Topic 12

microbiology bacteria bacterial strains resistance pathogen host antibiotic strain microbial resistant virulence isolates pathogens antimicrobial infections antibiotics infection coli escherichia microbiota pseudomonas gut microbiome production against growth bacterium isolated species biofilm gram pathogenic 16s aeruginosa were genes fungal microbes genomes microorganisms acid health colonization rrna genus communities community metabolic isolate was gene staphylococcus hosts susceptibility opportunistic carbon aureus presence sequencing metabolism diversity biofilms culture phage identified plasmid compounds produced fungi drug diverse products multidrug spp biosynthesis producing biosynthetic environmental metagenomic detected members pathogenicity genera streptococcus metabolites sp environment infected composition commensal bacillus concentrations soil revealed mycobacterium antibacterial pneumoniae phages susceptible

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Bacterial single-cell genomics enables phylogenetic analysis and reveals population structures from in vitro evolutionary studies 107 52 12 9 5 4

Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica 107 52 12 5

Linking phenotype, genotype and ecology: antimicrobial resistance in the zoonotic pathogen Streptococcus suis 107 52 12 5

Collateral Sensitivity Associated with Antibiotic Resistance Plasmids 52 12 5

Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples 158 143 29 12 5

Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera 107 52 12 5

PQS-Induced Outer Membrane Vesicles Enhance Biofilm Dispersion in Pseudomonas aeruginosa 52 12 10 3

Mapping the Role of AcrAB-TolC Efflux Pumps in the Evolution of Antibiotic Resistance Reveals Near-MIC Treatments Facilitate Resistance Acquisition 52 12 5

From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners 143 29 12 5

Glucose promotes resistance of human commensal Escherichia coli against contact-killing by pandemic Vibrio cholerae 158 79 12 3

An enhanced characterization of the human skin microbiome: a new biodiversity of microbial interactions 29 12 5

Dynamics of infection in a novel group of promiscuous phages and hosts of multiple bacterial genera retrieved from river communities 143 121 29 12 5

Integrated metabolic modeling, culturing and transcriptomics explains enhanced virulence of V. cholerae during co-infection with ETEC 114 12

Revisiting the Genomic Structure of the Genus Pseudomonas with Whole Genome Data: Insights into Diversity and Host-related Genetic Determinants 121 114 12 5

Prevalence of genetically similar Flavobacterium columnare phages across aquaculture environments reveals a strong potential for pathogen control 52 12 5

Transcriptional profiling of three Pseudomonas syringae pv. actinidiae biovars reveals different responses to apoplast-like conditions related to strain virulence 79 12 3

Amoeba predation of Cryptococcus neoformans results in pleiotropic changes to traits associated with virulence 114 12 5

High-throughput mapping of the phage resistance landscape in E. coli 143 12 5

Analysis of selection methods to develop novel phage therapy cocktails against antimicrobial resistant clinical isolates of bacteria 107 52 12

The small RNA ErsA plays a role in the regulatory network of Pseudomonas aeruginosa pathogenicity in airways infection 114 52 12 3

IlvY is an important regulator of Shigella infection in vitro and in vivo 52 12 10

Phage cocktail strategies for the suppression of a pathogen in a cross-feeding coculture 158 143 12 5

Pseudomonas aeruginosa isolates co-incubated with Acanthamoeba castellanii exhibit phenotypes similar to chronic cystic fibrosis isolates 114 79 12 5

Population analysis of Legionella pneumophila reveals the basis of resistance to complement-mediated killing 121 114 12 5

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance 143 29 12 5

Same, Same, but Different: Molecular Analyses of Streptococcus pneumoniae Immune Evasion Proteins Identifies new Domains and Reveals Structural Differences between PspC and Hic Variants 121 114 12 9 8

Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics 52 12 10 5

Metagenomic association analysis of gut symbiont Lactobacillus reuteri without host-specific genome isolation 121 29 12 5 4

