Dynamics of #resistance #plasmids in #ESBL-producing #Enterobacteriaceae during post-infection #colonization (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Dynamics of resistance plasmids in extended spectrum β-lactamase-producing Enterobacteriaceae during post-infection colonization

Alma Brolund, Fredrika Rajer, Christian G Giske, Öjar Melefors, Emilia Titelman, Linus Sandegren

DOI: 10.1128/AAC.02201-18



Extended spectrum β-lactamase-producing Enterobacteriaceae (EPE) are a major cause of bloodstream infections and the colonization rate of EPE in the gut microbiota of individuals lacking prior hospitalization or comorbidities is increasing. In this study we performed an in-depth investigation of the temporal dynamics of EPE and their plasmids during one year by collecting fecal samples from three patients initially seeking medical care for urinary tract infections. In two of the patients the same strain that caused the UTI was found at all consecutive samplings from the gut microbiota and no other EPEs were detected, while in the third patient the UTI strain was only found in the initial UTI sample. Instead, this patient presented a complex situation where a mixed microbiota of different EPE strain types, including three different E. coli ST131 variants, as well as different bacterial species was identified over the course of the study. Different plasmid dynamics were displayed in each of the patients including spread of plasmids between different strain types over time, transposition of blaCTX-M-15 from the chromosome to a plasmid followed by subsequent loss through homologous recombination. Small cryptic plasmids were found in all isolates from all patients and they appear to move frequently between different strains in the microbiota. In conclusion, we could demonstrate an extensive variation of EPE strain types, plasmid composition, rearrangements and horizontal gene transfer of genetic material illustrating the high dynamics nature and interactive environment of the gut microbiota during post UTI carriage.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Antibiotics; Drugs Resistance; Beta-lactams; E. Coli; Enterobacteriaceae; Bacteremia.



Conjugal Transfer, #WGS, and #Plasmid Analysis of Four #mcr1–bearing Isolates from #US Patients (Antimicrob Agents Chemother., asbtract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Conjugal Transfer, Whole Genome Sequencing, and Plasmid Analysis of Four mcr-1–bearing Isolates from U.S. Patients

Wenming Zhu, Adrian Lawsin, Rebecca L. Lindsey, Dhwani Batra, Kristen Knipe, Brian B. Yoo, K. Allison Perry, Lori A. Rowe, David Lonsway, Maroya S. Waters, J. Kamile Rasheed, Alison Laufer Halpin

DOI: 10.1128/AAC.02417-18



Four Enterobacteriaceae clinical isolates bearing mcr-1 gene-harboring plasmids were characterized. All isolates demonstrated the ability to transfer colistin resistance to E. coli;plasmids were stable in conjugants after multiple passages on non–selective media. mcr-1 was located on an IncX4 (n=3) or IncN (n=1) plasmid. The IncN plasmid harbored 13 additional antimicrobial resistance genes. Results indicate the mcr-1-bearing plasmids in this study are highly transferable in vitro and stable in the recipients.

This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

Keywords: Antibiotics; Drugs Resistance; USA; E. Coli; Enterobacteriaceae; Colistin; MCR1.


Updated #Prevalence of #mcr-like Genes among #Escherichia coli and #Klebsiella pneumoniae in SENTRY Program and Characterization of mcr-1.11 Variant (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Updated Prevalence of mcr-like Genes among Escherichia coli and Klebsiella pneumoniae in SENTRY Program and Characterization of mcr-1.11 Variant

Lalitagauri M. Deshpande, Cory Hubler, Andrew P. Davis, Mariana Castanheira

DOI: 10.1128/AAC.02450-18



Increased prevalence of infections caused by Gram-negative pathogens that are multidrug resistant has prompted the reconsideration of polymyxins as therapeutic options.…

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Antibiotics; Drugs Resistance; Polymyxins; MCR1.


Molecular characterisation of the #NDM-1-encoding #plasmid p2189-NDM in an #Escherichia coli ST410 clinical isolate from #Ghana (PLoS One, abstract)

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


Molecular characterisation of the NDM-1-encoding plasmid p2189-NDM in an Escherichia coli ST410 clinical isolate from Ghana

Alafate Ayibieke, Wakana Sato, Samiratu Mahazu, Isaac Prah, John Addow-Thompson, Mitsuko Ohashi, Toshihiko Suzuki, Shiroh Iwanaga, Anthony Ablordey, Ryoichi Saito

