Search

•Prevalence of ESBL-producing Enterobacteriaceae among Swiss broiler flocks is 21%.•The predominant blaESBLgene is blaSHV-12.•blaSHV-12genes are located on highly similar IncX3 plasmids co-harbouring qnrS1.

•Fresh herbs and salads are reservoirs of bacteria with antibiotic-resistant genes.•13% of the salads contained extended-spectrum ß-lactamase-producing bacteria.•85% of the contaminated salads were prewashed bagged salads.•5% of fresh herbs contained extended-spectrum ß-lactamase-producing bacteria.•6% of the fresh herbs contained carbapenemase-producing Enterobacterspp.

The use of florfenicol in farm animals may select enterococci that carry resistance genes that confer resistance to linezolid, a critically important oxazolidinone antibiotic used in human medicine. This cross-sectional study aimed to assess the occurrence of oxazolidinone resistance genes in florfenicol-resistant enterococci from fattening pigs in Switzerland and to characterize a subset of the isolates using whole genome sequencing. A total of 31 florfenicol-resistant enterococcal isolates were obtained from 27 (5%) of 565 cecal samples of fattening pigs from seven (11%) of 62 farms. Screening by PCR revealed the presence of cfr-poxtAin 1 of 31, optrAin 15 of 31, and poxtAin 15 of 31 enterococcal isolates. One randomly selected isolate per PCR-positive Enterococcusspecies and positive farm was selected for further analysis (n= 10). In nine of the 10 isolates, the presence of oxazolidinone resistance genes did not result in phenotypic resistance. Whole genome sequencing analysis showed the presence of E. faecalis(n= 1), E. faecium(n= 1), and E. hirae(n= 1), harboring optrA18, optrA7,and a new optrAallele, respectively. E. durans(n= 1), E. faecium(n= 4), and E. hirae(n= 1) carried the wild-type poxtA,and E. faecalis(n= 1) coharbored cfr(D)and poxtA2. Except for optrA7,all oxazolidinone resistance genes were found on plasmids. Multilocus sequence typing analysis identified E. faecalisST19 and ST376, E. faeciumST80 belonging to hospital-adapted clade A1, and E. faeciumST21, ST55, ST269, and ST416 belonging to clade A2, which represents human commensals and animal strains. The occurrence of cfr(D), optrA,and poxtAin various porcine Enterococcusspp. demonstrates the spread of oxazolidinone resistance genes among enterococci from fattening pigs in Switzerland. The presence in one sample of poxtA-carrying E. faeciumST80 emphasizes the potential risk to human health through dissemination of strains carrying oxazolidinone resistance genes into the food chain.

•191 samples from geographically-distributed water bodies were screened for vancomycin-resistant enterococci (VRE).•VRE were detected in six surface water samples from different sites throughout Switzerland.•The six isolates were identified as Enterococcus faeciumST133 (clade A2) and harboured vanAon a Tn1546element.•A similar dominance of ST133 in a recent animal screening suggests local spread of this clone in Switzerland.

Toxoplasma gondii,hepatitis E virus (HEV), and Salmonellaare zoonotic foodborne pathogens that may be transmitted to humans through the consumption of raw or undercooked pork. The aim of this study was to determine the seroprevalence of anti–T. gondii,anti-HEV, and anti-Salmonellaantibodies from healthy pigs at slaughter in Switzerland. From August to September 2020, the diaphragm muscle of Swiss fattening pigs was collected in three Swiss abattoirs from 188 farms. Two randomly chosen pig carcasses per farm were selected. On the basis of the slaughter data, we noted the production system and the canton of origin, comparing indoor (n= 120) and free-range (n= 68) farming and regional allocation. The meat juice of these samples was analyzed for pathogen-specific antibodies by using commercial enzyme-linked immunosorbent assay kits. The seroprevalences were 1.3% for T. gondii,71.8% for the HEV, and 5.3% for Salmonella,respectively. Comparing the origins, the results of many cantons were not meaningful due to the low number of samples. No regional accumulations were found for T. gondiiand HEV. The results showed that 2.1% of the farms had least one T. gondii–seropositive animal, 80.3% had at least one HEV-seropositive animal, and 8.5% had at least one Salmonella-seropositive animal, respectively. The seropositivity of T. gondiiwas higher in free-range pigs than in indoor pigs, whereas anti-Salmonellaantibodies were more common in pigs from indoor farming than in outdoor pigs. The seroprevalence of anti-HEV antibodies was similar in free-range and indoor farming pigs. Compared with studies from 2012, the seroprevalence of T. gondiihas decreased, whereas the seroprevalence of the HEV has increased and is highly prevalent among fattening pigs in Switzerland. The low seroprevalence of Salmonellahas remained stable in recent years.

