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

 

ABSTRACT

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.

 

IMPORTANCE

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.

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#Pig Movement and #Antimicrobial Use Drive #Transmission of #Livestock-Associated #Staphylococcus aureus CC398 (mBio, abstract)

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

Pig Movement and Antimicrobial Use Drive Transmission of Livestock-Associated Staphylococcus aureus CC398

Tara C. Smith, Meghan F. Davis, Christopher D. Heaney

DOI: 10.1128/mBio.02459-18

 

ABSTRACT

The epidemiology of methicillin-resistant Staphylococcus aureus has changed considerably over the last 3 decades, including the recognition of lineages associated with the community and with livestock exposure, in addition to nosocomial strains. A recent study by R. N. Sieber, R. L. Skov, J. Nielsen, J. Schulz, et al. (mBio 9:e02142-18, https://doi.org/10.1128/mBio.02142-18) demonstrates the importance of multisectoral cooperation at the intersection of occupational health, genomics, veterinary medicine practitioners, and farmers in order for us to better understand the epidemiology of antibiotic-resistant organisms.
The views expressed in this article do not necessarily reflect the views of the journal or of ASM.

Keywords: Antibiotics; Drugs Resistance; Pigs; Staphylococcus aureus.

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Diverse #vectors and mechanisms #spread #NDM beta-lactamases among #carbapenem resistant #Enterobacteriaceae in the Greater #Boston area (Antimicrob Agents Chemother., abstract)

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

Diverse vectors and mechanisms spread NDM beta-lactamases among carbapenem resistant Enterobacteriaceae in the Greater Boston area

Nicole Pecora, Xiaomin Zhao, Kathleen Nudel, Maria Hoffmann, Ning Li, Andrew B. Onderdonk, Deborah Yokoe, Eric Brown, Marc Allard, Lynn Bry

DOI: 10.1128/AAC.02040-18

 

ABSTRACT

New Delhi metallo-beta-lactamases (NDMs) are an uncommon but emerging cause of carbapenem resistance in the United States. Genomic factors promoting their domestic spread remain poorly characterized. A prospective genomic surveillance program among Boston-area hospitals identified multiple new occurrences of NDM carrying strains of E. coli and E. cloacaecomplex in inpatient and outpatient settings, representing the first occurrences of NDM-mediated resistance since initiating genomic surveillance in 2011. Cases included domestic patients with no international exposures. PacBio sequencing of isolates identified strain characteristics, resistance genes, and the complement of mobile vectors mediating spread. Analyses revealed a common 3114-bp region containing the blaNDM gene, with carriage of this conserved region among unique strains by diverse transposon and plasmid backbones. Functional studies revealed broad capacity for blaNDM transmission by conjugation, transposition, and complex inter-plasmid recombination events. NDMs represent a rapidly spreading form of drug resistance that can occur in inpatient and outpatient settings and in patients without international exposures. In contrast to Tn4401-based spread of Klebsiella pneumoniae carbapenemases (KPCs), diverse transposable elements mobilize NDM enzymes, commonly with other resistance genes, enabling naïve strains to acquire multi- and extensively-drug resistance profiles with single transposition or plasmid conjugation events. Genomic surveillance provides effective means to rapidly identify these gene-level drivers of resistance and mobilization, to inform clinical decisions to prevent further spread.

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

Keywords: Antibiotics; Drugs Resistance; Carbapenem; NDM1; USA; Enterobacteriaceae.

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#Spreading #patterns of #NDM-producing #Enterobacteriaceae in clinical and #environmental settings in #Yangon, #Myanmar (Antimicrob Agents Chemother., abstract)

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

Spreading patterns of NDM-producing Enterobacteriaceae in clinical and environmental settings in Yangon, Myanmar

Yo Sugawara, Yukihiro Akeda, Hideharu Hagiya, Noriko Sakamoto, Dan Takeuchi, Rathina Kumar Shanmugakani, Daisuke Motooka, Isao Nishi, Khwar Nyo Zin, Mya Mya Aye, Thuzar Myint,Kazunori Tomono, Shigeyuki Hamada

DOI: 10.1128/AAC.01924-18

 

