Campylobacter jejuni is the leading cause of bacterial food-borne diarrheal disease in the developed world (Dasti et al., 2010). Acute C. jejuni infection causes watery to bloody diarrhea, with fever, nausea, and vomiting, and can be fatal to vulnerable individuals (Butzler and Skirrow, 1979; Walker et al., 1986). Although the infection is often self-limiting, it has been reported to lead to the development of secondary autoimmune disorders such as the Guillain-Barré or Miller-Fisher syndromes (Wassenaar and Blaser, 1999; Young et al., 2007). C. jejuni is a prevalent human pathogen but is usually viewed as commensal in livestock, particularly in poultry (Inglis and Kalischuk, 2004; Boes et al., 2005; Gormley et al., 2008). The majority of human infections occur directly through consumption of raw or undercooked contaminated animal products, such as meat and milk, or indirectly through cross-contamination events in the consumer kitchen. Nevertheless, animal products are not the sole route of transmission of C. jejuni to humans. Analysis of waterborne outbreaks and sporadic cases show that water is an important environmental reservoir for C. jejuni (Bolton et al., 1982; Thomas et al., 1999; Huang et al., 2015). Contamination of surface water and well water may occur due to direct deposition of animal feces, sewage discharge and farmland run-offs (Vogt et al., 1982; Lind et al., 1996; Clark et al., 2003; O’Reilly et al., 2007; Bronowski et al., 2014; Huang et al., 2015).

Campylobacter jejuni is a microaerophilic bacterium that grows best at temperatures ranging from 37 to 42°C, and requires a rich growth medium (Skirrow, 1991). In the host digestive tract, C. jejuni encounters various challenges, such as acidity, antimicrobial bile salts, resident microorganisms, fluctuations in osmolarity, and effectors of the immune system (Fordtran and Locklear, 1966; Stintzi et al., 2005). Once expelled from one host, C. jejuni is exposed to and must survive a different set of stress conditions before colonizing another host (Bronowski et al., 2014). The conditions encountered within the different transmission routes are variable; transmission to humans through contaminated meat subjects the bacterium to stresses that are different from those found when its transmission occurs through water (Bronowski et al., 2014). Potential stresses encountered in water include nutrient scarcity, extreme temperatures, disinfectant and osmotic stresses (Thomas et al., 1999; Murphy et al., 2006; Jackson et al., 2009). C. jejuni must therefore overcome these challenges to survive and use water as a transmission route. Presumably, strains that survive the best in water are the most likely to be succesfully transmitted between hosts through this medium. Supporting this hypothesis, some Campylobacter multilocus sequence type (ST) complexes (ST-2381, ST-45, and ST-1225) were found to be more commonly associated to water (Sopwith et al., 2008; Carter et al., 2009). The high incidence of ST-45 in river water isolates and in human infections could indicate that it is well adapted to environmental transmission routes (Murphy et al., 2005; Lévesque et al., 2013). Indeed, C. jejuni strains assigned to ST-45 survive heat, aerobic and oxidative stresses better than other sequence types (Habib et al., 2010).

The multiple transmission routes of C. jejuni suggest that some strains may possesses effective mechanisms that allow it to sense and cope with a variety of stresses present in a given niche (Bronowski et al., 2014). Contributing to the survival success of C. jejuni is its ability to persist in natural environments by adapting lifestyles other than the planktonic form. Consequently, C. jejuni can be found as a free-living member of complex multispecies biofilm (Nguyen et al., 2011), internalized within some waterborne protozoa (Axelsson-Olsson et al., 2005; Snelling et al., 2005; Baffone et al., 2006), excreted within multilamellar bodies (MLBs) by ciliates (Trigui et al., 2016) and viable but non-culturable (VBNC) cells (Rollins and Colwell, 1986; Murphy et al., 2006). Given that water is a vehicle for the spread of C. jejuni, many studies have focused on the survival of Campylobacter in different types of water, such as tap water (Buswell et al., 1998; Cools et al., 2003), bottled mineral water (Tatchou-Nyamsi-König et al., 2007), artificial seawater (ASW) (Baffone et al., 2006; Trigui et al., 2015b) and a defined freshwater medium (Fraquil) (Trigui et al., 2015b). Notably, several Campylobacter strains were found to enter the VBNC state after exposure to the aforementioned water sources (Cools et al., 2003; Baffone et al., 2006; Trigui et al., 2015b). VBNC C. jejuni cells were able to maintain their ability to adhere to intestinal cells after 3 weeks in freshwater at 4°C (Patrone et al., 2013). In addition, Campylobacter-naïve chicks that consumed water contaminated by VBNC C. jejuni were successfully colonized by the bacterium (Pearson et al., 1993). Therefore, VBNC C. jejuni are considered a threat to public health (Murphy et al., 2006).

