Topic 107

isolates resistance resistant antimicrobial microbiology strains antibiotic escherichia coli isolated genome isolate amr clinical plasmid whole lactamase sequencing multidrug susceptibility klebsiella virulence genes hospital infections antibiotics identified surveillance pneumoniae sequence plasmids carbapenem collected bacterial were wgs prevalence countries genomes drug beta among carbapenemase public emergence spread genetic epidemiology genomic strain global health typing ciprofloxacin salmonella phylogenetic gene spectrum was pathogen genomics phenotypic concern carrying mic lactamases transmission mdr epidemiological globally producing extended clonal enterobacteriaceae esbl carried neisseria carriage blandm tetracycline blactx associated acquired patients study clone mobile cause dissemination antimicrobials sequences threat determinants belonged bacteria susceptible population detected azithromycin blaoxa

177 items. Top items listed below.

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

Genomic Epidemiology of Escherichia coli Isolates from a Tertiary Referral Center in Lilongwe, Malawi 107 52 12 5

Genomic Surveillance of Pseudomonas aeruginosa in the Philippines from 2013-2014 107 52 12 5

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

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

Extraintestinal pathogenic (ExPEC) lineages explain prolonged faecal carriage of travel-acquired extended-spectrum β-lactamase-producing Escherichia coli 107 52 12 5

Plasmidome analysis of carbapenem-resistant Enterobacteriaceae isolated in Vietnam 107 52 25 12 5

Genomic Surveillance of Neisseria gonorrhoeae in the Philippines from 2013-2014 107 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

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

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

See and Sequence: Integrating Whole-Genome Sequencing Within the National Antimicrobial Resistance Surveillance Program in the Philippines 107 52 12 5

Molecular epidemiology and clone transmission of carbapenem-resistant Acinetobacter baumannii in ICU rooms 107 52 12 5

Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients 107 52 12 5

Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399 107 40 12 5

Piperacillin/tazobactam resistant, cephalosporin susceptible Escherichia coli bloodstream infections driven by multiple resistance mechanisms across diverse sequence types 107 52 12

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

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

Predicting Antimicrobial Resistance Using Conserved Genes 182 107 52 26 4

Using whole-genome sequencing and a pentaplex real-time PCR to characterize third-generation cephalosporin-resistant Enterobacteriaceae from Southeast Queensland, Australia 107 52 12

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

Salmonella Typhi acquires diverse plasmids from other Enterobacteriaceae to develop cephalosporin resistance 107 52 12 5

Plasmid diversity among genetically related Klebsiella pneumoniae blaKPC-2 and blaKPC-3 isolates collected in the Dutch national surveillance 107 52 12 5

Molecular epidemiology of Escherichia coli producing CTX-M and plasmid AmpC-type β-lactamases from dairy farms identifies a dominant plasmid encoding CTX-M-32 but no evidence for transmission to humans in the same geographical region 107 12 5

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia 107 25 12 5

Clinical and genomic epidemiology of carbapenem-non-susceptible Citrobacter spp. at a tertiary healthcare center over two decades 107 52 12 5

Clinical extended-spectrum beta-lactamase antibiotic resistance plasmids have diverse transfer rates and can spread in the absence of antibiotic selection 107 52 12 5

Transmission and genetic adaptation of Achromobacter in cystic fibrosis 107 9 5

Within-patient evolution to piperacillin/tazobactam resistance in a clinical isolate of Escherichia coli due to IS26-mediated amplification of blaTEM-1B 107 52 12

Characterization of genomic variants associated with resistance to bedaquiline and delamanid in naïve Mycobacterium tuberculosis clinical strains 107 52 9 4

Genomic epidemiology and evolution of Escherichia coli in wild animals 107 52 12 5

Molecular Characterization of invasive Enterobacteriaceae from Pediatric Patients in Central and Northwestern Nigeria 107 52 12

Bacteriophage activity against and characterisation of avian pathogenic Escherichia coli isolated from colibacillosis cases in Uganda 107 52 12 5

Mutations in TAC1B: a novel genetic determinant of clinical fluconazole resistance in C. auris 107 12 9 5

Genomic Surveillance of Methicillin-Resistant Staphylococcus aureus in the Philippines from 2013-2014 107 52 12 5

Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates from Egyptian Patients 107 52 12

Collateral Sensitivity Associated with Antibiotic Resistance Plasmids 52 12 5

Situation of antibiotic resistance in Bangladesh and its association with resistance genes for horizontal transfer 107 52 12

Comparison of de-duplication methods used by WHO Global Antimicrobial Resistance Surveillance System (GLASS) and Japan Nosocomial Infections Surveillance (JANIS) in the surveillance of antimicrobial resistance 107 52 12 5

Occurrence, identification and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa. 107 52 12 5

Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly 25 12 9

Overexpression of blaOXA-58 Gene Driven by ISAba3 is Associated with Imipenem Resistance in a Clinical Acinetobacter baumannii Isolate from Vietnam 107 52 12

Near-infrared Spectroscopy evaluations for rapid differentiation of carbapenem resistant Enterobacteriaceae from susceptible strains 107 52 12

Antimicrobial Resistance Profile and mcr-1 gene Detection in Salmonella Isolates from Poultry in Bangladesh: Molecular and Bioinformatics Characterization 107 52 12

Population structure-guided profiling of antibiotic resistance patterns in clinical Listeria monocytogenes isolates from Germany identifies pbpB3 alleles associated with low levels of cephalosporin resistance 107 52 12 5

Genomic analysis of the diversity, antimicrobial resistance and virulence potential of Campylobacter jejuni and Campylobacter coli strains from Chile 107 12 5

Accessory genome dynamics and structural variation of Shigella from persistent infections 107 12 5

