Origin in Acinetobacter guillouiae and Dissemination of the Aminoglycoside-Modifying Enzyme Aph(3′)-VI

ABSTRACTThe amikacin resistance geneaphA6was first detected in the nosocomial pathogenAcinetobacter baumanniiand subsequently in other genera. Analysis of 133 whole-genome sequences covering the taxonomic diversity ofAcinetobacterspp. detectedaphA6in the chromosome of 2 isolates ofA. guillouiae, which is an environmental species, 1 of 8A. parvusisolates, and 5 of 34A. baumanniiisolates. The gene was also present in 29 out of 36A. guillouiaeisolates screened by PCR, indicating that it is ancestral to this species. ThePnativepromoter foraphA6inA. guillouiaeandA. parvuswas replaced inA. baumanniibyPaphA6, which was generated by use of the insertion sequence ISAba125, which brought a −35 sequence. Study of promoter strength inEscherichia coliandA. baumanniiindicated thatPaphA6was four times more potent thanPnative. There was a good correlation between aminoglycoside MICs andaphA6transcription inA. guillouiaeisolates that remained susceptible to amikacin. The marked topology differences of the phylogenetic trees ofaphA6and of the hosts strongly support its recent direct transfer withinAcinetobacterspp. and also to evolutionarily remote bacterial genera. Concomitant expression ofaphA6must have occurred because, contrary to the donors, it can confer resistance to the new hosts. Mobilization and expression ofaphA6via composite transposons and the upstream IS-generating hybridPaphA6, followed by conjugation, seems the most plausible mechanism. This is in agreement with the observation that, in the recipients,aphA6is carried by conjugative plasmids and flanked by IS that are common inAcinetobacterspp. Our data indicate that resistance genes can also be found in susceptible environmental bacteria.IMPORTANCEWe speculated that theaphA6gene for an enzyme that confers resistance to amikacin, the most active aminoglycoside for the treatment of nosocomial infections due toAcinetobacterspp., originated in this genus before disseminating to phylogenetically distant genera pathogenic for humans. Using a combination of whole-genome sequencing of a collection ofAcinetobacterspp. covering the breadth of the known taxonomic diversity of the genus, gene cloning, detailed promoter analysis, study of heterologous gene expression, and comparative analysis of the phylogenetic trees ofaphA6and of the bacterial hosts, we found thataphA6originated inAcinetobacter guillouiae, an amikacin-susceptible environmental species. The gene conferred, upon mobilization, high-level resistance to the new hosts. This work stresses that nonpathogenic bacteria can act as reservoirs of resistance determinants, and it provides an example of the use of a genomic library to study the origin and dissemination of an antibiotic resistance gene to human pathogens.

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New Macrolide-Lincosamide-Streptogramin B Resistance Gene erm(48) on the Novel Plasmid pJW2311 in Staphylococcus xylosus

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00066-17 ◽

2017 ◽

Vol 61 (7) ◽

Cited By ~ 9

Author(s):

Juliette R. K. Wipf ◽

Matthew C. Riley ◽

Stephen A. Kania ◽

David A. Bemis ◽

Sabrina Andreis ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Resistance Gene ◽

Genome Sequencing ◽

Bovine Mastitis ◽

Cloning And Expression ◽

Whole Genome ◽

The Novel ◽

Content Type ◽

Staphylococcus Xylosus ◽

Macrolide Resistance Gene

ABSTRACT Whole-genome sequencing of Staphylococcus xylosus strain JW2311 from bovine mastitis milk identified the novel 49.3-kb macrolide-lincosamide-streptogramin B (MLSB) resistance plasmid pJW2311. It contained the macrolide resistance gene mph(C), the macrolide-streptogramin B resistance gene msr(A), and the new MLSB resistance gene erm(48) and could be transformed into Staphylococcus aureus by electroporation. Functionality of erm(48) was demonstrated by cloning and expression in S. aureus.

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Plasmid with Colistin Resistance Genemcr-1in Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains Isolated from Pig Slurry in Estonia

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00443-16 ◽

2016 ◽

Vol 60 (11) ◽

pp. 6933-6936 ◽

Cited By ~ 29

Author(s):

Age Brauer ◽

Kaidi Telling ◽

Mailis Laht ◽

Piret Kalmus ◽

Irja Lutsar ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistance Gene ◽

Antibiotic Resistance Gene ◽

Dna Transfer ◽

The Other ◽

Pig Slurry ◽

Colistin Resistance ◽

Content Type ◽

Slurry Sample

ABSTRACTA plasmid carrying the colistin resistance genemcr-1was isolated from a pig slurry sample in Estonia. The gene was present on a 33,311-bp plasmid of the IncX4 group.mcr-1is the only antibiotic resistance gene on the plasmid, with the other genes mainly coding for proteins involved in conjugative DNA transfer (taxA,taxB,taxC,trbM, and thepilXoperon). The plasmid pESTMCR was present in three phylogenetically very differentEscherichia colistrains, suggesting that it has high potential for horizontal transfer.

