Breaking through the acid barrier: an orchestrated response to proton stress by enteric bacteria

The culturability of acid-tolerant Salmonella in mayonnaise, a raw egg-based sauce

Salmonella is one of the most common bacterial foodborne pathogens and is frequently found as a contaminant of raw egg-based foods. Food safety regulations recommend the use of food acids to mitigate the risk of Salmonella persistence in raw egg-based foods. Salmonella, however, can become tolerant to acidic environments and it is not known how this can affect bacterial persistence in food. This study investigated whether acid-tolerant strains of Salmonella persisted longer in mayonnaise compared with sensitive strains. Isolates of S. typhimurium, S. infantis, S. enteritidis, and S.hessarek were used in this project. Acid-tolerant Salmonella strains were generated using a three-day step-down method where pH was decreased every 24 h from pH 7 to pH 5. Growth curves were determined for both acid-sensitive and acid-tolerant strains. Time-kill experiments were conducted to compare the survivability of acid-sensitive and acid-tolerant Salmonella serotypes in mayonnaise stored at either 5 °C or 25 °C for 72 h. Salmonella exhibited an extended lag phase with increased acid concentration, and acid-tolerant strains recovered faster in media compared with acid-sensitive strains. Elevated biofilm formation was found in acid-habituated strains compared to sensitive strains, and this varied between serotypes. The culturability of Salmonella in mayonnaise stored at 5 °C declined slower than when stored at 25 °C. Acid-tolerant strains persisted longer in mayonnaise and there was a statistically significant difference in culturability (P < 0.05). In conclusion, the current safe food recommendations to control Salmonella in raw egg-based foods are not effective in eliminating it.

Key roles of two-component systems in intestinal signal sensing and virulence regulation in enterohemorrhagic Escherichia coli

Enterohemorrhagic Escherichia coli (EHEC) is a foodborne pathogen that infects humans by colonizing the large intestine. Upon reaching the large intestine, EHEC mediates local signal recognition and the transcriptional regulation of virulence genes to promote adherence and colonization in a highly site-specific manner. Two-component systems (TCSs) represent an important strategy used by EHEC to couple external stimuli with the regulation of gene expression, thereby allowing EHEC to rapidly adapt to changing environmental conditions. An increasing number of studies published in recent years have shown that EHEC senses a variety of host- and microbiota-derived signals present in the human intestinal tract and coordinates the expression of virulence genes via multiple TCS-mediated signal transduction pathways to initiate the disease-causing process. Here, we summarize how EHEC detects a wide range of intestinal signals and precisely regulates virulence gene expression through multiple signal transduction pathways during the initial stages of infection, with a particular emphasis on the key roles of TCSs. This review provides valuable insights into the importance of TCSs in EHEC pathogenesis, which has relevant implications for the development of antibacterial therapies against EHEC infection.

A current insight into Salmonella's inducible acid resistance

Salmonella is a diverse and ubiquitous group of bacteria and a major zoonotic pathogen implicated in several foodborne disease outbreaks worldwide. With more than 2500 distinct serotypes, this pathogen has evolved to survive in a wide spectrum of environments and across multiple hosts. The primary and most common source of transmission is through contaminated food or water. Although the main sources have been primarily linked to animal-related food products, outbreaks due to the consumption of contaminated plant-related food products have increased in the last few years. The perceived ability of Salmonella to trigger defensive mechanisms following pre-exposure to sublethal acid conditions, namely acid adaptation, has renewed a decade-long attention. The impact of acid adaptation on the subsequent resistance against lethal factors of the same or multiple stresses has been underscored by multiple studies. Α plethora of studies have been published, aiming to outline the factors that- alone or in combination- can impact this phenomenon and to unravel the complex networking mechanisms underlying its induction. This review aims to provide a current and updated insight into the factors and mechanisms that rule this phenomenon.

A Systemic Review on Fitness and Survival of Salmonella in Dynamic Environment and Conceivable Ways of Its Mitigation

Gastroenteritis caused by non-typhoidal Salmonella still prevails resulting in several recent outbreaks affecting many people worldwide. The presence of invasive non-typhoidal Salmonella is exemplified by several characteristic symptoms and their severity relies on prominent risk factors. The persistence of this pathogen can be attributed to its broad host range, complex pathogenicity and virulence and adeptness in survival under challenging conditions inside the host. Moreover, a peculiar aid of the ever-changing climatic conditions grants this organism with remarkable potential to survive within the environment. Abusive use of antibiotics for the treatment of gastroenteritis has led to the emergence of multiple drug resistance, making the infections difficult to treat. This review emphasizes the importance of early detection of Salmonella, along with strategies for accomplishing it, as well as exploring alternative treatment approaches. The exceptional characteristics exhibited by Salmonella, like strategies of infection, persistence, and survival parallelly with multiple drug resistance, make this pathogen a prominent concern to human health.

The transcriptional regulation of the horizontally acquired iron uptake system, yersiniabactin and its contribution to oxidative stress tolerance and pathogenicity of globally emerging salmonella strains

The bacterial species Salmonella enterica (S. enterica) is a highly diverse pathogen containing more than 2600 distinct serovars, which can infect a wide range of animal and human hosts. Recent global emergence of multidrug resistant strains, from serovars Infantis and Muenchen is associated with acquisition of the epidemic megaplasmid, pESI that augments antimicrobial resistance and pathogenicity. One of the main pESI's virulence factors is the potent iron uptake system, yersiniabactin encoded by fyuA, irp2-irp1-ybtUTE, ybtA, and ybtPQXS gene cluster. Here we show that yersiniabactin, has an underappreciated distribution among different S. enterica serovars and subspecies, integrated in their chromosome or carried by different conjugative plasmids, including pESI. While the genetic organization and the coding sequence of the yersiniabactin genes are generally conserved, a 201-bp insertion sequence upstream to ybtA, was identified in pESI. Despite this insertion, pESI-encoded yersiniabactin is regulated by YbtA and the ancestral Ferric Uptake Regulator (Fur), which binds directly to the ybtA and irp2 promoters. Furthermore, we show that yersiniabactin genes are specifically induced during the mid-late logarithmic growth phase and in response to iron-starvation or hydrogen peroxide. Concurring, yersiniabactin was found to play a previously unknown role in oxidative stress tolerance and to enhance intestinal colonization of S. Infantis in mice. These results indicate that yersiniabactin contributes to Salmonella fitness and pathogenicity in vivo and is likely to play a role in the rapid dissemination of pESI among globally emerging Salmonella lineages.

Bacterial battle against acidity

The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.

Intracellular replication of Inquilinus limosus in bronchial epithelial cells

Inquilinus limosus is an emerging multi-resistant opportunistic pathogen documented mainly in cystic fibrosis patients. Infection with I. limosus is accompanied by either an acute respiratory exacerbation or a progressive loss of pulmonary function. This study examined the interaction of Inquilinus limosus with the bronquial human epithelial cell line 16HBE14o^-. Almost 100% of the bacteria that attached to the bronquial cells were found internalized and located in acidic LAMP2 positive compartments. According to confocal studies combined with antibiotic protection assays, I. limosus is able to survive and eventually replicate in these compartments. I. limosus was found nontoxic to cells and did not induce neither IL-6 nor IL-8 cytokine production, a characteristic that may help the bacteria to evade host immune response. Overall, this study indicates that I. limosus displays pathogenic properties based on its ability to survive intracellularly in epithelial cells eventually leading to antibiotic failure and chronic infection.

