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Martin received a veterinary degree and a doctorate in Veterinary Medicine from the Ludwig-Maximilians University in Munich, and a Ph.D. in Food Science from Cornell, where he currently is the Gellert Family Professor of Food Safety. His research interests focus on farm-to-table microbial food quality and food safety and the application of molecular tools to study the transmission of foodborne pathogens and spoilage organisms. His team has published 400 peer reviewed publications, which have been cited >10,000 times. He and his team are regularly asked to help industry with a range of microbial food safety and quality challenges. He received the Young Scholars award from the American Dairy Science Association in 2002, the Samuel Cate Prescott Award from Institute of Food Technologists’ in 2003, the International Life Science Institute North America Future Leaders Award in 2004, and the American Meat Institute Foundation Scientific Achievement Award in 2011. He is a fellow of the American Association for the Advancement of Science (AAAS), a fellow of the Institute of Food Technologists (IFT), a fellow of the American Academy of Microbiology (AAM), and a member of the International Academy of Food Science and Technology.
Natural bacterial populations can display enormous genomic diversity, primarily in the form of gene content variation caused by the frequent exchange of DNA with the local environment. However, the ecological drivers of genomic variability and the role of selection remain controversial. Here, we address this gap by developing a nationwide atlas of 1,854 Listeria isolates, collected systematically from soils across the contiguous United States. We found that Listeria was present across a wide range of environmental parameters, being mainly controlled by soil moisture, molybdenum and salinity concentrations. Whole-genome data from 594 representative strains allowed us to decompose Listeria diversity into 12 phylogroups, each with large differences in habitat breadth and endemism. ‘Cosmopolitan’ phylogroups, prevalent across many different habitats, had more open pangenomes and displayed weaker linkage disequilibrium, reflecting higher rates of gene gain and loss, and allele exchange than phylogroups with narrow habitat ranges. Cosmopolitan phylogroups also had a large fraction of genes affected by positive selection. The effect of positive selection was more pronounced in the phylogroup-specific core genome, suggesting that lineage-specific core genes are important drivers of adaptation. These results indicate that genome flexibility and recombination are the consequence of selection to survive in variable environments. A population genomic analysis of 1,854 Listeria soil isolates collected across the contiguous United States identifies geographically prevalent phylogroups with increased pangenome openness and recombination, as a result of adaptation to variable environments.
Jingqiu Liao; Xiaodong Guo; Daniel L. Weller; Shaul Pollak; Daniel H. Buckley; Martin Wiedmann; Otto X. Cordero. Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution. Nature Microbiology 2021, 6, 1021 -1030.
AMA StyleJingqiu Liao, Xiaodong Guo, Daniel L. Weller, Shaul Pollak, Daniel H. Buckley, Martin Wiedmann, Otto X. Cordero. Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution. Nature Microbiology. 2021; 6 (8):1021-1030.
Chicago/Turabian StyleJingqiu Liao; Xiaodong Guo; Daniel L. Weller; Shaul Pollak; Daniel H. Buckley; Martin Wiedmann; Otto X. Cordero. 2021. "Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution." Nature Microbiology 6, no. 8: 1021-1030.
Tracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of the microbial composition.
Erika Ganda; Kristen L. Beck; Niina Haiminen; Justin D. Silverman; Ban Kawas; Brittany D. Cronk; Renee R. Anderson; Laura B. Goodman; Martin Wiedmann. DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid. mSystems 2021, 6, e0061921 .
AMA StyleErika Ganda, Kristen L. Beck, Niina Haiminen, Justin D. Silverman, Ban Kawas, Brittany D. Cronk, Renee R. Anderson, Laura B. Goodman, Martin Wiedmann. DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid. mSystems. 2021; 6 (3):e0061921.
Chicago/Turabian StyleErika Ganda; Kristen L. Beck; Niina Haiminen; Justin D. Silverman; Ban Kawas; Brittany D. Cronk; Renee R. Anderson; Laura B. Goodman; Martin Wiedmann. 2021. "DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid." mSystems 6, no. 3: e0061921.
Catharine R. Carlin; Jingqiu Liao; Daniel L. Weller; Xiaodong Guo; Renato Orsi; Martin Wiedmann. Corrigendum: Listeria cossartiae sp. nov., Listeria farberi sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov., isolated from agricultural water and natural environments. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 2021, 71, 004885 .
AMA StyleCatharine R. Carlin, Jingqiu Liao, Daniel L. Weller, Xiaodong Guo, Renato Orsi, Martin Wiedmann. Corrigendum: Listeria cossartiae sp. nov., Listeria farberi sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov., isolated from agricultural water and natural environments. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. 2021; 71 (6):004885.
Chicago/Turabian StyleCatharine R. Carlin; Jingqiu Liao; Daniel L. Weller; Xiaodong Guo; Renato Orsi; Martin Wiedmann. 2021. "Corrigendum: Listeria cossartiae sp. nov., Listeria farberi sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov., isolated from agricultural water and natural environments." INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 71, no. 6: 004885.
