A #cluster of #colistin- and #carbapenem-resistant #Klebsiella pneumoniae carrying #blaNDM-1 and #mcr-8.2 (J Infect Dis., abstract)

[Source: Journal of Infectious Diseases, full page: (LINK). Abstract, edited.]

A cluster of colistin- and carbapenem-resistant Klebsiella pneumoniae carrying blaNDM-1 and mcr-8.2

Ke Ma, Yu Feng, Lu Liu, Zhihong Yao, Zhiyong Zong

The Journal of Infectious Diseases, jiz519, https://doi.org/10.1093/infdis/jiz519

Published: 11 December 2019

 

Abstract

Background

Klebsiella pneumoniae resistant to both carbapenems and colistin imposes severe challenges for management. Here we report a cluster of five carbapenem-resistant K. pneumoniae clinical strains belonging to ST1 and K57 types, four of which were also resistant to colistin, from two hospitals.

Methods

The five strains were subjected to whole genome sequencing (WGS) using the short-read Illumina HiSeq platform and two strains were also selected for long-read WGS using MinION. Clonal relatedness of the five strains was determined based on single nucleotide polymorphisms (SNPs). Conjugation experiments were performed to obtain self-transmissible plasmids.

Results

All five strains carried the carbapenemase-encoding gene blaNDM-1, whereas the four colistin-resistant strains also harbored a new variant of the mcr-8 colistin resistance gene, namely mcr-8.2. Mcr-8.2 differs from Mcr-8.1 by four amino acid substitutions (A51V, A232S, N365Y, and N480K). mcr-8.2 was located on a large, hybrid, non-self-transmissible plasmid containing IncQ, IncR, and IncFII replicons, whereas blaNDM-1 was carried by self-transmissible IncX3 plasmids. Phylogenetic analysis based on SNPs revealed that the five strains were likely to have a common origin.

Conclusion

Both the intra- and inter-hospital transfer of strains carrying mcr-8 and blaNDM-1 were identified, which represents an emerging threat for clinical management and infection control.

colistin resistance, mcr, plasmid, Klebsiella pneumoniae

Topic: plasmids – colistin – klebsiella pneumoniae – single nucleotide polymorphism – beta-lactamase ndm-1 – carbapenem resistance – whole genome sequencing

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Author notes: These authors contributed equally.

© The Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Antibiotics; Drugs Resistance; Colistin; Carbapenem; Klebsiella pneumoniae; Nosocomial outbreaks; NDM1.

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#Transmission of #ESBL-producing #Escherichia coli between #broilers and #humans on broiler #farms (J Antimicrob Chemother., abstract)

[Source: Journal of Antimicrobial Chemotherapy, full page: (LINK). Abstract, edited.]

Transmission of ESBL-producing Escherichia coli between broilers and humans on broiler farms

Angela H A M van Hoek, Cindy Dierikx, Thijs Bosch, Leo Schouls, Engeline van Duijkeren, Michael Visser

Journal of Antimicrobial Chemotherapy, dkz507, https://doi.org/10.1093/jac/dkz507

Published: 04 December 2019

 

Abstract

Background

ESBL and AmpC β-lactamases are an increasing concern for public health. Studies suggest that ESBL/pAmpC-producing Escherichia coli and their plasmids carrying antibiotic resistance genes can spread from broilers to humans working or living on broiler farms. These studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these isolates.

Methods

Eleven suspected transmission events among broilers and humans living/working on eight broiler farms were investigated using whole-genome short-read (Illumina) and long-read sequencing (PacBio). Core genome MLST (cgMLST) was performed to investigate the occurrence of strain transmission. Horizontal plasmid and gene transfer were analysed using BLAST.

Results

Of eight suspected strain transmission events, six were confirmed. The isolate pairs had identical ESBL/AmpC genes and fewer than eight allelic differences according to the cgMLST, and five had an almost identical plasmid composition. On one of the farms, cgMLST revealed that the isolate pairs belonging to ST10 from a broiler and a household member of the farmer had 475 different alleles, but that the plasmids were identical, indicating horizontal transfer of mobile elements rather than strain transfer. Of three suspected horizontal plasmid transmission events, one was confirmed. In addition, gene transfer between plasmids was found.

Conclusions

The present study confirms transmission of strains as well as horizontal plasmid and gene transfer between broilers and farmers and household members on the same farm. WGS is an important tool to confirm suspected zoonotic strain and resistance gene transmission.

Issue Section: ORIGINAL RESEARCH

© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Antibiotics; Drugs Resistance; Beta-lactams; E. Coli; Poultry; Human.

