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Fresh produce is usually consumed raw or minimally processed, making it a potential vehicle for the transmission of antimicrobial-resistant (AMR) microorganisms to humans. The objective of the study was to assess the occurrence of extended-spectrum ß-lactamase (ESBL)- and carbapenemase-producing Enterobacterales (ESBL-E and CPE), respectively, in 118 fresh herbs and 101 bagged salads collected at retail level in Switzerland and to characterize the isolates' phenotypic and genotypic properties using culture-based methods and whole genome sequencing (WGS). Of the fresh herbs, 6/118 contained ESBL-E and 7/118 yielded CPE. Of the salads, 13/101 contained ESBL-E and 1/101 CPE. Antimicrobial susceptibility testing (AST) identified 9/29 isolates as multidrug-resistant (MDR). ESBL-E were Escherichia coli (n = 6), Klebsiella pneumoniae (n = 4) Enterobacter chuandaensis (n = 1), and Kluyvera spp. (n = 1) carrying ß-lactamase (bla) genes belonging to the cefotaximase-München (bla CTX-M )-groups, Proteus spp. (n = 1) containing Hôpital-Universitaire-de-Genève-bla (bla hugA ), Raoultella ornithinolytica (n = 1) carrying sulfhydryl reagent variable bla (bla SHV ), and Serratia fonticola (n = 7) carrying S. fonticula bla (bla FONA ) genes. CPE were Enterobacter asburiae (n = 1) E. cloacae (n = 6) and E. vonholyi (n = 1) carrying imipenemase bla (bla IMI ) genes. Several K. pneumoniae sequence types (STs) were identified (ST967, ST628, ST219, and ST1823), which have been linked to human disease and nosocomial outbreaks. They carried bla CTX-M-15 on plasmids detected globally in environmental and clinical samples. E. coli (ST10, ST48, ST609, ST2040, ST6215 and ST3580) and enterotoxigenic E. coli (ETEC) ST2040 carrying bla CTX-M-15 were found. E. cloacae (ST820 and ST1516) with bla IMI-1 have been found previously in clinical settings and community outbreaks. The occurrence and consumption of fresh produce containing MDR ESBL-E and CPE pose substantial public health risks and raise significant food safety concerns., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Extended-spectrum β-lactamase-producing Escherichia (E.) coli (ESBL-EC) in the clinical setting have emerged as a major threat to public and animal health. Wildlife, including Rattus spp. may serve as reservoirs and spreaders of ESBL-EC in the environment. Peridomestic rats are well adapted to living in proximity to humans and animals in a variety of urban and agricultural environments and may serve as sentinels to identify variations of ESBL-EC within their different habitats. In this study, a set of 221 rats (Rattus norvegicus, R. tanezumi, R. andamanensis, and Niviventer huang) consisting of 104 rats from city areas, 44 from chicken farms, 52 from pig farms, and 21 from stables of horse-riding schools were screened for ESBL-EC. Overall, a total of 134 ESBL-EC were isolated from the caecal samples of 130 (59%) rats. The predominant bla ESBL genes were bla CTX-M-14 , bla CTX-M-15 , bla CTX-M-55 , and bla CTX-M-65 . Phylogenetic analysis revealed a total of 62 sequence types (STs) and 17 SNP clusters. E. coli ST10 and ST155 were common to ESBL-EC from city areas and chicken farms, and ST44 were found among ESBL-EC from city areas and pig farms. Extra-intestinal pathogenic E. coli (ExPEC) ST69, ST131 and ST1193 were found exclusively among rats from city areas, and avian pathogenic E. coli (APEC) ST177 was restricted to ESBL-EC originating from chicken farms. Phylogenetic analysis showed that the populations of rodent ESBL-EC from city areas, chicken farms and pig farms were genetically different, suggesting a certain degree of partitioning between the human and animal locations. This study contributes to current understanding of ESBL-EC occurring in rats in ecologically diverse locations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Animal petting zoos and farm fairs provide the opportunity for children and adults to interact with animals, but contact with animals carries a risk of exposure to zoonotic pathogens and antimicrobial-resistant bacteria. The aim of this study was to assess the occurrence of Shiga toxin-producing Escherichia coli (STEC), Salmonella, extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae and methicillin-resistant Staphylococcus aureus (MRSA) in animal faeces from six animal petting zoos and one farm fair in Switzerland. Furthermore, hygiene facilities on the venues were evaluated. Of 163 faecal samples, 75 contained stx1, stx2 or stx1/stx2 genes, indicating the presence of STEC. Samples included faeces from sika deer (100%), sheep (92%), goats (88%), mouflons (80%), camels (62%), llamas (50%), yaks (50%), pigs (29%) and donkeys (6%), whereas no stx genes were isolated from faeces of calves, guinea pigs, hens, ostriches, ponies, zebras or zebus. Salmonella enterica subsp. enterica serovar Stourbridge (S. Stourbridge) was detected in faecal samples from camels. A total of four ESBL-producing E. coli strains were isolated from faeces of goats, camels and pigs. PCR and sequencing identified the presence of bla CTX-M-15 in three and bla CTX-M-65 in one E. coli. Antimicrobial resistance profiling using the disk diffusion method revealed two multidrug-resistant (MDR) E. coli with resistance to ciprofloxacin, gentamicin and azithromycin, all of which are critically important drugs for human medicine. Multilocus sequence typing identified E. coli ST162, E. coli ST2179, extraintestinal high-risk E. coli ST410 and E. coli ST4553, which belongs to the emerging extraintestinal clonal complex (CC) 648. No MRSA was detected. On all animal petting venues, there were inadequacies with regard to access to hygiene information and handwashing hygiene facilities. This study provides data that underscore the importance of hygiene measures to minimize the risk of transmission of zoonotic pathogens and MDR, ESBL-producing E. coli to visitors of animal petting venues., (© 2020 Wiley-VCH GmbH.)