ABSTRACT

The spread of carbapenemase-producing Enterobacteriaceae (CPE) has become a global concern, contributing to widespread carbapenem resistance. However, the specific dissemination patterns of carbapenemase genes have not been intensively investigated in developing countries, including Myanmar, where NDM-type carbapenemases are spreading in clinical settings. In the present study, we phenotypically and genetically characterized 91 CPE isolates obtained from clinical (n = 77) and environmental (n = 14) samples in Yangon, Myanmar. We determined the dissemination of plasmids harboring genes encoding NDM-1 and its variants using whole-genome sequencing and plasmid analysis. IncFII plasmids harboring blaNDM-5 and IncX3 plasmids harboring blaNDM-4 or blaNDM-7 were the most prevalent plasmid types identified among the isolates. The IncFII plasmids were predominantly carried by clinical isolates of Escherichia coli, and their clonal expansion was observed within the same ward of a hospital. By contrast, the IncX3 plasmids were found in phylogenetically divergent isolates from clinical and environmental samples classified into nine species, suggesting the widespread dissemination of plasmids via horizontal transfer. Half of the environmental isolates were found to possess IncX3 plasmids, and this type of plasmid was confirmed to transfer more effectively to recipient organisms at a relatively low temperature (25°C) compared to the IncFII plasmid. Moreover, various other plasmid types were identified harboring blaNDM-1, including IncFIB, IncFII, IncL/M, and IncA/C2, among clinical isolates of Klebsiella pneumoniae or Enterobacter cloacae complex. Overall, our results highlight three distinct patterns of the dissemination of blaNDM-harboring plasmids among CPE isolates in Myanmar, contributing to gaining a better understanding of their molecular epidemiology and dissemination in an endemic setting.

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

Keywords: Antibiotics; Drugs Resistance; Carbapenem; Myanmar; Enterobacteriaceae.

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#Klebsiella pneumoniae causing #UTIs in companion #animals and #humans: population structure, antimicrobial resistance and virulence genes (J Antimicrob Chemother., abstract)

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

Klebsiella pneumoniae causing urinary tract infections in companion animals and humans: population structure, antimicrobial resistance and virulence genes

Cátia Marques, Juliana Menezes, Adriana Belas, Catarina Aboim, Patrícia Cavaco-Silva, Graça Trigueiro, Luís Telo Gama, Constança Pomba

Journal of Antimicrobial Chemotherapy, dky499, https://doi.org/10.1093/jac/dky499

Published: 10 December 2018

 

Abstract

Objectives

To characterize the population structure, antimicrobial resistance and virulence genes of Klebsiella spp. isolated from dogs, cats and humans with urinary tract infections (UTIs).

Methods

Klebsiella spp. from companion animals (n = 27) and humans (n = 77) with UTI were tested by the disc diffusion method against 29 antimicrobials. Resistant/intermediate isolates were tested by PCR for 16 resistance genes. Seven virulence genes were screened for by PCR. All Klebsiella pneumoniae from companion animals and third-generation cephalosporin (3GC)-resistant isolates from humans were typed by MLST. All Klebsiella spp. were compared after PFGE XbaI macro-restriction using Dice/UPGMA with 1.5% tolerance.

Results

blaCTX-M-15 was detected in >80% of 3GC-resistant strains. K. pneumoniaehigh-risk clonal lineage ST15 predominated in companion animal isolates (60%, n = 15/25). Most companion animal ST15 K. pneumoniae belonged to two PFGE clusters (C4, C5) that also included human strains. Companion animal and human ST15-CTX-M-15 K. pneumoniae shared a fimH-1/mrkD/entB/ycfM/kfu virulence profile, with a few (n = 4) also harbouring the yersiniabactin siderophore-encoding genes. The hospital-adapted ST11 K. pneumoniae clonal lineage was detected in a cat (n = 1) and a human (n = 1); both were MDR, had 81.1% Dice/UPGMA similarity and shared several virulence and resistance genes. Two 3GC-resistant ST348 strains with 86.7% Dice/UPGMA similarity were isolated from a cat and a human.

Conclusions

Companion animals with UTI become infected with high-risk K. pneumoniaeclonal lineages harbouring resistance and virulence genes similar to those detected in strains from humans. The ST15-CTX-M-15 K. pneumoniae clonal lineage was disseminated in companion animals with UTI. Caution must be applied by companion animal caretakers to avoid the spread of K. pneumoniaehigh-risk clonal lineages.

Issue Section: ORIGINAL RESEARCH

© The Author(s) 2018. 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; Cephalosporins; Klebsiella pneumoniae; Cats; Human.