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Comparison of the inoculum size effects of #antibiotics on IMP-6 β-lactamase-producing #Enterobacteriaceae co-harboring #plasmid-mediated #quinolone #resistance genes (PLOS One, abstract)

[Source: PLOS One, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Comparison of the inoculum size effects of antibiotics on IMP-6 β-lactamase-producing Enterobacteriaceae co-harboring plasmid-mediated quinolone resistance genes

Yoshihiko Ogawa, Ryuichi Nakano , Kei Kasahara, Tomoki Mizuno, Nobuyasu Hirai, Akiyo Nakano, Yuki Suzuki, Naoki Kakuta, Takashi Masui, Hisakazu Yano, Keiichi Mikasa

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Published: November 13, 2019 / DOI: https://doi.org/10.1371/journal.pone.0225210

 

Abstract

Almost all cases of carbapenemase-producing Enterobacteriaceae infections in Japan are caused by blaIMP-positive Enterobacteriaceae (especially blaIMP-6) and infections caused by other types of carbapenemase-producing Enterobacteriaceae are quite rare. We examined drug resistance genes co-harboring with blaIMP-6 and their inoculum size effects. We screened β-lactamase genes, plasmid-mediated quinolone resistance (PMQR) genes, and aminoglycoside-modifying enzyme genes by PCR and performed sequencing for 14 blaIMP-6-positive Enterobacteriaceae. Further, all PMQR-positive isolates were submitted to conjugation and inoculum effect evaluation. Our data showed that 13 of the 14 isolates harbored CTX-M-2 and one co-harbored CTX-M-2 and CTX-M-1 as extended-spectrum β-lactamases. All isolates carried one or more PMQRs; aac(6’)-Ib-cr was the most prevalent (92.8%), and was followed by oqxA (64.3%), qnrS (50%), oqxAB (21.4%), and qnrB (14.3%). However, Klebsiella pneumoniae contains chromosomal OqxAB. Inoculum size effects were significant in all strains for meropenem, 13 strains for imipenem, 7 for levofloxacin, and 3 for amikacin. We observed that 11 of the experimental strains (100%), 8 strains (72.7%), and 1 strain showed inoculum size effects for meropenem, imipenem, and amikacin, respectively. However, four strains harbored qnr genes and two strains harbored qnr genes and QRDR mutations concurrently; no inoculum size effect was seen for levofloxacin. The blaIMP-6-positive Enterobacteriaceae that we studied was found to harbor at least one plasmid-mediated drug resistance gene. The inoculum size effect for carbapenems was thought to be mainly due to IMP-6-type metallo-β-lactamase; however qnrB and qnrS also had a minimal impact on the inoculum size effect for levofloxacin.

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Citation: Ogawa Y, Nakano R, Kasahara K, Mizuno T, Hirai N, Nakano A, et al. (2019) Comparison of the inoculum size effects of antibiotics on IMP-6 β-lactamase-producing Enterobacteriaceae co-harboring plasmid-mediated quinolone resistance genes. PLoS ONE 14(11): e0225210. https://doi.org/10.1371/journal.pone.0225210

Editor: Shampa Anupurba, Institute of Medical Sciences, Banaras Hindu University, INDIA

Received: July 22, 2019; Accepted: October 29, 2019; Published: November 13, 2019

Copyright: © 2019 Ogawa et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the manuscript.

Funding: This study was supported by JSPS KAKENHI (grant number: 17K10027 and 16K09940).

Competing interests: The authors have declared that no competing interests exist.

Keywords: Antibiotics; Drugs Resistance; Carbapenem; Beta-lactams; Quinolones; Enterobacteriaceae.

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#Evolution of #hypervirulence in #carbapenem-resistant #Klebsiella pneumoniae in #China: a multicentre, molecular epidemiological analysis (J Antimicrob Chemother., abstract)

[Source: Journal of Antimicrobial Chemotherapy, full page: (LINK). Abstract, edited.]

Evolution of hypervirulence in carbapenem-resistant Klebsiella pneumoniae in China: a multicentre, molecular epidemiological analysis

Yawei Zhang, Longyang Jin, Pengwen Ouyang, Qi Wang, Ruobing Wang, Juan Wang, Hua Gao, Xiaojuan Wang, Hui Wang on behalf of the China Carbapenem-Resistant Enterobacteriaceae (CRE) Network

Journal of Antimicrobial Chemotherapy, dkz446, https://doi.org/10.1093/jac/dkz446

Published: 12 November 2019

 

Abstract

Objectives

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) have been increasingly reported in China. Here, a multicentre, longitudinal surveillance study on CR-hvKP is described.

