Identification of Listeria monocytogenes genes involved in salt and alkaline-pH tolerance

Genomic landscapes of bacterial transposons and their applications in strain improvement

Transposons are mobile genetic elements that can give rise to gene mutation and genome rearrangement. Due to their mobility, transposons have been exploited as genetic tools for modification of plants, animals, and microbes. Although a plethora of reviews have summarized families of transposons, the transposons from fermentation bacteria have not been systematically documented, which thereby constrain the exploitation for metabolic engineering and synthetic biology purposes. In this review, we summarize the transposons from the most used fermentation bacteria including Escherichia coli, Bacillus subtilis, Lactococcus lactis, Corynebacterium glutamicum, Klebsiella pneumoniae, and Zymomonas mobilis by literature retrieval and data mining from GenBank and KEGG. We also outline the state-of-the-art advances in basic research and industrial applications especially when allied with other genetic tools. Overall, this review aims to provide valuable insights for transposon-mediated strain improvement. KEY POINTS: • The transposons from the most-used fermentation bacteria are systematically summarized. • The applications of transposons in strain improvement are comprehensively reviewed.

Listeria monocytogenes - How This Pathogen Survives in Food-Production Environments?

The foodborne pathogen Listeria monocytogenes is the causative agent of human listeriosis, a severe disease, especially dangerous for the elderly, pregnant women, and newborns. Although this infection is comparatively rare, it is often associated with a significant mortality rate of 20-30% worldwide. Therefore, this microorganism has an important impact on food safety. L. monocytogenes can adapt, survive and even grow over a wide range of food production environmental stress conditions such as temperatures, low and high pH, high salt concentration, ultraviolet lights, presence of biocides and heavy metals. Furthermore, this bacterium is also able to form biofilm structures on a variety of surfaces in food production environments which makes it difficult to remove and allows it to persist for a long time. This increases the risk of contamination of food production facilities and finally foods. The present review focuses on the key issues related to the molecular mechanisms of the pathogen survival and adaptation to adverse environmental conditions. Knowledge and understanding of the L. monocytogenes adaptation approaches to environmental stress factors will have a significant influence on the development of new, efficient, and cost-effective methods of the pathogen control in the food industry, which is critical to ensure food production safety.

A Central Role for Magnesium Homeostasis during Adaptation to Osmotic Stress

Osmotic stress is a significant physical challenge for free-living cells. Cells from all three domains of life maintain viability during osmotic stress by tightly regulating the major cellular osmolyte potassium (K+) and by import or synthesis of compatible solutes. It has been widely established that in response to high salt stress, many bacteria transiently accumulate high levels of K+, leading to bacteriostasis, with growth resuming only when compatible solutes accumulate and K+ levels are restored to biocompatible levels. Using Bacillus subtilis as a model system, we provide evidence that K+ fluxes perturb Mg2+ homeostasis: import of K+ upon osmotic upshift is correlated with Mg2+ efflux, and Mg2+ reimport is critical for adaptation. The transient growth inhibition resulting from hyperosmotic stress is coincident with loss of Mg2+ and a decrease in protein translation. Conversely, the reimport of Mg2+ is a limiting factor during resumption of growth. Furthermore, we show the essential signaling dinucleotide cyclic di-AMP fluctuates dynamically in coordination with Mg2+ and K+ levels, consistent with the proposal that cyclic di-AMP orchestrates the cellular response to osmotic stress. IMPORTANCE Environments with high concentrations of salt or other solutes impose an osmotic stress on cells, ultimately limiting viability by dehydration of the cytosol. A very common cellular response to high osmolarity is to immediately import high levels of potassium ion (K+), which helps prevent dehydration and allows time for the import or synthesis of biocompatible solutes that allow a resumption of growth. Here, using Bacillus subtilis as a model, we demonstrate that concomitant with K+ import there is a large reduction in intracellular magnesium (Mg2+) mediated by specific efflux pumps. Further, it is the reimport of Mg2+ that is rate-limiting for the resumption of growth. These coordinated fluxes of K+ and Mg2+ are orchestrated by cyclic-di-AMP, an essential second messenger in Firmicutes. These findings amend the conventional model for osmoadaptation and reveal that Mg2+ limitation is the proximal cause of the bacteriostasis that precedes resumption of growth.