Classification of bacterial pathogens into species has traditionally been an essential prerequisite for many aspects of infection control and food safety. Consequently, control measures, regulations, industry specifications, and other guidance documents for foodborne pathogens typically specify a pathogen species (or genus) as target. For example, current Codex Alimentarius guidelines recommend absence of Salmonella in two 375 g samples for infant formula (FAO, 2020). For other ready-to-eat (RTE) foods, absence in smaller samples size (e.g., 25 g) is typically expected. However, there is increasing evidence for Salmonella, as well as other foodborne pathogens, that subgroups, serovars, and/or clonal groups within a given species may differ considerably in their ability to cause human disease. Importantly, there is emerging evidence that use of “sub-species” (or “sub-genus”) classification for defining food safety hazards may allow for more effective management of foodborne pathogens. The genus Salmonella, a pathogen where all members of the genus are considered a food safety hazard, represents one key foodborne pathogen where there is increasing evidence that subtypes differ considerably in their likelihood of causing human disease and where science-based subtype-specific and risk-based approaches of control may have a positive public health impact. There is clear evidence that certain Salmonella subtypes (e.g., certain subtypes within serovars Kentucky and Cerro) show reduced human virulence, while being frequently isolated from food animal species (specifically poultry and cattle) (Rodriguez-Rivera et al., 2014; Haley et al., 2016). Additionally, under the current approach of considering all Salmonella equally likely to cause human disease, limited progress has been made worldwide to reduce foodborne salmonellosis cases (Havelaar et al., 2015; Tack et al., 2020). In some situations, there are counterproductive incentives to prioritize control of highly frequent Salmonella strains with limited human public health relevance (e.g., through poultry vaccines targeting S. Kentucky) over control of less frequent Salmonella strains commonly linked to human salmonellosis cases. We outline a new paradigm for incorporating strain-specific assessment of human public health significance into regulations and control strategies, which we propose should be used to incentivize control of Salmonella subtypes with the greatest public health impact, with a focus on pre-harvest control in meat and poultry. This paradigm could subsequently be applied to other foodborne pathogens, such as Listeria monocytogenes. The genus Salmonella consists of two species, Salmonella enterica and Salmonella bongori; S. enterica can be further divided into six recognized subspecies, the most clinically relevant of which is S. enterica subsp. enterica (Worley et al., 2018), a pathogen of warm-blooded mammals including humans. Within S. enterica subsp. enterica (hereafter referred to as “S.”), there are >1,500 serovars (Issenhuth-Jeanjean et al., 2014), which differ in their ability to cause human disease (Brenner et al., 2000). Typhoidal (i.e., S. Typhi) and paratyphoidal (e.g., S. Paratyphi A) serovars cause a systemic illness characterized by fever, headache, malaise, abdominal pain, and rash, while non-typhoidal serovars (e.g., S. Typhimurium) typically cause a self-limiting gastroenteritis. Additionally, S. Typhi and S. Paratyphi A are considered to be human-restricted (i.e., they only cause disease in and are spread by humans) serovars and are typically transmitted through food and/or water contaminated with human feces due to poor sanitation. Non-typhoidal serovars on the other hand are transmitted through both direct animal contact and food (as well as fomites) with contamination often linked to animal hosts and foods derived from warm-blooded animals (e.g., raw meat and poultry, raw eggs, raw milk and dairy products products) (Gal-Mor et al., 2014). However, a variety of foods have been sources of non-typhoidal Salmonella cases and outbreaks, including fruits and vegetables as well as dry products (e.g., spices, chocolate) and non-typhoidal Salmonella have been shown to also survive for extended times in extra-host environments such as soil and even processing plant environments (Waldner et al., 2012; Jechalke et al., 2019). Because typhoidal and paratyphoidal serovars typically cause systemic disease, they have traditionally been considered a higher public health risk than non-typhoidal serovars. Non-typhoidal serovars, despite differing in their ability to cause disease in humans, are considered an equal public health risk. With this current approach, efforts to decrease Salmonella human clinical cases in the United States have essentially failed (Tack et al., 2020). While Healthy People (2020) targeted a reduction in Salmonella incidence from 15.0 cases to 11.4 cases per 100,000 people by 2020, Salmonella incidence reached 17.1 cases per 100,000 people in 2019 (Tack et al., 2020). Similarly, at a global level, Salmonella continues to be the foodborne pathogen with the greatest public health impact based on disability-adjusted life years (Havelaar et al., 2015). While regulations in many countries consider all non-typhoidal Salmonella (NTS) serovars a hazard and equal public health risk, there is strong scientific evidence that NTS serovars and clonal groups differ in the public health risk they represent, as supported by (i) presence or absence of virulence genes that encode fully functional virulence factors; (ii) phenotypic data (e.g., in tissue culture or animal models); and (iii) epidemiological evidence (e.g., under-representation of certain serovars or clonal groups among human clinical cases relative to their presence in food, raw materials, or animals). Salmonella serovars or clonal groups may also show strong geographical associations which may need to be taken into...
Alexa R. Cohn; Rachel A. Cheng; Renato H. Orsi; Martin Wiedmann. Moving Past Species Classifications for Risk-Based Approaches to Food Safety: Salmonella as a Case Study. Frontiers in Sustainable Food Systems 2021, 5, 1 .
AMA StyleAlexa R. Cohn, Rachel A. Cheng, Renato H. Orsi, Martin Wiedmann. Moving Past Species Classifications for Risk-Based Approaches to Food Safety: Salmonella as a Case Study. Frontiers in Sustainable Food Systems. 2021; 5 ():1.
Chicago/Turabian StyleAlexa R. Cohn; Rachel A. Cheng; Renato H. Orsi; Martin Wiedmann. 2021. "Moving Past Species Classifications for Risk-Based Approaches to Food Safety: Salmonella as a Case Study." Frontiers in Sustainable Food Systems 5, no. : 1.
The foodborne pathogen Listeria monocytogenes is able to survive across a wide range of intra- and extra-host environments by appropriately modulating gene expression patterns in response to different stimuli. Positive Regulatory Factor A (PrfA) is the major transcriptional regulator of virulence gene expression in L. monocytogenes. It has long been known that activated charcoal is required to induce the expression of PrfA-regulated genes in complex media, such as Brain Heart Infusion (BHI), but not in chemically defined media. In this study, we show that the expression of the PrfA-regulated hly, which encodes listeriolysin O, is induced 5- and 8-fold in L. monocytogenes cells grown in Chelex-treated BHI (Ch-BHI) and in the presence of activated charcoal (AC-BHI), respectively, relative to cells grown in BHI medium. Specifically, we show that metal ions present in BHI broth plays a role in the reduced expression of the PrfA regulon. In addition, we show that expression of hly is induced when the levels of bioavailable extra- or intercellular iron are reduced. L. monocytogenes cells grown Ch-BHI and AC-BHI media showed similar levels of resistance to the iron-activated antibiotic, streptonigrin, indicating that activated charcoal reduces the intracellular labile iron pool. Metal depletion and exogenously added glutathione contributed synergistically to PrfA-regulated gene expression since glutathione further increased hly expression in metal-depleted BHI but not in BHI medium. Analyses of transcriptional reporter fusion expression patterns revealed that genes in the PrfA regulon are differentially expressed in response to metal depletion, metal excess and exogenous glutathione. Our results suggest that metal ion abundance plays a role in modulating expression of PrfA-regulated virulence genes in L. monocytogenes.
