12th International Meeting on Microbial Epidemiological Markers (IMMEM XII)
“Moving towards genome-based pathogen surveillance – lessons learnt and challenges ahead”
an ESCMID - ESGEM Conference
18-21 September 2019, Dubrovnik, Croatia
Abstract Submission
We can no longer accept abstracts.
The following abstracts have been accepted for IMMEM XII:
28 PCR-based typing methods for detecting S. pneumoniae serotypes in Bulgarian children
31 Streptococcus dysgalactiae a potential source of zoonotic infection in the kitchen
38 Potential transmission of methicillin resistance genes between staphylococcal species on German dairy farms
48 The molecular epidemiology of Salmonella Typhimurium in Africa
56 NGS based molecular typing of Staphylococcus haemolyticus - replacing PFGE to increase resolution
59 The bag of tricks of vancomycin variable enterococci: an alternative constitutive vanHAX-promoter, varying copy numbers and transferable resistance
62 Complete genome sequence of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7), isolate 16-SA00356, a serovar associated with sheep
67 The global phylogeography of a recently emerged Neisseria gonorrhoeae ST in Norway
74 Genome-based bacterial identification system improves the taxonomic identities of the genome sequences in the public database
81 Genomic analysis of Staphylococcus aureus along a pork production chain and in the community, Shandong Province, China
80 Core genome MLST investigation on MRSA spa type t172 isolates in a low-prevalence area, Southwest Finland, 2007-2016
82 In vivo structural alterations of a blaNDM-1 carrying IncA/C2 plasmid and complete sequence of its IncHI2-IncA/C2 co-integrate megaplasmid derivative generated during gastrointestinal passage in a broiler infection study
85 The impact of different MRSA typing methods on infection prevention and control strategies - a single-centre experience
88 Ciprofloxacin-resistant non-typhoid Salmonella isolated from food animals in South Korea
89 Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis: incidence in blood cultures in the Netherlands.
91 Genome-based pathogen surveillance: an use case of the new BIOMÉRIEUX EPISEQ® CS web-based software
93 bifrost: a platform for data analysis of collections with a start in quality control
94 Transfer dynamics of the antibiotic resistance plasmid pOXA-48 in a hospital
95 Characterisation of mcr-5-harbouring plasmids and mobile genetic elements in Salmonella using short-read and long-read sequencing technologies
96 Antibiotic exposure and impact on the gut microbiome and resistome: A prospective clinical metagenomics multicenter cohort study
97 Metagenomic profiling using curated reference genome database revealed hitherto unrecognized species in the genus Streptococcus.
99 Pseudomonas aeruginosa transmission efficacy determination by a novel algorithm based on whole genome sequencing in combination with patient data
101 High prevalence of vanB in non-enterococcal flora including a novel anaerobic species contributes to persistent outbreaks of vancomycin resistant enterococci in a Norwegian hospital
104 Intralaboratory comparison of the Oxford Nanopore’s MinION sequencing device for microbial applications
106 Comparative genomics of Escherichia coli from 13 European ICUs
109 LA-MRSA in German pigsty workers- Recolonization or persistence?
110 Helicase helP as prognostic biomarker in patients with Pseudomonas aeruginosa bloodstream infection
111 Genome-based analyses of Klebsiella pneumoniae to detect possible host- associations, host-adaptation and effects on virulence
112 Molecular evidence for persistence and adaptationof a vancomycin-resistant Enterococcus faeciumST-203 clone in a central European tertiary care hospital
113 Burkholderia cepacia complex infections caused by contaminated mouthwash solutions in German hospitals in 2018
103 Genome-based Surveillance for Rational Autogenous Vaccine Design to Control Campylobacter Infection in Poultry
107 Standardisation of Public Genomic Datasets of E. coli from Food-Animals: A First Step Towards Global Genomic Comparisons
114 Genomic analysis explaining long term carriage of ESBL-producing E. coli acquired during international travel
115 Developing novel epidemiological marker scheme for Klebsiella pneumoniae based on MLST, capsule synthesis type and lipopolysaccharide serotype
117 From sequence types to pathovars: Public health relevance of virulence markers in prospectively sequenced populations
123 Matrix-assisted laser desorption/ionization time-of flight mass spectrometry (MALDI-ToF MS) for epidemiological analysis of mastitis-associated pathogens in sheep flocks
126 Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans
128 A sentinel testing survey of plasmid-mediated (transferable) colistin resistance among Enterobacteriaceae in tertiary-care hospital.