Operational culture conditions determinate benzalkonium chloride resistance in L. monocytogenes-E. coli dual species biofilms

Biofilms pose a serious challenge to the food industry. Higher resistance of biofilms to any external stimuli is a major hindrance for their eradication. In this study, we compared the growth dynamics and benzalkonium chloride (BAC) resistance of dual species Listeria monocytogenes-Escherichia coli 48 h biofilms formed on stainless steel (SS) coupons surfaces under batch and fed-batch cultures. Differences between both operational culture conditions were evaluated in terms of total viable adhered cells (TVAC) in the coupons during 48 h of the mixed-culture and of reduction of viable adhered cells (RVAC) obtained after BAC-treatment of a 48 h biofilm of L. monocytogenes-E. coli formed under both culture conditions. Additionally, epifluorescence microscopy (EFM) and confocal scanning microscopy (CLSM) permitted to visualize the 2D and 3D biofilms structure, respectively. Observed results showed an increase in the TVAC of both strains during biofilm development, being the number of E. coli adhered cells higher than L. monocytogenes in both experimental systems (p < 0.05). Additionally, the number of both strains were higher approximately 2.0 log CFU/coupon in batch conditions compared to fed-batch system (p < 0.05). On the contrary, significantly higher resistance to BAC was observed in biofilms formed under fed-batch conditions. Furthermore, in batch system both strains had a similar reduction level of approximately 2.0 log CFU/coupon, while significantly higher resistance of E. coli compared to L. monocytogenes (reduction level of 0.69 and 1.72 log CFU/coupon, respectively) (p < 0.05) was observed in fed-batch system. Microscopic image visualization corroborated these results and showed higher complexity of 2D and 3D structures in dual species biofilms formed in batch cultures. Overall, we can conclude that the complexity of the biofilm structure does not always imply higher resistance to external stimuli, and highlights the need to mimic industrial operational conditions in the experimental systems in order to better assess the risk associated to the presence of pathogenic bacterial biofilms.

Environmental Nutrients Alter Bacterial and Fungal Gut Microbiomes in the Common Meadow Katydid, Orchelimum vulgare

Insect gut microbiomes consist of bacteria, fungi, and viruses that can act as mutualists to influence the health and fitness of their hosts. While much has been done to increase understanding of the effects of environmental factors that drive insect ecology, there is less understanding of the effects of environmental factors on these gut microbial communities. For example, the effect of environmental nutrients on most insect gut microbiomes is poorly defined. To address this knowledge gap, we investigated the relationship between environmental nutrients and the gut microbial communities in a small study of katydids (n = 13) of the orthopteran species Orchelimum vulgare collected from a costal prairie system. We sampled O. vulgare from unfertilized plots, as well as from plots fertilized with added nitrogen and phosphorus or sodium separately and in combination. We found significantly higher Shannon diversity for the gut bacterial communities in O. vulgare from plots fertilized with added sodium as compared to those collected from plots without added sodium. In contrast, diversity was significantly lower in the gut fungal communities of grasshoppers collected from plots with added nitrogen and phosphorus, as well as those with added sodium, in comparison to those with no added nutrients. There was also a strong positive correlation between the gut bacterial and gut fungal community diversity within each sample. Indicator group analysis for added sodium plots included several taxa with known salt-tolerant bacterial and fungal representatives. Therefore, despite the small sample number, these results highlight the potential for the gut bacterial and fungal constituents to respond differently to changes in environmental nutrient levels. Future studies with a larger sample size will help identify mechanistic determinants driving these changes. Based on our findings and the potential contribution of gut microbes to insect fitness and function, consideration of abiotic factors like soil nutrients along with characteristic gut microbial groups is necessary for better understanding and conservation of this important insect herbivore.