Ahmed Gaballa; Sriya Sunil; Etienne Doll; Sarah I. Murphy; Tyler Bechtel; Veronica Guariglia-Oropeza; Martin Wiedmann. Characterization of the roles of activated charcoal and Chelex in the induction of PrfA regulon expression in complex medium. PLOS ONE 2021, 16, e0250989 .
AMA StyleAhmed Gaballa, Sriya Sunil, Etienne Doll, Sarah I. Murphy, Tyler Bechtel, Veronica Guariglia-Oropeza, Martin Wiedmann. Characterization of the roles of activated charcoal and Chelex in the induction of PrfA regulon expression in complex medium. PLOS ONE. 2021; 16 (4):e0250989.
Chicago/Turabian StyleAhmed Gaballa; Sriya Sunil; Etienne Doll; Sarah I. Murphy; Tyler Bechtel; Veronica Guariglia-Oropeza; Martin Wiedmann. 2021. "Characterization of the roles of activated charcoal and Chelex in the induction of PrfA regulon expression in complex medium." PLOS ONE 16, no. 4: e0250989.
Listeria monocytogenes can regulate and fine-tune gene expression, to adapt to diverse stress conditions encountered during foodborne transmission. To further understand the contributions of alternative sigma (σ) factors to the regulation of L. monocytogenes gene expression, RNA-Seq was performed on L. monocytogenes strain 10403S and five isogenic mutants (four strains bearing in-frame null mutations in three out of four alternative σ factor genes, ΔCHL, ΔBHL, ΔBCL, and ΔBCH, and one strain bearing null mutations in all four genes, ΔBCHL), grown to stationary phase. Our data showed that 184, 35, 34, and 20 genes were positively regulated by σB, σL, σH, and σC (posterior probability > 0.9 and Fold Change (FC) > 5.0), respectively. Moreover, σB-dependent genes showed the highest FC (based on comparisons between the ΔCHL and the ΔBCHL strain), with 44 genes showing an FC > 100; only four σL-dependent, and no σH- or σC-dependent genes showed FC >100. While σB-regulated genes identified in this study are involved in stress-associated functions and metabolic pathways, σL appears to largely regulate genes involved in a few specific metabolic pathways, including positive regulation of operons encoding phosphoenolpyruvate (PEP)-dependent phosphotransferase systems (PTSs). Overall, our data show that (i) σB and σL directly and indirectly regulate genes involved in several energy metabolism-related functions; (ii) alternative σ factors are involved in complex regulatory networks and appear to have epistatic effects in stationary phase cells; and (iii) σB regulates multiple stress response pathways, while σL and σH positively regulate a smaller number of specific pathways.
Renato Orsi; Soraya Chaturongakul; Haley Oliver; Lalit Ponnala; Ahmed Gaballa; Martin Wiedmann. Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in Listeria monocytogenes under Stationary Phase Stress Condition. Pathogens 2021, 10, 411 .
AMA StyleRenato Orsi, Soraya Chaturongakul, Haley Oliver, Lalit Ponnala, Ahmed Gaballa, Martin Wiedmann. Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in Listeria monocytogenes under Stationary Phase Stress Condition. Pathogens. 2021; 10 (4):411.
Chicago/Turabian StyleRenato Orsi; Soraya Chaturongakul; Haley Oliver; Lalit Ponnala; Ahmed Gaballa; Martin Wiedmann. 2021. "Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in Listeria monocytogenes under Stationary Phase Stress Condition." Pathogens 10, no. 4: 411.
Spoilage of HTST- (high-temperature, short-time) and vat- pasteurized fluid milk due to introduction of Gram-negative bacteria post-pasteurization remains a challenge for the dairy industry. While processing facility level practices (e.g., sanitation practices) are known to impact the frequency of post-pasteurization contamination (PPC), the relative importance of different practices is not well defined, affecting the ability of facilities to select intervention targets that reduce PPC and provide the greatest return on investment. Thus, the goal of this study was to use an existing longitudinal dataset of bacterial spoilage indicators obtained for pasteurized fluid milk samples collected from 23 processing facilities between July 2015 and November 2017 (with 3 to 5 samplings per facility) and data from a survey on fluid milk quality management practices, to identify factors associated with PPC and rank their relative importance, using two separate approaches: (i) multimodel inference and (ii) conditional random forest. Data pre-processing for multimodel inference analysis showed (i) nearly all factors were significantly associated with PPC when assessed individually using univariable logistic regression and (ii) numerous pairs of factors were strongly associated with each other (Cramer’s V ³0.80). Multimodel inference and conditional random forest analyses identified similar drivers associated with PPC; factors identified as most important based on these analyses included cleaning and sanitation practices, activities related to good manufacturing practices, container type (which is a proxy for different filling equipment), in-house finished product testing, and designation of a quality department, indicating potential targets for reducing PPC. In addition, this study illustrates how machine learning approaches can be used with highly correlated and unbalanced data, as typical for food safety and quality, to facilitate improved data analyses and decision-making.
Sarah Ingersoll Murphy; Samuel J. Reichler; Nicole H. Martin; Kathryn J. Boor; Martin Wiedmann. Machine learning and advanced statistical modeling can identify key quality management practices that affect post-pasteurization contamination of fluid milk. Journal of Food Protection 2021, 1 .
