Denise Althaus

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.

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.

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.

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.

Performance of the Assurance GDSî Assay for the Detection of L. monocytogenes in Pure Cultures and Spiked Food Samples

Listeria monocytogenes is a foodborne pathogen with significant impacts on public health and economy worldwide. Reliable and fast detection of L. monocytogenes is of major importance for both diagnostic laboratories and the food industry. The current study evaluated the performance of the Assurance GDS® assay for the detection of L. monocytogenes in pure cultures and spiked food samples. In the pure culture experiments, the Assurance GDS® assay for Listeria monocytogenes accurately detected the target strains of different serotypes and was correctly negative for a variety of other Listeria species. For reliable detection of L. monocytogenes in pure culture experiments, colony counts >105 cfu/ml were required, which emphasizes the need for an adequate enrichment step. The challenge test experiments (steak tartare, bologna type sausage, Gorgonzola cheese) using a one-broth enrichment strategy showed that the Assurance GDS® assay reliably detected L. monocytogenes after 16 h of enrichment in Half-Fraser broth, provided that spiking levels of the different matrices were ≥102 cfu/g. Depending of the food matrix, longer incubation times of 24 h or 48 h were required when the initial spiking level was <102 cfu/g, as to be expected in a proportion of naturally contaminated food products. Thus, the Assurance GDS® Listeria monocytogenes assay has proven to be a reliable and easy to handle, rapid test system for the specific detection of L. monocytogenes. This system is a suitable tool for generating microbiological results used for a “positive batch release”, especially for RTE foods with short shelf lives. However, longer enrichment times (24 h or 48 h) are required in a one-broth enrichment strategy, when the contamination level of the food matrix is low (<102 cfu/g).