Systematic review of the Listeria monocytogenes σB regulon supports a role in stress response, virulence and metabolism

Aim: Among the alternative sigma factors of Listeria monocytogenes, σB controls the largest regulon. The aim of this study was to perform a comprehensive review of σB-regulated genes, and the functions they confer. Materials & methods: A systematic search of PubMed and Web of Knowledge was carried out to identify members of the σB regulon based on experimental evidence of σB-dependent transcription and presence of a consensus σB-dependent promoter. Results: The literature review identified σB-dependent transcription units encompassing 304 genes encoding different functions including stress response and virulence. Conclusion: Our review supports the well-known roles of σB in virulence and stress response and provides new insight into novel roles for σB in metabolism and overall resilience of L. monocytogenes.

Current Knowledge on Listeria monocytogenes Biofilms in Food-Related Environments: Incidence, Resistance to Biocides, Ecology and Biocontrol

Although many efforts have been made to control Listeria monocytogenes in the food industry, growing pervasiveness amongst the population over the last decades has made this bacterium considered to be one of the most hazardous foodborne pathogens. Its outstanding biocide tolerance capacity and ability to promiscuously associate with other bacterial species forming multispecies communities have permitted this microorganism to survive and persist within the industrial environment. This review is designed to give the reader an overall picture of the current state-of-the-art in L. monocytogenes sessile communities in terms of food safety and legislation, ecological aspects and biocontrol strategies.

The response of foodborne pathogens to osmotic and desiccation stresses in the food chain

In combination with other strategies, hyperosmolarity and desiccation are frequently used by the food processing industry as a means to prevent bacterial proliferation, and particularly that of foodborne pathogens, in food products. However, it is increasingly observed that bacteria, including human pathogens, encode mechanisms to survive and withstand these stresses. This review provides an overview of the mechanisms employed by Salmonella spp., Shiga toxin producing E. coli, Cronobacter spp., Listeria monocytogenes and Campylobacter spp. to tolerate osmotic and desiccation stresses and identifies gaps in knowledge which need to be addressed to ensure the safety of low water activity and desiccated food products.

Screening of a Leptospira biflexa mutant library to identify genes involved in ethidium bromide tolerance

Leptospira spp. are spirochete bacteria comprising both pathogenic and free-living species. The saprophyte L. biflexa is a model bacterium for studying leptospiral biology due to relative ease of culturing and genetic manipulation. In this study, we constructed a library of 4,996 random transposon mutants in L. biflexa. We screened the library for increased susceptibility to the DNA intercalating agent, ethidium bromide (EtBr), in order to identify genetic determinants that reduce L. biflexa susceptibility to antimicrobial agents. By phenotypic screening, using subinhibitory EtBr concentrations, we identified 29 genes that, when disrupted via transposon insertion, led to increased sensitivity of the bacteria to EtBr. At the functional level, these genes could be categorized by function as follows: regulation and signaling (n=11), transport (n=6), membrane structure (n=5), stress response (n=2), DNA damage repair (n=1), and other processes (n=3), while 1 gene had no predicted function. Genes involved in transport (including efflux pumps) and regulation (two-component systems, anti-sigma factor antagonists, etc.) were overrepresented, demonstrating that these genes are major contributors to EtBr tolerance. This finding suggests that transport genes which would prevent EtBr to enter the cell cytoplasm are critical for EtBr resistance. We identified genes required for the growth of L. biflexa in the presence of sublethal EtBr concentration and characterized their potential as antibiotic resistance determinants. This study will help to delineate mechanisms of adaptation to toxic compounds, as well as potential mechanisms of antibiotic resistance development in pathogenic L. interrogans.

MudPIT profiling reveals a link between anaerobic metabolism and the alkaline adaptive response of Listeria monocytogenes EGD-e

Listeria monocytogenes is a foodborne human pathogen capable of causing life-threatening disease in susceptible populations. Previous proteomic analysis we performed demonstrated that different strains of L. monocytogenes initiate a stringent response when subjected to alkaline growth conditions. Here, using multidimensional protein identification technology (MudPIT), we show that in L. monocytogenes EGD-e this response involves an energy shift to anaerobic pathways in response to the extracellular pH environment. Importantly we show that this supports a reduction in relative lag time following an abrupt transition to low oxygen tension culture conditions. This has important implications for the packaging of fresh and ready-to-eat foods under reduced oxygen conditions in environments where potential exists for alkaline adaptation.