Methods

We retrospectively investigated carbapenem-resistant K. pneumoniae (CRKP) in 56 centres across China during 2015–17 and screened the virulence genes (iucA, iroN, rmpA and rmpA2) for the presence of virulence plasmids. Hypermucoviscosity, serum killing and Galleria mellonella lethality experiments were conducted to identify CR-hvKP among strains with all four virulence genes. Capsule typing, fitness and plasmid features of CR-hvKP were also investigated.

Results

A total of 1052 CRKP were collected. Among these, 34.2% (360/1052) carried virulence genes and 72 of them had all four of the virulence genes tested. Fifty-five (76.4%) were considered to be CR-hvKP using the G. mellonella infection model, with KPC-2-producing K64-ST11 being the most common type (80%, 44/55). Prevalence of CR-hvKP differed greatly between regions, with the highest in Henan (25.4%, 17/67) and Shandong (25.8%, 25/97). A significant increase in CR-hvKP among KPC-2-producing ST11 strains was observed, from 2.1% (3/141) in 2015 to 7.0% (23/329) in 2017 (P = 0.045). Alarmingly, compared with classic CRKP, no difference in growth was found among CR-hvKP (P = 0.7028), suggesting a potential risk for dissemination. The hybrid virulence and resistance-encoding plasmid evolved from pLVPK and the resistance plasmid harbouring blaKPC-2, indicating evolution existed between the hypervirulence and hyper-resistance plasmid.

Conclusions

CR-hvKP were more frequently detected than previously assumed, especially among KPC-2-producing ST11. Dissemination of hypervirulence could be extremely rapid due to limited fitness cost. Also, the evolution of resistance genes into hypervirulence plasmids was identified, presenting significant challenges for public health and infection control.

Issue Section: ORIGINAL RESEARCH

© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Antibiotics; Drugs Resistance; Carbapenem; Klebsiella pneumoniae; Plasmids; China.

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From #farm to #fork: identical #clones and Tn6674-like elements in #linezolid-resistant #Enterococcus faecalis from #food-producing #animals and #retail meat (J Antimicrob Chemother., abstract)

[Source: Journal of Antimicrobial Chemotherapy, full page: (LINK). Abstract, edited.]

From farm to fork: identical clones and Tn6674-like elements in linezolid-resistant Enterococcus faecalis from food-producing animals and retail meat

Houyem Elghaieb, Ana P Tedim, Mohamed S Abbassi, Carla Novais, Bárbara Duarte, Abdennaceur Hassen, Luísa Peixe, Ana R Freitas

Journal of Antimicrobial Chemotherapy, dkz419, https://doi.org/10.1093/jac/dkz419

Published: 11 October 2019

 

Abstract

Objectives

Increasing numbers of linezolid-resistant Enterococcus carrying optrA are being reported across different niches worldwide. We aimed to characterize the first optrA-carrying Enterococcus faecalis obtained from food-producing animals and retail meat samples in Tunisia.

Methods

Seven optrA-carrying E. faecalis obtained from chicken faeces (n = 3, August 2017) and retail chicken meat (n = 4, August 2017) in Tunisia were analysed. Antimicrobial susceptibility was determined by disc diffusion, broth microdilution and Etest against 13 antibiotics, linezolid and tedizolid, respectively (EUCAST/CLSI). optrA stability (∼600 bacterial generations), transfer (filter mating) and location (S1-PFGE/hybridization) were characterized. WGS (Illumina-HiSeq) was done for four representatives that were analysed through in silico and genomic mapping tools.

Results

Four MDR clones carrying different virulence genes were identified in chicken faeces (ST476) and retail meat (the same ST476 clone plus ST21 and ST859) samples. MICs of linezolid and tedizolid were stably maintained at 8 and 1–2 mg/L, respectively. optrA was located in the same transferable chromosomal Tn6674-like element in ST476 and ST21 clones, similar to isolates from pigs in Malaysia and humans in China. ST859 carried a non-conjugative plasmid of ∼40 kb with an impB-fexA-optrA segment, similar to plasmids from pigs and humans in China.

Conclusions

The same chromosomal and transferable Tn6674-like element was identified in different E. faecalis clones from humans and animals. The finding of retail meat contaminated with the same linezolid-resistant E. faecalis strain obtained from a food-producing animal highlights the potential role of the food chain in the worrisome dissemination of optrA that can be stably maintained without selective pressure over generations.