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The #phylogeography and incidence of #MDR #typhoid fever in sub-Saharan #Africa (Nat Commun., abstract)

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

Article | OPEN | Published: 30 November 2018

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

Se Eun Park, Duy Thanh Pham, […] Stephen Baker

Nature Communications, volume 9, Article number: 5094 (2018)

 

Abstract

There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) SalmonellaTyphi in sub-Saharan Africa. Here we present a phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolated between 2008-2015 in 11 sub-Saharan African countries, in context of the 2,057 global S. Typhi genomic framework. Despite the broad genetic diversity, the majority of organisms (225/249; 90%) belong to only three genotypes, 4.3.1 (H58) (99/249; 40%), 3.1.1 (97/249; 39%), and 2.3.2 (29/249; 12%). Genotypes 4.3.1 and 3.1.1 are confined within East and West Africa, respectively. MDR phenotype is found in over 50% of organisms restricted within these dominant genotypes. High incidences of MDR S. Typhi are calculated in locations with a high burden of typhoid, specifically in children aged <15 years. Antimicrobial stewardship, MDR surveillance, and the introduction of typhoid conjugate vaccines will be critical for the control of MDR typhoid in Africa.

Keywords: Antibiotics; Drugs Resistance; Salmonella typhi; Typhoid fever; Africa Region.

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#Antimicrobial-resistant #pathogens in #Canadian #ICUs: results of the #CANWARD 2007 to 2016 study (J Antimicrob Chemother., abstract)

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

Antimicrobial-resistant pathogens in Canadian ICUs: results of the CANWARD 2007 to 2016 study

Andrew J Denisuik, Lauren A Garbutt, Alyssa R Golden, Heather J Adam, Melanie Baxter, Kimberly A Nichol, Philippe Lagacé-Wiens, Andrew J Walkty, James A Karlowsky, Daryl J Hoban, Michael R Mulvey, George G Zhanel

Journal of Antimicrobial Chemotherapy, dky477, https://doi.org/10.1093/jac/dky477

Published: 29 November 2018

 

Abstract

Objectives

To describe the microbiology and antimicrobial resistance patterns of cultured samples acquired from Canadian ICUs.

Methods

From 2007 to 2016, tertiary care centres from across Canada submitted 42 938 bacterial/fungal isolates as part of the CANWARD surveillance study. Of these, 8130 (18.9%) were from patients on ICUs. Susceptibility testing guidelines and MIC interpretive criteria were defined by CLSI.

Results

Of the 8130 pathogens collected in this study, 58.2%, 36.3%, 3.1% and 2.4% were from respiratory, blood, wound and urine specimens, respectively. The top five organisms collected from Canadian ICUs accounted for 55.4% of all isolates and included Staphylococcus aureus (21.5%), Pseudomonas aeruginosa (10.6%), Escherichia coli (10.4%), Streptococcus pneumoniae (6.5%) and Klebsiella pneumoniae (6.4%). MRSA accounted for 20.7% of S. aureus collected, with community-associated (CA) MRSA genotypes increasing in prevalence over time (P < 0.001). The highest susceptibility rates among MRSA were 100% for vancomycin, 100% for ceftobiprole, 100% for linezolid, 99.7% for ceftaroline, 99.7% for daptomycin and 99.7% for tigecycline. The highest susceptibility rates among E. coli were 100% for tigecycline, 99.9% for meropenem, 99.7% for colistin and 94.2% for piperacillin/tazobactam. MDR was identified in 26.3% of E. coli isolates, with 10.1% producing an ESBL. The highest susceptibility rates among P. aeruginosa were 97.5% for ceftolozane/tazobactam, 96.1% for amikacin, 94.7% for colistin and 93.3% for tobramycin.

Conclusions

The most active agents against Gram-negative bacilli were the carbapenems, tigecycline and piperacillin/tazobactam. Against Gram-positive cocci, the most active agents were vancomycin, daptomycin and linezolid. The prevalence of CA-MRSA genotypes and ESBL-producing E. coli collected from ICUs increased significantly over time.

Topic: pseudomonas aeruginosa – vancomycin – staphylococcus aureus – amikacin – carbapenem – colistin – canada – daptomycin – drug resistance, microbial – genotype – gram-positive cocci – klebsiella pneumoniae – streptococcus pneumoniae – guidelines – microbiology – tobramycin – meropenem – piperacillin/tazobactam – pathogenic  organism – linezolid – antimicrobials – escherichia coli – tazobactam – surveillance, medical – methicillin-resistant staphylococcus aureus – tigecycline – extended-spectrum beta lactamases – ceftobiprole – community – gram-negative bacillus – ceftaroline – ceftolozane – urine specimens

Issue Section: ORIGINAL RESEARCH

© The Author(s) 2018. 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; Canada; Nosocomial Outbreaks; ICUs.

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