scholarly journals Adjacent Terrestrial Landscapes Impact the Biogeographical Pattern of Soil Escherichia coli Strains in Produce Fields by Modifying the Importance of Environmental Selection and Dispersal

2021 ◽  
Vol 87 (6) ◽  
Author(s):  
Jingqiu Liao ◽  
Peter Bergholz ◽  
Martin Wiedmann
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Land Use ◽  
Enteric Bacteria ◽  
Content Type ◽  
E Coli ◽  
Biogeographic Pattern ◽  
Environmental Selection ◽  
Forest Sites ◽  
Land Use Types

ABSTRACT High-quality habitats for wildlife (e.g., forest) provide essential ecosystem services while increasing species diversity and habitat connectivity. Unfortunately, the presence of such habitats adjacent to produce fields may increase risk for contamination of fruits and vegetables by enteric bacteria, including Escherichia coli. E. coli survives in extrahost environments (e.g., soil) and could be dispersed across landscapes by wildlife. Understanding how terrestrial landscapes impact the distribution of soil E. coli strains is of importance in assessing the contamination risk of agricultural products. Here, using multilocus sequence typing, we characterized 938 E. coli soil isolates collected from two watersheds with different landscape patterns in New York State, USA, and compared the distribution of E. coli and the influence that environmental selection and dispersal have on the distribution between these two watersheds. Results showed that for the watershed with widespread produce fields, sparse forests, and limited interaction between the two land use types, E. coli composition was significantly different between produce field sites and forest sites; this distribution appears to be shaped by relatively strong environmental selection, likely from soil phosphorus, and slight dispersal limitation. For the watershed with more forested areas and stronger interaction between produce field sites and forest sites, E. coli composition between these two land use types was relatively homogeneous; this distribution appeared to be a consequence of wildlife-driven dispersal, inferred by competing models. Collectively, our results suggest that terrestrial landscape attributes could impact the biogeographic pattern of enteric bacteria by adjusting the importance of environmental selection and dispersal. IMPORTANCE 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. Agricultural areas in such watersheds may have a higher risk of produce contamination due to fewer environmental constraints and higher potential of dispersal of enteric bacteria between locations. Thus, there is a perceived trade-off between priorities of environmental conservation and public health in on-farm food safety, with limited ecological data supporting or refuting the role of wildlife in dispersing pathogens under normal operating conditions. By combining field sampling and spatial modeling, we explored ecological principles underlying the biogeographic pattern of enteric bacteria at the regional level, which can benefit agricultural, environmental, and public health scientists who aim to reduce the risk of food contamination by enteric bacteria while minimizing negative impacts on wildlife habitats.

scholarly journals Adjacent terrestrial landscapes impact the biogeographical pattern of soil Escherichia coli in produce fields by modifying the importance of environmental selection and dispersal

2020 ◽  
Author(s):  
Jingqiu Liao ◽  
Peter Bergholz ◽  
Martin Wiedmann
Keyword(s):  
Escherichia Coli ◽  
Land Use ◽  
New York State ◽  
Enteric Bacteria ◽  
Landscape Patterns ◽  
E Coli ◽  
Biogeographic Pattern ◽  
Environmental Selection ◽  
Forest Sites ◽  
Land Use Types

ABSTRACTHigh-quality habitats for wildlife (e.g., forest) provide essential ecosystem services while increasing species diversity and habitat connectivity. Unfortunately, presence of such habitats adjacent to produce fields may increase risk for contamination of fruits and vegetables by enteric bacteria, including Escherichia coli. E. coli survives in extra-host environments (e.g., soil) and could disperse across landscapes by wildlife. Understanding how terrestrial landscapes impact the distribution of soil E. coli is of importance in assessing the contamination risk of agricultural products. Here, using multi-locus sequence typing, we characterized 938 E. coli soil isolates collected from two watersheds with different landscape patterns in New York state, USA, and compared the distribution of E. coli and the influence of two ecological forces (environmental selection and dispersal) on the distribution between these two watersheds. Results showed that for the watershed with widespread produce fields, sparse forests, and limited interaction between the two land-use types, E. coli composition was significantly different between produce field sites and forest sites; this distribution was shaped by relatively strong environmental selection likely from soil phosphorus and slight dispersal limitation. For the watershed with more forested areas and stronger interaction between produce field sites and forest sites, E. coli composition between these two land-use types was relatively homogeneous; this distribution appeared to a consequence of wildlife-driven dispersal, inferred by competing models. Collectively, our results suggest that terrestrial landscape attributes could impact the biogeographic pattern of enteric bacteria by adjusting the importance of environmental selection and dispersal.IMPORTANCEUnderstanding the ecology of enteric bacteria in extra-host environments is important to allow for development and implementation of strategies to minimize pre-harvest 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. For watersheds with widespread produce fields, E. coli appears to experience local adaptation, possibly due to exposure to environmental stresses associated with agricultural activities. In contrast, for watersheds with high forest coverage we found evidence for wildlife-driven dispersal of E. coli, which might facilitate more frequent genetic exchange in this environment. Agricultural areas in such watersheds may have a higher risk of produce contamination due to less environmental constraints and higher potential of dispersal of enteric bacteria between locations. The significance of our research lies in exploring ecological principles underlying the biogeographic pattern of enteric bacteria at the regional level, which can inform agricultural, environmental and public health scientists that aim to reduce the risk of food contamination by enteric bacteria.