Objectives: Carbapenem-resistant Escherichia coli have 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. coli belonging to sequence type 617 isolated from wastewater treatment plant effluent in Switzerland., Methods: Whole-genome sequencing of E. coli 657SK2 was performed using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology RS2 reads (C4/P6 chemistry). De novo assembly was carried out using Canu 1.6, and sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP)., Results: The genome of E. coli 657SK2 consists of a 4.9-Mbp chromosome containing bla CTX-M-15 , genes associated with virulence [fyuA, hlyE, the pyelonephritis-associated pili (pap) gene cluster and the yad gene cluster], the copper resistance gene pco, and genes associated with resistance to quaternary ammonium compound (QAC) disinfectants (emrA, mdfA and sugE). A 173.9-kb multidrug resistance IncFII-FIA-FIB plasmid was detected harbouring aadA2, aadA5, bla NDM-5 , bla OXA-1 , cat, drfA, drfA17, the mph(A)-mrx-mphR cluster, the tetA-tetC-tetR cluster, and the virulence genes iutA and ylpA., Conclusions: The genome sequence of E. coli 657SK2 provides information on resistance mechanisms and virulence characteristics of pathogenic E. coli harbouring bla NDM-5 and bla CTX-M-15 that are spreading into the environment via urban wastewater., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: Carbapenem-resistant Klebsiella pneumoniae have emerged worldwide and represent a major threat to human health. Here we report the genome sequence of K. pneumoniae 002SK2, 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)., Methods: Whole-genome sequencing of K. pneumoniae 002SK2 was performed using Pacific Biosciences (PacBio) single-molecule, real-time (SMRT) technology RS2 reads (C4/P6 chemistry). De novo assembly was performed using Canu assembler, and sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP)., Results: The genome of K. pneumoniae 002SK2 consists of a 5.4-Mbp chromosome containing bla SHV-11 and fosA6, a 159-kb IncFIB(K) plasmid carrying the heavy metal resistance genes ars and sil, and a 77-kb IncR plasmid containing bla CTX-M-15 , bla NDM-9 , bla OXA-9 and bla TEM-1 ., Conclusions: Multidrug-resistant K. pneumoniae harbouring bla NDM-9 and bla CTX-M-15 are spreading into the environment, most probably via wastewater from clinical settings., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