AMA StyleSarah Ingersoll Murphy, Samuel J. Reichler, Nicole H. Martin, Kathryn J. Boor, Martin Wiedmann. Machine learning and advanced statistical modeling can identify key quality management practices that affect post-pasteurization contamination of fluid milk. Journal of Food Protection. 2021; ():1.
Chicago/Turabian StyleSarah Ingersoll Murphy; Samuel J. Reichler; Nicole H. Martin; Kathryn J. Boor; Martin Wiedmann. 2021. "Machine learning and advanced statistical modeling can identify key quality management practices that affect post-pasteurization contamination of fluid milk." Journal of Food Protection , no. : 1.
Contamination of dairy powders with sporeforming bacteria is a concern for dairy processors who wish to penetrate markets with stringent spore count specifications (e.g., infant powders). Despite instituted specifications, no standard methodology is used for spore testing across the dairy industry. Instead, a variety of spore enumeration methods are in use, varying primarily by heat-shock treatments, plating method, recovery medium, and incubation temperature. Importantly, testing the same product using different methodologies leads to differences in spore count outcomes, which is a major issue for those required to meet specifications. As such, we set out to identify method(s) to recommend for standardized milk powder spore testing. To this end, 10 commercial milk powders were evaluated using methods varying by (1) heat treatment (e.g., 80°C/12 min), (2) plating method (e.g., spread plating), (3) medium type (e.g., plate count milk agar), and (4) incubation time and temperature combinations (e.g., 32°C for 48 h). The resulting data set included a total of 48 methods. With this data set, we used a stepwise process to identify optimal method(s) that would explain a high proportion of variance in spore count outcomes and would be practical to implement across the dairy industry. Ultimately, spore pasteurized mesophilic spore count (80°C/12 min, incubated at 32°C for 48 h), highly heat resistant thermophilic spore count (100°C/30 min, incubated at 55°C for 48 h), and specially thermoresistant spore enumeration (106°C/30 min, incubated at 55°C for 48 h) spread plating on plate count milk agar were identified as the optimal method set for reliable enumeration of spores in milk powders. Subsequently, we assessed different powder sampling strategies as a way to reduce variation in powder spore testing outcomes using our recommended method set. Results indicated that 33-g composite sampling may reduce variation in spore testing outcomes for highly heat resistant thermophilic spore count over 11-g and 33-g discrete sampling, whereas there was no significant difference across sampling strategies for specially thermoresistant spore enumeration or spore pasteurized mesophilic spore count. Finally, an interlaboratory study using our recommended method set and a modified method set (using tryptic soy agar with 1% starch) among both university and industry laboratories showed increased variation in spore count outcomes within milk powders, which not only was due to natural variation in powders but also was hypothesized to be due to technical errors, highlighting the need for specialized training for technicians who perform spore testing on milk powders. Overall, this study addresses challenges to milk powder spore testing and recommends a method set for standardized spore testing for implementation across the dairy industry.
S.I. Murphy; D. Kent; J. Skeens; M. Wiedmann; N.H. Martin. A standard set of testing methods reliably enumerates spores across commercial milk powders. Journal of Dairy Science 2021, 104, 2615 -2631.
AMA StyleS.I. Murphy, D. Kent, J. Skeens, M. Wiedmann, N.H. Martin. A standard set of testing methods reliably enumerates spores across commercial milk powders. Journal of Dairy Science. 2021; 104 (3):2615-2631.
Chicago/Turabian StyleS.I. Murphy; D. Kent; J. Skeens; M. Wiedmann; N.H. Martin. 2021. "A standard set of testing methods reliably enumerates spores across commercial milk powders." Journal of Dairy Science 104, no. 3: 2615-2631.
S.J. Reichler; S.I. Murphy; N.H. Martin; M. Wiedmann. Identification, subtyping, and tracking of dairy spoilage-associated Pseudomonas by sequencing the ileS gene. Journal of Dairy Science 2021, 104, 2668 -2683.
AMA StyleS.J. Reichler, S.I. Murphy, N.H. Martin, M. Wiedmann. Identification, subtyping, and tracking of dairy spoilage-associated Pseudomonas by sequencing the ileS gene. Journal of Dairy Science. 2021; 104 (3):2668-2683.
Chicago/Turabian StyleS.J. Reichler; S.I. Murphy; N.H. Martin; M. Wiedmann. 2021. "Identification, subtyping, and tracking of dairy spoilage-associated Pseudomonas by sequencing the ileS gene." Journal of Dairy Science 104, no. 3: 2668-2683.
Our findings suggest that inclusion of multiple pregrowth conditions in inoculation studies can best capture the range of growth and survival patterns expected for Salmonella enterica and Escherichia coli present on produce. This is particularly important for fresh and fresh-cut produce, where stress conditions encountered by pathogens prior to contamination can vary widely, making selection of a typical pregrowth condition virtually impossible.
Anna Sophia Harrand; Veronica Guariglia-Oropeza; Jordan Skeens; David Kent; Martin Wiedmann. Nature versus Nurture: Assessing the Impact of Strain Diversity and Pregrowth Conditions on Salmonella enterica, Escherichia coli, and Listeria Species Growth and Survival on Selected Produce Items. Applied and Environmental Microbiology 2021, 87, 1 .
AMA StyleAnna Sophia Harrand, Veronica Guariglia-Oropeza, Jordan Skeens, David Kent, Martin Wiedmann. Nature versus Nurture: Assessing the Impact of Strain Diversity and Pregrowth Conditions on Salmonella enterica, Escherichia coli, and Listeria Species Growth and Survival on Selected Produce Items. Applied and Environmental Microbiology. 2021; 87 (6):1.
