Clonal Diversity, Virulence Potential and Antimicrobial Resistance of Escherichia coli Causing Community Acquired Urinary Tract Infection in Switzerland.

Objectives: The aim of this study was to assess the clonal structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli (UPEC) isolates causing community acquired urinary tract infection (CAUTI) in unselected primary care patients in Switzerland. Methods: We performed multilocus sequence typing, virulence factor determination, and phenotypic and genotypic antimicrobial resistance testing on 44 non-duplicate UPEC isolates. Results: Twenty-seven different sequence types (STs) were identified. Major UPEC clones were represented by 19 (43.2%) of the isolates, including E. coli ST131, ST69 (both 13.6%), ST73 (6.8%), ST10 (4.5%), ST127, ST140, (both 2.3%). Five (11.4%) isolates belonged to ST141. Aggregate virulence factor (VF) scores were highest among isolates belonging to ST127 and ST141. Overall, 50% of the isolates were susceptible to all 12 antimicrobials tested, and all isolates remained susceptible to fosfomycin and nitrofurantoin. Resistance to sulfamethoxazole and ciprofloxacin were found in 31.8, and 15.9% of the isolates, respectively. Plasmid-mediated resistance genes were detected in ST69 and ST131 and included aac(6')-Ib-cr (2.3% of all isolates) blaCTX-M-14 and blaCTX-M-15 (9%), and mph(A) (13.6%). None of the isolates tested positive for mcr-1 or mcr-2. Conclusions: Our results show that CAUTI in Switzerland is caused by a wide variety of UPEC STs for which fosfomycin remains a good treatment option. We suggest that ST141 is an emerging clone associated with UTI in the community, and warrants closer attention. Moreover, the high rate of E. coli harboring mph(A) from patients without a history of antimicrobial therapy or hospitalization indicates that UPEC is an important reservoir for mph(A).

Screening for fecal carriage of MCR-producing Enterobacteriaceae in healthy humans and primary care patients.

BACKGROUND: The extent of the occurrence of the plasmid-encoded colistin resistance genes mcr-1 and mcr-2 among humans is currently sparsely studied in Western Europe. OBJECTIVES: To determine the occurrence of MCR-producing Enterobacteriaceae in fecal samples of healthy humans with high occupational exposure to food and primary care patients in Switzerland. METHODS: Stool samples from 1091 healthy individuals and fecal swabs from 53 primary care patients were screened for polymyxin-resistant Enterobacteriaceae using LB agar containing 4 mg/L colistin. Minimal inhibitory concentrations (MICs) of colistin were determined for non-intrinsic colistin-resistant isolates. Isolates were screened by PCR for the presence of mcr-1 and mcr-2 genes. RESULTS: The fecal carriage rate of colistin resistant (MIC value >2 mg/l) Enterobacteriaceae was 1.5% for healthy people and 3.8% for primary care patients. Isolates included Hafnia alvei (n = 9), Escherichia coli (n = 3), Enterobacter cloacae (n = 4), Klebsiella pneumoniae (n = 1) and Raoultella ornithinolytica (n = 1). None of the isolates harbored the mcr-1 or mcr-2 genes. CONCLUSIONS: There is no evidence for the presence of MCR-producers in the fecal flora of healthy people or primary care patients. Therefore, the risk of transfer of mcr genes from animals, food or the environment to humans is likely to be low in Switzerland.

Detection of Shigella sonnei in a respiratory specimen in a patient with subacute atypical pneumonia.

BACKGROUND: Pneumonia caused by shigellosis with or without typical dysentery in immunocompetent patients is an uncommon entity. CASE REPORT: We describe a case of pneumonia in an immunocompetent, previously healthy middle-aged man from Switzerland without relevant travel history which was presumably caused by Shigella sonnei. He was originally admitted for suspected lung cancer. The clinical picture was remarkable as the patient presented with cough and purulent sputum production, but otherwise no classical signs of pneumonia. Furthermore, there was no diarrhoeal episode in the recent history. It is an uncommon presentation of shigellosis in an immunocompetent person without underlying severe predisposing conditions. CONCLUSION: We report an unusual identification of S. sonnei as the only identified pathogen from respiratory specimens, which we therefore consider the most likely etiology of this subacute atypical pneumonia. This case illustrates the importance of a complete work-up in a patient whose suspected malignancy could not be proven.

Draft Genome Sequence of Escherichia coli 26R 793, a Plasmid-Free Recipient Strain Commonly Used in Conjugation Assays.

Here, we report the draft genome sequence of the lactose-negative, rifampin-resistant, Escherichia coli strain 26R 793. This isolate has been widely used in conjugation experiments as a general recipient strain.

Horizontal Acquisition of a Multidrug-Resistance Module (R-type ASSuT) Is Responsible for the Monophasic Phenotype in a Widespread Clone of Salmonella Serovar 4,[5],12:i:.