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Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

Journal of Clinical Microbiology ◽

10.1128/jcm.01818-15 ◽

2015 ◽

Vol 54 (3) ◽

pp. 593-612 ◽

Cited By ~ 44

Author(s):

Margaret A. Fitzpatrick ◽

Egon A. Ozer ◽

Alan R. Hauser

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Phylogenetic Trees ◽

Acinetobacter Calcoaceticus ◽

Whole Genome ◽

Strain Typing ◽

Nucleotide Polymorphisms ◽

Content Type ◽

Carbapenem Resistant ◽

Outbreak Investigations

Acinetobacter baumanniifrequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinicalAcinetobacterisolates and analyzing a carbapenem-resistantA. baumannii(CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148Acinetobacter calcoaceticus-A. baumanniicomplex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed threeAcinetobacterspecies within this collection. Four majorA. baumanniiclonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguishedA. baumanniiisolates from different clonal lineages. The band-based techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques forA. baumanniistrain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts.

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Various Sequence Types of Escherichia coli Isolates Coharboring blaNDM-5 and mcr-1 Genes from a Commercial Swine Farm in China

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02167-16 ◽

2016 ◽

Vol 61 (3) ◽

Cited By ~ 33

Author(s):

Ling-Han Kong ◽

Chang-Wei Lei ◽

Su-Zhen Ma ◽

Wei Jiang ◽

Bi-Hui Liu ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Gene ◽

Genome Sequencing ◽

Carbapenem Resistance ◽

Whole Genome ◽

Swine Farm ◽

Colistin Resistance ◽

Content Type ◽

E Coli ◽

Sequence Types

ABSTRACT Sixteen different sequence types (STs) of Escherichia coli isolates from a commercial swine farm in China were confirmed to coharbor the carbapenem resistance gene bla NDM-5 and the colistin resistance gene mcr-1. Whole-genome sequencing revealed that bla NDM-5 and mcr-1 were located on a 46-kb IncX3 plasmid and a 32-kb IncX4 plasmid, respectively. The two plasmids can transfer together with a low fitness cost, which might explain the presence of various STs of E. coli coharboring bla NDM-5 and mcr-1.

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First Report of OXA-181-Producing Escherichia coli in China and Characterization of the Isolate Using Whole-Genome Sequencing

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00442-15 ◽

2015 ◽

Vol 59 (8) ◽

pp. 5022-5025 ◽

Cited By ~ 51

Author(s):

Yanbin Liu ◽

Yu Feng ◽

Wenjing Wu ◽

Yi Xie ◽

Xiaohui Wang ◽

...

Keyword(s):

Escherichia Coli ◽

Whole Genome Sequencing ◽

Resistance Gene ◽

Genome Sequencing ◽

Chinese Patient ◽

Sequence Type ◽

Whole Genome ◽

Travel History ◽

Content Type

ABSTRACTWe report the first OXA-181-producing strain in China.blaOXA-181was found in sequence type 410 (ST410)Escherichia colistrain WCHEC14828 from a Chinese patient without recent travel history. Genome sequencing and conjugation experiments were performed.blaOXA-181was carried on a 51-kb self-transmissible IncX3 plasmid and was linked withqnrS1, a quinolone resistance gene.blaOXA-181was introduced onto the IncX3 plasmid from a ColE2-type plasmid, and IncX3 plasmids have the potential to mediate the dissemination ofblaOXA-181.

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Centre-specific bacterial pathogen typing affects infection-control decision making

Microbial Genomics ◽

10.1099/mgen.0.000612 ◽

2021 ◽

Vol 7 (8) ◽

Author(s):

Jordy P. M. Coolen ◽

Casper Jamin ◽

Paul H. M. Savelkoul ◽

John W. A. Rossen ◽

Heiman F. L. Wertheim ◽

...

