Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours... more Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA h...
Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involv... more Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains a...
Cronobacter species are considered an opportunistic group of foodborne pathogenic bacteria capabl... more Cronobacter species are considered an opportunistic group of foodborne pathogenic bacteria capable of causing both intestinal and systemic human disease. This review describes common virulence themes shared among the seven Cronobacter species and describes multiple exoproteins secreted by Cronobacter, many of which are bacterial toxins that may play a role in human disease. The review will particularly concentrate on the virulence factors secreted by C. sakazakii, C. malonaticus, and C. turicensis, which are the primary human pathogens of interest. It has been discovered that various species-specific virulence factors adversely affect a wide range of eukaryotic cell processes including protein synthesis, cell division, and ion secretion. Many of these factors are toxins which have been shown to also modulate the host immune response. These factors are encoded on a variety of mobile genetic elements such as plasmids and transposons; this genomic plasticity implies ongoing re-assortme...
Bacteria belonging to the genus Cronobacter have been recognized as causative agents of life-thre... more Bacteria belonging to the genus Cronobacter have been recognized as causative agents of life-threatening systemic infections primarily in premature and low-birthweight neonates. Validation of putative bacterial virulence components as well as host factors potentially involved in the response to infection has been hampered in the past by the availability of suitable neonatal animal models. In the current study, the zebrafish embryo model was employed to study the interaction of the zinc metalloproteinase Zpx present in Cronobacter turicensis LMG 23827 , with the eukaryotic MMP-9, a proteinase that functions to cleave extracellular matrix gelatin and collagen. Cleavage and activation of the human recombinant pro-MMP-9 by zpx-expressing C. turicensis cells were demonstrated in vitro, and the presence and increase of the processed, active form of zebrafish pro-MMP-9 were shown in vivo. We provided evidence that Zpx induces the expression of the mmp-9 but also increases the levels of pro...
Malonate utilization, an important differential trait, well recognized as being possessed by six ... more Malonate utilization, an important differential trait, well recognized as being possessed by six of the seven species is thought to be largely absent in (Csak). The current study provides experimental evidence that confirms the presence of a malonate utilization operon in 24 strains of sequence type (ST) 64, obtained from Europe, Middle East, China, and USA; it offers explanations regarding the genomic diversity and phylogenetic relatedness among these strains, and that of other strains. In this study, the presence of a malonate utilization operon in these strains was initially identified by DNA microarray analysis (MA) out of a pool of 347 strains obtained from various surveillance studies involving clinical, spices, milk powder sources and powdered infant formula production facilities in Ireland and Germany, and dried dairy powder manufacturing facilities in the USA. All ST64 strains tested could utilize malonate. Zebrafish embryo infection studies showed that ST64 strains are as ...
Cronobacter (C.) sakazakii is an opportunistic pathogen and has been associated with serious infe... more Cronobacter (C.) sakazakii is an opportunistic pathogen and has been associated with serious infections with high mortality rates predominantly in pre-term, low-birth weight and/or immune compromised neonates and infants. Infections have been epidemiologically linked to consumption of intrinsically and extrinsically contaminated lots of reconstituted powdered infant formula (PIF), thus contamination of such products is a challenging task for the PIF producing industry. We present the draft genome of C. sakazakii H322, a highly persistent sequence type (ST) 83, clonal complex (CC) 65, serotype O:7 strain obtained from a batch of non-released contaminated PIF product. The presence of this strain in the production environment was traced back more than 4 years. Whole genome sequencing (WGS) of this strain together with four more ST83 strains (PIF production environment-associated) confirmed a high degree of sequence homology among four of the five strains. Phylogenetic analysis using mi...
Antimicrobial resistance and infection control, 2017
The extent of the occurrence of the plasmid-encoded colistin resistance genes mcr-1 and mcr-2 amo... more 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. 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. 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. 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 ...
Cronobacter (previously known as Enterobacter sakazakii) is a genus of Gram-negative, facultative... more Cronobacter (previously known as Enterobacter sakazakii) is a genus of Gram-negative, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped bacteria of the family Enterobacteriaceae. These organisms cause a variety of illnesses such as meningitis, necrotizing enterocolitis, and septicemia in neonates and infants, and urinary tract, wound, abscesses or surgical site infections, septicemia, and pneumonia in adults. The total gene content of 379 strains of Cronobacter spp. and taxonomically-related isolates was determined using a recently reported DNA microarray. The Cronobacter microarray as a genotyping tool gives the global food safety community a rapid method to identify and capture the total genomic content of outbreak isolates for food safety, environmental, and clinical surveillance purposes. It was able to differentiate the seven Cronobacter species from one another and from non-Cronobacter species. The microarray was also able to cluster strains within each ...
Here, we report the draft genome sequence of the lactose-negative, rifampin-resistant, Escherichi... more 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.
We present the draft genome of Escherichia coli S51, a colistin-resistant extended-spectrum β-lac... more We present the draft genome of Escherichia coli S51, a colistin-resistant extended-spectrum β-lactamase-producing strain isolated in 2015 from raw chicken meat imported from Germany. Assembly and annotation of this draft genome resulted in a 4,994,918-bp chromosome and revealed a chromosomally encoded mcr-1 gene responsible for the colistin resistance of the strain.