Published: December 21, 2018 / DOI: https://doi.org/10.1371/journal.pone.0209623



Global dissemination of New Delhi metallo-β-lactamase (NDM)-producing bacteria has become a major health threat. However, there are few reports regarding the identification and characterisation of NDM-producing bacteria from West Africa, including Ghana. An Escherichia coli strain with resistance to meropenem was isolated from the Tamale Teaching Hospital in Ghana. Its identification and determination of antibiotic susceptibility profile were carried out using commercial systems. The antibiotic resistance mechanism was analysed by phenotypic detection kits, PCR, and DNA sequencing. Conjugation experiments, S1 nuclease pulsed field gel electrophoresis, and Southern blotting were performed. Finally, the NDM-1-harbouring plasmid was characterised using next-generation sequencing and phylogenetic analysis. The meropenem-resistant Escherichia coli strain EC2189 harboured blaNDM-1 and belonged to sequence type 410. blaNDM-1 was located on the IncHI type transferrable plasmid p2189-NDM (248,807 bp long), which co-carried multiple resistance genes, such as blaCTX-M-15, aadA1, aac(6′)-Ib, sul3, dfrA12, and cmlA1. p2189-NDM phylogenetically differed from previously identified blaNDM-1-positive IncHI type plasmids. A truncated Tn125 containing blaNDM-1 was bracketed by an ISSm-1-like insertion sequence upstream and by a site-specific integrase downstream. To the best of our knowledge, we have, for the first time identified and molecularly characterised an NDM-1-producing Enterobacteriaceae strain in Ghana with blaNDM-1 that had a novel genetic structure. Our findings indicate a possibility of NDM-1 dissemination in Ghana and underscore the need for constant monitoring of carbapenemase-producing bacteria.


Citation: Ayibieke A, Sato W, Mahazu S, Prah I, Addow-Thompson J, Ohashi M, et al. (2018) Molecular characterisation of the NDM-1-encoding plasmid p2189-NDM in an Escherichia coli ST410 clinical isolate from Ghana. PLoS ONE 13(12): e0209623. https://doi.org/10.1371/journal.pone.0209623

Editor: Yung-Fu Chang, Cornell University, UNITED STATES

Received: September 26, 2018; Accepted: December 7, 2018; Published: December 21, 2018

Copyright: © 2018 Ayibieke 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 and its Supporting Information files.

Funding: This study was supported by the Japan Agency for Medical Research and Development (AMED, URL: http://www.amed.go.jp/en/) under Grant Number 17fm0108010h0003 (MO, TS, SI, RS). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

Keywords: Antibiotics; Drugs resistance; NMD1; Carbapene; Ghana.


Acquisition and Loss of #CTX-M-Producing and Non-Producing #Escherichia coli in the Fecal #Microbiome of #Travelers to South #Asia (mBio, abstract)

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

Acquisition and Loss of CTX-M-Producing and Non-Producing Escherichia coli in the Fecal Microbiome of Travelers to South Asia

Edward R. Bevan, Alan McNally, Christopher M. Thomas, Laura J. V. Piddock, Peter M. Hawkey

George A. Jacoby, Editor

DOI: 10.1128/mBio.02408-18



Over 80% of travelers from the United Kingdom to the Indian subcontinent acquire CTX-M-producing Escherichia coli (CTX-M-EC), but the mechanism of CTX-M-EC acquisition is poorly understood. We aimed to investigate the dynamics of CTX-M-EC acquisition in healthy travelers and how this relates to populations of non-CTX-M-EC in the fecal microbiome. This is a prospective observational study of healthy volunteers traveling from the United Kingdom to South Asia. Fecal samples were collected pre- and post-travel at several time points up to 12 months post-travel. A toothpicking experiment was used to determine the proportion of cephalosporin-sensitive E. coli in fecal samples containing CTX-M-EC. MLST and SNP type of pre-travel and post-travel E. coli were deduced by WGS. CTX-M-EC was acquired by 89% (16/18) of volunteers. Polyclonal acquisition of CTX-M-EC was seen in 8/15 volunteers (all had >3 STs across post-travel samples), suggesting multiple acquisition events. Indistinguishable CTX-M-EC clones (zero SNPs apart) are detectable in serial fecal samples up to 7 months after travel, indicating stable maintenance in the fecal microbiome on return to the United Kingdom in the absence of selective pressure. CTX-M-EC-containing samples were often co-colonized with novel, non-CTX-M strains after travel, indicating that acquisition of non-CTX-M-EC occurs alongside CTX-M-EC. The same pre-travel non-CTX-M strains (<10 SNPs apart) were found in post-travel fecal samples after CTX-M-EC had been lost, suggesting return of the fecal microbiome to the pre-travel state and long-term persistence of minority strains in travelers who acquire CTX-M-EC.



Escherichia coli strains which produce CTX-M extended-spectrum beta-lactamases are endemic as colonizers of humans and in the environment in South Asia. This study demonstrates that acquisition of CTX-M-producing E. coli (CTX-M-EC) in travelers from the United Kingdom to South Asia is polyclonal, which is likely due to multiple acquisition events from contaminated food and drinking water during travel. CTX-M-EC frequently persists in the fecal microbiome for at least 1 year after acquisition, often alongside newly acquired non-CTX-M E. coli strains. In travelers who acquire CTX-M-EC, pre-travel non-CTX-M E. coli remains as a minority population in the gut until the CTX-M-EC strains are lost. The non-CTX-M strains are then reestablished as the predominant E. coli population. This study has shed light on the dynamics of CTX-M-EC acquisition, colonization, and loss after travel. Future work involving manipulation of nonvirulent resident E. coli could be used to prevent colonization with antibiotic-resistant E. coli.