130 Emergence of a new KPC-3 variant in the high-risk clone ST307-K. pneumoniae after ceftazidime-avibactam exposure in a Tertiary Hospital in Madrid
135 Whole genome sequencing of Campylobacter jejuni strains isolated from human, broiler chicken and wild bird faecal samples
138 Epidemiology of carbapenemase-producing Klebsiella pneumoniae in a Portuguese hospital: surveillance over a 6-year period (2013-2018)
139 International occurrence of an OXA-48 encoding plasmid in four European countries.
133 The swansong of MLST: Comparative analysis of the two Acinetobacter baumannii schemes
140 Pathogenwatch: A Global Platform for Genomic Surveillance
144 Comparison of wgMLST (BioNumerics) vs mapping and core-genome SNPs approach for the epidemiological investigations of Pseudomonas aeruginosa
146 Integrated Aquaculture Contributes to the Transfer of mcr-1 between Animals and Humans Via the Aquaculture Supply Chain
147 Usefulness of whole genome sequencing in the investigation of discordant phenotypes and genotypes in paired Staphylococcus aureus blood culture isolates
148 Global Salmonella plasmid population dynamics and associations with known antimicrobial resistance genes
154 A Nosocomial Respiratory Infection Outbreak of Carbapenem-non-susceptible Escherichia coli ST131 with multiple transmissible blaKPC-2 carrying plasmids
155 Evaluation of Staphylococcus aureus subtyping module for MRSA detection based on MALDI-TOF MS
156 Evolutionary Snapshot of Australian Methicillin-resistant Staphylococcus aureus (MRSA) bacteraemia isolates in 2015-2017
157 Molecular characteristics of the van operon in vancomycin resistant E. faecium blood stream infection isolates in Australia
159 Rapid prospective strain typing to identify unsuspected nosocomial transmission of MRSA and VRE
158 Colistin resistant Escherichia coli isolated from a mixed farm (bovine, swine and the farmer): a One-health study applying Nanopore sequencing for metagenomics.
162 Use of MLVA and WGS based approaches for investigation of outbreak caused by monophasic Salmonella Typhimurium
163 Characterisation of Neisseria gonorrhoeae isolates using a core-genome MLST scheme
161 Increased prevalence of linezolid resistance among clinical enterococci in Norway mainly due to spread of optrA E. faecalis
165 Mapping Antimicrobial Resistance in Livestock in Low- and Middle-Income Countries
168 Three genotyping methods to assess diversity of pathogenic Yersinia enterocolitica in its reservoir, the pig.
171 Characterisation of a vancomycin-resistant and a vancomycin-susceptible Enterococcus faecium isolate from the same blood culture
172 Combination of epidemiological and Next-generation sequencing data to determine the contribution of the aqueous environment for Pseudomonas aeruginosa colonization of high-risk haemato-oncology patients
174 Tracking carbapenemase harbouring plasmids by application of long-read sequencing technology: a new dimension of surveillance of MDR bacteria within the hospital setting
175 Antimicrobial resistance and virulence factors in cephalosporin resistant E. coli from retail meat
169 Within-host evolution of Streptococcus pneumoniae among children attending a day-care center
173 Retrospective genome analysis of Acinetobacter baumannii to investigate local population structure
177 A double multi-fragment recombination event originated the Streptococcus pneumoniae serotype 11A-PMEN3 clone that is spreading in Southwest Europe.