Genes influencing phage host range in Staphylococcus aureus on a species-wide scale 52 12 5

Infection with novel Bacteroides phage BV01 alters host transcriptome and bile acid metabolism in a common human gut microbe 143 29 12 9 5

Acquisition of Oral Microbiota is Driven by Environment, Not Host Genetics 29 12 5

Taxonomic variability over functional stability in the microbiome of Cystic Fibrosis patients chronically infected by Pseudomonas aeruginosa 29 12 5

Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert 52 29 12 5

Comparative genomics identified a genetic locus in plant-associated Pseudomonas spp. that is necessary for induced systemic susceptibility 143 114 79 12 5

Comparative genomics identified a genetic locus in plant-associated Pseudomonas spp. that is necessary for induced systemic susceptibility 143 114 79 12 5

Lytic Bacteroides uniformis bacteriophages exhibiting host tropism congruent with diversity generating retroelement 143 121 29 12 5

Computational Model to Quantify the Growth of Antibiotic Resistant Bacteria in Wastewater 52 12 5

Heterogenous response to R-pyocin killing in populations of Pseudomonas aeruginosa sourced from cystic fibrosis lungs 52 12 10

Comparison of transcriptional responses of three multidrug resistant model microorganisms, Staphylococcus aureus ATCC BAA-39, Escherichia coli ATCC BAA-196 and Acinetobacter baumannii ATCC BAA-1790, on exposure to iodine-containing nano-micelle drug FS-1 52 12 10

Elucidating essential genes in plant-associated Pseudomonas protegens Pf-5 using transposon insertion sequencing 79 12 9

Genome-scale mapping reveals complex regulatory activities of RpoN in Yersinia pseudotuberculosis 79 31 12 9 3

Predicting Antimicrobial Resistance Using Conserved Genes 182 107 52 26 4

Strain background, species frequency and environmental conditions are important in determining population dynamics and species co-existence between Pseudomonas aeruginosa and Staphylococcus aureus 99 5

Limited and strain-specific transcriptional and growth responses to acquisition of a multidrug resistance plasmid in genetically diverse Escherichia coli lineages 52 12 5

Diversity of Antimicrobial-Resistant Aeromonas Species Isolated from Aquatic Environments in Brazil 107 52 12 5

Systematic characterization and genetic interaction analysis of adhesins in Candida albicans virulence 114 79 12

Bacteriophages targeting Acinetobacter baumannii capsule induce antimicrobial resensitization 52 12 10

Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations 52 12 5

Secondary metabolism in the gill microbiota of shipworms (Teredinidae) as revealed by comparison of metagenomes and nearly complete symbiont genomes 143 121 29 12 5

Characterization of the antimicrobial activity of the cell-penetrating peptide TAT-RasGAP317-326 52 12

Natural infection with Giardia is associated with altered community structure of the human and canine gut microbiome. 101 29 12 5

Short chain fatty acid butyrate promotes virus infection by repressing interferon stimulated genes 27 10 3

Multiplex CRISPRi-Cas9 silencing of planktonic and stage-specific biofilm genes in Enterococcus faecalis 52 12

Halophytic bacterial endophytome: a potential source of beneficial microbes for a sustainable agriculture 143 29 12 5

Phenotypic delay in the evolution of bacterial antibiotic resistance: mechanistic models and their implications 185 21 5

Functional insights from KpfR, a new transcriptional regulator of fimbrial expression that is crucial for Klebsiella pneumoniae pathogenicity 114 79 52 12 3

The impact of genetic diversity on gene essentiality within the E. coli species 139 121 12 5

Ceragenins and antimicrobial peptides kill bacteria through distinct mechanisms 52 12

Characterising the methylome of Legionellalongbeachae serogroup 1 clinical isolates and assessing geo-temporal genetic diversity 121 40 12 5

A Genome-based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates 26 4

Antibiotic-induced DNA damage results in a controlled loss of pH homeostasis and genome instability 52 12 3