scholarly journals Functional Analysis of Genes Comprising the Locus of Heat Resistance in Escherichia coli

2017 ◽  
Vol 83 (20) ◽  
Author(s):  
Ryan Mercer ◽  
Oanh Nguyen ◽  
Qixing Ou ◽  
Lynn McMullen ◽  
Michael G. Gänzle
Keyword(s):  
Escherichia Coli ◽  
Heat Shock ◽  
Heat Shock Proteins ◽  
Heat Resistance ◽  
Growth Phase ◽  
Genomic Island ◽  
Enteric Bacteria ◽  
Content Type ◽  
E Coli ◽  
Shock Proteins

ABSTRACT The locus of heat resistance (LHR) is a 15- to 19-kb genomic island conferring exceptional heat resistance to organisms in the family Enterobacteriaceae, including pathogenic strains of Salmonella enterica and Escherichia coli. The complement of LHR-comprising genes that is necessary for heat resistance and the stress-induced or growth-phase-induced expression of LHR-comprising genes are unknown. This study determined the contribution of the seven LHR-comprising genes yfdX1 GI, yfdX2, hdeD GI, orf11, trx GI, kefB, and psiE GI by comparing the heat resistances of E. coli strains harboring plasmid-encoded derivatives of the different LHRs in these genes. (Genes carry a subscript “GI” [genomic island] if an ortholog of the same gene is present in genomes of E. coli.) LHR-encoded heat shock proteins sHSP20, ClpKGI, and sHSPGI are not sufficient for the heat resistance phenotype; YfdX1, YfdX2, and HdeD are necessary to complement the LHR heat shock proteins and to impart a high level of resistance. Deletion of trx GI, kefB, and psiE GI from plasmid-encoded copies of the LHR did not significantly affect heat resistance. The effect of the growth phase and the NaCl concentration on expression from the putative LHR promoter p2 was determined by quantitative reverse transcription-PCR and by a plasmid-encoded p2:GFP promoter fusion. The expression levels of exponential- and stationary-phase E. coli cells were not significantly different, but the addition of 1% NaCl significantly increased LHR expression. Remarkably, LHR expression in E. coli was dependent on a chromosomal copy of evgA. In conclusion, this study improved our understanding of the genes required for exceptional heat resistance in E. coli and factors that increase their expression in food. IMPORTANCE The locus of heat resistance (LHR) is a genomic island conferring exceptional heat resistance to several foodborne pathogens. The exceptional level of heat resistance provided by the LHR questions the control of pathogens by current food processing and preparation techniques. The function of LHR-comprising genes and their regulation, however, remain largely unknown. This study defines a core complement of LHR-encoded proteins that are necessary for heat resistance and demonstrates that regulation of the LHR in E. coli requires a chromosomal copy of the gene encoding EvgA. This study provides insight into the function of a transmissible genomic island that allows otherwise heat-sensitive enteric bacteria, including pathogens, to lead a thermoduric lifestyle and thus contributes to the detection and control of heat-resistant enteric bacteria in food.

scholarly journals Inactivation of Escherichia coli by Polychromatic Simulated Sunlight: Evidence for and Implications of a Fenton Mechanism Involving Iron, Hydrogen Peroxide, and Superoxide

2013 ◽  
Vol 80 (3) ◽  
pp. 935-942 ◽  
Author(s):  
Michael B. Fisher ◽  
Kara L. Nelson
Keyword(s):  
Escherichia Coli ◽  
Hydrogen Peroxide ◽  
Enteric Bacteria ◽  
Growth Conditions ◽  
Simulated Sunlight ◽  
Wild Type ◽  
Intracellular Iron ◽  
Content Type ◽  
E Coli ◽  
Degree Of Sensitization