Dissemination routes of the carbapenem resistance plasmid pOXA-48 in a hospital setting 107 52 12

Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically-relevant bacteria 107 52 12

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

The household resistome - frequency of beta-lactamases, class 1 integron and antibiotic resistant bacteria in the domestic environment 107 52 12 5

Genetic characterization of AmpC and extended-spectrum beta-lactamase (ESBL) phenotypes in Escherichia coli and Salmonella from Alberta poultry 107 52 12

Real-time sampling of travelers shows intestinal colonization by multidrug-resistant bacteria to be a dynamic process with multiple transient acquisitions 107 52 12 5

Characterization of a clinical Enterobacter hormaechei strain belonging to epidemic clone ST418 co-carrying blaNDM-1, blaIMP-4 and mcr-9.1 107 52 12

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

Prevalence and global distribution of blaKPC-2 and blaNDM-1 genes in Klebsiella Pneumoniae 107 52 12 5

GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure 107 52 4

Strain and lineage-level methylome heterogeneity in the multi-drug resistant pathogenic Escherichia coli ST101 clone 107 12 9 5

Identification of antimicrobial resistance-associated genes through whole genome sequencing of high and low MIC isolates of Mycoplasma bovis 107 12 9

Exploration of the Neisseria resistome reveals resistance mechanisms in commensals that may be acquired by N. gonorrhoeae through horizontal gene transfer 107 52 12

Virulence potential of a multidrug-resistant Escherichia coli strain belonging to the emerging clonal group ST101-B1 isolated from bloodstream infection 107 52 12

Population genomics and antimicrobial resistance in Corynebacterium diphtheriae 107 52 12 5

Comparative Genomic Analysis of Fifty-Two Staphylococcus aureus Isolates Identified from Uncharacterized Staphylococcus Genomes in the NCBI database 107 12 5

Emergence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing 107 25 12 5

Concurrence of Porin Loss and Modular Amplification of β-Lactamase Encoding Genes Drives Carbapenem Resistance in a Cohort of Recurrent Enterobacterales Bacteremia 107 25 12 9

Staphylococcus sciuri C2865 from a distinct subspecies cluster as reservoir of the novel transferable trimethoprim resistance gene, dfrE, and adaptation driving mobile elements 107 52 12 5

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

Microevolution of acquired colistin resistance in Enterobacteriaceae from ICU patients receiving selective decontamination of the digestive tract. 107 52 12

Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes 107 52 12 5

Population genomic molecular epidemiological study of macrolide resistant Streptococcus pyogenes in Iceland,1995-2016: Identification of a large clonal population with a pbp2x mutation conferring reduced in vitro beta-lactam susceptibility 107 52 12

A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes within Vibrio cholerae infected patients 107 12 5

A 21-year survey of <Escherichia coil> from bloodstream infections (BSIs) in a tertiary hospital reveals how community-hospital dynamics, influence local BSI rates, the trends of the B2 phylogroup and the STc131 pandemic clone 107 52 12 5

Whole Genome Sequences of Aedes aegypti (Linn.) Field Isolates from Southern India 48 25 9 5 4

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment 107 52 12 5

Genomic and phenotypic heterogeneity of clinical isolates of the human pathogens Aspergillus fumigatus, Aspergillus lentulus and Aspergillus fumigatiaffinis 121 114 107 12 5

Genetic characterisation of a large antibiotic resistant environmental ST131 E. coli plasmid using a long read hybrid assembly approach 107 52 12

Genomic diversity of Escherichia coli isolates from healthy children in rural Gambia 107 40 5

Increased power from bacterial genome-wide association conditional on known effects identifies Neisseria gonorrhoeae macrolide resistance mutations in the 50S ribosomal protein L4 107 52 19 12 9 5

Genomic investigation of a suspected multi-drug resistant Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa 107 52 12 9

Ecological niche adaptation of a bacterial pathogen associated with reduced zoonotic potential 107 12 5

Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia 107 12 5

Acquired fluoroquinolone resistance genes in corneal isolates of Pseudomonas aeruginosa 107 52 25 12

Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning 107 52 4

Elucidation of global and local epidemiology of Salmonella Enteritidis through multilevel genome typing 107 37 5 4

Genome-wide analysis in Escherichia coli unravels an unprecedented level of genetic homoplasy associated with cefotaxime resistance. 107 52 12 7

Antibiotic-resistant Salmonella species and Escherichia coli in broiler chickens from farms, abattoirs and open markets in selected districts of Zambia 107 52 12

Multidrug Resistance and High Prevalence of class 1 Integrons in Escherichia coli Isolated from Irrigation Water and Vegetables in Parts of Nsukka and Enugu, Nigeria 107 52 12

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing 107 25 12 4

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

Dissemination of carbapenem-resistance and plasmids encoding carbapenemases in Gram-negative bacteria isolated from India 107 52 12

Specialised functions of two common plasmid mediated toxin-antitoxin systems, ccdAB and pemIK, in Enterobacteriaceae 107 52 12 5

Phylogenetic and evolutionary analysis reveals the recent dominance of ciprofloxacin resistant S. sonnei and local persistence of S. flexneri clones in India 107 40 5

Incidence and susceptibility patterns of urine bacterial flora in young females 107 52 12 5

Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses 37 5

Global population genomic analysis of Mycoplasma bovis isolates reveals transcontinental variations and potential virulence genes 121 107 40 12 5

Spontaneous emergence of azithromycin resistance in independent lineages of Salmonella Typhi in Northern India 107 52 12

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

The prevalence and genomic context of Shiga toxin 2a genes in E. coli found in cattle 107 12 5

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

Bacteriophages targeting Acinetobacter baumannii capsule induce antimicrobial resensitization 52 12 10