Serotypes and virulence profiles of Shiga toxin-producing Escherichia coli strains isolated during 2017 from human infections in Switzerland.

Since 2015, the Swiss Federal Office of Public Health registered an increase of notifications of STEC, probably due to the adoption of culture independent stx screening tests in diagnostic laboratories. This study aimed to identify the serotypes and virulence genes of 120 STEC isolated from human clinical stx positive specimens during 2017 in order to estimate any changes in serotype distribution and toxin profiles of STEC compared to the time span 2010-2014. Culturing of STEC from stool samples was achieved using the streak plate technique on MacConkey agar. We performed O and H serotyping by PCR and by micro array. Virulence genes were identified and subtyped using molecular methods, including stx1 and stx2 subtypes, and the intimin encoding gene, eae. STEC were recovered from 27.5% of the stx positive samples. STEC O157:H7 accounted for 7.5% of all isolates, and STEC O80:H2, O91:H10/H14/H21, O103:H2/H11, and O26:H11 accounted for 36.9% of the non-O157 strains. Forty-five isolates with stx1 variants, 47 with stx2 variants and 28 isolates with both stx1 and stx2 variants were identified. Forty (33.3% of all isolates) carried the subtypes associated with high pathogenic potential, stx2a, stx2c, or stx2d. The eae gene for intimin was detected in 54 strains (45% of all strains). Compared to 2010-2014, our data show that the proportion of the so called "top five" serogroups, STEC O26, O111, O103, and O157 declined from 53.7% to 28.3% in 2017. The proportion of isolates with stx2a, stx2c, or stx2d decreased from 50.5% to 33.3%. We also observed an increase of STEC harbouring the low pathogenic subtypes stx2b and stx2e from 12.6% to 29.2%, and of eae negative STEC from 29.5% in 2010-2014 to 55% in 2017. Simultaneously, there was a sharp increase of the patients' median age from 24 years to 46.5 years. Clinical manifestations in the patients included abdominal pain without diarrhea (22.3%), diarrhea (77.7%), and the haemolytic-uremic syndrome (HUS) (7.4%). Our data show that a greater number and a wider range of STEC serotypes are detected by culture-independent testing, with implications for public health services.

Complete and Assembled Genome Sequence of Salmonella enterica subsp. enterica Serotype Senftenberg N17-509, a Strain Lacking Salmonella Pathogen Island 1.

The genome of Salmonella enterica subsp. enterica serotype Senftenberg N17-509, a strain isolated from desiccated coconut, was sequenced using single-molecule real-time sequencing. It consists of a 5.1-Mbp chromosome and a 29-kb linear plasmid.

Salmonella enterica serovar Infantis from Food and Human Infections, Switzerland, 2010-2015: Poultry-Related Multidrug Resistant Clones and an Emerging ESBL Producing Clonal Lineage.

Objectives: The aim of this study was to characterize a collection of 520 Salmonella enterica serovar Infantis strains isolated from food (poultry meat), human infections and environmental sources from the years 2010, 2013 and 2015 in Switzerland. Methods: We performed antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE) analysis on all 520 S. Infantis isolates, and whole genome sequencing (WGS) on 32 selected isolates. Results: The majority (74.8%) of the isolates was multidrug resistant (MDR). PFGE analysis revealed that 270 (51.9%) isolates shared an identity of 90%. All isolates subjected to WGS belonged to sequence type (ST) 32 or a double-locus variant thereof (one isolate). Seven (21.9%) of the sequenced isolates were phylogenetically related to the broiler-associated clone B that emerged in Hungary and subsequently spread within and outside of Europe. In addition, three isolates harboring blaCTX-M-65 on a predicted large (∼320 kb) plasmid grouped in a distinct cluster. Conclusion: This study documents the presence of the Hungarian clone B and related clones in food and human isolates between 2010 and 2015, and the emergence of a blaCTX-M-65 harboring MDR S. serovar Infantis lineage.

Local Outbreak of Listeria monocytogenes Serotype 4b Sequence Type 6 Due to Contaminated Meat Pâté.