Transcriptome Analyses of Chicken Primary Macrophages Infected With Attenuated Salmonella Typhimurium Mutants

Salmonella enterica is one of the most common foodborne illnesses in the United States and worldwide, with nearly one-third of the cases attributed to contaminated eggs and poultry products. Vaccination has proven to be an effective strategy to reduce Salmonella load in poultry. The Salmonella Typhimurium Δcrp-cya (MeganVac1) strain is the most commonly used vaccine in the United States; however, the mechanisms of virulence attenuation and host response to this vaccine strain are poorly understood. Here, we profiled the invasion and intracellular survival phenotypes of Δcrp-cya and its derivatives (lacking key genes required for intra-macrophage survival) in HD11 macrophages and the transcriptome response in primary chicken macrophages using RNA-seq. Compared to the parent strain UK1, all the mutant strains were highly defective in metabolizing carbon sources related to the TCA cycle and had greater doubling times in macrophage-simulating conditions. Compared to UK1, the majority of the mutants were attenuated for invasion and intra-macrophage survival. Compared to Δcrp-cya, while derivatives lacking phoPQ, ompR-envZ, feoABC and sifA were highly attenuated for invasion and intracellular survival within macrophages, derivatives lacking ssrAB, SPI13, SPI2, mgtRBC, sitABCD, sopF, sseJ and sspH2 showed increased ability to invade and survive within macrophages. Transcriptome analyses of macrophages infected with UK1, Δcrp-cya and its derivatives lacking phoPQ, sifA and sopF demonstrated that, compared to uninfected macrophages, 138, 148, 153, 155 and 142 genes were differentially expressed in these strains, respectively. Similar changes in gene expression were observed in macrophages infected with these strains; the upregulated genes belonged to innate immune response and host defense and the downregulated genes belonged to various metabolic pathways. Together, these data provide novel insights on the relative phenotypes and early response of macrophages to the vaccine strain and its derivatives. The Δcrp-cya derivatives could facilitate development of next-generation vaccines with improved safety.

Visualizing the pH in Escherichia coli Colonies via the Sensor Protein mCherryEA Allows High-Throughput Screening of Mutant Libraries

Cytoplasmic pH in bacteria is tightly regulated by diverse active mechanisms and interconnected regulatory processes. Many processes and regulators underlying pH homeostasis have been identified via phenotypic screening of strain libraries for nongrowth at low or high pH values. Direct screens with respect to changes of the internal pH in mutant strain collections are limited by laborious methods, which include fluorescent dyes and radioactive probes. Genetically encoded biosensors equip single organisms or strain libraries with an internal sensor molecule during the generation of the strain. Here, we used the pH-sensitive mCherry variant mCherryEA as a ratiometric pH biosensor. We visualized the internal pH of Escherichia coli colonies on agar plates by the use of a GelDoc imaging system. Combining this imaging technology with robot-assisted colony picking and spotting allowed us to screen and select mutants with altered internal pH values from a small transposon mutagenesis-derived E. coli library. Identification of the transposon (Tn) insertion sites in strains with altered internal pH levels revealed that the transposon was inserted into trkH (encoding a transmembrane protein of the potassium uptake system) or rssB (encoding the adaptor protein RssB, which mediates the proteolytic degradation of the general stress response regulator RpoS), two genes known to be associated with pH homeostasis and pH stress adaptation. This successful screening approach demonstrates that the pH sensor-based analysis of arrayed colonies on agar plates is a sensitive approach for the rapid identification of genes involved in pH homeostasis or pH stress adaptation in E. coli.

IMPORTANCE Phenotypic screening of strain libraries on agar plates has become a versatile tool to understand gene functions and to optimize biotechnological platform organisms. Screening is supported by genetically encoded biosensors that allow to easily measure intracellular processes. For this purpose, transcription factor-based biosensors have emerged as the sensor type of choice. Here, the target stimulus initiates the activation of a response gene (e.g., a fluorescent protein), followed by transcription, translation, and maturation. Due to this mechanistic principle, biosensor readouts are delayed and cannot report the actual intracellular state of the cell in real time. To capture rapid intracellular processes adequately, fluorescent reporter proteins are extensively applied. However, these sensor types have not previously been used for phenotypic screenings. To take advantage of their properties, we established here an imaging method that allows application of a rapid ratiometric sensor protein for assessing the internal pH of colonies in a high-throughput manner.

Innovative Treatments Enhancing the Functionality of Gut Microbiota to Improve Quality and Microbiological Safety of Foods of Animal Origin

The gastrointestinal tract, or gut, microbiota is a microbial community containing a variety of microorganisms colonizing throughout the gut that plays a crucial role in animal health, growth performance, and welfare. The gut microbiota is closely associated with the quality and microbiological safety of foods and food products originating from animals. The gut microbiota of the host can be modulated and enhanced in ways that improve the quality and safety of foods of animal origin. Probiotics—also known as direct-fed microbials—competitive exclusion cultures, prebiotics, and synbiotics have been utilized to achieve this goal. Reducing foodborne pathogen colonization in the gut prior to slaughter and enhancing the chemical, nutritional, or sensory characteristics of foods (e.g., meat, milk, and eggs) are two of many positive outcomes derived from the use of these competitive enhancement–based treatments in food-producing animals.

Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Enterobacteriaceae in food safety with an emphasis on raw milk and meat

There has been a growing interest in traditional dairy (such as raw milk cheeses) and meat products, in recent years. However, these products are suitable and nutrient medium and may be easily contaminated by microorganisms such as Enterobacteriaceae. Enterobacteriaceae are considered to be the indicator bacteria for microbiological quality of food and hygiene status of a production process. Additionally, the food contaminated by Enterobacteriaceae poses a microbiological risk for consumers. In fact, the contamination of raw milk and meat by Enterobacteriaceae amid manufacturing may easily occur from various environmental sources, and this group of bacteria is frequently detected in dairy and meat products. Therefore, monitoring the microbiological quality of the used raw material and maintaining high standards of hygiene in the production process are mandatory for a high quality of traditional products and the safety of the potential consumers. The goal of this review is to present the most recent survey on Enterobacteriaceae growth, number, and distribution in raw milk cheeses and meat, as well as to discuss the sources of contamination and methods of control. KEY POINTS: • Enterobacteriaceae: role and importance in milk and meat products, EU legal regulations • Dynamics, distribution, and survival of Enterobacteriaceae in milk and meat • Mechanisms of control of Enterobacteriaceae in dairy products.

Molecular Insights into Conformational Heterogeneity and Enhanced Structural Integrity of Helicobacter pylori DNA Binding Protein Hup at Low pH

The summarized amalgam of internal relaxation modulations and external forces like pH, temperature, and solvent conditions determine the protein structure, stability, and function. In a free-energy landscape, although conformers are arranged in vertical hierarchy, there exist several adjacent parallel sets with conformers occupying equivalent energy cleft. Such conformational states are pre-requisites for the functioning of proteins that have oscillating environmental conditions. As these conformational changes have utterly small re-arrangements, nuclear magnetic resonance (NMR) spectroscopy is unique in elucidating the structure-dynamics-stability-function relationships for such conformations. Helicobacter pylori survives and causes gastric cancer at extremely low pH also. However, least is known as to how the genome of the pathogen is protected from reactive oxygen species (ROS) scavenging in the gut at low pH under acidic stress. In the current study, biophysical characteristics of H. pylori DNA binding protein (Hup) have been elucidated at pH 2 using a combination of circular dichroism, fluorescence, NMR spectroscopy, and molecular dynamics simulations. Interestingly, the protein was found to have conserved structural features, differential backbone dynamics, enhanced stability, and DNA binding ability at low pH as well. In summary, the study suggests the partaking of Hup protein even at low pH in DNA protection for maintaining the genome integrity.