Keyword(s):

Phylogenetic Trees ◽

De Novo ◽

Bacterial Pathogen ◽

Snp Analysis ◽

Whole Genome ◽

Single Nucleotide ◽

Content Type ◽

Extended Spectrum Beta Lactamase ◽

Bioinformatic Tools ◽

Control Decision

Whole-genome sequencing is becoming the de facto standard for bacterial outbreak surveillance and infection prevention. This is accompanied by a variety of bioinformatic tools and needs bioinformatics expertise for implementation. However, little is known about the concordance of reported outbreaks when using different bioinformatic workflows. In this multi-centre proficiency testing among 13 major Dutch healthcare-affiliated centres, bacterial whole-genome outbreak analysis was assessed. Centres who participated obtained two randomized bacterial datasets of Illumina sequences, a Klebsiella pneumoniae and a Vancomycin-resistant Enterococcus faecium, and were asked to apply their bioinformatic workflows. Centres reported back on antimicrobial resistance, multi-locus sequence typing (MLST), and outbreak clusters. The reported clusters were analysed using a method to compare landscapes of phylogenetic trees and calculating Kendall–Colijn distances. Furthermore, fasta files were analysed by state-of-the-art single nucleotide polymorphism (SNP) analysis to mitigate the differences introduced by each centre and determine standardized SNP cut-offs. Thirteen centres participated in this study. The reported outbreak clusters revealed discrepancies between centres, even when almost identical bioinformatic workflows were used. Due to stringent filtering, some centres failed to detect extended-spectrum beta-lactamase genes and MLST loci. Applying a standardized method to determine outbreak clusters on the reported de novo assemblies, did not result in uniformity of outbreak-cluster composition among centres.

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Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms

Microbial Genomics ◽

10.1099/mgen.0.000638 ◽

2021 ◽

Vol 7 (10) ◽

Author(s):

Sara E. Pidcock ◽

Timofey Skvortsov ◽

Fernanda G. Santos ◽

Stephen J. Courtney ◽

Karen Sui-Ting ◽

...

Keyword(s):

Type Species ◽

Phylogenetic Trees ◽

Glycosyl Hydrolase ◽

Anaerobic Bacteria ◽

Taxonomic Diversity ◽

Genomic Variation ◽

Gene Marker ◽

Phylogenetic Systematics ◽

Content Type ◽

Link Type

Butyrivibrio and Pseudobutyrivibrio dominate in anaerobic gastrointestinal microbiomes, particularly the rumen, where they play a key role in harvesting dietary energy. Within these genera, five rumen species have been classified ( Butyrivibrio fibrisolvens , Butyrivibrio hungatei , Butyrivibrio proteoclasticus , Pseudobutyrivibrio ruminis and Pseudobutyrivibrio xylanivorans ) and more recently an additional Butyrivibrio sp. group was added. Given the recent increase in available genomes, we re-investigated the phylogenetic systematics and evolution of Butyrivibrio and Pseudobutyrivibrio . Across 71 genomes, we show using 16S rDNA and 40 gene marker phylogenetic trees that the current six species designations ( P. ruminis , P. xylanivorans , B. fibrisolvens , Butyrivibrio sp., B. hungatei and B. proteclasticus) are found. However, pangenome analysis showed vast genomic variation and a high abundance of accessory genes (91.50–99.34 %), compared with core genes (0.66–8.50 %), within these six taxonomic groups, suggesting incorrectly assigned taxonomy. Subsequent pangenome accessory genomes under varying core gene cut-offs (%) and average nucleotide identity (ANI) analysis suggest the existence of 42 species within 32 genera. Pangenome analysis of those that still group within B. fibrisolvens , B. hungatei and P. ruminis , based on revised ANI phylogeny, also showed possession of very open genomes, illustrating the diversity that exists even within these groups. All strains of both Butyrivibrio and Pseudobutyrivibrio also shared a broad range of clusters of orthologous genes (COGs) (870), indicating recent evolution from a common ancestor. We also demonstrate that the carbohydrate-active enzymes (CAZymes) predominantly belong to glycosyl hydrolase (GH)2, 3, 5, 13 and 43, with numerous within family isoforms apparent, likely facilitating metabolic plasticity and resilience under dietary perturbations. This study provides a major advancement in our functional and evolutionary understanding of these important anaerobic bacteria.

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Prevalence and Genetic Analysis ofmcr-3-PositiveAeromonasSpecies from Humans, Retail Meat, and Environmental Water Samples

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00404-18 ◽

2018 ◽

Vol 62 (9) ◽

Cited By ~ 22

Author(s):

Yingbo Shen ◽

Chunyan Xu ◽

Qiaoling Sun ◽

Stefan Schwarz ◽

Yanran Ou ◽

...