Chicago/Turabian StyleAnna Sophia Harrand; Veronica Guariglia-Oropeza; Jordan Skeens; David Kent; Martin Wiedmann. 2021. "Nature versus Nurture: Assessing the Impact of Strain Diversity and Pregrowth Conditions on Salmonella enterica, Escherichia coli, and Listeria Species Growth and Survival on Selected Produce Items." Applied and Environmental Microbiology 87, no. 6: 1.
Antibiotic resistance (AR) phenotypes and acquired resistance determinants (ARDs) detected by in silico analysis of genome sequences were examined in 55 Shiga toxin-producing Escherichia coli (STEC) isolates representing diverse serotypes recovered from surfaces waters and sediments in a mixed use urban/agricultural landscape in British Columbia, Canada. The isolates displayed decreased susceptibility to florfenicol (65.5%), chloramphenicol (7.3%), tetracycline (52.7%), ampicillin (49.1%), streptomycin (34.5%), kanamycin (20.0%), gentamycin (10.9%), amikacin (1.8%), amoxicillin/clavulanic acid (21.8%), ceftiofur (18.2%), ceftriaxone (3.6%), trimethoprim-sulfamethoxazole (12.7%), and cefoxitin (3.6%). All surface water and sediment isolates were susceptible to ciprofloxacin, nalidixic acid, ertapenem, imipenem and meropenem. Eight isolates (14.6%) were multidrug resistant. ARDs conferring resistance to phenicols (floR), trimethoprim (dfrA), sulfonamides (sul1/2), tetracyclines (tetA/B), and aminoglycosides (aadA and aph) were detected. Additionally, narrow-spectrum β-lactamase blaTEM-1b and extended-spectrum AmpC β-lactamase (cephalosporinase) blaCMY-2 were detected in the genomes, as were replicons from plasmid incompatibility groups IncFII, IncB/O/K/Z, IncQ1, IncX1, IncY and Col156. A comparison with surveillance data revealed that AR phenotypes and ARDs were comparable to those reported in generic E. coli from food animals. Aquatic environments in the region are potential reservoirs for the maintenance and transmission of antibiotic resistant STEC, associated ARDs and their plasmids.
Yvonne Ma; Jessica Chen; Karen Fong; Stephanie Nadya; Kevin Allen; Chad Laing; Kim Ziebell; Ed Topp; Laura Carroll; Martin Wiedmann; Pascal Delaquis; Siyun Wang. Antibiotic Resistance in Shiga Toxigenic Escherichia coli Isolates from Surface Waters and Sediments in a Mixed Use Urban Agricultural Landscape. Antibiotics 2021, 10, 237 .
AMA StyleYvonne Ma, Jessica Chen, Karen Fong, Stephanie Nadya, Kevin Allen, Chad Laing, Kim Ziebell, Ed Topp, Laura Carroll, Martin Wiedmann, Pascal Delaquis, Siyun Wang. Antibiotic Resistance in Shiga Toxigenic Escherichia coli Isolates from Surface Waters and Sediments in a Mixed Use Urban Agricultural Landscape. Antibiotics. 2021; 10 (3):237.
Chicago/Turabian StyleYvonne Ma; Jessica Chen; Karen Fong; Stephanie Nadya; Kevin Allen; Chad Laing; Kim Ziebell; Ed Topp; Laura Carroll; Martin Wiedmann; Pascal Delaquis; Siyun Wang. 2021. "Antibiotic Resistance in Shiga Toxigenic Escherichia coli Isolates from Surface Waters and Sediments in a Mixed Use Urban Agricultural Landscape." Antibiotics 10, no. 3: 237.
Understanding the ecology of enteric bacteria in extrahost environments is important for the development and implementation of strategies to minimize preharvest contamination of produce with enteric pathogens. Our findings suggest that watershed landscape is an important factor influencing the importance of ecological drivers and dispersal patterns of E. coli .
Jingqiu Liao; Peter Bergholz; Martin Wiedmann. Adjacent Terrestrial Landscapes Impact the Biogeographical Pattern of Soil Escherichia coli Strains in Produce Fields by Modifying the Importance of Environmental Selection and Dispersal. Applied and Environmental Microbiology 2021, 87, 1 .
AMA StyleJingqiu Liao, Peter Bergholz, Martin Wiedmann. Adjacent Terrestrial Landscapes Impact the Biogeographical Pattern of Soil Escherichia coli Strains in Produce Fields by Modifying the Importance of Environmental Selection and Dispersal. Applied and Environmental Microbiology. 2021; 87 (6):1.
Chicago/Turabian StyleJingqiu Liao; Peter Bergholz; Martin Wiedmann. 2021. "Adjacent Terrestrial Landscapes Impact the Biogeographical Pattern of Soil Escherichia coli Strains in Produce Fields by Modifying the Importance of Environmental Selection and Dispersal." Applied and Environmental Microbiology 87, no. 6: 1.
Food loss and waste is a major concern in the United States and globally, with dairy foods representing one of the top categories of food lost and wasted. Estimates indicate that in the United States, approximately a quarter of dairy products are lost at the production level or wasted at the retail or consumer level annually. Premature microbial spoilage of dairy products, including fluid milk, cheese, and cultured products, is a primary contributor to dairy food waste. Microbial contamination may occur at various points throughout the production and processing continuum and includes organisms such as gram-negative bacteria (e.g., Pseudomonas), gram-positive bacteria (e.g., Paenibacillus), and a wide range of fungal organisms. These organisms grow at refrigerated storage temperatures, often rapidly, and create various degradative enzymes that result in off-odors, flavors, and body defects (e.g., coagulation), rendering them inedible. Reducing premature dairy food spoilage will in turn reduce waste throughout the dairy continuum. Strategies to reduce premature spoilage include reducing raw material contamination on-farm, physically removing microbial contaminants, employing biocontrol agents to reduce outgrowth of microbial contaminants, tracking and eliminating microbial contaminants using advanced molecular microbiological techniques, and others. This review will address the primary microbial causes of premature dairy product spoilage and methods of controlling this spoilage to reduce loss and waste in dairy products.