Extremophilic Microalgae Galdieria Gen. for Urban Wastewater Treatment: Current State, the Case of “POWER” System, and Future Prospects

Over the past decades, wastewater research has increasingly focused on the use of microalgae as a tool to remove contaminants, entrapping nutrients, and whose biomass could provide both material and energy resources. This review covers the advances in the emerging research on the use in wastewater sector of thermoacidophilic, low-lipid microalgae of the genus Galdieria, which exhibit high content of protein, reserve carbohydrates, and other potentially extractable high-value compounds. The natural tolerance of Galdieria for high toxic environments and hot climates recently made it a key player in a single-step process for municipal wastewater treatment, biomass cultivation and production of energetic compounds using hydrothermal liquefaction. In this system developed in New Mexico, Galdieria proved to be a highly performing organism, able to restore the composition of the effluent to the standards required by the current legislation for the discharge of treated wastewater. Future research efforts should focus on the implementation, in the context of wastewater treatment, of more energetically efficient cultivation systems, potentially capable of generating water with increasingly higher purity levels.

The Different Response to an Acid Shock of Two Salmonella Strains Marks Their Resistance to Thermal Treatments

Microbial cells respond to sub-lethal stresses with several physiological changes to increase their chance of survival. These changes are of high relevance when combined treatments (hurdle technology) are applied during food production, as the cells surviving the first hurdle may have greater resistance to subsequent treatments than untreated cells. In this study, we analyzed if Salmonella develops increased resistance to thermal treatments after the application of an acid shock. We compared the heat resistance of acid-shocked (pH 4.5 achieved with citric acid) Salmonella cells with that of cells maintained at pH 7 (control cells). Thermal treatments were performed between 57.5 and 65°C. We observed a differential response between the two strains studied. Acid-shocked cells of Salmonella Senftenberg exhibited reduced heat resistance, e.g., for a treatment at 60.0°C and pH 7.0 the time required to reduce the population by 3 log cycles was lowered from 10.75 to 1.98min with respect to control cells. Salmonella Enteritidis showed a different response, with acid-shocked cells having similar resistance than untreated cells (the time required to reduce 3 log cycles at 60.0°C and pH 7.0 was 0.30min for control and 0.31min for acid-shock cells). Based on results by differential plating (with or without adding the maximum non-inhibitory concentration of NaCl to the recovery medium), we hypothesize that the differential response between strains can be associated to sub-lethal damage to the cell membrane of S. Senftenberg caused by the acid shock. These results provide evidence that different strains of the same species can respond differently to an acid shock and highlight the relevance of cross-resistances for microbial risk assessment.

Comparative phenotypic characterization of hybrid Shiga toxin-producing / uropathogenic Escherichia coli, canonical uropathogenic and Shiga toxin-producing Escherichia coli

Hybrid Shiga toxin (Stx)-producing Escherichia coli (STEC) and uropathogenic E. coli (UPEC) strains are phylogenetically positioned between STEC and UPEC and can cause both diarrhea and urinary tract infections (UTIs). However, their virulence properties and adaptation to different host milieu in comparison to canonical UPEC and STEC strains are unknown. We determined phenotypes of the STEC/UPEC hybrid with respect to virulence including acid resistance, motility, biofilm formation, siderophore production, and adherence to human colonic Caco-2 and bladder T24 cells and compared to phenotypes of commensal strain MG1655, UPEC strain 536, and STEC strains B2F1 and Sakai. Moreover, we assessed the adaptation of the hybrid to artificial urine medium (AUM) and simulated colonic environment medium (SCEM). Overall acid resistance at pH 2.5 was high except in strains B2F1 and hybrid 05-00787 which showed reduced and extremely low acid resistance, respectively. Motility was reduced in hybrid 05-00787 and 09-05501 but strong in the remaining hybrids. While some hybrids showed high biofilm formation in LB, overall biofilm formation in SCEM and AUM were low and non-existent, respectively. All strains tested showed siderophore activity at equilibrium. All strains except MG1655 adhered to Caco-2 cells with the hybrid having similar adherence when compared to 536 but exhibited 2 and 3 times lower adherence when compared to B2F1 and Sakai, respectively. All Stx-producing strains adhered stronger to T24 cells than strains 536 and MG1655. Overall growth in LB, SCEM and AUM was consistent within the hybrid strains, except hybrid 05-00787 which showed significantly different growth patterns. Our data suggest that the hybrid is adapted to both, the intestinal and extraintestinal milieu. Expression of phenotypes typical of intestinal and extraintestinal pathogens thereby supports its potential to cause diarrhea and UTI.

Role of microbial dysbiosis in the pathogenesis of esophageal mucosal disease: A paradigm shift from acid to bacteria?

Genomic sequencing, bioinformatics, and initial speciation (e.g., relative abundance) of the commensal microbiome have revolutionized the way we think about the “human” body in health and disease. The interactions between the gut bacteria and the immune system of the host play a key role in the pathogenesis of gastrointestinal diseases, including those impacting the esophagus. Although relatively stable, there are a number of factors that may disrupt the delicate balance between the luminal esophageal microbiome (EM) and the host. These changes are thought to be a product of age, diet, antibiotic and other medication use, oral hygiene, smoking, and/or expression of antibiotic products (bacteriocins) by other flora. These effects may lead to persistent dysbiosis which in turn increases the risk of local inflammation, systemic inflammation, and ultimately disease progression. Research has suggested that the etiology of gastroesophageal reflux disease-related esophagitis includes a cytokine-mediated inflammatory component and is, therefore, not merely the result of esophageal mucosal exposure to corrosives (i.e., acid). Emerging evidence also suggests that the EM plays a major role in the pathogenesis of disease by inciting an immunogenic response which ultimately propagates the inflammatory cascade. Here, we discuss the potential role for manipulating the EM as a therapeutic option for treating the root cause of various esophageal disease rather than just providing symptomatic relief (i.e., acid suppression).

Salmonella enterica serovar Typhi genomic regions involved in low pH resistance and in invasion and replication in human macrophages

Purpose

Salmonella enterica serovar Typhi, the etiological agent of typhoid fever, causes a systemic life-threatening disease. To carry out a successful infection process, this bacterium needs to survive alkaline and acid pH conditions presented in the mouth, stomach, small intestine, and gallbladder. Therefore, in this work, a genetic screening to identify S. Typhi genes involved in acid and circumneutral pH resistance was performed.

Methods

A collection of S. Typhi mutants deleted of fragments ranging from 6 to 80 kb were obtained by the Datsenko and Wanner method. Bacterial growth rate assays of each mutant were performed to identify S. Typhi genes involved in circumneutral and acid pH resistance. S. Typhi mutants deficient to growth at specific pH were evaluated in their capacity to invade and replicate in phagocytic cells.