Keyword(s):

Resistance Gene ◽

Aquatic Environment ◽

Genetic Relationships ◽

Screening Method ◽

Amino Acid Identity ◽

Whole Genome Sequence ◽

Whole Genome ◽

Colistin Resistance ◽

Content Type ◽

Rectal Swabs

ABSTRACTThe mobile colistin resistance genemcr-3is globally disseminated in bothEnterobacteriaceaeandAeromonasspecies, with the latter potentially serving as a reservoir for this gene. Here, we investigated the prevalence ofmcr-3in rectal swabs from humans, in food-producing animals and their products, and in the aquatic environment, and we investigated the genetic relationships between themcr-3-positive isolates. An enriched broth screening method was used to detectmcr-3in samples, and species identification of isolates from positive samples was carried out by matrix-assisted laser desorption ionization–time of flight mass spectrometry and shotgun sequencing. Allmcr-3-positive isolates were subjected to antimicrobial susceptibility testing, conjugation, and whole-genome sequencing. TenAeromonasisolates, including 2 from human rectal swabs, 1 from pork, 3 from chicken meat, and 4 from the aquatic environment, were positive formcr-3, but only 2 showed resistance to colistin. In addition to themcr-3variants identified previously (the novel variants were termedmcr-3.13tomcr-3.18), all isolates harboredmcr-3-like genes downstream of themcr-3variants. The MCR-3.13 to MCR-3.18 proteins exhibited only 89.2% to 96.1% amino acid identity to the original MCR-3 protein. Whole-genome sequence analysis indicated diversity within the genetic environments ofmcr-3-positiveAeromonasisolates and possible transmission between different sources in China and even worldwide. Close relationships betweenmcr-3-positive andmcr-3-negativeAeromonasisolates suggested thatmcr-3might be common inAeromonasspecies, which are not inherent hosts ofmcr-3but may act as an important reservoir of this mobile colistin resistance gene.

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PacBio Genome Sequences of Escherichia coli Serotype O157:H7, Diffusely Adherent E. coli, and Salmonella enterica Strains, All Carrying Plasmids with an mcr-1 Resistance Gene

Microbiology Resource Announcements ◽

10.1128/mra.01025-18 ◽

2018 ◽

Vol 7 (14) ◽

Cited By ~ 3

Author(s):

Rebecca L. Lindsey ◽

Dhwani Batra ◽

Peyton Smith ◽

Pooja N. Patel ◽

Kaitlin A. Tagg ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Gene ◽

Salmonella Enterica ◽

Whole Genome ◽

Genome Sequences ◽

Content Type ◽

E Coli ◽

Serotype O

We report here Illumina-corrected PacBio whole-genome sequences of an Escherichia coli serotype O157:H7 strain (2017C-4109), an E. coli serotype O[undetermined]:H2 strain (2017C-4173W12), and a Salmonella enterica subsp. enterica serovar Enteritidis strain (2017K-0021), all of which carried the mcr-1 resistance gene on an IncI2 or IncX4 plasmid.

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Population Dynamics of Staphylococcus aureus in Cystic Fibrosis Patients To Determine Transmission Events by Use of Whole-Genome Sequencing

Journal of Clinical Microbiology ◽

10.1128/jcm.00164-17 ◽

2017 ◽

Vol 55 (7) ◽

pp. 2143-2152 ◽

Cited By ~ 13

Author(s):

Andrea Ankrum ◽

Barry G. Hall

Keyword(s):

Cystic Fibrosis ◽

Staphylococcus Aureus ◽

Population Dynamics ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Phylogenetic Trees ◽

Hospital Environment ◽

Snp Analysis ◽

Whole Genome ◽

Content Type

ABSTRACT Strict infection control practices have been implemented for health care visits by cystic fibrosis (CF) patients in an attempt to prevent transmission of important pathogens. This study used whole-genome sequencing (WGS) to determine strain relatedness and assess population dynamics of Staphylococcus aureus isolates from a cohort of CF patients as assessed by strain relatedness. A total of 311 S. aureus isolates were collected from respiratory cultures of 115 CF patients during a 22-month study period. Whole-genome sequencing was performed, and using single nucleotide polymorphism (SNP) analysis, phylogenetic trees were assembled to determine relatedness between isolates. Methicillin-resistant Staphylococcus aureus (MRSA) phenotypes were predicted using PPFS2 and compared to the observed phenotype. The accumulation of SNPs in multiple isolates obtained over time from the same patient was examined to determine if a genomic molecular clock could be calculated. Pairs of isolates with ≤71 SNP differences were considered to be the “same” strain. All of the “same” strain isolates were either from the same patient or siblings pairs. There were 47 examples of patients being superinfected with an unrelated strain. The predicted MRSA phenotype was accurate in all but three isolates. Mutation rates were unable to be determined because the branching order in the phylogenetic tree was inconsistent with the order of isolation. The observation that transmissions were identified between sibling patients shows that WGS is an effective tool for determining transmission between patients. The observation that transmission only occurred between siblings suggests that Staphylococcus aureus acquisition in our CF population occurred outside the hospital environment and indicates that current infection prevention efforts appear effective.

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