Research & Projects

ESCMID Panorama

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


The text must be formatted in Arial font size 10. ALL CAPS for text (other than abbreviations or acronyms) are not allowed. The abstract text may not be longer than a maximum of 350 words.



Authors may include a maximum of one picture or graph or one table (of up to ten rows x ten columns) per abstract. Words within the table count towards the total maximum of words allowed. 



Abstract titles must be submitted according to the scientific rules. This includes any special characters and special words that need to be capitalized or in italics. Abstract titles will be proofread. Titles in ALL CAPS (other than abbreviations or acronyms) are not allowed.


Submit your abstract

You can save your abstract at any time. Please make sure to have all fields completed before you finally submit your abstract. You will receive a confirmation by email after the submission (please make sure to state your correct email address!). Please note that emails regarding the submission will be sent to the submitter. All correspondence regarding acceptance or rejection, including further information on the mode of presentation etc. will be sent to the presenting author.

If you have any questions or need any assistance, please do not hesitate to contact us at IMMEMconf2019[at]


Spelling guidelines

The International System of Units (SI) should be used wherever appropriate. Genus and species names should be written in full on first mention and then abbreviated on subsequent mention.

        The following scientific rules apply (examples in brackets):

  • Systematic names (genus, family and higher orders): capitalized (Chlamydia, Enterobacteriaceae, Picornaviridae).
  • Non-English expressions: non-English expressions in English texts are written in italics, e.g. force majeure, in vitro/in vivo, ad hoc, ex officio
  • Taxonomic names: are to be italicized, e.g. Staphylococcus aureus, Clostridium difficile.
  • Non-systematic names (e.g. plural): lower case and not italicized (group A streptococci, mycobacteria, chlamydiae).
  • Generic drug names: lower case (penicillin).
  • Avoid using brand names; if needed: capitalized with trademark symbol (Rocephin®).
  • Diseases and viruses: lower case (hepatitis, herpes zoster, herpesvirus, West Nile virus).
  • Please observe standard English grammar rules including a space after full stops and commas.
  • Only common abbreviations may be used without definition.

Scientific Secretariat

ESCMID Executive Office
P.O. Box 214
4010 Basel, Switzerland
Phone +41 61 508 01 72
Email IMMEMconf2019[at]