•Linezolid-resistant Enterococcus faecalisST16 strain F102 was recovered from surface water.•E. faecalisF102 carried the optrAgene on a Tn6674-like element.•E. faecalisST16 harboured a large number of antimicrobial resistance genes and virulence genes.•The aquatic environment is important in view of dissemination of antimicrobial-resistant bacteria.

Wheat flour has recently been described as a novel vehicle for transmission of Shiga toxin–producing Escherichia coli(STEC). Very recently, an outbreak of STEC O121 and STEC O26 infections was linked to flour in the United States. The aim of the present study was to generate baseline data for the occurrence of STEC in flour samples from different retailers in Switzerland. In total, 70 flour samples were analyzed. After enrichment, the samples were screened for stx1and stx2by the Assurance GDS MPX ID assay. STEC strains were isolated and serotyped by the E. coliSeroGenoTyping AS-1 kit. The determination of stxsubtypes was performed with conventional PCR amplification. Screening for eae, aggR, elt,and estIa/Ibwas performed by real-time PCR. Nine (12.9%) of the flour samples tested positive for stxby PCR. STEC was recovered from eight (88.9%) of the positive samples. Two isolates were STEC O11:H48 harboring stx1c/stx1d, two were O146:H28 containing stx2b, one was O103:H2 containing stx1aand eae,and three were O nontypeable: Ont:H12 (stx2a), Ont:H14 (stx2a/stx2g), and Ont:H31 (stx1c/stx1d). STEC O103 belongs to the “top five” serogroups of human pathogenic STEC in the European Union, and STEC O146 is frequently isolated from diseased humans in Switzerland. Our results show that flour may be contaminated with a variety of STEC serogroups. Consumption of raw or undercooked flour may constitute a risk for STEC infection.

AbstractIn January and February 2016, five cases of confirmed and two cases of probable infection due to Listeria monocytogenesserotype 4b, sequence type (ST) 6 belonging to a single pulsed-field gel electrophoresis pulsotype pattern were registered in a region of southern Switzerland. L. monocytogeneswas detected in blood samples (four cases) and pleural fluid (one case). Furthermore, L. monocytogenes4b 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. monocytogenescontamination 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. monocytogenes4b ST6 in the mincing machine as the cause of the food contamination.

AbstractDuring the summer of 2013, an increase of Salmonella entericassp. entericaserovar 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 entericaserovar 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 SalmonellaSzentes 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.

Ready-to-eat (RTE) prepacked salads and fruit have been successfully marketed for the last decade in Switzerland and are increasingly important as a component of everyday diets. To determine whether extended-spectrum β-lactamase (ESBL)–producing Enterobacteriaceaeare present in RTE salads, fresh-cut fruit, and sprouts on the Swiss market, samples of 238 mixed and unmixed RTE produce from a large production plant and 23 sprout samples from two sprout farms were analyzed. Further, four samples from the production plant’s recycled wash water, which is used for crop irrigation, were analyzed. Twelve (5%) of the 238 RTE products and one of the recycled wash water samples yielded ESBL-producing Enterobacteriaceae. Strain identification and PCR analysis of the blaESBLgenes revealed Kluyvera ascorbataisolated from a tomato sample harboring a blaCTX-M-2-like gene; multidrug-resistant (MDR) Enterobacter cloacaedetected in a chives sample imported from Spain harboring the clinically important blaCTX-M-15gene; and 10 Serratiaspp. isolated from mixed salads (blaFONA-2and blaFONA-2-like genes were found in 6 [60%] and blaFONA-4-like and blaFONA-5-like genes were each found in 2 [20%] of the isolates). The recycled wash water sample tested positive for one extraintestinal pathogenic MDR Escherichia coliB2:ST131 harboring blaCTX-M-27and for one MDR E. coliA:ST88 containing blaCTX-M-3. None of the sprout samples tested positive for ESBL-producing Enterobacteriaceae. Overall, the majority of the Enterobacteriaceaedetected in Swiss RTE produce were environmental strains producing minor ESBLs. The detection of an isolate producing a clinically important ESBL in a single sample and of an international circulating pathogenic strain (B2:ST131) in recycled wash water highlights the importance of surveillance of fresh produce and of recycled wash water that will be reused for irrigation purposes.

Hepatitis E virus (HEV) is the causative agent of an acute and self-limiting hepatitis and is increasingly detected in food products containing pork. In this study, 102 raw sausages containing pig liver (mortadella di fegato) and 18 raw pork sausages (salami type sausage) collected at retail level in a region of southern Switzerland were screened for the presence of HEV by quantitative real-time reverse transcription PCR. HEV was detected in 12 (11.8%) of 102 mortadella di fegato products but not in any of the salami sausages. Viral loads in the mortadella di fegato sausages ranged from log HEV 2.3 to 5.7 genome copies per gram of food product. This study identifies mortadella di fegato type sausages made with raw pig liver as a potential source of HEV infection in humans.