ABSTRACTSunlight inactivation ofEscherichia colihas previously been shown to accelerate in the presence of oxygen, exogenously added hydrogen peroxide, and bioavailable forms of exogenously added iron. In this study, mutants unable to effectively scavenge hydrogen peroxide or superoxide were found to be more sensitive to polychromatic simulated sunlight (without UVB wavelengths) than wild-type cells, while wild-type cells grown under low-iron conditions were less sensitive than cells grown in the presence of abundant iron. Furthermore, prior exposure to simulated sunlight was found to sensitize cells to subsequent hydrogen peroxide exposure in the dark, but this effect was attenuated for cells grown with low iron. Mutants deficient in recombination DNA repair were sensitized to simulated sunlight (without UVB wavelengths), but growth in the presence of iron chelators reduced the degree of sensitization conferred by this mutation. These findings support the hypothesis that hydrogen peroxide, superoxide, and intracellular iron all participate in the photoinactivation ofE. coliand further suggest that the inactivation rate of enteric bacteria in the environment may be strongly dependent on iron availability and growth conditions.

scholarly journals What Is the Appropriate Meropenem MIC for Screening of Carbapenemase-Producing Enterobacteriaceae in Low-Prevalence Settings?

2015 ◽  
Vol 60 (3) ◽  
pp. 1556-1559 ◽  
Author(s):  
Ramzi Fattouh ◽  
Nathalie Tijet ◽  
Allison McGeer ◽  
Susan M. Poutanen ◽  
Roberto G. Melano ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Treatment Options ◽  
Large Set ◽  
Wild Type ◽  
Content Type ◽  
The Public ◽  
E Coli ◽  
Low Prevalence ◽  
Screening Approaches

Infection with carbapenemase-producingEnterobacteriaceae(CPE) has been shown to cause significant illness among hospitalized patients. Given the paucity of treatment options, there is a critical need to stop the spread of CPE. However, screening for the presence of CPE in laboratory settings has been challenging. In order to assess the effectiveness of current CPE detection guidelines, we analyzed the meropenem MIC distribution for a large set of clinicalEnterobacteriaceaeisolates. A total of 1,022 isolates submitted to the Public Health Ontario Laboratories (PHOL) from January 2011 to March 2014 were examined. Only isolates displaying a meropenem or ertapenem MIC of ≥0.25 or ≥1 μg/ml, respectively, were included. Carbapenemase-positive isolates were identified by multiplex PCR. We identified 189 isolates positive for carbapenemases, which primarily comprised NDM, KPC, and OXA-48-like carbapenemases, and these isolates were largelyKlebsiellaspp.,Escherichia coli, andEnterobacterspp. Interestingly, 14 to 20% of these isolates displayed meropenem MICs within the susceptible range on the basis of CLSI and EUCAST breakpoint interpretive criteria. While the majority of meropenem-susceptible CPE isolates were observed to beE. coli, meropenem susceptibility was not exclusive to any one species/genus or carbapenemase type. Application of CLSI screening recommendations captured only 86% of carbapenemase-producing isolates, whereas application of EUCAST recommendations detected 98.4% of CPE isolates. In a region with a low carbapenemase prevalence, meropenem-based screening approaches require a cutoff MIC near the epidemiological wild-type threshold in order to achieve nearly optimal CPE identification.

scholarly journals Indole Production Promotes Escherichia coli Mixed-Culture Growth with Pseudomonas aeruginosa by Inhibiting Quorum Signaling

2011 ◽  
Vol 78 (2) ◽  
pp. 411-419 ◽  
Author(s):  
Weihua Chu ◽  
Tesfalem R. Zere ◽  
Mary M. Weber ◽  
Thomas K. Wood ◽  
Marvin Whiteley ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Mixed Culture ◽  
Receptor Gene ◽  
Enteric Bacteria ◽  
Wild Type ◽  
Content Type ◽  
E Coli ◽  
Culture Growth ◽  
Indole Production