Evolution of Honey Resistance in Experimental Populations of Bacteria Depends on the Type of Honey, and Has no Major Side Effects for Antibiotic Susceptibility 52 12 5

Non-clonal emergence of colistin resistance associated with mutations in the BasRS two component system in Escherichia coli bloodstream isolates 107 52 12

An investigation of Burkholderia cepacia complex methylomes via SMRT sequencing and mutant analysis 79 12 9 5

Similar gut bacterial microbiota in two fruit-feeding moth pests collected from different host species and locations 29 12 5

Aerobic metabolism in Vibrio cholerae is required for population expansion during infection 114 79 67 12

Sterol-response pathways mediate alkaline survival in diverse fungi 114 79 12 3


In vitro evolution of colistin resistance in the Klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics. 52 12 10

Correlation of pathogenic factors with antimicrobial resistance of clinical Proteus mirabilis strains 52 12 5

Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes 29 16 12 5

Development of a whole cell biosensor for detection of 2, 4-diacetylphloroglucinol (DAPG) producing bacteria from grassland soil 143 12 5

Acinetobacter baumannii NCIMB8209: A rare environmental strain displaying extensive insertion sequence-mediated genome remodeling resulting in the loss of exposed cell structures and defensive mechanisms 107 12 5

Amino Sugars Reshape Interactions between Streptococcus mutans and Streptococcus gordonii. 12 5

Genomic and phenotypic diversity of Enterococcus faecalis isolated from endophthalmitis 107 52 12 5

Prevalence of Diversified Antibiotic Resistant Bacteria within Sanitation Related Facilities of Human Populated Workplaces in Abbottabad 52 12 5

Pathway-based and phylogenetically adjusted quantification of metabolic interaction between microbial species 143 29 4

A Universal Stress Protein upregulated by hypoxia may contribute to chronic lung colonisation and intramacrophage survival in cystic fibrosis. 79 12 3

Long-read shotgun metagenome sequencing using PromethION uncovers novel bacteriophages, their abundance, and interaction with host bacterial immunity in the oral microbiota 25 12 5 4

Composition of the North American wood frog (Rana sylvatica) skin microbiome and seasonal variation in community structure 29 17 5

Computational Modeling of the Gut Microbiota Predicts Metabolic Mechanisms of Recurrent Clostridioides difficile Infection 101 29 12 10

The heart microbiome of insectivorous bats from Central and South Eastern Europe 29 12 5

The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins 143 79 12 3

Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection 114 12 5

Candida auris phenotypic heterogeneity determines pathogenicity in vitro 114 12

Functional characterization of clinical isolates of the opportunistic fungal pathogen Aspergillus nidulans 114 12 10

Genomic characterisation and context of the blaNDM-1 carbapenemase in Escherichia coli ST101. 107 52 25 12 5

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics and proteomics 29 12 5

MogR is a ubiquitous transcriptional repressor affecting motility, biofilm formation and virulence in the Bacillus cereus group 79 12 3

Genomic insights into adaptations of TMA-utilizing methanogens to diverse habitats including the human gut 29 5

In vitro and in vivo characterization of a recombinant rhesus cytomegalovirus containing a complete genome 41 27 12 10

Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus 21 5

The generation of persister cells is regulated at the initiation of translation by (p)ppGpp 52 12 3

Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples 158 29 17 12 5

Pseudomonas aeruginosa is capable of natural transformation in biofilms 79 52 12 5

Short-chain fatty acid production by gut microbiota from children with obesity is linked to bacterial community composition and prebiotic choice 101 29 12 5

Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and Type IX Secretion System 52 12 5

Comparative genomics of ocular Pseudomonas aeruginosa strains from keratitis patients with different clinical outcomes 52 12 9

A novel role for the C-terminal domain of the influenza A virus host shutoff endoribonuclease PA-X in mediating rapid turnover of the PA-X protein 41 3

Candida albicans genetic background influences mean and heterogeneity of drug responses and genome stability during evolution to fluconazole 21 5