Results

In this work, it is reported that S. Typhi ∆F4 (pH 4.5), S. Typhi ∆F44 (pH 4.5, 5.5, and 6.5), and S. Typhi ∆F73 (pH 4.5, 5.5, 6.5, and 7.5) were deficient to grow in the pH indicated. These three mutant strains were also affected in their ability to invade and replicate in human macrophages.

Conclusions

S. Typhi contains defined genomic regions that influence the survival at specific pH values, as well as the invasion and replication inside human cells. Thus, this genetic information probably allows the bacteria to survive in different human compartments for an efficient infection cycle.

Characterization of Salmonella spp. Isolates from Swine: Virulence and Antimicrobial Resistance

Simple Summary

Salmonella is a pathogenic bacterium able to infect both humans and animals. It is diffused worldwide and, generally, animals are a source of infection for humans. Among domestic animals, swine represents an important reservoir and a frequent source of human infection, especially in some countries like Italy. To acquire information on Salmonella, in particular about epidemiology, but also virulence, pathogenesis and antimicrobial resistance, is the basis for a cohesive control program. This manuscript describes an investigation conducted on Salmonella isolates from swine, where two important characteristics were evaluated: the pathogenicity and the antimicrobial resistance. A great variability was observed among investigated strains. Salmonella serovar Typhimurium was confirmed as one of the most virulent serovars; indeed, most isolates belonging to this serovar presented many of the searched virulence factors. A high level of antimicrobial resistance was observed for some compounds (sulfonamide, tetracycline, streptomycin and ampicillin), but not for the so-called “last line antibiotics”, such as, for example, ciprofloxacin. The constant monitoring on circulating strains in reservoir animals is important to acquire information and set up adequate prophylaxis measures.

Abstract

Salmonella is one of the most important zoonotic pathogens worldwide. Swine represent typical reservoirs of this bacterium and a frequent source of human infection. Some intrinsic traits make some serovars or strains more virulent than others. Twenty-nine Salmonella spp. isolated from pigs belonging to 16 different serovars were analyzed for gastric acid environment resistance, presence of virulence genes (mgtC, rhuM, pipB, sopB, spvRBC, gipA, sodCI, sopE), antimicrobial resistance and presence of antimicrobial resistance genes (bla_TEM, bla_PSE-1, aadA1, aadA2, aphA1-lab, strA-strB, tetA, tetB, tetC, tetG, sul1, sul2, sul3). A percentage of 44.83% of strains showed constitutive and inducible gastric acid resistance, whereas 37.93% of strains became resistant only after induction. The genes sopB, pipB and mgtC were the most often detected, with 79.31%, 48.28% and 37.93% of positive strains, respectively. Salmonella virulence plasmid genes were detected in a S. enterica sup. houtenae ser. 40:z₄,z₂₃:-strain. Fifteen different virulence profiles were identified: one isolate (ser. Typhimurium) was positive for 6 genes, and 6 isolates (3 ser. Typhimurium, 2 ser. Typhimurium monophasic variant and 1 ser. Choleraesuis) scored positive for 5 genes. None of the isolates resulted resistant to cefotaxime and ciprofloxacin, while all isolates were susceptible to ceftazidime, colistin and gentamycin. Many strains were resistant to sulfonamide (75.86%), tetracycline (51.72%), streptomycin (48.28%) and ampicillin (31.03%). Twenty different resisto-types were identified. Six strains (4 ser. Typhimurium, 1 ser. Derby and 1 ser. Typhimurium monophasic variant) showed the ASSuT profile. Most detected resistance genes sul2 (34.48%), tetA (27.58%) and strA-strB (27.58%). Great variability was observed in analyzed strains. S. ser. Typhimurium was confirmed as one of the most virulent serovars. This study underlines that swine could be a reservoir and source of pathogenic Salmonella strains.

Prior exposure to different combinations of pH and undissociated acetic acid can affect the induced resistance of Salmonella spp. strains in mayonnaise stored under refrigeration and the regulation of acid-resistance related genes

The innate and inducible resistance of six Salmonella strains (4/74, FS8, FS115, P167807, ATCC 13076, WT) in mayonnaise at 5 °C following adaptation to different pH/undissociated acetic acid (UAA) combinations (15mM/pH5.0, 35mM/pH5.5, 45mM/pH6.0) was investigated. The inherent and acid-induced responses were strain-dependent. Two strains (ATCC 13076, WT), albeit not the most resistant innately, exhibited the most prominent adaptive potential. Limited/no adaptability was observed regarding the rest strains, though being more resistant inherently. The individual effect of pH and UAA adaptation in the phenotypic and transcriptomic profiles of ATCC 13076 and WT was further examined. The type (pH, UAA) and magnitude of stress intensity affected their responses. Variations in the type and magnitude of stress intensity also determined the relative gene expression of four genes (adiA, cadB, rpoS, ompR) implicated in Salmonella acid resistance mechanisms. adiA and cadB were overexpressed following adaptation to some treatments; rpoS and ompR were downregulated following adaptation to 15mM/pH5.0 and 35mM/pH5.5, respectively. Nonetheless, the transcriptomic profiles did not always correlate with the corresponding phenotypes. In conclusion, strain variations in Salmonella are extensive. The ability of the strains to adapt and induce resistant phenotypes and acid resistance-related genes is affected by the type and magnitude of the stress applied during adaptation.

The "Little Iron Waltz": The Ternary Response of Paracoccidioides spp. to Iron Deprivation

Paracoccidioides is a genus of thermodimorphic fungi that causes paracoccidioidomycosis. When in the host, the fungus undergoes several challenges, including iron deprivation imposed by nutritional immunity. In response to the iron deprivation triggered by the host, the fungus responds in a ternary manner using mechanisms of high affinity and specificity for the uptake of Fe, namely non-classical reductive iron uptake pathway, uptake of host iron proteins, and biosynthesis and uptake of siderophores. This triple response resembles the rhythmic structure of a waltz, which features three beats per compass. Using this connotation, we have constructed this review summarizing relevant findings in this area of study and pointing out new discoveries and perspectives that may contribute to the expansion of this "little iron waltz".

Salmonella survival after exposure to heat in a model meat juice system

The effect of heat against eleven Salmonella strains in model meat juices was examined. Juices from beef, lamb and goat were made from either the fatty layer (FL), muscle (M) or a mixture of both (FLM). The pH of each FLM sample was altered to match the pH of PBS and vice versa to determine the pH effect on the survival of Salmonella against the effect of heat. Salmonella were exposed to either gradual heating to 70 °C in FLM, M and FL or heat shock at 70 °C for 5 min in FLM. Fat, fatty acid profile and iron content of the juices were determined. Gradual heat treatment significantly (p ≤ 0.05) reduced Salmonella as compared to the untreated controls (~1.92-7.61 log CFU ml^-1) while heat shock significantly (p ≤ 0.05) reduced Salmonella as compared to the untreated controls (~5.80-7.36 log CFU ml^-1). Survival of Salmonella was higher in lamb juices than other juices. The fat content in lamb FL (3.25%) was significantly higher (p ≤ 0.05) than beef (1.30%) and goat FL (1.42%). Iron content in lamb FLM (~127 mg kg^-1) was significantly (p ≤ 0.05) lower than beef (~233 mg kg^-1) and goat FLM (~210 mg kg^-1). The omega 6 and linoleic acid content in goat FLM (~36.0% and ~34.4%) was significantly higher (p ≤ 0.05) than beef (~29.1% and ~27.1%). Fat, fatty acids and iron may differentially protect Salmonella against the effect of heat in these juices.