Listeria monocytogenes mutants with altered growth phenotypes at refrigeration temperature and high salt concentrations

Listeria monocytogenes can survive and grow in refrigerated temperatures and high-salt environments. In an effort to better understand the associated mechanisms, a library of ∼ 5,200 transposon mutants of LS411, a food isolate from the Jalisco cheese outbreak, were screened for their ability to grow in brain heart infusion (BHI) broth at 5°C or in the presence of 7% NaCl and two mutants with altered growth profiles were identified. The LS522 mutant has a transposon insertion between secA2 and iap and showed a significant reduction in growth in BHI broth at 5°C and in the presence of 7% NaCl. Reverse transcriptase quantitative PCR (RT-qPCR) revealed a substantial reduction in the expression of iap. Additionally, a hypothetical gene (met), containing a putative S-adenosylmethionine-dependent methyltransferase domain, downstream of iap had downregulated expression. In-frame deletion mutants of iap and met were created in LS411. The LS560 (LS411 Δiap) mutant showed reduced growth at 5°C and in the presence of 7% salt, confirming its role in cold and salt growth attenuation. Surprisingly, the LS655 (LS411 Δmet) mutant showed slightly increased growth during refrigeration, though no alteration was seen in salt growth relative to the wild-type strain. The LS527 mutant, containing an insertion 36 bp upstream of the gbu operon, showed reduced expression of the gbu transcript by RT-qPCR and also showed growth reduction at 5°C and in the presence of 7% salt. This attenuation was severely exacerbated when the mutant was grown under the combined stresses. Analysis of the gbu operon deletion mutant showed decreased growth in 7% salt and refrigeration, supporting the previously characterized role for this gene in cold and salt adaptation. These studies indicate the potential for an intricate relationship between environmental stress regulation and virulence in L. monocytogenes.

The contribution of transcriptomic and proteomic analysis in elucidating stress adaptation responses of Listeria monocytogenes

The foodborne transmission of Listeria monocytogenes requires physiological adaptation to various conditions, including the cold, osmotic, heat, acid, alkaline, and oxidative stresses, associated with food hygiene, processing, and preservation measures. We review the current knowledge on the molecular stress adaptation responses in L. monocytogenes cells as revealed through transcriptome, proteome, genetic, and physiological analysis. The adaptation of L. monocytogenes to stress exposure is achieved through global expression changes in a large number of cellular components. In addition, the cross-protection of L. monocytogenes exposed to different stress environments might be conferred through various cellular machineries that seem to be commonly activated by the different stresses. To assist in designing L. monocytogenes mitigation strategies for ready-to-eat food products, further experiments are warranted to specifically evaluate the effects of food composition, additives, preservatives, and processing technologies on the modulation of L. monocytogenes cellular components in response to specific stresses.

Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification

Background

Bacterial pathogens often show significant intraspecific variations in ecological fitness, host preference and pathogenic potential to cause infectious disease. The species of Listeria monocytogenes, a facultative intracellular pathogen and the causative agent of human listeriosis, consists of at least three distinct genetic lineages. Two of these lineages predominantly cause human sporadic and epidemic infections, whereas the third lineage has never been implicated in human disease outbreaks despite its overall conservation of many known virulence factors.

Results

Here we compare the genomes of 26 L. monocytogenes strains representing the three lineages based on both in silico comparative genomic analysis and high-density, pan-genomic DNA array hybridizations. We uncover 86 genes and 8 small regulatory RNAs that likely make L. monocytogenes lineages differ in carbohydrate utilization and stress resistance during their residence in natural habitats and passage through the host gastrointestinal tract. We also identify 2,330 to 2,456 core genes that define this species along with an open pan-genome pool that contains more than 4,052 genes. Phylogenomic reconstructions based on 3,560 homologous groups allowed robust estimation of phylogenetic relatedness among L. monocytogenes strains.

