High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei

Monahan, Leigh G.; DeMaere, Matthew Z.; Cummins, Max L.; Djordjevic, Steven P.; Chowdhury, Piklu Roy; Darling, Aaron E.

doi:10.1186/s13099-019-0288-7

Cited by 26 publications

(22 citation statements)

References 25 publications

(35 reference statements)

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“…Isolate E. cloacae C15117, used in this study for the make-up of the mock community, was recently found to be most closely related to the Enterobacter hormaechei phylogenomic group C type strain DSM 16687 and therefore re-identi ed as Enterobacter hormaechei subsp. oharae 90 . For this reason, taxonomic assignment by MetaPhlAn2 attributed the reads to E. cloacae instead.…”

Section: Resultsmentioning

confidence: 99%

Community composition and development of the post-weaning piglet gut microbiome

Gaio

DeMaere

Anantanawat

et al. 2020

Preprint

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BackgroundEarly weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. Studies have previously investigated the effects of probiotics as alternatives to antibiotic treatment for the prevention of post-weaning diarrhea. In order to describe the post-weaning gut microbiota, and the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we processed over 800 faecal time-series samples from 126 piglets and 42 sows, generating over 8Tbp of metagenomic shotgun sequence data. Here we describe the animal trial procedures, the generation of our metagenomic dataset and the analysis of the microbial community composition using a phylogenetic framework.ResultsFactors such as age, litter effects, and breed, by significantly correlating with gut microbial community shifts, can be major confounding factors in the assessment of treatment effects. Intramuscular antibiotic treatment and probiotic treatments were found to correlate with alpha and beta diversity, as well as with a transient establishment of Mollicutes and Lactobacillales, respectively. We found the abundance of certain taxa to correlate with weight gain.ConclusionsOur findings demonstrate that breed, litter, and age, are important contributors to variation in the community composition, and that treatment effects of the antibiotic and probiotic treatments were subtle, while host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The current study shows, by means of a phylogenetic diversity framework, that the post-weaning pig gut microbiome appears to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life.

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Section: Resultsmentioning

confidence: 99%

Community composition and development of the post-weaning piglet gut microbiome

Gaio

DeMaere

Anantanawat

et al. 2020

Preprint

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“…2 As one of the most frequently isolated bacteria of ECC, E. hormaechei has become an important pathogen causing human clinical infection. 30,31 Some reports exhibited that an E. hormaechei outbreak strain ever occurred nationwide in the Netherlands, 32 in addition, this bacterium also appeared in several outbreaks of sepsis, most notably in the United States and Brazil. 33 At present, it is recognized as capable of persisting in the hospital environment and developing resistance to multiple antibiotics.…”

Section: Discussionmentioning

confidence: 99%

Carbapenem-Resistant Enterobacter hormaechei ST1103 with IMP-26 Carbapenemase and ESBL Gene blaSHV-178

Gou¹,

Liu²,

Guo³

et al. 2020

IDR

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To investigate the occurrence and genetic characteristics of the bla IMP-26-positive plasmid from a multidrug-resistant clinical isolate, Enterobacter hormaechei L51. Methods: Species identification was determined by MALDI-TOF MS and Sanger sequencing. Antimicrobial susceptibility testing was performed by the agar dilution and broth microdilution. Whole-genome sequencing was conducted using Illumina HiSeq 4000-PE150 and PacBio Sequel platforms, and the genome was annotated by the RAST annotation server. The ANI analysis of genomes was performed using OAT. Phylogenetic reconstruction and analyses were performed using the Harvest suite based on the core-genome SNPs of 61 publicly available E. hormaechei genomes. Results: The E. hormaechei L51 genome consists of a 5,018,729 bp circular chromosome and a 343,918 bp conjugative IncHI2/2A plasmid pEHZJ1 encoding bla IMP-26 which surrounding genetic context was intI1-bla IMP-26-ltrA-qacEΔ1-sul1. A new sequence type (ST1103) was assigned for the isolate L51 which was resistant to cephalosporins, carbapenems, but sensitive to piperacillin-tazobactam, amikacin, tigecycline, trimethoprimsulfamethoxazole and colistin. Phylogenetic analysis demonstrated that E. hormaechei L51 belonged to the same subspecies as the reference strain E. hormaechei SCEH020042, however 18,248 divergent SNP were identified. Resistance genes in pEHZJ1 including aac (3)-IIc, aac(6ʹ)-IIc, bla SHV-178 , bla DHA-1 , bla TEM-1 , bla IMP-26 , ereA2, catII, fosA5, qnrB4, tet(D), sul1 and dfrA19. Conclusion: In our study, we identified a conjugative IncHI2/2A plasmid carrying bla IMP-26 and bla SHV-178 in E. hormaechei ST1103, a novel multidrug-resistant strain isolated from China, and describe the underlying resistance mechanisms of the strain and detailed genetic context of mega plasmid pEHZJ1.

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“…In Australia, IncHI2 plasmids carrying a diverse range of antimicrobial resistance genes have been found in MDR E. coli (Dolejska et al, 2016;Saputra et al, 2017), Salmonella enterica serovar Typhimurium (Cain et al, 2010;Cain and Hall, 2012;Billman-Jacobe et al, 2018), Enterobacter cloacae (Sidjabat et al, 2015), and Enterobacter hormaechei susbp. Oharae (Monahan et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia

Wyrsch

Reid

DeMaere

et al. 2019

Front. Sustain. Food Syst.

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IncHI2 ST3 plasmids are known carriers of multiple antimicrobial resistance genes. Complete plasmid sequences from multiple drug resistant Escherichia coli circulating in Australian swine is however limited. Here we sequenced two related IncHI2 ST3 plasmids, pSDE-SvHI2, and pSDC-F2_12BHI2, from phylogenetically unrelated multiple-drug resistant Escherichia coli strains SvETEC (CC23:O157:H19) and F2_12B (ST93:O7:H4) from geographically disparate pig production operations in New South Wales, Australia. Unicycler was used to co-assemble short read (Illumina) and long read (PacBio SMRT) nucleotide sequence data. The plasmids encoded three drug-resistance loci, two of which carried class 1 integrons. One integron, hosting drfA12-orfF-aadA2, was within a hybrid Tn1721/Tn21, with the second residing within a copper/silver resistance transposon, comprising part of an atypical sul3-associated structure. The third resistance locus was flanked by IS15DI and encoded neomycin resistance (neoR). An oqx-encoding transposon (quinolone resistance), similar in structure to Tn6010, was identified only in pSDC-F2_12BHI2. Both plasmids showed high sequence identity to plasmid pSTM6-275, recently described in Salmonella enterica serotype 1,4,[5],12:i:-that has risen to prominence and become endemic in Australia. IncHI2 ST3 plasmids circulating in commensal and pathogenic E. coli from Australian swine belong to a lineage of plasmids often in association with sul3 and host multiple complex antibiotic and metal resistance structures, formed in part by IS26.

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High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei

Cited by 26 publications

References 25 publications

Community composition and development of the post-weaning piglet gut microbiome

Community composition and development of the post-weaning piglet gut microbiome

<p>Carbapenem-Resistant <em>Enterobacter hormaechei</em> ST1103 with IMP-26 Carbapenemase and ESBL Gene <em>bla</em><sub>SHV-178</sub></p>

Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia

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