Metabolic Traits of Bovine Shiga Toxin-Producing Escherichia Coli (STEC) Strains with Different Colonization Properties

Cattle harbor Shiga toxin-producing Escherichia coli (STEC) in their intestinal tract, thereby providing these microorganisms with an ecological niche, but without this colonization leading to any clinical signs. In a preceding study, genotypic characterization of bovine STEC isolates unveiled that their ability to colonize cattle persistently (STEC^per) or only sporadically (STEC^spo) is more closely associated with the overall composition of the accessory rather than the core genome. However, the colonization pattern could not be unequivocally linked to the possession of classical virulence genes. This study aimed at assessing, therefore, if the presence of certain phenotypic traits in the strains determines their colonization pattern and if these can be traced back to distinctive genetic features. STEC^spo strains produced significantly more biofilm than STEC^per when incubated at lower temperatures. Key substrates, the metabolism of which showed a significant association with colonization type, were glyoxylic acid and L-rhamnose, which were utilized by STEC^spo, but not or only by some STEC^per. Genomic sequences of the respective glc and rha operons contained mutations and frameshifts in uptake and/or regulatory genes, particularly in STEC^per. These findings suggest that STEC^spo conserved features leveraging survival in the environment, whereas the acquisition of a persistent colonization phenotype in the cattle reservoir was accompanied by the loss of metabolic properties and genomic mutations in the underlying genetic pathways.

Using hydrochloric acid and bile resistance for optimized detection and isolation of Shiga toxin-producing Escherichia coli (STEC) from sprouts

Shiga toxin-producing Escherichia coli (STEC) in sprouts have caused large scale outbreaks in the past involving severe illness. The combination of this very diverse pathogen and a food matrix with high numbers of background microbiota poses a particular challenge for detection and isolation. An acid treatment of the enrichment before plating on agar has been shown to improve the recovery of STEC from sprouts. After enrichment in buffered peptone water (BPW) at 37 °C we applied an acid treatment, followed by plating on tryptone bile x-glucuronide (TBX) agar (acid bile method). An inter-laboratory study was organized with 21 laboratories taking part to evaluate the performance parameters and applicability of the acid bile method. A sample set of six sprout samples was prepared consisting of two uninoculated samples and four spiked samples, each containing one of two STEC strains at one of two concentrations (low and high). Analyzing a set of six samples at the National Reference Laboratory (NRL E. coli), we determined the relative abundance of STEC without, after acid-, after bile- and after acid-bile treatment using real-time PCR. The participating laboratories successfully applied the acid bile method and were better able to detect (sensitivity 92.9% vs. 70.0%) and isolate (sensitivity 87.5% vs. 31.3%) STEC from positive samples using the acid bile method compared to non-acid methods. The relative limit of detection (RLOD) after isolation using the acid bile method (vs. non-acid method) was <1 for both STEC strains used, BfR-EC-14434 O133:H25 (0.146) and BfR-EC-16015 O26:H11 (0.073). A collection of STEC (n = 71) of diverse type and characteristics was assessed for their resistance towards the acid bile treatment selection. The majority (n = 65) of STEC strains could be recovered after acid treatment on TBX plates. However, a few strains (n = 6), among them clinical isolates were (partly) sensitive. These results suggest that an acid bile method is a rapid and reasonable approach to improve the recovery of STEC from sprouts when used in combination with methods targeting other selection markers.

New Roles for Two-Component System Response Regulators of Salmonella enterica Serovar Typhi during Host Cell Interactions

In order to survive external stresses, bacteria need to adapt quickly to changes in their environment. One adaptive mechanism is to coordinate and alter their gene expression by using two-component systems (TCS). TCS are composed of a sensor kinase that activates a transcriptional response regulator by phosphorylation. TCS are involved in motility, virulence, nutrient acquisition, and envelope stress in many bacteria. The pathogenic bacteria Salmonella enterica serovar Typhi (S. Typhi) possess 30 TCSs, is specific to humans, and causes typhoid fever. Here, we have individually deleted each of the 30 response regulators. We have determined their role during interaction with host cells (epithelial cells and macrophages). Deletion of most of the systems (24 out of 30) resulted in a significant change during infection. We have identified 32 new phenotypes associated with TCS of S. Typhi. Some previously known phenotypes associated with TCSs in Salmonella were also confirmed. We have also uncovered phenotypic divergence between Salmonella serovars, as distinct phenotypes between S. Typhi and S. Typhimurium were identified for cpxR. This finding highlights the importance of specifically studying S. Typhi to understand its pathogenesis mechanisms and to develop strategies to potentially reduce typhoid infections.

Escherichia coli O157:H7 Stationary-Phase Acid Resistance and Assessment of Survival in a Model Vegetable Fermentation System

ABSTRACT

Escherichia coli O157:H7 (STEC) acid resistance may aid the pathogen's ability to cross the human gastric barrier, which makes it an organism of concern in acidic foods. Our objective was to determine how STEC acid resistance may correlate with survival during vegetable fermentations. Seven E. coli O157:H7 strains were screened to assess acid resistance in simulated stomach acid at pH 2. The strains were separated into two groups that differed in acid resistance (P < 0.05), with three being acid sensitive and four acid resistant. The growth rates of these strains were measured in a Luria broth at pH values from 4.2 to 6.8. Two strains having similar growth kinetics, B201 (acid sensitive) and B241 (acid resistant), were selected for further analysis. B201 was found to be missing (compared with B241) two glutamic acid decarboxylase regulatory genes required for acid resistance, gadE and gadX. These strains were challenged in lactic acid (100 mM) solutions, including cucumber juice (CJ) media at pH 3.3. As expected, B201 was more acid sensitive than B241, and a filtered fermented CJ was more inhibitory than similarly acidified CJ. In competitive growth studies with Lactobacillus plantarum LA445 in CJ, B201 or B241 grew from approximately 104 to 108 CFU/mL within 24 h, but the STEC strains were below the limit of detection by 48 h. In all fermentations, L. plantarum reached 108 CFU/mL by 48 h. However, in three of four independent fermentation experiments, strain B201 survived longer than B241. This was possibly due to buffering in B241-LA445 fermentation brines that had increased lactic acid for a given pH compared with B201-LA445. These data indicate that stationary-phase acid resistance may not accurately predict STEC survival during vegetable fermentations.

