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Background In the last decade, the growth of the pig-farming industry has led to an increase in antibiotic use, including several used in human medicine, e.g. (fluoro)quinolones. Data from several studies suggest that there is a link between the agricultural use of antibiotics and the prevalence of antibiotic-resistant bacteria in the pig farm environment, including (fluoro)quinolone resistance. This poses a threat to human and animal health. Our goal was to phenotypically and genotypically characterize 174 E. coli showing non-susceptibility to quinolones isolated from environmental samples from pig farms. Antimicrobial susceptibility testing (AST) was performed using the disk diffusion method. PCR and sequence analysis were performed to identify chromosomal mutations in the quinolone resistance-determining regions (QRDR) of gyrA and the isolates were screened for the presence of the plasmid-mediated quinolone resistance (PMQR) genes aac-(6')-Ib-cr, qepA, qnrA, qnrB, qnrC, qnrD and qnrS. Strain relatedness was assessed by phylogenetic classification and multilocus sequence typing (MLST). Results Of 174 isolates, 81% (n = 141) were resistant to nalidixic acid, and 19% (n = 33) were intermediately resistant. Overall, 68.4% (n = 119) were multidrug resistant. This study revealed a prevalence of 79.9% (n = 139) for gyrA QRDR mutations, and detected 21.8% (n = 38) isolates with at least one PMQR gene. The two most frequently detected PMQR genes were qnrB and qnrS (13.8% (n = 24) and 9.8% (n = 17, respectively). E. coli belonging to phylogenetic group A (48.3%/n = 84) and group B1 (33.3% /n = 58) were the most frequent. E. coli ST10 (n = 20) and ST297 (n = 20) were the most common STs. Conclusions E. coli with non-susceptibility to quinolones are widespread among the environment of Swiss pig farms and are often associated with an MDR phenotype. In several cases these isolates possess at least one PMQR gene, which could spread by horizontal gene transfer. E. coli from pig farms have diverse STs, some of which are associated with human and animal disease. Electronic supplementary material The online version of this article (10.1186/s40813-019-0116-y) contains supplementary material, which is available to authorized users.

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 stx1 and stx2 by the Assurance GDS MPX ID assay. STEC strains were isolated and serotyped by the E. coli SeroGenoTyping AS-1 kit. The determination of stx subtypes was performed with conventional PCR amplification. Screening for eae, aggR, elt, and estIa/Ib was performed by real-time PCR. Nine (12.9%) of the flour samples tested positive for stx by 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 stx1a and 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.

Data on the occurrence, population structure and toxinogenic potential of Bacillus cereus sensu lato isolated from flour is essential to enable improved risk assessment. We aimed to provide data on the occurrence of B. cereus sensu lato in flour products at retail level. In addition, we screened the isolates for Bacillus thuringiensis and Bacillus cytotoxicus and determined population structure and toxin gene profiles. We screened 89 flour products for presence of B. cereus sensu lato, resulting in 75 positive samples (84%). We were able to show that the population structure of members of the B. cereus group isolated from flour is highly diverse. Isolates were assigned to panC types II (4%), III (21%), IV (39%) and V (36%). Production of parasporal crystals characteristic for Bacillus thuringiensis was detected in seven isolates assigned to panC type III, IV and V. No B. cytotoxicus were detected. Two of the isolates harbored ces encoding cereulide, which causes the emetic syndrome. Various enterotoxin genes were found, with all isolates harboring nhe, 75% of isolates harboring hbl and 51% of the isolates harboring cytK-2. Our findings suggest that toxinogenic B. cereus sensu lato are common in flour products at retail level.

This study was conducted to determine the distribution of antimicrobial resistance among Escherichia coli isolated from feces of healthy dromedary camels in Kenya. A total of 162 fecal samples were cultivated for E. coli. Samples were also subcultivated to detect E. coli with extended-spectrum ß-lactamases (ESBLs). Antimicrobial susceptibility testing (AST) was performed by disk diffusion using a panel of 16 antimicrobials. In addition, isolates were screened for the presence of the plasmid-mediated colistin resistance genes mcr-1 to mcr-5.Samples from 20 (12.4%) of the camels contained antimicrobial resistant (AMR) E. coli, and 85% of the AMR isolates were multidrug resistant (MDR). The highest frequency of resistance was observed to tetracycline (11.7%), followed by ampicillin and streptomycin (both 10.5%), and sulfamethoxazole/trimethoprim (9.9%). Two (1.2%) of the isolates showed intermediate resistance to cefazolin and streptomycin, respectively. All the isolates were susceptible to amoxycillin/clavulanic acid, ciprofloxacin, fosfomycin, aztreonam and kanamycin, and 86.4% of the isolates were susceptible to all 16 antimicrobials used in this study. The prevalence of fecal carriage of ESBL producing E. coli was 0.6%. PCR and amplicon sequencing showed that the ESBL producer belonged to E. coli phylogenetic group A, sequence type (ST) 48, and harbored blaCTX-M-15. None of the isolates contained mcr genes. The results indicate that dromedary camels in Kenya may be reservoirs of AMR E. coli, including ESBL producers, that could potentially be transmitted to humans by direct contact or via the food chain. Keywords: Kenya, Dromedary camels, Escherichia coli, Antimicrobial resistance, ESBL

A total of 294 fecal swabs from 294 wild birds in Switzerland were cultivated for antimicrobial resistant (AMR) Escherichia coli. Samples were also subcultivated to detect E. coli with extended‐spectrum β‐lactamases (ESBL), carbapenemases, and plasmid‐mediated aminoglycoside or colistin resistance, respectively. Samples from 17 (5.8%) of the birds contained 19 AMR E. coli, whereof 26.3% were multidrug resistant. Five (1.7%) ESBL‐producing E. coli were detected. The isolates harbored bla CTX‐M‐1 (two isolated from carrion crows and from one great spotted woodpecker, respectively), bla CTX‐M‐15 (originating from a grey heron), bla CTX‐M‐55 (from a carrion crow), and bla CTX‐M‐65 (from a common blackbird). Phylogenetic analysis assigned three isolates to commensal phylogroups A and B1, one to extraintestinal pathogenic group B2, and one to phylogroup F. Multilocus sequence typing identified sequence types (STs) that have been found previously in ESBL E. coli in wild birds (ST58, ST205, ST540). One isolate harboring bla CTX‐M‐55 was assigned to the recently emerged fluoroquinolone‐resistant, extraintestinal pathogenic E. coli clone ST1193. Wild birds have the potential to disperse AMR, including clinically important resistance genes, from anthropogenic‐influenced habitats to diverse areas, including vulnerable natural environments such as surface waters or mountain regions., Of 294 fecal samples from resident and short‐distance migratory wild birds, 5.8% contained antimicrobial resistant (AMR) Escherichia coli. Moreover, 1.7% of the samples yielded E. coli producing the extended‐spectrum β‐lactamases CTX‐M‐1, CTX‐M‐15, CTX‐M‐55, or CTX‐M‐65. Wild birds have the potential to disperse AMR bacteria from anthropogenic‐influenced habitats to diverse areas, including vulnerable natural environments such as surface waters or mountain regions.