Salmonella enterica serovar 4,[5],12:i:- is a monophasic variant of S. Typhimurium incapable of expressing the second-phase flagellar antigen (fljAB operon), and it is recognized to be one of the most prevalent serovars causing human infections. A clonal lineage characterized by phage type DT193, PulseNet PFGE profile STYMXB.0131 and multidrug resistance to ampicillin, streptomycin, sulphonamides and tetracycline (R-type ASSuT) is commonly circulating in Europe. In this study we determined the deletions affecting the fljAB operon and the resistance region responsible for the R-type ASSuT in a strain of Salmonella enterica serovar 4,5,12:i:- DT193/STYMXB.0131, through an approach based on PCRs and Southern blot hybridization of genomic DNA. Using a set of nine specific PCRs, the prevalence of the resistance region was assessed in a collection of 144 S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 strains isolated from Germany, Switzerland and Italy. A 28 kb-region is embedded between the loci STM2759 and iroB, replacing the DNA located in between, including the fljAB operon. It encompasses the genes bla TEM-1, strA-strB, sul2 and tet(B) responsible for the R-type ASSuT together with genes involved in plasmid replication and orfs of unknown function characteristically located on IncH1 plasmids. Its location and internal structure is fairly conserved in S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 strains regardless of the isolation source or country. Hence, in the S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 clonal lineage widespread in Germany, Switzerland and Italy, a resistance region derived from IncH1 plasmids has replaced the chromosomal region encoding the second flagellar phase and is an example of the stabilization of new plasmid-derived genetic material due to integration into the bacterial chromosome.

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.

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.

Assessment of the Prevalence of Extended-Spectrum ß-Lactamase-Producing Enterobacteriaceae in Ready-to-Eat Salads, Fresh-Cut Fruit, and Sprouts from the Swiss Market.

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 ß-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.

Emergence of Escherichia coli producing OXA-48 ß-lactamase in the community in Switzerland.

BACKGROUND: The emergence and worldwide spread of carbapenemase-producing Enterobacteriaceae is of great concern to public health services. The aim of this study was to investigate the occurrence of carbapenemase-producing Enterobacteriaceae in the community in Switzerland. FINDINGS: One thousand and eighty-six stool samples of healthy humans (staff members of a food-processing company which were screened for the occurrence of salmonellae) were collected in September 2014. After an initial enrichment-step, carbapenemase-producing Enterobacteriaceae were isolated from the carbapenem-containing selective medium SUPERCARBA II. Grown colonies from 11 samples were screened by PCR for the presence of bla KPC, bla NDM, bla OXA-48 and bla VIM. A single OXA-48-producing Escherichia coli was detected. Phylogenetic grouping and multi-locus sequence typing (MLST) revealed that this strain belonged to D:ST38, a type which had been previously reported in the UK, France, Lebanon and Egypt. CONCLUSIONS: The results of this study show that OXA-48-producing Enterobacteriaceae have started to spread into the community in Switzerland, and a continuous monitoring is necessary to better understand their dissemination in the human population as well as in animals and the environment.

Replicon typing of plasmids carrying blaCTX-M-15 among Enterobacteriaceae isolated at the environment, livestock and human interface.

One of the currently most important antibiotic resistance mechanisms in Enterobacteriaceae is based on the production of ESBL enzymes that inactivate ß-lactam antibiotics including cephalosporins and monobactams by hydrolyzing their ß-lactam ring. In humans, the most prevalent ESBL enzyme type is encoded by blaCTX-M-15. CTX-M-15 producing enterobacterial strains were also frequently isolated from environmental samples including surface water and freshwater fish. Plasmids, which can be grouped in different plasmid incompatibility types, play a key role in the horizontal spread of these multidrug resistance genes. The purpose of this study was to investigate the diversity of plasmids that carry blaCTX-M-15 genes among Enterobacteriaceae isolated at the environment, livestock and human interface. In total, 81 blaCTX-M-15-harboring isolates collected between 2009 and 2014 were tested for its ability to transfer blaCTX-M-15 by conjugation. These plasmids were further typed. Transfer of a single blaCTX-M-15-harboring plasmid was observed in 32 (39.5%) of the isolates. The most frequent replicon types detected among these plasmids are IncF-type plasmids (n=12) (mostly multi replicon plasmids with a combination of following replicons: IncFII, IncFIA and IncFIB), followed by IncI1 (n=8), IncK (n=3) and IncR (n=1). A noticeable number of plasmids (n=8) could not be assigned to any of the tested replicon types. Knowledge about the plasmid types circulating in bacterial populations is indispensable for understanding epidemiological dynamics and for establishing intervention strategies to stop further dissemination of particular plasmids.

Extended-spectrum-ß-lactamase-producing Enterobacteriaceae isolated from vegetables imported from the Dominican Republic, India, Thailand, and Vietnam.