The aim of this study was to evaluate wastewater for carbapenemase-producing Enterobacteriaceae (CPE) and 16S rRNA methylase-producing Gram-negative bacteria (MPB) and to assess their occurrence following wastewater treatment. Wastewater samples were collected between June 2015 and March 2016 in the sewage network of the city of Basel (Switzerland) from sites located before and after influx of wastewater from the hospital into the sewage network. Samples were also obtained from the influent and effluent of the receiving wastewater treatment plant. Samples were screened for CPE and MPB using selective media. Escherichia coli and Klebsiella pneumoniae were typed by multilocus sequence typing (MLST). Carbapenemase and 16S rRNA methylase genes were identified by PCR and sequencing. Resistance profiles were determined by the disk diffusion test and Etest. The occurrence of CPE and MPB was increased downstream of hospital wastewater influx. Of 49 CPE isolates, 9 belonged to OXA-48-producing E. coli clone D:ST38, 7 were OXA-48-producing Citrobacter freundii, and 6 were KPC-2- or OXA-48-producing K. pneumoniae belonging to clonal complex 258. NDM (NDM-1, -5 and -9) and VIM (VIM-1) producers were detected sporadically. MPB included ArmA- and RmtB-producing E. coli and Citrobacter spp. Isolates corresponding to strains from wastewater were detected in the effluent of the treatment plant. Conclusively, CPE and MPB, predominantly OXA-48-producing Enterobacteriaceae, are readily detected in wastewater, survive wastewater treatment and are released into the aquatic environment. OXA-48-producers may represent an emerging threat to public health and environmental integrity., (Copyright © 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.)

Here, 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-1 localized 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., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

In this study, extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli isolates recovered from the following sources were characterized with regard to the occurrence and distribution of uropathogenic and enteric pathogenic virulence factors: surface waters (rivers and lakes, n=60), the intestines of freshwater fish (n=33), fresh vegetables (n=26), retail poultry meat (n=13) and the fecal samples of livestock (n=28), healthy humans (n=34) and primary care patients (n=13). Among the 207 isolates, 82% tested positive by PCR for one or more of the virulence factors (VF) that predict uropathogenicity, TraT, fyuA, chuA, PAI, yfcv or vat. Uropathogenic E. coli (UPEC) were detected in each of the analyzed sources. Regarding virulence factors for intestinal pathogenic E. coli, these were found more rarely and predominantly associated with the aquatic environment, with aagR (EAEC) found in isolates from surface waters and STp (porcine heat stable enterotoxin) and LT (heat-labile enterotoxin) associated with isolates from fish. Aggregate VF scores (the number of unique virulence factors detected for each isolate) were lowest among isolates belonging to phylogenetic group B1 and highest among group B2. Clustering of the isolates by phylogenetic group, multilocus sequence type (MLST) and ESBL-types revealed clonal overlaps of A:ST10(CTX-M-1) and D:ST350(CTX-M-1) between the sources of livestock, poultry meat and healthy humans, suggesting livestock, in particular poultry, represents a potential reservoir for these particular UPEC clones. The clones A:ST10(CTX-M-55) and B2:ST131(CTX-M-27), harboring uropathogenic virulence factors were significantly associated with fresh vegetables and with fish, respectively. Further clonal complexes with source overlaps included D:ST38(CTX-M-14), D:ST69(CTX-M-15), D:ST405(CTX-M-15) and D:ST648(CTX-M-15), which were found in surface water and healthy humans. Identifying potential reservoirs of UPEC in the environment, animals, food and humans is important in order to assess routes of transmission and risk factors for acquiring UPEC., (Copyright © 2015 Elsevier B.V. All rights reserved.)

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 Enterobacteriaceae are 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 blaESBL genes revealed Kluyvera ascorbata isolated from a tomato sample harboring a blaCTX-M-2-like gene; multidrug-resistant (MDR) Enterobacter cloacae detected in a chives sample imported from Spain harboring the clinically important bla(CTX-M-15) gene; and 10 Serratia spp. isolated from mixed salads (bla(FONA-2) and bla(FONA-2)-like genes were found in 6 [60%] and bla(FONA-4)-like and bla(FONA-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 coli B2:ST131 harboring bla(CTX-M-27) and for one MDR E. coli A:ST88 containing bla(CTX-M-3). None of the sprout samples tested positive for ESBL-producing Enterobacteriaceae. Overall, the majority of the Enterobacteriaceae detected 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.

