com/jac/article/76/2/531/5974115 by Freie Universitaet Berlin user on 15 April 2021origin. Co-location of these genes was reported only for a singlehuman clinical Aeromonas caviae isolate (KR869764) in 2014.6 Thecorresponding plasmid belonged to the replicon type IncA/C andshowed no substantial similarities to pEC17-AB02384. SHV-12 isan extended-spectrum b-lactamase that is commonly detected inisolates from poultry, but rarely from pigs.7 Alonso et al.7 providedfurther data on blaSHV-12-carrying plasmids from human, animaland food sources. Among them, the E. coli plasmid pCAZ590(LT669764) exhibits a similar SHV-12 region as the one identified inpEC17-AB02384. In general, blaSHV-12 seems to be associated withIS26 elements, which might support its mobility. The ability of IS26to mobilize neighbouring genes might play an important role in thepersistence of antimicrobial resistances.8A comparison of the few known blaVIM-1-carrying plasmidsfrom German livestock revealed close relationships. This might in-dicate that a prototype-plasmid has adapted to bacteria in differ-ent animal populations and persists in an unknown reservoir. Thecharacterization of CPE isolates and their plasmids will contributeto the further understanding of reservoirs, potential transmissionpathways and persistence factors for plasmid maintenance in bac-teria from animal husbandry.AcknowledgementsWe gratefully acknowledge the support of the regional laboratories andauthorities in their general support during sampling and providing iso-lates in the framework of the monitoring. We also thank the laboratoryteam of the NRL-AR, especially Britta Lesniewsky and Silvia Schmoger,for excellent technical assistance.FundingThis work was supported by the German Federal Institute for RiskAssessment (43-001), by funding from the European Union’s Horizon2020 Research and Innovation programme under grant agreementnumber 773830: One Health European Joint Programme, and theGerman Federal Ministry of Education and Research (BMBF) under proj-ect number 01KI1727D as part of the Research Network ZoonoticInfectious Diseases.Transparency declarationsWe declare that the research was conducted in the absence of any com-mercial or financial relationships that could be construed as a potentialconflict of interest.Supplementary dataTables S1 and S2 are available as Supplementary data at JAC Online.References1 Köck R, Daniels-Haardt I, Becker K et al. Carbapenem-resistantEnterobacteriaceae in wildlife, food-producing, and companion animals: asystematic review. Clin Microbiol Infect 2018; 24: 1241–50.Figure 1. (a) Schematic illustrations of plasmids pRH-R178 and pSE15-SA01028 in comparison with plasmid pEC17-AB02384 described in this sudy.(b) Schematic illustration of the multidrug resistance region of plasmid pEC17-AB02384. The reading frames are displayed as arrows with the arrow-head showing the dirction of transcription. The numbers refer to the whole plasmid sequence of pEC17-AB02384, which is deposited in the GenBankdatabase under accession no. MT163739. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.Research letters532Downloaded from https://academic.oup.com/jac/article/76/2/531/5974115 by Freie Universitaet Berlin user on 15 April 20212 Fischer J, Hille K, Ruddat I et al. Simultaneous occurrence of MRSA andESBL-producing Enterobacteriaceae on pig farms and in nasal and stool sam-ples from farmers. Vet Microbiol 2017; 200: 107–13.3 Irrgang A, Tenhagen BA, Pauly N et al. Characterization of VIM-1-producing E. coli isolated from a German fattening pig farm by an improvedisolation procedure. Front Microbiol 2019; 10: 2256.4 Zhang Q, Lv L, Huang X et al. Rapid increase in carbapenemase-producingEnterobacteriaceae in retail meat driven by the spread of the blaNDM-5-carry-ing IncX3 plasmid in China from 2016 to 2018. Antimicrob Agents Chemother2019; 63: e00573–19.5 Falgenhauer L, Ghosh H, Guerra B et al. Comparative genome analysis ofIncHI2 VIM-1 carbapenemase-encoding plasmids of Escherichia coli andSalmonella enterica isolated from a livestock farm in Germany. Vet Microbiol2017; 200: 114–7.6 Antonelli A, D’Andrea MM, Montagnani C et al. Newborn bacteraemiacaused by an Aeromonas caviae producing the VIM-1 and SHV-12 b-lacta-mases, encoded by a transferable plasmid. J Antimicrob Chemother 2016;71: 272–4.7 Alonso CA, Michael GB, Li J et al. Analysis of blaSHV-12-carrying Escherichiacoli clones and plasmids from human, animal and food sources. J AntimicrobChemother 2017; 72: 1589–96.8 Harmer CJ, Moran RA, Hall RM. Movement of IS26-associated antibi-otic resistance genes occurs via a translocatable unit that includes a sin-gle IS26 and preferentially inserts adjacent to another IS26. mBio 2014;5: e01801-14.9.J Antimicrob Chemother 2021; 76: 533–535doi:10.1093/jac/dkaa450Advance Access publication 5 November 2020Distinct evolution of colistin resistanceassociated with experimentalresistance evolution models inKlebsiella pneumoniaeL. B. S. Aulin 1, C. I. M. Koumans1, Y. Haakman1,W. van Os1, M. E. M. Kraakman2, J. Gooskens2,W. K. Smits 2, A. Liakopoulos 3† andJ. G. C. van Hasselt 1*†1Leiden Academic Centre for Drug Research, Leiden University,Leiden, The Netherlands; 2Department of Medical Microbiology,Leiden University Medical Center, Leiden, The Netherlands;3Institute of Biology, Leiden University, Leiden, The Netherlands*Corresponding author. E-mail: coen.vanhasselt@lacdr.leidenuniv.nl†These authors made an equal contribution.Sir,Klebsiella pneumoniae ranks at the top of the global priority listof pathogens regarding demand for new treatment options.1Colistin represents a last-resort antibiotic for treatment of MDRK. pneumoniae infections.2 Colistin resistance in K. pneumoniae isattributed to the accumulation of chromosomal mutations, mainlyin pmrAB, phoPQ, ccrAB and mgrB.3 In order to maintain the effi-cacy of such last-resort antibiotics, we need to design rationaltreatment strategies that consider resistance development associ-ated with clinical antibiotic concentration–time profiles. In vitroexperiments in the context of pharmacokinetic (PK) profiles repre-sent a relevant approach to characterize the evolution of resis-tance. However, experimental evolution studies for colistin havemainly focused on approaches such as serial passaging thatdo not consider PK. The role of the experimental model and inparticular the impact of clinical drug concentrations on evolutionof resistance is poorly understood.We aimed to study the impact of experimental evolutionapproaches for the development of resistance to colistin inK. pneumoniae. We performed experiments with a continuousculture chemostat replicating clinical PK profiles of colistin, astatic clinical colistin concentration and standard serial passagingexperiments, comparing the phenotypic and the genotypicchanges.Two colistin-susceptible clinical isolates of K. pneumoniae(KML9749 and KML9884) obtained from Leiden University MedicalVC The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creati-vecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, providedthe original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comResearch letters JAC533Downloaded from https://academic.oup.com/jac/article/76/2/531/5974115 by Freie Universitaet Berlin user on 15 April 2021

Co-occurrence of the bla(VIM-1) and bla(SHV-12) genes on an IncHI2 plasmid of an Escherichia coli isolate recovered from German livestock

https://refubium.fu-berlin.de/bitstream/fub188/30361/1/dkaa436.pdf

Co-occurrence of the bla(VIM-1) and bla(SHV-12) genes on an IncHI2 plasmid of an Escherichia coli isolate recovered from German livestock

Abstract

Similar works

Full text

Available Versions

Institutional Repository of the Freie Universität Berlin