143 Surveillance of methicillin-resistant Staphylococcus aureus by standard molecular typing and deciphering of unusual carriage in a maternity ward by whole genome sequencing
179 Preliminary study of the transmission potential of AMR and virulence genes in the E.coli wild boars isolates
180 Chlamydia trachomatis outbreak: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature
185 A story of success: rmtB methylase gene, pHN7A8 plasmid and Escherichia coli ST1196 in Waste Water Treatment Plants
186 Complete genome sequencing: a new standard for typing of molluscum contagiosum virus isolates?
189 Gastrointestinal colonization of mcr-4.6 and blaIMP-4 co-harboring Leclercia adcarboxglata isolate from an intensive care patient
193 Whole genome sequencing gives n“ewe” insights into the role of Dichelobacter nodosus in the pathogenesis of footrot in sheep
196 The rise of Enterococcus faecium ST117 - a 20 years longitudinal analysis of a successful hospital-adapted lineage
195 Whole Genome Sequencing for cluster detection and characterization of Salmonella Rissen isolates from Portugal
194 Clinical Enterococcus faecalis isolates resistant to tigecycline
200 Typing and monitoring of emerging group B Streptococcus strain types using MALDI-TOF-MS in Hong Kong.
201 MBL-producing non-aeruginosa Pseudomonas spp. in Poland in 2003-2016 – population structure and resistome
203 Genome wide association studies reveals the genetic factors that contribute to the success of Staphylococcus saprophyticus as a uropathogen
204 The AFROStrep Registry: Report of the prevalence of pharyngeal group A streptococcal emm-types in Cape Town, South Africa
206 Genome – based surveillance of Clostridioides difficile ribotype 017 sublineages circulating in Portugal
207 Combining WGS, epidemiological data and contact network-based analyses to disclose transmission events and population changes of VRE within a hospital setting
210 Comparing SNP- and cgMLST- based analyses of Enterococcus faecium and Enterococcus faecalis
211 Genetic basis for antimicrobial resistance (AMR) and population structure of Campylobacter jejuni isolated from broilers and turkeys in Italy
214 Virulence and antibiotic resistance plasticity of Arcobacter butzleri: insights on the genomic diversity of an emerging human pathogen
213 Strengthening Mycobacterium tuberculosis surveillance through culture-independent whole-genome sequencing
215 Canada’s Integrated Rapid Infectious Disease Analysis Platform (IRIDA)
216 Empowering data sharing for genomics-based public health surveillance using ontologies
217 Genomic investigations into Serratia marcescens causing outbreaks in neonatological intensive care units
218 Time-resolved evolution and host association of mammal associated Campylobacter fetus
221 Use of whole genome sequencing for analysis of Staphylococcus aureus transmission from mother`s milk to infant: a case report.
225 MRSA in the age of migration: data from the German National Reference Centre for Staphylococci and Enterococci 2014 - 2017
224 WGS - based analysis of Salmonella Newport and Bardo strains isolated from different sources
226 ESBL Escherichia coli diversity amongst meat and meat sellers in North-Western Tanzania
222 In-host genetic diversity and persistence of ESBL-producing Enterobacteriales over time
228 Transmission of methicillin-resistant Staphylococcus aureus (MRSA) ST398 through the food chain in Portugal
229 MRSA in bloodstream infections in Portugal: diversification and dissemination patterns of the EMRSA-15 clone
209 Added value of implementing whole genome sequencing – a double-edged sword
231 Analysis of NGS reads for surveillance and clonality: an example with ESBL-producing K. pneumoniae
234 Prevalence and contribution of mobile genetic elements and virulence genes in extended-spectrum beta-lactamase-producing Klebsiella pneumoniae outbreaks in three parallel neonatal intensive care units
235 Genomics-based risk factor analysis: identification of drivers associated with the spread of antimicrobial resistance in Salmonella enterica subsp. enterica serovar Heidelberg in Ontario, Canada
237 Implementation of Next generation sequencing for routine surveillance and characterization of Listeria monocytogenes in Israel, 2016-2019
238 Whole genome sequence characterization of DSA-Shigella in Israel
243 PulseNet USA experience with the implementation of whole genome sequencing (WGS) for foodborne disease surveillance
236 Development of strain nomenclature for outbreak surveillance based on core genome MLST for Salmonella enterica
244 FT-IR spectroscopy: an effective method for real-time outbreak investigation
245 Campylobacter plasmids and niche adaptation
247 Application of Whole genome sequencing for typing and surveillance of Clostridioides difficile in Denmark
250 Nation-wide outbreak of Klebsiella pneumoniae ST11 NDM-1 in Poland, 2012-2018, analysed by the WGS approach
251 A long-term MRSA t5147/ST88 outbreak among iv drug abusers and homeless people in Copenhagen
246 Taxonomic vote: a new method to assign taxonomy after similarity searches
248 Whole genome sequencing data analysis pipelines for definition of clonality, genetic distances, gene content, and phylogeny of bacterial pathogens
254 High comparability despite use of different laboratory and analysis approaches for Listeria monocytogenes cluster identification by Whole Genome Sequencing.