Conclusions

Our pan-genome approach enables accurate co-analysis of DNA sequence and hybridization array data for both core gene estimation and phylogenomics. Application of our method to the pan-genome of L. monocytogenes sheds new insights into the intraspecific niche expansion and evolution of this important foodborne pathogen.

Implications of salt and sodium reduction on microbial food safety

Excess sodium consumption has been cited as a primary cause of hypertension and cardiovascular diseases. Salt (sodium chloride) is considered the main source of sodium in the human diet, and it is estimated that processed foods and restaurant foods contribute 80% of the daily intake of sodium in most of the Western world. However, ample research demonstrates the efficacy of sodium chloride against pathogenic and spoilage microorganisms in a variety of food systems. Notable examples of the utility and necessity of sodium chloride include the inhibition of growth and toxin production by Clostridium botulinum in processed meats and cheeses. Other sodium salts contributing to the overall sodium consumption are also very important in the prevention of spoilage and/or growth of microorganisms in foods. For example, sodium lactate and sodium diacetate are widely used in conjunction with sodium chloride to prevent the growth of Listeria monocytogenes and lactic acid bacteria in ready-to-eat meats. These and other examples underscore the necessity of sodium salts, particularly sodium chloride, for the production of safe, wholesome foods. Key literature on the antimicrobial properties of sodium chloride in foods is reviewed here to address the impact of salt and sodium reduction or replacement on microbiological food safety and quality.

Differentially expressed genes after hyper- and hypo-salt stress in the halophilic archaeonMethanohalophilus portucalensis

Methanohalophilus portucalensis FDF1 can grow over a range of external NaCl concentrations, from 1.2 to 2.9 mol/L. Differential gene expression in response to long-term hyper-salt stress (3.1 mol/L of NaCl) and hypo-salt stress (0.9 mol/L of NaCl) were compared by differential display RT-PCR. Fourteen differentially expressed genes responding to long-term hyper- or hypo-salt stress were detected, cloned, and sequenced. Several of the differentially expressed genes were related to the unique energy-acquiring methanogenesis pathway in this organism, including the transmembrane protein MttP, cobalamin biosynthesis protein, methenyl-H4MPT cyclohydrolase and monomethylamine methyltransferase. One signal transduction histidine kinase was identified from the hyper-salt stress cultures. Moreover, 3 known stress-response gene homologues — the DNA mismatch repair protein, MutS, the universal stress protein, UspA, and a member of the protein-disaggregating multichaperone system, ClpB — were also detected. The transcriptional analysis of these long-term salt stress response and adaptation-related genes for cells immediately after salt stress indicated that the expression of the energy metabolism genes was arrested during hyper-salt shock, while the chaperone clpB gene was stimulated by both hypo- and hyper-salt shock.

Studies on the susceptibility of different culture morphotypes of Listeria monocytogenes to uptake and survival in human polymorphonuclear leukocytes

This study demonstrated that atypical virulent filaments of Listeria monocytogenes (rough variant type II and designated FR for this study), isolated from clinical specimens or generated during exposure to pulsed-plasma gas discharge in liquids, were shown to be capable of survival when engulfed by human polymorphonuclear leukocytes (PMNLs). Factors shown to significantly influence the maximal respiratory burst response in PMNLs and survival of different internalized cell or filament forms of L. monocytogenes were bacterial strain, culture form, degree of opsonization (with and without the use of 10% serum) and composition of the bacterial growth media used before uptake by PMNLs. Opsonized regular-sized L. monocytogenes cells grown on blood agar (BA) elicited the greatest respiratory burst response and survived best in PMNLs. The filamentous (FR) and multiple cell chain (MCR) rough variants were significantly less susceptible to uptake and survival in PMNLs. Supplementation of tryptone soya agar with hemin resulted in significantly reduced chemiluminescence responses in phagocytosing PMNLs compared with the maximal levels observed from prior bacterial growth on BA or brain heart infusion agar that also contained a source of iron. The MCR variants secreting decreased levels of a peptidoglycan hydrolase CwhA protein exhibited the lowest percentage survival when internalized in PMNLs compared with wild-type smooth or FR culture variants as determined by the macrophage-killing assay.