HIGHLIGHTS

Pathogenicity island excision during an infection by Salmonella enterica serovar Enteritidis is required for crossing the intestinal epithelial barrier in mice to cause systemic infection

Pathogenicity island excision is a phenomenon that occurs in several Salmonella enterica serovars and other members of the family Enterobacteriaceae. ROD21 is an excisable pathogenicity island found in the chromosome of S. Enteritidis, S. Dublin and S. Typhi among others, which contain several genes encoding virulence-associated proteins. Excision of ROD21 may play a role in the ability of S. Enteritidis to cause a systemic infection in mice. Our previous studies have shown that Salmonella strains unable to excise ROD21 display a reduced ability to colonize the liver and spleen. In this work, we determined the kinetics of ROD21 excision in vivo in C57BL/6 mice and its effect on virulence. We quantified bacterial burden and excision frequency in different portions of the digestive tract and internal organs throughout the infection. We observed that the frequency of ROD21 excision was significantly increased in the bacterial population colonizing mesenteric lymph nodes at early stages of the infective cycle, before 48 hours post-infection. In contrast, excision frequency remained very low in the liver and spleen at these stages. Interestingly, excision increased drastically after 48 h post infection, when intestinal re-infection and mortality begun. Moreover, we observed that the inability to excise ROD21 had a negative effect on S. Enteritidis capacity to translocate from the intestine to deeper organs, which correlates with an abnormal transcription of invA in the S. Enteritidis strain unable to excise ROD21. These results suggest that excision of ROD21 is a genetic mechanism required by S. Enteritidis to produce a successful invasion of the intestinal epithelium, a step required to generate systemic infection in mice.

Salmonella is a bacterial genus that causes foodborne illnesses worldwide. The ability of Salmonella to cause disease is related to the presence of Pathogenicity Islands (PAIs), which are clusters of genes within the bacterial chromosome that are involved in virulence. Interestingly, some PAIs excise and re-integrate into the bacterial chromosome, which is a process probably involved in the capacity of Salmonella to cause infection in their hosts. Here we show that the excision of Region of Difference 21 (ROD21), one of the excisable PAIs within the genome of Salmonella enterica serovar Enteritidis, occurs with high frequency in the mesenteric lymph node at early stages of infection, suggesting that excision is required by S. Enteritidis to reach this organ from the intestinal tract. Accordingly, S. Enteritidis strains unable to excise ROD21 are unable to invade intestinal host cells, delaying the infective cycle and showing attenuated virulence. We propose that ROD21 excision in vivo is required by S. Enteritidis to cross the intestinal barrier, a fundamental step to further colonize deep organs, due to modulation of virulence genes transcription. Thus, ROD21 excision may play an important role in the capacity of the bacteria to cause a successful systemic infection in the mouse. Our data suggest that the excision of PAIs is a mechanism used by Salmonella and probably other Gram-negative enterobacteria to modulate the expression of virulence genes and may provide insights to design novel therapies to control the infection caused by these pathogens.

Prior Exposure to Dry-Cured Meat Promotes Resistance to Simulated Gastric Fluid in Salmonella Typhimurium

This study assessed if exposure of foodborne Salmonella enterica in Brazilian dry-cured loin (BDL) affects pathogen inactivation in simulated gastric fluid (SGF). The acid tolerance responses of three Salmonella enterica serovars, Typhimurium, Derby and Panama, were assessed by an acid challenge trial at pH 3.0 for 4 h following pre-adaptation to three conditions: neutral pH, acidic pH (4.5) or BDL matrix. The influence of Salmonella exposure temperature and time in the BDL on pathogen gastric fluid resistance was evaluated by the response surface methodology. The Salmonella serovars acquired acid tolerance when exposed to the BDL matrix and their response to acid stress was strain-dependent, with S. Typhimurium being the most tolerant strain. S. Typhimuirum exposed to temperatures >25 °C in the BDL matrix displayed increased resistance to SGF. By using the response surface methodology, it was determined that S. Typhimurium becomes less resistant against SGF if maintained in the BDL matrix at temperatures <7 °C, reinforcing the recommendation to store dry-cured meat under refrigeration in order to minimize consumer risks. The results presented herein point to a novel aspect of hurdle technology that should be taken into account to further understand the risks associated with hurdle-stable meat product, such as dry-cured meats, concerning foodborne pathogen contamination.

RstA, a two-component response regulator, plays important roles in multiple virulence-associated processes in enterohemorrhagic Escherichia coli O157:H7

Background

Enterohemorrhagic Escherichia coli O157:H7 (EHEC O157) causes bloody diarrhea and hemolytic-uremic syndrome. EHEC O157 encounters varied microenvironments during infection, and can efficiently adapt to these using the two-component system (TCS). Recently, a functional TCS, RstAB, has been implicated in the regulation of virulence of several bacterial pathogens. However, the regulatory function of RstAB in EHEC O157 is poorly understood. This study aimed at providing insights into the global effects of RstA on gene expression in EHEC O157.

Results

In the present study, we analyzed gene expression differences between the EHEC O157 wild-type strain and a ΔrstA mutant using RNA-seq technology. Genes with differential expression in the ΔrstA mutant compared to that in the wild-type strain were identified and grouped into clusters of orthologous categories. RstA promoted EHEC O157 LEE gene expression, adhesion in vitro, and colonization in vivo by indirect regulation. We also found that RstA could bind directly to the promoter region of hdeA and yeaI to enhance acid tolerance and decrease biofilm formation by modulating the concentration of c-di-GMP.

Conclusions

In summary, the RstAB TCS in EHEC O157 plays a major role in the regulation of virulence, acid tolerance, and biofilm formation. We clarified the regulatory function of RstA, providing an insight into mechanisms that may be potential drug targets for treatment of EHEC O157-related infections.

Salmonella and Reactive Oxygen Species: A Love-Hate Relationship

Salmonella enterica represents an enterobacterial species including numerous serovars that cause infections at, or initiated at, the intestinal epithelium. Many serovars also act as facultative intracellular pathogens with a tropism for phagocytic cells. These bacteria not only survive in phagocytes but also undergo de facto replication therein. Phagocytes, through the activities of phagocyte NADPH-dependent oxidase and inducible nitric oxide synthase, are very proficient in converting molecular oxygen to reactive oxygen (ROS) and nitrogen species (RNS). These compounds represent highly efficient effectors of the innate immune defense. Salmonella is by no means resistant to these effectors, which may stand in contrast to the host niches chosen. To cope with this paradox, these bacteria rely on an array of detoxification and repair systems. Combination these systems allows for a high enough tolerance to ROS and RNS to enable establishment of infection. In addition, salmonella possesses protein factors that have the potential to dampen the infection-associated inflammation, which evidently results in a reduced exposure to ROS and RNS. This review attempts to summarize the activities and strategies by which salmonella tries to cope with ROS and RNS and how the bacterium can make use of these innate defense factors.

Increased Resistance of Salmonella enterica Serovar Typhimurium and Escherichia coli O157:H7 to 222-Nanometer Krypton-Chlorine Excilamp Treatment by Acid Adaptation