ABSTRACTIndole production byEscherichia coli, discovered in the early 20th century, has been used as a diagnostic marker for distinguishingE. colifrom other enteric bacteria. By using transcriptional profiling and competition studies with defined mutants, we show that cyclic AMP (cAMP)-regulated indole formation is a major factor that enablesE. coligrowth in mixed biofilm and planktonic populations withPseudomonas aeruginosa. Mutants deficient in cAMP production (cyaA) or the cAMP receptor gene (crp), as well as indole production (tnaA), were not competitive in coculture withP. aeruginosabut could be restored to wild-type competitiveness by supplementation with a physiologically relevant indole concentration.E. colisdiAmutants, which lacked the receptor for both indole andN-acyl-homoserine lactones (AHLs), showed no change in competitive fitness, suggesting that indole acted directly onP. aeruginosa. AnE. colitnaAmutant strain regained wild-type competiveness if grown withP. aeruginosaAHL synthase (rhlIandrhlI lasI) mutants. In contrast to the wild type,P. aeruginosaAHL synthase mutants were unable to degrade indole. Indole produced during mixed-culture growth inhibited pyocyanin production and other AHL-regulated virulence factors inP. aeruginosa. Mixed-culture growth withP. aeruginosastimulated indole formation inE. colicpdA, which is unable to regulate cAMP levels, suggesting the potential for mixed-culture gene activation via cAMP. These findings illustrate how indole, an early described feature ofE. colicentral metabolism, can play a significant role in mixed-culture survival by inhibiting quorum-regulated competition factors inP. aeruginosa.

scholarly journals Molecular Characterization of Escherichia coli Isolates Carrying mcr-1, fosA3, and Extended-Spectrum-β-Lactamase Genes from Food Samples in China

2017 ◽  
Vol 61 (6) ◽  
Author(s):  
Xiaobo Liu ◽  
Ruichao Li ◽  
Zhiwei Zheng ◽  
Kaichao Chen ◽  
Miaomiao Xie ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Molecular Characterization ◽  
Food Products ◽  
Multidrug Resistant ◽  
Food Samples ◽  
Content Type ◽  
E Coli ◽  
Extended Spectrum

ABSTRACT This study surveyed the prevalence of mcr-1 in extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli strains of food origin in China and identified strains that carried mcr-1, fosA3, and ESBL genes, which were carried in various plasmids. The mcr-1 and ESBL genes could be cotransferred by one or more types of plasmids. The presence of these multidrug-resistant E. coli strains in food products might pose a huge threat to public health.

scholarly journals High Incidence of Escherichia coli Strains Coharboring mcr-1 and blaNDM from Chickens

2017 ◽  
Vol 61 (3) ◽  
Author(s):  
Bao-Tao Liu ◽  
Feng-Jing Song ◽  
Ming Zou ◽  
Qi-Di Zhang ◽  
Hu Shan
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Resistance Genes ◽  
Content Type ◽  
E Coli ◽  
High Incidence ◽  
Chicken Farm

ABSTRACT This study investigated the characteristics of Escherichia coli isolates carrying mcr-1-bla NDM from a chicken farm in China. Of the 78 E. coli isolates, 21 clonally unrelated isolates carried mcr-1-bla NDM. Diverse IncI2 plasmids disseminated mcr-1, while the dissemination of bla NDM was mediated by diverse IncB/O plasmids. More striking was the colocalization of resistance genes mcr-1 and bla NDM-4 in an IncHI2/ST3 plasmid, which might pose a great challenge for public health.

scholarly journals Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Alan McNally ◽  
Teemu Kallonen ◽  
Christopher Connor ◽  
Khalil Abudahab ◽  
David M. Aanensen ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Anaerobic Metabolism ◽  
Multidrug Resistant ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Content Type ◽  
E Coli ◽  
Negative Frequency Dependent Selection ◽  
Tract Infections

ABSTRACT Escherichia coli is a major cause of bloodstream and urinary tract infections globally. The wide dissemination of multidrug-resistant (MDR) strains of extraintestinal pathogenic E. coli (ExPEC) poses a rapidly increasing public health burden due to narrowed treatment options and increased risk of failure to clear an infection. Here, we present a detailed population genomic analysis of the ExPEC ST131 clone, in which we seek explanations for its success as an emerging pathogenic strain beyond the acquisition of antimicrobial resistance (AMR) genes. We show evidence for evolution toward separate ecological niches for the main clades of ST131 and differential evolution of anaerobic metabolism, key colonization, and virulence factors. We further demonstrate that negative frequency-dependent selection acting across accessory loci is a major mechanism that has shaped the population evolution of this pathogen. IMPORTANCE Infections with multidrug-resistant (MDR) strains of Escherichia coli are a significant global public health concern. To combat these pathogens, we need a deeper understanding of how they evolved from their background populations. By understanding the processes that underpin their emergence, we can design new strategies to limit evolution of new clones and combat existing clones. By combining population genomics with modelling approaches, we show that dominant MDR clones of E. coli are under the influence of negative frequency-dependent selection, preventing them from rising to fixation in a population. Furthermore, we show that this selection acts on genes involved in anaerobic metabolism, suggesting that this key trait, and the ability to colonize human intestinal tracts, is a key step in the evolution of MDR clones of E. coli.