In January and February 2016, five cases of confirmed and two cases of probable infection due to Listeria monocytogenes serotype 4b, sequence type (ST) 6 belonging to a single pulsed-field gel electrophoresis pulsotype pattern were registered in a region of southern Switzerland. L. monocytogenes was detected in blood samples (four cases) and pleural fluid (one case). Furthermore, L. monocytogenes 4b ST6 was detected in a stool sample of an asymptomatic person exposed to a common food. Forthwith, the food safety authority and a local gourmet meat producer reported L. monocytogenes contamination of meat pâté. Analysis of further food and environmental samples from the premises of the producer yielded isolates matching the clinical strains and confirmed the presence of L. monocytogenes 4b ST6 in the mincing machine as the cause of the food contamination.

Analysis of a poultry slaughter process: Influence of process stages on the microbiological contamination of broiler carcasses.

In a large-scale Swiss poultry abattoir, a microbiological process analysis of broiler carcasses was performed. At each selected process stage (scalding, plucking, evisceration, washing, and chilling), 90 carcasses from 30 flocks were sampled and examined for Campylobacter, Salmonella, Escherichia coli, Enterobacteriaceae, and extended-spectrum b-lactamases-producing Enterobacteriaceae. With regard to Campylobacter counts on carcasses, plucking tended to slightly increase the results (on average by 0.4 log CFU/g), whereas mean counts from plucked and chilled carcasses were comparable (3.1 log CFU/g after plucking, 3.0 log CFU/g in the chiller). The Campylobacter results of chilled carcasses are thereby likely to comply with the newly defined requirements of the European Union (process hygiene criterion for Campylobacter). With regard to Escherichia coli and Enterobacteriaceae counts on carcasses, plucking clearly reduced the results (on average by 0.8 and 0.9 log CFU/g), whereas mean counts from plucked and chilled carcasses were comparable (3.4 and 3.5 log CFU/g after plucking, 3.4 log CFU/g in the chiller). In contrast, Salmonella spp. were not detected on broiler carcasses and extended-spectrum b-lactamases- producing Enterobacteriaceae only rarely (1.8%). Such abattoir-specific data are of central importance for assessment of slaughter process performance and if necessary for the implementation of effective measures in the slaughter process.

Shigella Antimicrobial Drug Resistance Mechanisms, 2004-2014.

To determine antimicrobial drug resistance mechanisms of Shigella spp., we analyzed 344 isolates collected in Switzerland during 2004-2014. Overall, 78.5% of isolates were multidrug resistant; 10.5% were ciprofloxacin resistant; and 2% harbored mph(A), a plasmid-mediated gene that confers reduced susceptibility to azithromycin, a last-resort antimicrobial agent for shigellosis.

High-resolution subtyping of Staphylococcus aureus strains by means of Fourier-transform infrared spectroscopy.

Staphylococcus aureus causes a variety of serious illnesses in humans and animals. Subtyping of S. aureus isolates plays a crucial role in epidemiological investigations. Metabolic fingerprinting by Fourier-transform infrared (FTIR) spectroscopy is commonly used to identify microbes at species as well as subspecies level. In this study, we aimed to assess the suitability of FTIR spectroscopy as a tool for S. aureus subtyping. To this end, we compared the subtyping performance of FTIR spectroscopy to other subtyping methods such as pulsed field gel electrophoresis (PFGE) and spa typing in a blinded experimental setup and investigated the ability of FTIR spectroscopy for identifying S. aureus clonal complexes (CC). A total of 70 S. aureus strains from human, animal, and food sources were selected, for which clonal complexes and a unique virulence and resistance gene pattern had been determined by DNA microarray analysis. FTIR spectral analysis resulted in high discriminatory power similar as obtained by spa typing and PFGE. High directional concordance was found between FTIR spectroscopy based subtypes and capsular polysaccharide expression detected by FTIR spectroscopy and the cap specific locus, reflecting strain specific expression of capsular polysaccharides and/or other surface glycopolymers, such as wall teichoic acid, peptidoglycane, and lipoteichoic acid. Supervised chemometrics showed only limited possibilities for differentiation of S. aureus CC by FTIR spectroscopy with the exception of CC45 and CC705. In conclusion, FTIR spectroscopy represents a valuable tool for S. aureus subtyping, which complements current molecular and proteomic strain typing.