Keywords: Antibiotics; Drugs Resistance; Cephalosporins; E. Coli; UK; Asian region.


Emergence of #resistance to #quinolones and #betalactam #antibiotics in enteroaggregative and enterotoxigenic #Ecoli causing #traveler’s #diarrhea (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Emergence of resistance to quinolones and β–lactam antibiotics in enteroaggregative and enterotoxigenic Escherichia coli causing traveler’s diarrhea.

Elisabet Guiral, Milene Gonçalves Quiles, Laura Muñoz, Javier Moreno-Morales, Izaskun Alejo-Cancho, Pilar Salvador, Miriam J. Alvarez-Martinez, Francesc Marco, Jordi Vila

DOI: 10.1128/AAC.01745-18



The objective of this study was to assess the antimicrobial resistance of enteroaggregative Escherichia coli (EAEC) and enterotoxigenic E. coli (ETEC) causing traveler’s diarrhea (TD) and investigate the molecular characterization of antimicrobial resistance genes to third generation cephalosporins, chepamycins and quinolones. Overall, 39 EAEC and 43 ETEC clinical isolates were studied. The susceptibility of EAEC and ETEC against ampicillin, amoxicillin-clavulanic acid, cefotaxime, imipenem, chloramphenicol, tetracycline, cotrimoxazole, nalidixic acid, ciprofloxacin, azithromycin and rifaximin was determined. All genes encoding resistant determinants were detected by PCR or PCR and DNA sequencing. The epidemiology of selected EAEC and ETEC strains was studied using MLST. The resistance to quinolones of EAEC and ETEC strains causing TD has significantly increased over the last decades, and high percentages has been found especially in patients traveling to India and sub-Saharan Africa. The ST38 and ST131 carrying the blaCTX-M-15 and blaCTX-M-27 genes, respectively, are highly prevalent among ESBL-producing EAEC and ETEC. The cephamycinase ACT-20 is described in the present study for the first time in EAEC and ETEC strains causing TD in patients who had traveled to Central America. The percentages of resistance to azithromycin in EAEC and ETEC isolates from patients to South-East Asia/India and Africa are above 25%. Meanwhile, rifaximin is still active against EAEC and ETEC with the prevalence of resistant strains not being high. In conclusion, fluoroquinolones should no longer be considered the drugs of choice for the prevention or treatment in TD for travelers traveling to India and Africa. Azithromycin and rifaximin are still a good alternative to treat TD caused by EAEC or ETEC.

Copyright © 2018 American Society for Microbiology. All Rights Reserved.

Keywords: Antibiotics; Drugs Resistance; Beta-lactams; Quinolones; Azithromycin; Rifaximin.


#Phylogenomic analysis of extraintestinal pathogenic #Ecoli ST1193, an emerging #MDR clonal group (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Phylogenomic analysis of extraintestinal pathogenic Escherichia coli ST1193, an emerging multidrug-resistant clonal group

Timothy J. Johnson, Ehud Elnekave, Elizabeth A. Miller, Jeannette Munoz-Aguayo, Cristian Flores Figueroa, Brian Johnston, Daniel W. Nielson, Catherine M. Logue, James R. Johnson

DOI: 10.1128/AAC.01913-18



The fluoroquinolone-resistant ST1193 clonal group of Escherichia coli, from the ST14 clonal complex (STc14) within phylogenetic group B2, has appeared recently as an important cause of extraintestinal disease in humans. Although this emerging lineage has been characterized to some extent using conventional methods, it has not been studied extensively at the genomic level. Here, we used whole genome sequence analysis to compare 355 ST1193 isolates with 72 isolates from other STs within STc14. Using core genome phylogeny, the ST1193 isolates formed a tightly clustered clade with many genotypic similarities, as compared to ST14 isolates. All ST1193 isolates possessed the same set of three chromosomal mutations conferring fluoroquinolone resistance, carried the fimH64 allele, and were lactose non-fermenting. Analysis revealed an evolutionary progression from K1 to K5 capsular types and acquisition of an F-type virulence plasmid followed by changes in plasmid structure congruent with genome phylogeny. In contrast, the numerous identified antimicrobial resistance genes were distributed incongruently with the underlying phylogeny, suggesting frequent gain or loss of the corresponding resistance gene cassettes despite retention of the presumed carrier plasmids. Pangenome analysis revealed gains and losses of genetic loci occurring during the transition from ST14 to ST1193, and from the K1 to K5 capsular types. Using time-scaled phylogenetic analysis, we estimated that current ST1193 clades first emerged approximately 25 years ago. Overall, ST1193 appears to be a recently emerged clone in which both stepwise and mosaic evolution likely have contributed to epidemiologic success.

Copyright © 2018 American Society for Microbiology. All Rights Reserved.

Keywords: Antibiotics; Drugs Resistance; E. Coli; Fluoroquinolones.