LadR, a new PadR-related transcriptional regulator from Listeria monocytogenes, negatively regulates the expression of the multidrug efflux pump MdrL

The Listeria monocytogenes genome encodes putative multidrug efflux transporters but only the MdrL transporter has been partially characterized in the wild-type LO28 strain. Here, we show in the LO28 strain, that the expression of MdrL is repressed at the transcriptional level, under standard growth conditions, by the product of a new gene ladR (lmo1408), and the expression of MdrL is induced in the presence of rhodamine. Phylogenetic analysis in related firmicutes shows that LadR, conserved in all sequenced Listeria genomes, forms an independent group from the large and diverse PadR transcriptional regulator family (PF03551). This is the first report of a bacterial multidrug transporter controlled by a member of the PadR family.

Influence of different histories of the inoculum on lag phase and growth of Listeria monocytogenes in meat models

The aim of this study was to determine the effect of history of inoculum and preservatives on the lag phase and growth rate of Listeria monocytogenes strains in meat products packaged under modified atmosphere conditions. Inocula with different histories were added to meat models, and growth rate and lag phase of two strains of L. monocytogenes were measured at 5 and 10 degrees C. The meat model stored at 10 degrees C contained sodium lactate, but the model stored at 5 degrees C did not. The five different histories of the inocula included cold propagation, biofilm formation, and starvation. The lag phase ranged from 1 to 10 days and was affected by the history of the inoculum, whereas the growth rate was constant except for one combination of history of inoculum and strain, where growth did not start during the incubation period. In a second series of experiments, the growth rate and lag phase of the two Listeria strains and the effects of two different histories of inoculum were tested in meat models with pH 5.7 or 6.5 and increasing amounts of NaCl. The growth rate depended on salt concentration, bacterial strain, and pH, whereas lag phase duration depended on history of inoculum, salt concentration, and pH. The lag phase duration was highly dependent on the history of the inoculum, and higher amounts of preservative (NaCl) made these effects even more noticeable. The results of this study underline the importance of the effects of the history of the inoculum on lag phase duration and could be used to predict lag phase in industrial meat products.

Sensitivity of Escherichia coli O157:H7 to commercially available alkaline cleaners and subsequent resistance to heat and sanitizers

The effects of seven commercially available alkaline cleaners used in the food processing industry, 0.025 M NaOH, and 0.025 M KOH on viability of wild-type (EDL 933) and rpoS-deficient (FRIK 816-3) strains of Escherichia coli O157:H7 in logarithmic and stationary phases of growth were determined. Cells were treated at 4 or 23 degrees C for 2, 10, or 30 min. Cleaners 2, 4, 6, and 7, which contained hypochlorite and <11% NaOH and/or KOH (pH 11.2 to 11.7), killed significantly higher numbers of cells than treatment with cleaner 3, containing sodium metasilicate (pH 11.4) and <10% KOH, and cleaner 5, containing ethylene glycol monobutyl ether (pH 10.4). There were no differences in the sensitivities of logarithmic and stationary-phase cells to the alkaline cleaners. Treatment with KOH or NaOH (pH 12.2) was not as effective as four out of seven commercial cleaners in killing E. coli O157:H7, indicating that chlorine and other cleaner components have bactericidal activity at high pH. Stationary-phase cells of strain EDL 933 that had been exposed to cleaner 7 at 4 or 23 degrees C and strain FRIK 816-3 exposed to cleaner 7 at 23 degrees C had significantly higher D(55 degrees C) (decimal reduction time, minutes at 55 degrees C) values than control cells or cells exposed to cleaner 5, indicating that exposure to cleaner 7 confers cross-protection to heat. Cells of EDL 933 treated with cleaner 7 at 12 degrees C showed significantly higher D(55 degrees C) values than cells of FRIK 816-3, indicating that rpoS may play a role in cross-protection. Stationary-phase cells treated with cleaner 5 or cleaner 7 at 4 or 12 degrees C were not cross-protected against subsequent exposure to sanitizers containing quaternary ammonium compounds or sodium hypochlorite, or to cetylpyridinium chloride and benzalkonium chloride.