In this study, we examined the change in resistance of Salmonella enterica serovar Typhimurium and Escherichia coli O157:H7 to 222-nm krypton-chlorine (KrCl) excilamp treatment as influenced by acid adaptation and identified a mechanism of resistance change. In addition, we measured changes in apple juice quality indicators, such as color, total phenols, and 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity, during treatment. Non-acid-adapted and acid-adapted pathogens were induced by growing the cells in tryptic soy broth without dextrose (TSB w/o D) at pH 7.3 and in TSB w/o D at pH 5.0 (adjusted with HCl), respectively. For the KrCl excilamp treatment, acid-adapted pathogens exhibited significantly (P < 0.05) higher D5d values, which indicate dosages required to achieve a 5-log reduction, than those for non-acid-adapted pathogens in both commercially clarified apple juice and phosphate-buffered saline (PBS), and the pathogens in the juice showed significantly (P < 0.05) higher D5d values than those for pathogens in PBS because of the UV-absorbing characteristics of apple juice. Through mechanism identification, it was found that the generation of lipid peroxidation in the cell membrane, inducing cell membrane destruction, was significantly (P < 0.05) lower in acid-adapted cells than in non-acid-adapted cells for the same amount of reactive oxygen species (ROS) generated at the same dose because the ratio of unsaturated to saturated fatty acids (USFA/SFA) in the cell membrane was significantly (P < 0.05) decreased as a result of acid adaptation. Treated apple juice showed no significant (P > 0.05) difference in quality indicators compared to those of untreated controls during treatment at 1,773 mJ/cm2IMPORTANCE There is a need for novel, mercury-free UV lamp technology to replace germicidal lamps containing harmful mercury, which are routinely utilized for UV pasteurization of apple juice. In addition, consideration of the changes in response to antimicrobial treatments that may occur when pathogens are adapted to the acid in an apple juice matrix is critical to the practical application of this technology. Based on this, an investigation using 222-nm KrCl excilamp technology, an attractive alternative to mercury lamps, was conducted. Our study demonstrated increased resistance to 222-nm KrCl excilamp treatment as pathogens adapted to acids, and this was due to changes in reactivity to ROS with changes in the fatty acid composition of the cell membrane. Despite increased resistance, the 222-nm KrCl excilamp achieved pathogen reductions of 5 log or more at laboratory scale without affecting apple juice quality. These results provide valuable baseline data for application of 222-nm KrCl excilamps in the apple juice industry.

Modulation of Enterohaemorrhagic Escherichia coli Survival and Virulence in the Human Gastrointestinal Tract

Enterohaemorrhagic Escherichia coli (EHEC) is a major foodborne pathogen responsible for human diseases ranging from diarrhoea to life-threatening complications. Survival of the pathogen and modulation of virulence gene expression along the human gastrointestinal tract (GIT) are key features in bacterial pathogenesis, but remain poorly described, due to a paucity of relevant model systems. This review will provide an overview of the in vitro and in vivo studies investigating the effect of abiotic (e.g., gastric acid, bile, low oxygen concentration or fluid shear) and biotic (e.g., gut microbiota, short chain fatty acids or host hormones) parameters of the human gut on EHEC survival and/or virulence (especially in relation with motility, adhesion and toxin production). Despite their relevance, these studies display important limitations considering the complexity of the human digestive environment. These include the evaluation of only one single digestive parameter at a time, lack of dynamic flux and compartmentalization, and the absence of a complex human gut microbiota. In a last part of the review, we will discuss how dynamic multi-compartmental in vitro models of the human gut represent a novel platform for elucidating spatial and temporal modulation of EHEC survival and virulence along the GIT, and provide new insights into EHEC pathogenesis.

Food-Associated Stress Primes Foodborne Pathogens for the Gastrointestinal Phase of Infection

The incidence of foodborne outbreaks and product recalls is on the rise. The ability of the pathogen to adapt and survive under stressful environments of food processing and the host gastrointestinal tract may contribute to increasing foodborne illnesses. In the host, multiple factors such as bacteriolytic enzymes, acidic pH, bile, resident microflora, antimicrobial peptides, and innate and adaptive immune responses are essential in eliminating pathogens. Likewise, food processing and preservation techniques are employed to eliminate or reduce human pathogens load in food. However, sub-lethal processing or preservation treatments may evoke bacterial coping mechanisms that alter gene expression, specifically and broadly, resulting in resistance to the bactericidal insults. Furthermore, environmentally cued changes in gene expression can lead to changes in bacterial adhesion, colonization, invasion, and toxin production that contribute to pathogen virulence. The shared microenvironment between the food preservation techniques and the host gastrointestinal tract drives microbes to adapt to the stressful environment, resulting in enhanced virulence and infectivity during a foodborne illness episode.

Distribution of Salmonella Enteritidis in internal organs and variation of cecum microbiota in chicken after oral challenge

The aim study was to explore the distribution of Salmonella Enteritidis (S. enteritidis) in internal organs and variation of cecum microbiota in newly hatched chicken after oral challenge during a 21-day period. The quantities of S. enteritidis DNA in different internal organs (heart, liver, spleen, stomach, pancreas, small intestine, blood and cecum contents) were determined by real-time fluorescent quantitative polymerase chain reaction (FQ-PCR). The result showed that all of the above-mentioned samples were positive at 12 h post inoculation (PI) after oral challenge. The highest copy numbers of S. enteritidis in all tissue were heart and liver, with about 2 × 10² to 6 × 10⁶ copies of DNA target sequences/0.5 g. The copy number of S. enteritidis in the stomach was only lower than the heart and liver. The blood at 8 d PI, the pancreas at 10 d PI, the heart at 14 d PI and the stomach at 17 d PI didn't have a positive result. However, the liver, spleen, cecum contents and small intestine were all positive during the 21-day period. The cecum contents at 0 d PI, 4 d PI and 10 d PI from the control group and experiment group were collected for bacterial 16 S rRNA sequencing targeting the V3-V4 hypervariable region. The result showed that at the 0 d PI, the main cecum microbiota ingredient of the two-day old chicken was Enterobacteriaceae (Proteobacteria) and the other microbiology species were fewer. At the 10 d PI, the microbiota ingredient of cecum became abundant and stable mainly including the families Ruminococcaceae (Firmicutes), Enterobacteriaceae (Proteobacteria), Lachnospiraceae (Firmicutes) and clostridiacaea (Firmicutes) both of the two group, suggesting Salmonella infection with 2-day old chicken might not significantly change cecum microbiota community. The study indicated the major organs, which carried numerous S. enteritidis, providing a significantly guideline for salmonella detection in poultry and revealed the main microbiota ingredient of chicken cecum.

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi

Insights into disease susceptibility as well as the efficacy of vaccines against typhoid and other enteric pathogens may be informed by better understanding the relationship between the effector immune response and the gut microbiota. In the present study, we characterized the composition (16S rRNA gene profiling) and function (RNA sequencing [RNA-seq]) of the gut microbiota following immunization and subsequent exposure to wild-type Salmonella enterica serovar Typhi in a human challenge model to further investigate the central hypothesis that clinical outcomes may be linked to the gut microbiota. Metatranscriptome analysis of longitudinal stool samples collected from study subjects revealed two stable patterns of gene expression for the human gut microbiota, dominated by transcripts from either Methanobrevibacter or a diverse representation of genera in the Firmicutes phylum. Immunization with one of two live oral attenuated vaccines against S. Typhi had minimal effects on the composition or function of the gut microbiota. It was observed that subjects harboring the methanogen-dominated transcriptome community at baseline displayed a lower risk of developing symptoms of typhoid following challenge with wild-type S. Typhi. Furthermore, genes encoding antioxidant proteins, metal homeostasis and transport proteins, and heat shock proteins were expressed at a higher level at baseline or after challenge with S. Typhi in subjects who did not develop symptoms of typhoid. These data suggest that functional differences relating to redox potential and ion homeostasis in the gut microbiota may impact clinical outcomes following exposure to wild-type S. Typhi.IMPORTANCES. Typhi is a significant cause of systemic febrile morbidity in settings with poor sanitation and limited access to clean water. It has been demonstrated that the human gut microbiota can influence mucosal immune responses, but there is little information available on the impact of the human gut microbiota on clinical outcomes following exposure to enteric pathogens. Here, we describe differences in the composition and function of the gut microbiota in healthy adult volunteers enrolled in a typhoid vaccine trial and report that these differences are associated with host susceptibility to or protection from typhoid after challenge with wild-type S Typhi. Our observations have important implications in interpreting the efficacy of oral attenuated vaccines against enteric pathogens in diverse populations.