Cross-border outbreak of Salmonella enterica ssp. enterica serovar Bovismorbificans: multiple approaches for an outbreak investigation in Germany and Switzerland.

QUESTION UNDER STUDY: In July 2014, an outbreak of Salmonella enterica ssp. enterica serovar Bovismorbificans was detected in Switzerland. The goal of the outbreak investigation was to rapidly identify and eliminate the contamination source in order to prevent new cases. METHODS: A case-case study design was applied comprising reported cases of S. Bovismorbificans and cases of other serovars. A trawling questionnaire was administered by telephone interview. Data were collected for 34 cases (20 S. Bovismorbificans and 14 Salmonella spp.) pertaining to food consumption during the 72 hours prior to symptom onset. RESULTS: A statistically significant association between an S. Bovismorbificans infection and the consumption of 'salads' (odds ratio [OR] 14.3, 95% confidence interval [CI] 1.47-138.27) as well as the consumption of 'sprouts' (OR 10.6, 95% CI 1.16-97.59) was found. Principal places of consumption of 'salads' and 'sprouts' in outbreak cases were restaurants in southern Germany (80.0%, 95% CI 56.3%-94.3%). Microbiological analysis in Germany identified S. Bovismorbificans on sprouts, and genotype analysis confirmed that Swiss and German cases shared the same outbreak strain. The contaminated products were removed from the market in Germany, preventing an on-going outbreak. CONCLUSION: The combination of the applied methods and the collaboration between the two countries proved to be crucial elements of this investigation. A series of sprouts-associated salmonellosis outbreaks underpin the importance of this vegetable as a potential food-borne pathogen carrier.

Salmonella enterica Serovar Szentes, a Rare Serotype Causing a 9-Month Outbreak in 2013 and 2014 in Switzerland.

During the summer of 2013, an increase of Salmonella enterica ssp. enterica serovar Szentes isolates from human clinical cases was registered by the Swiss National Centre for Enteropathogenic Bacteria and Listeria. In the course of the ensuing 9 months, 18 isolates originating from 13 patients and from one food sample were collected. Of the 13 human cases, 10 (77%) were female. The patients' ages ranged from 27 to 83 years (median age 49 years). Pulsed-field gel electrophoresis (PFGE) performed with XbaI, and multilocus sequence typing (MLST) were used to type the strains. PFGE as well as MLST showed the strains as indistinguishable. The PFGE pattern and MLST sequence type (ST427) were identical to those of Salmonella enterica serovar Szentes isolated in previous years (2002-2013) from sporadic cases in Switzerland and Germany. The increased isolation frequency continued for 6 months after the detection of Salmonella Szentes in sprouts. No common food exposure could be established. Due to lack of information on the potential food source, further investigations were not possible. The outbreak of this unusual serotype was detected because of its temporal clustering.

Characterization of Listeria monocytogenes strains isolated during 2011-2013 from human infections in Switzerland.

Listeria monocytogenes, an emerging foodborne pathogen, can cause in the population at risk severe infections that are associated with high case fatality rates. A total of 93 L. monocytogenes strains isolated from different patients in Switzerland from July 2011 to September 2013 were further characterized. Septicemia was reported for 74.2% of the patients, meningitis for 10.8%, and abortion for 3.2%. The majority of the strains belonged to serotype 1/2a (n=58) followed by serotype 4b (n=28), 1/2b (n=5), and 1/2c (n=2). The strains represented 35 multilocus sequence typing sequence types, 8 of which were designated for the first time. Sequence analysis of the inlA gene in the 35 sequence types showed that most of the strains encoded full-length proteins. Screening for Listeriolysin S showed the presence of this virulence factor in 29 of the 33 genetic lineage I strains. By using ApaI and AscI for pulsed-field gel electrophoresis, most strains showed distinguishable patterns.