N.H. Martin; P. Torres-Frenzel; M. Wiedmann. Invited review: Controlling dairy product spoilage to reduce food loss and waste. Journal of Dairy Science 2021, 104, 1251 -1261.
AMA StyleN.H. Martin, P. Torres-Frenzel, M. Wiedmann. Invited review: Controlling dairy product spoilage to reduce food loss and waste. Journal of Dairy Science. 2021; 104 (2):1251-1261.
Chicago/Turabian StyleN.H. Martin; P. Torres-Frenzel; M. Wiedmann. 2021. "Invited review: Controlling dairy product spoilage to reduce food loss and waste." Journal of Dairy Science 104, no. 2: 1251-1261.
As risk-based approaches are increasingly recognized and used to manage food safety hazards, their implementation requires a recognition and appreciation of residual risk. We define residual risk as the one that remains even after a fully compliant food safety system has been implemented. As true ‘zero risk’ is essentially unattainable, understanding and assessing the residual risks for different products is essential for the different actors involved in the food production system. Understanding residual risk is particularly critical as improved surveillance systems (e.g. facilitated by whole genome sequencing) can detect small outbreaks and potentially link cases to a product, even when they are consequences of residual risk rather than a non-compliant food safety system. Future work on assessing residual risk for different pathogen-food combinations are essential at both the company and governmental level to further fine tune food safety systems with the definition of an acceptable residual risk.
Marcel H Zwietering; Alberto Garre; Martin Wiedmann; Robert L Buchanan. All food processes have a residual risk, some are small, some very small and some are extremely small: zero risk does not exist. Current Opinion in Food Science 2021, 39, 83 -92.
AMA StyleMarcel H Zwietering, Alberto Garre, Martin Wiedmann, Robert L Buchanan. All food processes have a residual risk, some are small, some very small and some are extremely small: zero risk does not exist. Current Opinion in Food Science. 2021; 39 ():83-92.
Chicago/Turabian StyleMarcel H Zwietering; Alberto Garre; Martin Wiedmann; Robert L Buchanan. 2021. "All food processes have a residual risk, some are small, some very small and some are extremely small: zero risk does not exist." Current Opinion in Food Science 39, no. : 83-92.
Salmonella enterica serotype Typhimurium (S. Typhimurium) boasts a broad host range and can be transmitted between livestock and humans. While members of this serotype can acquire resistance to antimicrobials, the temporal dynamics of this acquisition is not well understood. Using New York State (NYS) and its dairy cattle farms as a model system, 87 S. Typhimurium strains isolated from 1999 to 2016 from either human clinical or bovine-associated sources in NYS were characterized using whole-genome sequencing. More than 91% of isolates were classified into one of four major lineages, two of which were largely susceptible to antimicrobials but showed sporadic antimicrobial resistance (AMR) gene acquisition, and two that were largely multidrug-resistant (MDR). All four lineages clustered by presence and absence of elements in the pan-genome. The two MDR lineages, one of which resembled S. Typhimurium DT104, were predicted to have emerged circa 1960 and 1972. The two largely susceptible lineages emerged earlier, but showcased sporadic AMR determinant acquisition largely after 1960, including acquisition of cephalosporin resistance-conferring genes after 1985. These results confine the majority of AMR acquisition events in NYS S. Typhimurium to the twentieth century, largely within the era of antibiotic usage.
Laura M. Carroll; Jana S. Huisman; Martin Wiedmann. Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State. Scientific Reports 2020, 10, 1 -15.
AMA StyleLaura M. Carroll, Jana S. Huisman, Martin Wiedmann. Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State. Scientific Reports. 2020; 10 (1):1-15.
Chicago/Turabian StyleLaura M. Carroll; Jana S. Huisman; Martin Wiedmann. 2020. "Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State." Scientific Reports 10, no. 1: 1-15.
B. cereus is responsible for thousands of cases of foodborne disease each year worldwide, causing two distinct forms of illness: (i) intoxication via cereulide (i.e., emetic syndrome) or (ii) toxicoinfection via multiple enterotoxins (i.e., diarrheal syndrome). Here, we show that emetic B. cereus is not a clonal, homogenous unit that resulted from a single cereulide synthetase gain event followed by subsequent proliferation; rather, cereulide synthetase acquisition and loss is a dynamic, ongoing process that occurs across lineages, allowing some group III B. cereus sensu lato populations to oscillate between diarrheal and emetic foodborne pathogens over the course of their evolutionary histories. We also highlight the care that must be taken when selecting a reference genome for whole-genome sequencing-based investigation of emetic B. cereus sensu lato outbreaks, since some reference genome selections can lead to a confounding loss of resolution and potentially hinder epidemiological investigations.
Laura M. Carroll; Martin Wiedmann. Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group III Bacillus cereus Sensu Lato Facilitate the Transition between Emetic and Diarrheal Foodborne Pathogens. mBio 2020, 11, 1 .
AMA StyleLaura M. Carroll, Martin Wiedmann. Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group III Bacillus cereus Sensu Lato Facilitate the Transition between Emetic and Diarrheal Foodborne Pathogens. mBio. 2020; 11 (4):1.
Chicago/Turabian StyleLaura M. Carroll; Martin Wiedmann. 2020. "Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group III Bacillus cereus Sensu Lato Facilitate the Transition between Emetic and Diarrheal Foodborne Pathogens." mBio 11, no. 4: 1.
AbstractUntargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis could reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in the food industry. However, before these approaches can be applied, it is imperative to verify that the most appropriate methods are used at every step of the process: gathering primary material, laboratory methods, data analysis, and interpretation.The focus of this study is in gathering the primary material, in this case, DNA. We used bovine milk as a model to 1) evaluate commercially available kits for their ability to extract nucleic acids from inoculated bovine milk; 2) evaluate host DNA depletion methods for use with milk, and 3) develop and evaluate a selective lysis-PMA based protocol for host DNA depletion in milk.Our results suggest that magnetic-based nucleic acid extraction methods are best for nucleic acid isolation of bovine milk. Removal of host DNA remains a challenge for untargeted sequencing of milk, highlighting that the individual matrix characteristics should always be considered in food testing. Some reported methods introduce bias against specific types of microbes, which may be particularly problematic in food safety where the detection of Gram-negative pathogens and indicators is essential. Continuous efforts are needed to develop and validate new approaches for untargeted metagenomics in samples with large amounts of DNA from a single host.ImportanceTracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of what the relative composition looks like. Because the genetic material of higher organisms present in food (e.g., cow in milk or beef, wheat in flour) is around one thousand times larger than the bacterial content, challenges exist in gathering the information of interest. Additionally, specific bacterial characteristics can make them easier or harder to detect, adding another layer of complexity to this issue. In this study, we demonstrate the impact of using different methods in the ability of detecting specific bacteria and highlight the need to ensure that the most appropriate methods are being used for each particular sample.
Erika Ganda; Kristen L. Beck; Niina Haiminen; Ban Kawas; Brittany Cronk; Renee R. Anderson; Laura Brunengraber Goodman; Martin Wiedmann. DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid. 2020, 1 .
AMA StyleErika Ganda, Kristen L. Beck, Niina Haiminen, Ban Kawas, Brittany Cronk, Renee R. Anderson, Laura Brunengraber Goodman, Martin Wiedmann. DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid. . 2020; ():1.
Chicago/Turabian StyleErika Ganda; Kristen L. Beck; Niina Haiminen; Ban Kawas; Brittany Cronk; Renee R. Anderson; Laura Brunengraber Goodman; Martin Wiedmann. 2020. "DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid." , no. : 1.
Postpasteurization contamination (PPC) with gram-negative bacteria adversely affects the quality and shelf-life of milk through the development of flavor, odor, texture, and visual defects. Through evaluation of milk quality at 4 large fluid milk processing facilities in the northeast United States, we examined the efficacy of 3 strategies designed to reduce the occurrence of PPC in fluid milk: (1) employee training (focusing on good manufacturing practices) alone and (2) with concurrent implementation of modified clean-in-place chemistry and (3) preventive maintenance (PM) focused on replacement of wearable rubber components. Despite increases in employee knowledge and self-reported behavior change, microbiological evaluation of fluid milk before and after interventions indicated that neither training alone nor training combined with modified clean-in-place interventions significantly decreased PPC. Furthermore, characterization of gram-negative bacterial isolates from milk suggested that specific bacterial taxonomic groups (notably, Pseudomonas sequence types) continued to contribute to PPC even after interventions and that no major changes in the composition of the spoilage-associated microbial populations occurred as a consequence of the interventions. More specifically, in 3 of 4 facilities, gram-negative bacteria with identical 16S rDNA sequence types were isolated on multiple occasions. Evaluation of a PM intervention showed that used rubber goods harbored PPC-associated bacteria and that PPC may have been less frequent following a PM intervention in which wearable rubber goods were replaced (reduction from 3/3 samples with PPC before to 1/3 samples after). Overall, our findings suggest that commonly used "broad stroke interventions" may have a limited effect on reducing PPC. Our case study also demonstrates the inherent complexities of identifying and successfully addressing sanitation problems in large and complex fluid milk processing facilities. For example, broad changes to sanitation practices without improvements in PM and sanitary equipment design may not always lead to reduced PPC. Our data also indicate that although short-term evaluations, such as pre- and post-tests for employee training, may suggest improvements after corrective and preventive actions, extensive microbial testing, ideally in combination with isolate characterization, may be necessary to evaluate return on investment of different interventions.
S.J. Reichler; S.I. Murphy; A.W. Erickson; N.H. Martin; A.B. Snyder; M. Wiedmann. Interventions designed to control postpasteurization contamination in high-temperature, short-time-pasteurized fluid milk processing facilities: A case study on the effect of employee training, clean-in-place chemical modification, and preventive maintenance programs. Journal of Dairy Science 2020, 103, 7569 -7584.
AMA StyleS.J. Reichler, S.I. Murphy, A.W. Erickson, N.H. Martin, A.B. Snyder, M. Wiedmann. Interventions designed to control postpasteurization contamination in high-temperature, short-time-pasteurized fluid milk processing facilities: A case study on the effect of employee training, clean-in-place chemical modification, and preventive maintenance programs. Journal of Dairy Science. 2020; 103 (8):7569-7584.
Chicago/Turabian StyleS.J. Reichler; S.I. Murphy; A.W. Erickson; N.H. Martin; A.B. Snyder; M. Wiedmann. 2020. "Interventions designed to control postpasteurization contamination in high-temperature, short-time-pasteurized fluid milk processing facilities: A case study on the effect of employee training, clean-in-place chemical modification, and preventive maintenance programs." Journal of Dairy Science 103, no. 8: 7569-7584.