Ready-to-eat (RTE) prepacked salads and fruit have been successfully marketed for the last decade... more 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 im...
Cronobacter sakazakii is a food-borne pathogenic bacterium that may cause severe illness in neona... more Cronobacter sakazakii is a food-borne pathogenic bacterium that may cause severe illness in neonates and the elderly. We present the genome sequence of a rare strain (ST40, CC45), commonly found in multiple food processing facilities and in powdered infant formula and only indicted in a single clinical case.
Human isolates of Salmonella enterica serovars Hadar, Kentucky, Virchow, Schwarzengrund, and the ... more 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.
We report the draft genome sequence of Enterobacter helveticus strain LMG 23733, isolated from fr... more We report the draft genome sequence of Enterobacter helveticus strain LMG 23733, isolated from fruit powder. The draft genome assembly for E. helveticus strain LMG 23733 has a size of 4,635,476 bp and a G+C content of 55.9%.
Extended-spectrum β-lactamase (ESBL)-encoding genes are frequently mapped to plasmids, yet few of... more Extended-spectrum β-lactamase (ESBL)-encoding genes are frequently mapped to plasmids, yet few of these structures have been characterized at the molecular level, to date. Eighty-seven ESBL-producing Escherichia coli were isolated from fecal samples of food-producing animals and healthy humans in Switzerland from 2009 to 2011. Plasmid DNA of all isolates was purified. Broth mating assays were carried out individually for 32 isolates to determine if the ESBL marker could be transferred by conjugation. The plasmid sizes were determined by S1-nuclease pulsed-field gel electrophoresis (PFGE) and the plasmids were typed by PCR-based replicon typing. Susceptibility tests by disk diffusion followed with a re-analysis S1-nuclease PFGE and PCRs were performed to confirm plasmid transfer. Microarray was performed to detect additional antibiotic resistance markers and multi-locus sequence typing was also performed in selected donor strains. The phylotypes were identified by triplex PCR. About ...
We report the draft genome sequences of the Enterobacter pulveris strains 601/05(T) (=LMG24057(T)... more We report the draft genome sequences of the Enterobacter pulveris strains 601/05(T) (=LMG24057(T) =DSM19144(T)) and 1160/04 (=LMG24058 =DSM19146), isolated from fruit powder. The genome assemblies for the E. pulveris type strain, LMG24057, and strain LMG24058 have sizes of 4,708,624 and 4,811,103 bp and G+C contents of 56.6% and 56.5%, respectively.
Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours... more Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA h...
Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involv... more Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains a...
Cronobacter species are considered an opportunistic group of foodborne pathogenic bacteria capabl... more Cronobacter species are considered an opportunistic group of foodborne pathogenic bacteria capable of causing both intestinal and systemic human disease. This review describes common virulence themes shared among the seven Cronobacter species and describes multiple exoproteins secreted by Cronobacter, many of which are bacterial toxins that may play a role in human disease. The review will particularly concentrate on the virulence factors secreted by C. sakazakii, C. malonaticus, and C. turicensis, which are the primary human pathogens of interest. It has been discovered that various species-specific virulence factors adversely affect a wide range of eukaryotic cell processes including protein synthesis, cell division, and ion secretion. Many of these factors are toxins which have been shown to also modulate the host immune response. These factors are encoded on a variety of mobile genetic elements such as plasmids and transposons; this genomic plasticity implies ongoing re-assortme...
Bacteria belonging to the genus Cronobacter have been recognized as causative agents of life-thre... more Bacteria belonging to the genus Cronobacter have been recognized as causative agents of life-threatening systemic infections primarily in premature and low-birthweight neonates. Validation of putative bacterial virulence components as well as host factors potentially involved in the response to infection has been hampered in the past by the availability of suitable neonatal animal models. In the current study, the zebrafish embryo model was employed to study the interaction of the zinc metalloproteinase Zpx present in Cronobacter turicensis LMG 23827 , with the eukaryotic MMP-9, a proteinase that functions to cleave extracellular matrix gelatin and collagen. Cleavage and activation of the human recombinant pro-MMP-9 by zpx-expressing C. turicensis cells were demonstrated in vitro, and the presence and increase of the processed, active form of zebrafish pro-MMP-9 were shown in vivo. We provided evidence that Zpx induces the expression of the mmp-9 but also increases the levels of pro...
Malonate utilization, an important differential trait, well recognized as being possessed by six ... more Malonate utilization, an important differential trait, well recognized as being possessed by six of the seven species is thought to be largely absent in (Csak). The current study provides experimental evidence that confirms the presence of a malonate utilization operon in 24 strains of sequence type (ST) 64, obtained from Europe, Middle East, China, and USA; it offers explanations regarding the genomic diversity and phylogenetic relatedness among these strains, and that of other strains. In this study, the presence of a malonate utilization operon in these strains was initially identified by DNA microarray analysis (MA) out of a pool of 347 strains obtained from various surveillance studies involving clinical, spices, milk powder sources and powdered infant formula production facilities in Ireland and Germany, and dried dairy powder manufacturing facilities in the USA. All ST64 strains tested could utilize malonate. Zebrafish embryo infection studies showed that ST64 strains are as ...