scholarly journals Landscape-Scale Factors Affecting the Prevalence of Escherichia coli in Surface Soil Include Land Cover Type, Edge Interactions, and Soil pH

2018 ◽  
Vol 84 (10) ◽  
Author(s):  
Nicholas Dusek ◽  
Austin J. Hewitt ◽  
Kaycie N. Schmidt ◽  
Peter W. Bergholz
Keyword(s):  
Escherichia Coli ◽  
Land Cover ◽  
Surface Soil ◽  
Landscape Scale ◽  
Life Cycles ◽  
Soil Conditions ◽  
Content Type ◽  
E Coli ◽  
Environmental Selection ◽  
New Findings

ABSTRACT Escherichia coli is deposited into soil with feces and exhibits subsequent population decline with concomitant environmental selection. Environmentally persistent strains exhibit longer survival times during this selection process, and some strains have adapted to soil and sediments. A georeferenced collection of E. coli isolates was developed comprising 3,329 isolates from 1,428 soil samples that were collected from a landscape spanning the transition from the grasslands to the eastern deciduous forest biomes. The isolate collection and sample database were analyzed together to discover how land cover, site characteristics, and soil chemistry influence the prevalence of cultivable E. coli in surface soil. Soils from forests and pasture lands had equally high prevalences of E. coli . Edge interactions were also observed among land cover types, with proximity to forests and pastures affecting the likelihood of E. coli isolation from surrounding soils. E. coli is thought to be more prevalent in sediments with high moisture, but this was observed only in grass- or crop-dominated lands in this study. Because differing E. coli phylogroups are thought to have differing ecology profiles, isolates were also typed using a novel single-nucleotide polymorphism (SNP) genotyping assay. Phylogroup B1 was the dominant group isolated from soil, as has been reported in all other surveys of environmental E. coli . Although differences were small, isolates belonging to phylogroups B2 and D were associated with wooded areas, slightly more acidic soils, and soil sampling after rainfall events. In contrast, isolates from phylogroups B1 and E were associated with pasture lands. IMPORTANCE The consensus is that complex niches or life cycles should select for complex genomes in organisms. There is much unexplained biodiversity in E. coli , and its cycling through complex extrahost environments may be a cause. In order to understand the evolutionary processes that lead to adaptation for survival and growth in soil, an isolate collection that associates soil conditions and isolate genome sequences is required. An equally important question is whether traits selected in soil or other extrahost habitats can be transmitted to E. coli residing in hosts via gene flow. The new findings about the distribution of E. coli in soil at the landscape scale (i) enhance our capability to study how extrahost environments influence the evolution of E. coli and other bacteria, (ii) advance our knowledge of the environmental biology of this microbe, and (iii) further affirm the emerging scientific consensus that E. coli in waterways originates from nonpoint sources not associated with human activity or livestock farming.

scholarly journals Identification and Characterization of Conjugative Plasmids That Encode Ciprofloxacin Resistance inSalmonella

2018 ◽  
Vol 62 (8) ◽  
Author(s):  
Kaichao Chen ◽  
Ning Dong ◽  
Shaohua Zhao ◽  
Lizhang Liu ◽  
Ruichao Li ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Infection Control ◽  
Conjugative Plasmid ◽  
Content Type ◽  
E Coli ◽  
Conjugative Plasmids ◽  
Ciprofloxacin Resistance ◽  
Identification And Characterization

ABSTRACTThis study aimed to characterize novel conjugative plasmids that encode transferable ciprofloxacin resistance inSalmonella. In this study, 157 nonduplicatedSalmonellaisolates were recovered from food products, of which 55 were found to be resistant to ciprofloxacin. Interestingly, 37 of the 55 CiprSalmonellaisolates (67%) did not harbor any mutations in the quinolone resistance-determining regions (QRDR). SixSalmonellaisolates were shown to carry two novel types of conjugative plasmids that could transfer the ciprofloxacin resistance phenotype toEscherichia coliJ53 (azithromycin resistant [Azir]). The first type of conjugative plasmid belonged to the ∼110-kb IncFIB-type conjugative plasmids carryingqnrB-bearing andaac(6′)-Ib-cr-bearing mobile elements. Transfer of the plasmid betweenE. coliandSalmonellacould confer a ciprofloxacin MIC of 1 to 2 μg/ml. The second type of conjugative plasmid belonged to ∼240-kb IncH1/IncF plasmids carrying a single PMQR gene,qnrS. Importantly, this type of conjugative ciprofloxacin resistance plasmid could be detected in clinicalSalmonellaisolates. The dissemination of these conjugative plasmids that confer ciprofloxacin resistance poses serious challenges to public health andSalmonellainfection control.

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