258 Genetic analysis of plasmid-encoded mcr-1 mediated resistance in Enterobacteriaceae
261 Development and application of a whole genome MLST scheme for Cutibacterium acnes
262 BARiSTA: A framework for Bayesian allele recovery in sequence typing analysis
241 Hepatitis C virus subtyping in a clinical setting with Next Generation Sequencing provides additional information now and in the future.
263 Molecular diagnostics reveals persistence of serotype 3 as the main cause of pediatric complicated pneumonia in Portugal despite extensive PCV13 use
266 SOLIDNESS - Surveillance Of mobiLome meDiated aNtibiotic rEsiStance Spread
267 Characterization of the genetic lineages responsible for pediatric invasive pneumococcal disease in Portugal (1999-2015)
269 Food origin and gut human carriage of Enterobacter spp. isolates harbouring the rare extended-spectrum beta-lactamase SFO-1.
270 Methicillin-resistant Staphylococcus pseudintermedius (MRSP) surveillance with nanopore long reads: Whole Genome Sequencing, antimicrobial resistance and within-host variability in infection
268 A genome-wide epidemiological study on Pseudomonas aeruginosa distribution and circulation in Northeast Italy
273 Genomic Diversity, Antimicrobial Resistance and Virulence of Klebsiella pneumoniaefrom Animal Carriage: a Comprehensive Analysis in an One Health Perspective
274 Dru-repeats and the origin of the Staphylococcal Cassette Chromosome mec (SCCmec)
272 Extensively drug-resistant Salmonella typhi in a pregnant traveler returning from Pakistan to Denmark, 2019
275 Comparative genomics analysis of optrA-carrying Enterococcus faecalis strains: new insights on clonal and genetic hotspots for optrA acquisition
276 Multidimensional Sequence Typing (MDST): a new method to localize particular sequences in the universe of bacterial genomes
279 Pangenome Analysis TOolkit (PATO): A new integrative suite to analyze very large numbers of genomes.
280 Whole genome sequencing of influenza: applications in infection control and surveillance
281 Analysis of the intestinal resistome of Amerindians from the French Guiana and individuals from European countries
282 Metagenomic tools comparison on 16S rRNA Sequences
284 ONEIDA-INNUENDO - A bioinformatic platform for the integration of genomics in surveillance and outbreak detection
285 Validation of Fourier-Transform Infrared spectroscopy for cost-effective detection of nosocomial outbreaks
286 Identification and typing of dengue viruses directly from patient samples with DEN-IM
287 An outbreak of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae in a regional teaching hospital
289 Introduction and clonal spread of vanB E. faecium in Copenhagen, Denmark 2019
290 Genomic analysis of Enterococcus faecium isolates causing bacteremia in Madrid, Spain.
296 Clonal contamination of laying hens farm by Salmonella enterica serovar Enteritidis responsible for a multi-annual outbreak demonstrated through phylodynamic reconstruction
300 I-4-1-Health: Multi-centre surveillance of multidrug resistant Enterobacteriaceae reveals strong host specificity and no spread between livestock and humans.
301 Molecular characterization and genomic epidemiology of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae isolated from children in Qatar
302 Ongoing outbreak of OXA-244 carbapenemase-producing Enterobacterales in Germany is driven by clonal expansion of E. coli ST38
303 A genus-wide genomics survey of antibiotic resistance in Klebsiella species recovered from multiple human, animal and environmental niches within a single town in northern Italy
305 Lyb-2-4, a unique genomic region of carbapenem-resistantAcinetobacter baumannii associated with fatal outcome
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