To examine to what extent fresh vegetables imported into Switzerland represent carriers of extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae, 169 samples of different types of fresh vegetables imported into Switzerland from the Dominican Republic, India, Thailand, and Vietnam were analyzed. Overall, 25.4% of the vegetable samples yielded one or more ESBL-producing Enterobacteriaceae, 78.3% of which were multidrug resistant. Sixty isolates were obtained: Escherichia coli, 26; Klebsiella pneumoniae, 26; Enterobacter cloacae, 6; Enterobacter aerogenes, 1; and Cronobacter sakazakii, 1. We found 29 isolates producing CTX-M-15, 8 producing CTX-M-14, 7 producing CTX-M-55, 3 producing CTX-M-65, 1 each producing CTX-M-1, CTX-M-3, CTX-M-27, and CTX-M-63, 5 producing SHV-2, 3 producing SHV-12, and 1 producing SHV-2a. Four of the E. coli isolates belonged to epidemiologically important clones: CTX-M-15-producing B2:ST131 (1 isolate), D:ST405 (1 isolate), and D:ST38 (2 isolates). One of the D:ST38 isolates belonged to the extraintestinal enteroaggregative E. coli (EAEC) D:ST38 lineage. Two of the K. pneumoniae isolates belonged to the epidemic clones sequence type 15 (ST15) and ST147. The occurrence of antibiotic-resistant pathogenic and commensal Enterobacteriaceae in imported agricultural foodstuffs constitutes a source of ESBL genes and a concern for food safety., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

Sixty extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from rivers and lakes in Switzerland were screened for individual strains additionally exhibiting a reduced quinolone susceptibility phenotype. Totally, 42 such isolates were found and further characterized for their molecular (fluoro)quinolone resistance mechanisms. PCR and sequence analysis were performed to identify chromosomal mutations in the quinolone resistance-determining regions (QRDR) of gyrA, gyrB, parC and parE and to describe the occurrence of the following plasmid-mediated quinolone resistance genes: qepA, aac-6'-Ib-cr, qnrA, qnrB, qnrC, qnrD and qnrS. The contribution of efflux pumps to the resistance phenotype of selected strains was further determined by the broth microdilution method in the presence and absence of the efflux pump inhibitor phe-arg-β-naphthylamide (PAβN). Almost all strains, except two isolates, showed at least one mutation in the QRDR of gyrA. Ten strains showed only one mutation in gyrA, whereas thirty isolates exhibited up to four mutations in the QRDR of gyrA, parC and/or parE. No mutations were detected in gyrB. Most frequently the amino-acid substitution Ser83→Leu was detected in GyrA followed by Asp87→Asn in GyrA, Ser80→Ile in ParC, Glu84→Val in ParC and Ser458→Ala in ParE. Plasmid-mediated quinolone resistance mechanisms were found in twenty isolates bearing QnrS1 (4/20), AAC-6'-Ib-cr (15/20) and QepA (1/20) determinants, respectively. No qnrA, qnrB, qnrC and qnrD were found. In the presence of PAβN, the MICs of nalidixic acid were decreased 4- to 32-fold. (Fluoro) quinolone resistance is due to various mechanisms frequently associated with ESBL-production in E. coli from surface waters in Switzerland.

One of the currently most relevant resistance mechanisms in Enterobacteriaceae is the production of enzymes that lead to modern expanded-spectrum cephalosporin and even carbapenem resistance, mainly extended-spectrum β-lactamases (ESBLs) and carbapenemases. A worrisome aspect is the spread of ESBL and carbapenemase producers into the environment. The aim of the present study was to assess the occurrence of ESBL- and carbapenemase-producing Enterobacteriaceae and to further characterize ESBL- and carbapenemase-producing Enterobacteriaceae in rivers and lakes in Switzerland. ESBL-producing Enterobacteriaceae were detected in 21 (36.2%) of the 58 bodies of water sampled. One river sample tested positive for a carbapenemase-producing Klebsiella pneumoniae subsp. pneumoniae strain. Seventy-four individual strains expressing an ESBL phenotype were isolated. Species identification revealed 60 Escherichia coli strains, seven Klebsiella pneumoniae subsp. pneumoniae strains, five Raoultella planticola strains, one Enterobacter cloacae strain, and one Enterobacter amnigenus strain. Three strains were identified as SHV-12 ESBL producers, and 71 strains carried genes encoding CTX-M ESBLs. Of the 71 strains with CTX-M ESBL genes, 8 isolates expressed CTX-M-1, three produced CTX-M-3, 46 produced CTX-M-15, three produced CTX-M-55, one produced CTX-M-79, six produced CTX-M-14, and four produced CTX-M-27. Three of the four CTX-M-27 producers belonged to the multiresistant pandemic sequence type E. coli B2:ST131 that is strongly associated with potentially severe infections in humans and animals.