ABSTRACTHuman isolates of Salmonella entericaserovars Hadar, Kentucky, Virchow, Schwarzengrund, and the monophasic variant of S. Typhimurium, Salmonella entericasubsp. entericaserovar 4,5,12:i:− were examined for mutations within the quinolone resistance target genes gyrA, gyrB, parC, and parEand for plasmid-mediated resistance genes. Differences were observed among the serovars. A novel variant of qnrD, qnrD2, was detected in an S. Hadar isolate.

AbstractSalmonella entericasubsp. entericaserovar 4,[5],12:i:- is a monophasic variant of SalmonellaTyphimurium. In this study, a total of 651 human and 107 food and environmental isolates of serovar 4,[5],12:i:- recovered from 2007 through 2011 in Switzerland were characterized by antibiotic resistance profiles and pulsed-field gel electrophoresis (PFGE). In addition, a selection of isolates belonging to the most frequent PFGE patterns was further subjected to multilocus variable-number tandem-repeat analysis (MLVA) and phage typing. Over the years 2007–2011, the reports of salmonellosis caused by Salmonella entericaserovar 4,[5],12:i:- significantly increased. A high prevalence of multidrug-resistant isolates, mainly showing an ampicillin–streptomycin–sulfonamide–tetracycline resistance pattern (ASSuT), was observed. In addition, four extended spectrum beta lactamase (ESBL) (CTX-M-55)–producing isolates were found. XbaI PFGE analysis of all isolates revealed over 150 different pulsotypes, and generally showed a considerable diversity within the monophasic isolates. Nevertheless, among these we identified seven dominant profiles, which encompassed 66% of all isolates tested. The PFGE type STYMXB.0131 dominated among human as well as food isolates. Multilocus variable-number tandem-repeat analysis profile 3-12-10-0-0211, which, in many cases, coincided with PFGE type STYMXB.0131 and phage type DT193 were the most prevalent types found for the isolates further characterized by these typing methods. Our data provide strong evidence for a spread of two specific Salmonellaserovar 4,[5],12:i:- clones (PFGE pattern STYMXB.0131, resistance type ASSuT) and (PFGE pattern STYMXB.0131, resistance type SSuT). In contrast to the human isolates, the pork/poultry isolates expressed predominantly the SSuT resistance type.

ABSTRACTHere, we present the full sequences of three mcr-1-carrying plasmids isolated from extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli. The plasmids belong to three different replicon types and are 34,640 bp, 209,401 bp, and 247,885 bp in size. We describe for the first time a composite transposon containing mcr-1localized on a multidrug-resistant (MDR) IncHI2 plasmid harboring additional determinants of resistance to six different classes of antibiotics, including the ESBL gene blaCTX-M-1, and heavy metal resistance.

Carbapenem-resistant Escherichia colihave emerged worldwide and represent a major challenge to effective healthcare management. Here we report the genome sequence of an NDM-5- and CTX-M-15-producing E. colibelonging to sequence type 617 isolated from wastewater treatment plant effluent in Switzerland.

Carbapenem-resistant Klebsiella pneumoniaehave emerged worldwide and represent a major threat to human health. Here we report the genome sequence of K. pneumoniae002SK2, an NDM-9- and CTX-M-15-producing strain isolated from wastewater in Switzerland and belonging to the international high-risk clone sequence type 147 (ST147).

Escherichia coliis an important aetiological agent of bovine mastitis worldwide. In this study, 82 E. colifrom bovine mastitis milk samples from 49 farms were analysed for their genetic diversity using phylogenetic grouping and multilocus sequence typing. The isolates were examined by PCR for a selection of virulence factors (VFs). Antimicrobial susceptibility profiles were assessed using the disk diffusion method. The most prevalent phylogroups were group B1 (41.5 per cent of the isolates) and group A (30.5 per cent). A variety of 35 different sequence types (STs) were identified, including ST1125 (11 per cent), ST58 (9.8 per cent), ST10 (8.5 per cent) and ST88 (7.3 per cent). Aggregate VF scores (the number of unique VFs detected for each isolate) ranged from 1 to 3 for 63.4 per cent of the isolates and were at least 4 for 12.2 per cent. For 24.4 per cent of the isolates, the score was 0. The three most frequent VFs were traT, fyuAand iutA. The majority (72 per cent) of the isolates harboured traT. The majority (68.3 per cent) of the isolates were fully susceptible to all antimicrobials tested, with 22 per cent resistant to ampicillin and 14.6 per cent to tetracycline. Resistance rates were low for gentamicin (3.7 per cent), amoxicillin/clavulanic acid (2.4 per cent) and ceftiofur (1.2 per cent), respectively. Among the study's sample population, E. colistrains were genotypically diverse, even in cows from the same farm, although some STs occurred more frequently than others. Susceptibility to clinically relevant compounds remained high.