Listeria monocytogenes is a human pathogen that is commonly found in environments associated with cold-smoked salmon. Nisin is a natural antimicrobial that can be used as a food preservative. While nisin is active against a number of Gram-positive bacteria, including L. monocytogenes, environmental stresses encountered in cold-smoked salmon processing facilities might affect L. monocytogenes' nisin susceptibility. The objective of this study was to investigate the effect of seafood-relevant pre-growth conditions and L. monocytogenes strain diversity on nisin treatment efficacy on cold-smoked salmon. Six L. monocytogenes strains representing serotypes most commonly associated with cold-smoked salmon (1/2a, 1/2b, and 4b) were initially pre-grown under a number of seafood-relevant conditions and challenged with nisin in growth media modified to represent the characteristics of cold-smoked salmon. The pre-growth conditions with the lowest mean log reduction due to nisin and the highest strain-to-strain variability were selected for experiments on cold-smoked salmon; these included: (i) 4.65% w.p. NaCl (“NaCl”); (ii) pH = 6.1 (“pH”); (iii) 0.5 μg/ml benzalkonium chloride (“Quat”); and a control (“BHI”). Cold-smoked salmon slices with or without nisin were inoculated with L. monocytogenes pre-grown in one of the conditions above, vacuum-packed, and incubated at 7 °C. L. monocytogenes were enumerated on days 1, 15, and 30. A linear mixed effects model was constructed to investigate the effect of pre-growth condition, day in storage, serotype, source of isolation as well as their interactions on nisin efficacy against L. monocytogenes. Compared to pre-growth in “BHI”, significant reduction (P < 0.05) in nisin efficacy was induced by pre-growth in “pH” and “Quat” on both days 15 and 30, and by pre-growth in “NaCl” on day 30, indicating a time-dependent cross-protection effect. Additionally, an effect of L. monocytogenes' serotype on the cross-protection to nisin was observed; pre-growth in “pH” significantly reduced nisin efficacy against serotype 1/2a and 4b strains, but not against 1/2b strains. In conclusion, pre-exposure to mildly acidic environment, high salt content, and sublethal concentrations of quaternary ammonium compounds, is likely to provide cross-protection against a subsequent nisin treatment of L. monocytogenes on cold-smoked salmon. Therefore, challenge studies that use pre-growth in “BHI”, as well as more susceptible L. monocytogenes strains, may overestimate the efficacy of nisin as a control strategy for cold-smoked salmon.
Ruixi Chen; Jordan Skeens; Renato H. Orsi; Martin Wiedmann; Veronica Guariglia-Oropeza. Pre-growth conditions and strain diversity affect nisin treatment efficacy against Listeria monocytogenes on cold-smoked salmon. International Journal of Food Microbiology 2020, 333, 108793 .
AMA StyleRuixi Chen, Jordan Skeens, Renato H. Orsi, Martin Wiedmann, Veronica Guariglia-Oropeza. Pre-growth conditions and strain diversity affect nisin treatment efficacy against Listeria monocytogenes on cold-smoked salmon. International Journal of Food Microbiology. 2020; 333 ():108793.
Chicago/Turabian StyleRuixi Chen; Jordan Skeens; Renato H. Orsi; Martin Wiedmann; Veronica Guariglia-Oropeza. 2020. "Pre-growth conditions and strain diversity affect nisin treatment efficacy against Listeria monocytogenes on cold-smoked salmon." International Journal of Food Microbiology 333, no. : 108793.
The emergence of multidrug-resistant bacterial strains worldwide has become a serious problem for public health over recent decades. The increase in antimicrobial resistance has been expanding via plasmids as mobile genetic elements encoding antimicrobial resistance (AMR) genes that are transferred vertically and horizontally. This study focuses on Salmonella enterica, one of the leading foodborne pathogens in industrialized countries. S. enterica is known to carry several plasmids involved not only in virulence but also in AMR. In the current paper, we present an integrated strategy to detect plasmid scaffolds in whole genome sequencing (WGS) assemblies. We developed a two-step procedure to predict plasmids based on i) the presence of essential elements for plasmid replication and mobility, as well as ii) sequence similarity to a reference plasmid. Next, to confirm the accuracy of the prediction in 1750 S. enterica short-read sequencing data, we combined Oxford Nanopore MinION long-read sequencing with Illumina MiSeq short-read sequencing in hybrid assemblies for 84 isolates to evaluate the proportion of plasmid that has been detected. At least one scaffold with an origin of replication (ORI) was predicted in 61.3% of the Salmonella isolates tested. The results indicated that IncFII and IncI1 ORIs were distributed in many S. enterica serotypes and were the most prevalent AMR genes carrier, whereas IncHI2A/IncHI2 and IncA/C2 were more serotype restricted but bore several AMR genes. Comparison between hybrid and short-read assemblies revealed that 81.1% of plasmids were found in the short-read sequencing using our pipeline. Through this process, we established that plasmids are prevalent in S. enterica and we also substantially expand the AMR genes in the resistome of this species.
Jean-Guillaume Emond-Rheault; Jérémie Hamel; Julie Jeukens; Luca Freschi; Irena Kukavica-Ibrulj; Brian Boyle; Sandeep Tamber; Danielle Malo; Eelco Franz; Elton Burnett; France Daigle; Gitanjali Arya; Kenneth Sanderson; Martin Wiedmann; Robin M. Slawson; Joel T. Weadge; Roger Stephan; Sadjia Bekal; Samantha Gruenheid; Lawrence D. Goodridge; Roger C. Levesque. The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance. Microorganisms 2020, 8, 1016 .
AMA StyleJean-Guillaume Emond-Rheault, Jérémie Hamel, Julie Jeukens, Luca Freschi, Irena Kukavica-Ibrulj, Brian Boyle, Sandeep Tamber, Danielle Malo, Eelco Franz, Elton Burnett, France Daigle, Gitanjali Arya, Kenneth Sanderson, Martin Wiedmann, Robin M. Slawson, Joel T. Weadge, Roger Stephan, Sadjia Bekal, Samantha Gruenheid, Lawrence D. Goodridge, Roger C. Levesque. The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance. Microorganisms. 2020; 8 (7):1016.
Chicago/Turabian StyleJean-Guillaume Emond-Rheault; Jérémie Hamel; Julie Jeukens; Luca Freschi; Irena Kukavica-Ibrulj; Brian Boyle; Sandeep Tamber; Danielle Malo; Eelco Franz; Elton Burnett; France Daigle; Gitanjali Arya; Kenneth Sanderson; Martin Wiedmann; Robin M. Slawson; Joel T. Weadge; Roger Stephan; Sadjia Bekal; Samantha Gruenheid; Lawrence D. Goodridge; Roger C. Levesque. 2020. "The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance." Microorganisms 8, no. 7: 1016.