To examine to what extent fresh vegetables imported into Switzerland represent carriers of extended-spectrum-ß-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.

Repeated isolation of Salmonella enterica Goverdhan, a very rare serovar, from Danish poultry surveillance samples.

We report here the appearance of a very rare serovar of Salmonella, S. enterica subsp. enterica serovar Goverdhan, in routine Salmonella surveillance samples from Danish poultry production. S. Goverdhan was found on nine occasions: in one broiler breeder farm in October 2010, four broiler farms and one broiler breeder farm in June-September 2012, two broiler breeder flocks simultaneously in June 2013, and one layer flock in July 2013. The five isolates from 2012 and the three isolates from 2013 had identical pulsed-field gel electrophoresis profiles, whereas the profile of the isolate from 2010 deviated in a single band. It is the first time this serovar has been described in samples from poultry. The origin of the bacterium is still unknown, but it is suggested that it may have been a pseudo-outbreak caused by contaminated sampling material.

Replicon typing of plasmids carrying bla CTX-M-1 in Enterobacteriaceae of animal, environmental and human origin.

OBJECTIVES: The aim of this work was to determine the plasmid replicon profiles of a collection of bla CTX-M-1-positive enterobacterial strains. The isolates originated from chicken in the production pyramid, healthy food-producing animals at slaughter (chicken, calves, and pigs), chicken retail meat, environmental isolates originating from water bodies, and isolates from humans. A selection of IncI and IncN plasmids were characterized by multilocus sequence typing in order to determine their epidemiological relatedness. METHODS: Transconjugants of 74 bla CTX-M-1-positive isolates were analyzed by PCR-based replicon typing and by PCR-based plasmid multilocus sequence typing. RESULTS: The incompatibility groups detected among the bla CTX-M-1-harboring plasmids included IncI1, IncN, IncHI1B, IncF, IncFIIS, IncFIB, and IncB/O, with plasmid lineage IncI1/ST3 predominating in isolates from chicken and from humans. Lineage IncN/ST1 was detected mainly in isolates from pigs. For the first time, bla CTX-M-1 genes encoded on IncHI1 plasmids were detected in isolates from cattle and from water bodies. CONCLUSIONS: This study identifies plasmid lineages that are contributing to the dissemination of bla CTX-M-1 genes in the food chain, the environment, and humans.

Nucleotide sequences of 16 transmissible plasmids identified in nine multidrug-resistant Escherichia coli isolates expressing an ESBL phenotype isolated from food-producing animals and healthy humans.

OBJECTIVES: Nine extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli isolated from healthy humans and food-producing animals were found to transfer their cefotaxime resistance marker at high frequency in laboratory conjugation experiments. The objective of this study was to completely characterize 16 transmissible plasmids that were detected in these bacterial isolates. METHODS: The nucleotide sequences of all 16 plasmids were determined from transconjugants using next-generation sequencing technology. Open reading frames were assigned using Rapid Annotation using Subsystem Technology and analysed by BLASTn and BLASTp. The standard method was used for plasmid multilocus sequence typing (pMLST) analysis. Plasmid structures were subsequently confirmed by PCR amplification of selected regions. RESULTS: The complete circularized nucleotide sequence of 14 plasmids was determined, along with that of a further two plasmids that could not be confirmed as closed. These ranged in size from 1.8 to 166.6 kb. Incompatibility groups and pMLSTs identified included IncI1/ST3, IncI1/ST36, IncN/ST1, IncF and IncB/O, and those of the same Inc types presented a similar backbone structure despite being isolated from different sources. Eight plasmids contained bla(CTX-M-1) genes that were associated with either ISEcp1 or IS26 insertion sequence elements. Six plasmids isolated from humans and chickens were identical or closely related to the IncI1 reference plasmid, R64. CONCLUSIONS: These data, based on comparative sequence analysis, highlight the successful spread of blaESBL-harbouring plasmids of different Inc types among isolates of human and food-producing animal origin and provide further evidence for potential dissemination routes.

Quinolone resistance mechanisms among extended-spectrum beta-lactamase (ESBL) producing Escherichia coli isolated from rivers and lakes in Switzerland.

Sixty extended-spectrum ß-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-ß-naphthylamide (PAßN). 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 PAßN, 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.

Extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae: a threat from the kitchen.

Food is an established source of extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae. Hand hygiene and cooking prevent transmission, but hands could be recontaminated by touching used cutting boards. ESBL-producing Escherichia coli were identified on 12% of cutting boards and 50% of gloves after poultry preparation, pointing to an important source for transmission.

Quinolone resistance mechanisms in Salmonella enterica serovars Hadar, Kentucky, Virchow, Schwarzengrund, and 4,5,12:i:-, isolated from humans in Switzerland, and identification of a novel qnrD variant, qnrD2, in S. Hadar.

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