Category Archives: Microbiology

Research – ECDC TECHNICAL REPORT Proficiency test for Listeria monocytogenes whole genome assembly

ECDC ecdclogo

Executive summary
Within its mission to operate EU surveillance networks, ECDC supports the integration of whole genome sequencing (WGS) data into surveillance and multi-country outbreak investigations of foodborne diseases including listeriosis as one of the priority diseases. To evaluate the inter-laboratory reproducibility and portability of Listeria monocytogenes genome assemblies, ECDC organised a proficiency test for national public health reference laboratories with WGS typing capabilities in the EU/EEA, as well as EFSA and the EU Reference Laboratory for L. monocytogenes.
This report presents the results of the proficiency test. Each participant received a total of 15 sets of raw sequence reads, which were to be assembled by one or more pipelines of their choice. The resulting assemblies were then compared to the reference assembly generated by ECDC on several quality metrics. There were 16 participants, submitting results for 29 pipelines. Twelve participants, including 10 of the 14 participating public health reference laboratories, had at least one concordant pipeline for Illumina reads. The other participants were provided with individual feedback on possibilities to improve their pipeline(s). Participants with a concordant pipeline are recommended to use that for their own analyses as well as for any sharing of assemblies with other organisations including ECDC. For EU-level surveillance purposes ECDC will only accept assemblies generated with a concordant pipeline. Any new pipelines or updates to existing pipelines should go through the same proficiency testing before being used for sharing data with ECDC. For outbreak investigation purposes when more detailed analysis can be needed, raw sequence reads are proposed to be shared instead of or in addition to assemblies for isolates included in the cluster. For Ion Torrent reads, it was not possible to establish concordance. ECDC suggests that any countries producing
these reads share not only the reads with other organisations but also the extracted allele sequences for at least the core genome in the form of a fasta file. This was shown to produce acceptable results and allows other organisations, including ECDC, to perform their allele calling as with any regular assembly. It was also found that the assembly process can be used to remove low-level contamination. Conversely, low-level
contamination can give rise to much longer assembly lengths than the expected length due to the presence of a
large number of very small contigs with very low quality. It is recommended that assembly pipelines include
removal of such small and unreliable contigs, ideally in a way that still alerts the user to the likely presence of
low-level contamination.
EU laboratories that have installed a new or updated pipeline are welcome to have its concordance assessed by
ECDC at any time.


Research – Nisin penetration and efficacy against Staphylococcus aureus biofilms under continuous-flow conditions

Microbiology Research

Biofilms may enhance the tolerance of bacterial pathogens to disinfectants, biocides and other stressors by restricting the penetration of antimicrobials into the matrix-enclosed cell aggregates, which contributes to the recalcitrance of biofilm-associated infections. In this work, we performed real-time monitoring of the penetration of nisin into the interior of Staphylococcus aureus biofilms under continuous flow and compared the efficacy of this lantibiotic against planktonic and sessile cells of S. aureus . Biofilms were grown in Center for Disease Control (CDC) reactors and the spatial and temporal effects of nisin action on S. aureus cells were monitored by real-time confocal microscopy. Under continuous flow, nisin caused loss of membrane integrity of sessile cells and reached the bottom of the biofilms within ~20 min of exposure. Viability analysis using propidium iodide staining indicated that nisin was bactericidal against S. aureus biofilm cells. Time-kill assays showed that S. aureus viability reduced 6.71 and 1.64 log c.f.u. ml for homogenized planktonic cells in exponential and stationary phase, respectively. For the homogenized and intact S. aureus CDC biofilms, mean viability decreased 1.25 and 0.50 log c.f.u. ml, respectively. Our results demonstrate the kinetics of biofilm killing by nisin under continuous-flow conditions, and shows that alterations in the physiology of S. aureus cells contribute to variations in sensitivity to the lantibiotic. The approach developed here could be useful to evaluate the antibiofilm efficacy of other bacteriocins either independently or in combination with other antimicrobials.

Information – Campylobacteriosis – Annual Epidemiological Report for 2017



Image CDC

Campylobacteriosis is the most commonly reported gastrointestinal disease in the EU/EEA.  In 2017, 29 EU/EEA countries reported 250 161 confirmed cases of campylobacteriosis.

Research – Prevalence, Levels, and Viability of Salmonella in and on Raw Chicken Livers

Journal of Food Protection


We surveyed chicken livers from various sources for the presence and levels of Salmonella. The pathogen was recovered from 148 (59.4%) of 249 chicken livers purchased at retail stores in Delaware, New Jersey, and Pennsylvania over about a 9-month period. Positive samples harbored Salmonella at levels of 6.4 most probable number (MPN)/g to 2.4 log CFU/g. The percentage of Salmonella-positive livers purchased at retail outlets in New Jersey (72%, 59 of 82 livers) was significantly higher (P < 0.05) than the percentage for livers purchased in Delaware (48%, 36 of 75 livers); however, this percentage was not significantly different (P > 0.05) from that for livers purchased in Pennsylvania (57.6%, 53 of 92 livers). The pathogen was also recovered more often (P = 0.019) from livers that were packaged by retailers (81 of 121 livers, 66.9%) than from livers packaged directly by processors (67 of 128 livers, 52.3%). In related studies, 12 (5.8%) of 207 chicken livers harvested from birds on a research farm tested positive for Salmonella at levels of 0.4 to 2.2 MPN/g. The recovery rate of Salmonella was 4.4% (6 of 135 livers) from livers with the gall bladder attached and 8.3% (6 of 72 livers) from livers when the gall bladder was removed at harvest on the research farm. We also quantified the levels of a nine-strain cocktail (ca. 6.5 log CFU/g) of Salmonella strains inoculated externally onto or internally into livers both before and after extended cold storage. Storage for at least 2 days at 4°C or 15 days at −20°C resulted in a decrease of about 1.0 log CFU/g in pathogen levels. Given the relatively high recovery rate (ca. 6.0 to 60.0%) and high (possibly illness causing) levels (0.4 MPN/g to 2.4 CFU/g) of Salmonella associated with chicken livers in the present study, further interventions for processors are needed to lower the prevalence and levels of this pathogen on poultry liver.

India -Four children die of ‘food poisoning’

The Hindu

Four children belonging to the aboriginal Kolam tribe from Narnoor mandal in Adilabad district died after developing symptoms of food poisoning on Wednesday while 24 other children, all aged between six and seven years, were undergoing treatment for the same symptoms at Utnoor hospital. This happened after some children consumed chicken curry that had been cooked the previous day for a wedding feast at Kothapalli Kolamguda village.

RASFF Alert – Animal Feed- Enterobacteriaceae – Pet Food


RASFF – too high count of Enterobacteriaceae (between 70 and 645 CFU/g) in pet food from China in Sweden

RASFF Alerts – Animal Feed – Salmonella – Fish Meal – Rabbit Meal


RASFF – Salmonella (O:7 in 2 out of 5 samples /25g) in fishmeal from South Africa, via Denmark in Germany

RASFF – Salmonella enterica ser. Montevideo (presence /25g) in rabbit meal from France in Belgium