Cronobacter (C.) sakazakii is an opportunistic pathogen and has been associated with serious infe... more Cronobacter (C.) sakazakii is an opportunistic pathogen and has been associated with serious infections with high mortality rates predominantly in pre-term, low-birth weight and/or immune compromised neonates and infants. Infections have been epidemiologically linked to consumption of intrinsically and extrinsically contaminated lots of reconstituted powdered infant formula (PIF), thus contamination of such products is a challenging task for the PIF producing industry. We present the draft genome of C. sakazakii H322, a highly persistent sequence type (ST) 83, clonal complex (CC) 65, serotype O:7 strain obtained from a batch of non-released contaminated PIF product. The presence of this strain in the production environment was traced back more than 4 years. Whole genome sequencing (WGS) of this strain together with four more ST83 strains (PIF production environment-associated) confirmed a high degree of sequence homology among four of the five strains. Phylogenetic analysis using mi...
Antimicrobial resistance and infection control, 2017
The extent of the occurrence of the plasmid-encoded colistin resistance genes mcr-1 and mcr-2 amo... more 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. 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. 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. 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 ...
Cronobacter (previously known as Enterobacter sakazakii) is a genus of Gram-negative, facultative... more Cronobacter (previously known as Enterobacter sakazakii) is a genus of Gram-negative, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped bacteria of the family Enterobacteriaceae. These organisms cause a variety of illnesses such as meningitis, necrotizing enterocolitis, and septicemia in neonates and infants, and urinary tract, wound, abscesses or surgical site infections, septicemia, and pneumonia in adults. The total gene content of 379 strains of Cronobacter spp. and taxonomically-related isolates was determined using a recently reported DNA microarray. The Cronobacter microarray as a genotyping tool gives the global food safety community a rapid method to identify and capture the total genomic content of outbreak isolates for food safety, environmental, and clinical surveillance purposes. It was able to differentiate the seven Cronobacter species from one another and from non-Cronobacter species. The microarray was also able to cluster strains within each ...
Here, we report the draft genome sequence of the lactose-negative, rifampin-resistant, Escherichi... more 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.
We present the draft genome of Escherichia coli S51, a colistin-resistant extended-spectrum β-lac... more We present the draft genome of Escherichia coli S51, a colistin-resistant extended-spectrum β-lactamase-producing strain isolated in 2015 from raw chicken meat imported from Germany. Assembly and annotation of this draft genome resulted in a 4,994,918-bp chromosome and revealed a chromosomally encoded mcr-1 gene responsible for the colistin resistance of the strain.
Ready-to-eat (RTE) prepacked salads and fruit have been successfully marketed for the last decade... more 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 im...
Cronobacter sakazakii is a food-borne pathogenic bacterium that may cause severe illness in neona... more Cronobacter sakazakii is a food-borne pathogenic bacterium that may cause severe illness in neonates and the elderly. We present the genome sequence of a rare strain (ST40, CC45), commonly found in multiple food processing facilities and in powdered infant formula and only indicted in a single clinical case.
Human isolates of Salmonella enterica serovars Hadar, Kentucky, Virchow, Schwarzengrund, and the ... more 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.
We report the draft genome sequence of Enterobacter helveticus strain LMG 23733, isolated from fr... more We report the draft genome sequence of Enterobacter helveticus strain LMG 23733, isolated from fruit powder. The draft genome assembly for E. helveticus strain LMG 23733 has a size of 4,635,476 bp and a G+C content of 55.9%.
Extended-spectrum β-lactamase (ESBL)-encoding genes are frequently mapped to plasmids, yet few of... more Extended-spectrum β-lactamase (ESBL)-encoding genes are frequently mapped to plasmids, yet few of these structures have been characterized at the molecular level, to date. Eighty-seven ESBL-producing Escherichia coli were isolated from fecal samples of food-producing animals and healthy humans in Switzerland from 2009 to 2011. Plasmid DNA of all isolates was purified. Broth mating assays were carried out individually for 32 isolates to determine if the ESBL marker could be transferred by conjugation. The plasmid sizes were determined by S1-nuclease pulsed-field gel electrophoresis (PFGE) and the plasmids were typed by PCR-based replicon typing. Susceptibility tests by disk diffusion followed with a re-analysis S1-nuclease PFGE and PCRs were performed to confirm plasmid transfer. Microarray was performed to detect additional antibiotic resistance markers and multi-locus sequence typing was also performed in selected donor strains. The phylotypes were identified by triplex PCR. About ...
We report the draft genome sequences of the Enterobacter pulveris strains 601/05(T) (=LMG24057(T)... more We report the draft genome sequences of the Enterobacter pulveris strains 601/05(T) (=LMG24057(T) =DSM19144(T)) and 1160/04 (=LMG24058 =DSM19146), isolated from fruit powder. The genome assemblies for the E. pulveris type strain, LMG24057, and strain LMG24058 have sizes of 4,708,624 and 4,811,103 bp and G+C contents of 56.6% and 56.5%, respectively.
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