Topic: antibiotics – enterococcus – plasmids – diffusion – chickens – china – chromosomes – clone cells – electrophoresis, gel, pulsed-field – enterococcus faecalis – feces – food – food chain – genes – genome – malaysia – meat – suidae – tunisia – virulence – linezolid – antimicrobial susceptibility – transfer technique – filters – mating – tedizolid – malnutrition-inflammation-cachexia syndrome – whole genome sequencing

Issue Section: ORIGINAL RESEARCH

© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Antibiotics; Drugs Resistance; Linezolid; Enterococci; Pigs; Poultry; Food Safety; Plasmids.

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#Plasmid #Dissemination and #Selection of a #MDR #Klebsiella pneumoniae Strain during #Transplant-Associated #Antibiotic #Therapy (mBio, abstract)

[Source: mBio, full page: (LINK). Abstract, edited.]

Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy

Sean Conlan, Anna F. Lau, Clay Deming, Christine D. Spalding, ShihQueen Lee-Lin, Pamela J. Thomas, Morgan Park, John P. Dekker, Karen M. Frank, Tara N. Palmore, Julia A. Segre

Robert A. Bonomo, Editor

DOI: 10.1128/mBio.00652-19

 

ABSTRACT

Antibiotics, which are used both to prevent and to treat infections, are a mainstay therapy for lifesaving procedures such as transplantation. For this reason, and many others, increased antibiotic resistance among human-associated pathogens, such as the carbapenem-resistant Enterobacteriaceae species, is of grave concern. In this study, we report on a hematopoietic stem cell transplant recipient in whom cultures detected the emergence of carbapenem resistance and spread across five strains of bacteria that persisted for over a year. Carbapenem resistance in Citrobacter freundii, Enterobacter cloacae, Klebsiella aerogenes, and Klebsiella pneumoniae was linked to a pair of plasmids, each carrying the Klebsiella pneumoniae carbapenemase gene (blaKPC). Surveillance cultures identified a carbapenem-susceptible strain of Citrobacter freundii that may have become resistant through horizontal gene transfer of these plasmids. Selection of a multidrug-resistant Klebsiella pneumoniae strain was also detected following combination antibiotic therapy. Here we report a plasmid carrying the blaKPC gene with broad host range that poses the additional threat of spreading to endogenous members of the human gut microbiome.

 

IMPORTANCE

Antibiotic-resistant bacteria are a serious threat to medically fragile patient populations. The spread of antibiotic resistance through plasmid-mediated mechanisms is of grave concern as it can lead to the conversion of endogenous patient-associated strains to difficult-to-treat pathogens.

Keywords: Antibiotics; Drugs Resistance; Klebsiella pneumoniae; Plasmids.

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A novel #plasmid-encoded #mcr-4.3 gene in a #colistin-resistant #Acinetobacter baumannii clinical strain (J Antimicrob Chemother., abstract)

[Source: Journal of Antimicrobial Chemotherapy, full page: (LINK). Abstract, edited.]

A novel plasmid-encoded mcr-4.3 gene in a colistin-resistant Acinetobacter baumannii clinical strain

Natacha Martins-Sorenson, Erik Snesrud, Danilo Elias Xavier, Luciana Camila Cacci, Anthony T Iavarone, Patrick McGann, Lee W Riley, Beatriz Meurer Moreira

Journal of Antimicrobial Chemotherapy, dkz413, https://doi.org/10.1093/jac/dkz413

Published: 03 October 2019

 

Abstract

Objectives

To identify the molecular mechanism of colistin resistance in an MDR Acinetobacter baumannii clinical strain isolated in 2008 from a meningitis case in Brazil.

Methods

Long- and short-read WGS was used to identify colistin resistance genes in A. baumannii strain 597A with a colistin MIC of 64 mg/L. MS was used to analyse lipid A content. mcr was cloned into pET-26b (+) and transformed into Escherichia coli BL21(λDE3)pLysS for analysis.

Results

A novel plasmid (pAb-MCR4.3) harbouring mcr-4.3 within a Tn3-like transposon was identified. The A. baumannii 597A lipid A MS spectra showed a main molecular ion peak at m/z = 2034, which indicated the addition of phosphoethanolamine to the lipid A structure. E. coli BL21 transformed with pET-26b-mcr-4.3 gained colistin resistance with a colistin MIC of 8 mg/L.

Conclusions

Colistin resistance in A. baumannii 597A was correlated with the presence of a novel plasmid-encoded mcr-4.3 gene.

Issue Section: ORIGINAL RESEARCH

© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Antibiotics; Drugs Resistance; MCR4; Colistin; Acinetobacter baumannii; Brazil.

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