Dissecting the Acid Stress Response of Rhizobium tropici CIAT 899

Rhizobium tropici CIAT899 is a nodule-forming α-proteobacterium displaying intrinsic resistance to several abiotic stress conditions such as low pH and high temperatures, which are common in tropical environments. It is a good competitor for Phaseolus vulgaris (common bean) nodule occupancy at low pH values, however little is known about the genetic and physiological basis of the tolerance to acidic conditions. To identify genes in R. tropici involved in pH stress response we combined two different approaches: (1) A Tn5 mutant library of R. tropici CIAT899 was screened and 26 acid-sensitive mutants were identified. For 17 of these mutants, the transposon insertion sites could be identified. (2) We also studied the transcriptomes of cells grown under different pH conditions using RNA-Seq. RNA was extracted from cells grown for several generations in minimal medium at 6.8 or 4.5 (adapted cells). In addition, we acid-shocked cells pre-grown at pH 6.8 for 45 min at pH 4.5. Of the 6,289 protein-coding genes annotated in the genome of R. tropici CIAT 899, 383 were differentially expressed under acidic conditions (pH 4.5) vs. control condition (pH 6.8). Three hundred and fifty one genes were induced and 32 genes were repressed; only 11 genes were induced upon acid shock. The acid stress response of R. tropici CIAT899 is versatile: we found genes encoding response regulators and membrane transporters, enzymes involved in amino acid and carbohydrate metabolism and proton extrusion, in addition to several hypothetical genes. Our findings enhance our understanding of the core genes that are important during the acid stress response in R. tropici.

Salmonella Vaccines: Conduits for Protective Antigens

Vaccines afford a better and more cost-effective approach to combatting infectious diseases than continued reliance on antibiotics or antiviral or antiparasite drugs in the current era of increasing incidences of diseases caused by drug-resistant pathogens. Recombinant attenuated Salmonella vaccines (RASVs) have been significantly improved to exhibit the same or better attributes than wild-type parental strains to colonize internal lymphoid tissues and persist there to serve as factories to continuously synthesize and deliver rAgs. Encoded by codon-optimized pathogen genes, Ags are selected to induce protective immunity to infection by that pathogen. After immunization through a mucosal surface, the RASV attributes maximize their abilities to elicit mucosal and systemic Ab responses and cell-mediated immune responses. This article summarizes many of the numerous innovative technologies and discoveries that have resulted in RASV platforms that will enable development of safe efficacious RASVs to protect animals and humans against a diversity of infectious disease agents.

Soil microbial community responses to acid exposure and neutralization treatment

Changes in microbial community induced by acid shock were studied in the context of potential release of acids to the environment due to chemical accidents. The responses of microbial communities in three different soils to the exposure to sulfuric or hydrofluoric acid and to the subsequent neutralization treatment were investigated as functions of acid concentration and exposure time by using 16S-rRNA gene based pyrosequencing and DGGE (Denaturing Gradient Gel Electrophoresis). Measurements of soil pH and dissolved ion concentrations revealed that the added acids were neutralized to different degrees, depending on the mineral composition and soil texture. Hydrofluoric acid was more effectively neutralized by the soils, compared with sulfuric acid at the same normality. Gram-negative ß-Proteobacteria were shown to be the most acid-sensitive bacterial strains, while spore-forming Gram-positive Bacilli were the most acid-tolerant. The results of this study suggest that the Gram-positive to Gram-negative bacterial ratio may serve as an effective bio-indicator in assessing the impact of the acid shock on the microbial community. Neutralization treatments helped recover the ratio closer to their original values. The findings of this study show that microbial community changes as well as geochemical changes such as pH and dissolved ion concentrations need to be considered in estimating the impact of an acid spill, in selecting an optimal remediation strategy, and in deciding when to end remedial actions at the acid spill impacted site.

Mechanisms of Salmonella pathogenesis in animal models

Animal models play an important role in understanding the mechanisms of bacterial pathogenesis. Here we review recent studies of Salmonella infection in various animal models. Although mice are a classic animal model for Salmonella, mice do not normally get diarrhea, raising the question of how well the model represents normal human infection. However, pretreatment of mice with oral streptomycin, which apparently reduces the normal microbiota, leads to an inflammatory diarrheal response upon oral infection with Salmonella. This has led to a re-evaluation of the role of various Salmonella virulence factors in colonization of the intestine and induction of diarrhea. Indeed, it is now clear that Salmonella purposefully induces inflammation, which leads to the production of both carbon sources and terminal electron acceptors by the host that allow Salmonella to outgrow the normal intestinal microbiota. Overall use of this modified mouse model provides a more nuanced understanding of Salmonella intestinal infection in the context of the microbiota with implications for the ability to predict human risk.

Noisy Response to Antibiotic Stress Predicts Subsequent Single-Cell Survival in an Acidic Environment

Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to "cross-protect" bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors.

Benzoate- and Salicylate-Tolerant Strains of Escherichia coli K-12 Lose Antibiotic Resistance during Laboratory Evolution

Escherichia coli K-12 W3110 grows in the presence of membrane-permeant organic acids that can depress cytoplasmic pH and accumulate in the cytoplasm. We conducted experimental evolution by daily diluting cultures in increasing concentrations of benzoic acid (up to 20 mM) buffered at external pH 6.5, a pH at which permeant acids concentrate in the cytoplasm. By 2,000 generations, clones isolated from evolving populations showed increasing tolerance to benzoate but were sensitive to chloramphenicol and tetracycline. Sixteen clones grew to stationary phase in 20 mM benzoate, whereas the ancestral strain W3110 peaked and declined. Similar growth occurred in 10 mM salicylate. Benzoate-evolved strains grew like W3110 in the absence of benzoate, in media buffered at pH 4.8, pH 7.0, or pH 9.0, or in 20 mM acetate or sorbate at pH 6.5. Genomes of 16 strains revealed over 100 mutations, including single-nucleotide polymorphisms (SNPs), large deletions, and insertion knockouts. Most strains acquired deletions in the benzoate-induced multiple antibiotic resistance (Mar) regulon or in associated regulators such as rob and cpxA, as well as the multidrug resistance (MDR) efflux pumps emrA, emrY, and mdtA Strains also lost or downregulated the Gad acid fitness regulon. In 5 mM benzoate or in 2 mM salicylate (2-hydroxybenzoate), most strains showed increased sensitivity to the antibiotics chloramphenicol and tetracycline; some strains were more sensitive than a marA knockout strain. Thus, our benzoate-evolved strains may reveal additional unknown drug resistance components. Benzoate or salicylate selection pressure may cause general loss of MDR genes and regulators.

IMPORTANCE

Benzoate is a common food preservative, and salicylate is the primary active metabolite of aspirin. In the gut microbiome, genetic adaptation to salicylate may involve loss or downregulation of inducible multidrug resistance systems. This discovery implies that aspirin therapy may modulate the human gut microbiome to favor salicylate tolerance at the expense of drug resistance. Similar aspirin-associated loss of drug resistance might occur in bacterial pathogens found in arterial plaques.