Some of the C. jejuni stress response mechanisms and their regulators that have been studied to-date are distinct from those in other enteric Gram-negative pathogens, while others remain poorly understood. For example, full genome analyses of C. jejuni strains suggest that this pathogen has a relatively small genome (Parkhill et al., 2000) and lacks many classical stress tolerance regulators, such as the stationary phase sigma factor RpoS, the oxidative stress response regulators SoxRS and OxyR, and the osmotic shock regulator BetAB (Murphy et al., 2006). In contrast, genes related to iron metabolism and oxidative stress defense, which are controlled by the ferric uptake regulator (Fur) and the peroxide responsive regulator (PerR), respectively, are key factors for C. jejuni’s survival in vivo (Palyada et al., 2009; Flint et al., 2014; Butcher et al., 2015).

Recently, we investigated the survival of C. jejuni chicken cecal isolates in Fraquil, artificial sea water and Fraquil supplemented with salt (Trigui et al., 2015b). Fraquil is an artificial freshwater medium used to study the behavior of bacteria in water (Mendis et al., 2015). The strains tested varied significantly in their ability to survive in the three aforementioned water systems, presumably due to genetic differences between the isolates. In the present study, the survival of two additional model strains was evaluated in Fraquil. Strain 81116 remained culturable and viable longer than strain 81-176 in Fraquil. Moreover, strain 81116 was more resistant to oxidative stress and exposure to bile salts after incubation in water relative to 81-176. Given that 81116 was better adapted to surviving this aquatic environment, we performed a microarray analysis to uncover its transcriptomic response when exposed to water.

Transmission of campylobacteriosis to humans occurs via consumption of contaminated foods or water. The ability of C. jejuni to survive in water determines its ability to be transmitted by water to humans, or from one animal reservoir to another (Bronowski et al., 2014). The ability to survive in water varies greatly between C. jejuni strains (Buswell et al., 1998; Thomas et al., 1999; Tatchou-Nyamsi-König et al., 2007; Trigui et al., 2015b), resulting in some sequence types (ST) being isolated more frequently from water than others (Sopwith et al., 2008; Carter et al., 2009; Lévesque et al., 2013). This suggests that some strains are better adapted for utilizing water as a vehicle for transmission. This study aims at identifying phenotypes associated with the ability to survive in freshwater, and determining the transcriptomic response of a strain adapted to survive in water. Since the composition of tap water is variable, the experiments were carried out in the chemically defined freshwater medium Fraquil, which approximates the composition of freshwater of North America (Morel et al., 1975; Trigui et al., 2015b). First, the ability of each strain to survive in Fraquil was assessed using CFU counts and the LIVE/DEAD assay. 81116, a strain isolated during a water-borne outbreak of campylobacteriosis (Palmer et al., 1983), was found to survive in water better than 81-176, an epidemic strain isolated from contaminated milk (Figure 1) (Korlath et al., 1985). We hypothesized that the capacity of each strain to survive in different environmental conditions explains their mode of transmission and their respective outbreaks (Bronowski et al., 2014).

In addition, we report that exposure to Fraquil also affects the sensitivity of these strains to oxidative stress and bile salts (Figures 2, 3). Oxidative disinfectants, such as chlorine, are routinely used in processing plant chiller water to prevent cross contamination and reduce C. jejuni loads on carcasses (Kameyama et al., 2012). Our results suggest that some strains, such as 81116, are better than others at resisting these disinfection procedures during chilling and are more likely to contaminate the final product. A recent study reports that some flaA genotypes are selected by the slaughtering process and appear more frequently on the finished product (Kudirkienė et al., 2011).

The resistance of strain 81116 to bile salts was not affected by exposure to Fraquil or rich broth (Figure 3). In contrast, 81-176 was markedly more sensitive to this stress (Figure 3). The CmeABC efflux pump mediates resistance to bile salt and is essential for colonization of the intestinal tract (Lin et al., 2003, 2005, 2007; Gibreel et al., 2007; Young et al., 2007; Caldwell et al., 2008). While 81116 induced the expression of cmeB in response to Fraquil, the remaining components of the efflux system were not differentially expressed in water relative to rich broth, suggesting that this system is expressed at the same level in water and in broth (Supplementary Table S1). Possibly, the expression of this efflux pump is reduced in 81-176, which results in lower resistance to bile salts. C. jejuni is unlikely to be exposed to sodium choleate at concentrations used in this study in the natural environment. Nevertheless, the increased sensitivity of 81-176 to bile salts after exposure to water (Figure 3) suggests that some strains are better at colonizing the intestinal tract following transmission by water compared to other strains.

To better understand the genetic elements that contribute to the enhanced survival of 81116 in water, its transcriptome in Fraquil was compared to that in Brucella broth. To this end, 81116 was exposed to Fraquil at 4°C since it survives better at this temperature compared to 25°C (Figure 1). The exposure time was limited to 4 h because transcriptional changes are known to happen quickly in response to a new condition (Hinton et al., 2004). Moreover, the rate of transcription is reduced dramatically during starvation (Srivatsan and Wang, 2008), as evidenced in Legionella pneumophila exposed to water (Li et al., 2015). Since phenotypic differences were observed between Fraquil and rich Brucella broth (Figures 2, 3), suspension in rich Brucella broth at 4°C for 4 h was used as the control condition. In addition, this control allows the study of the starvation response of C. jejuni, which is likely necessary to survive in the nutrient-poor water environment. Starvation of C. jejuni in Ringer solution induces heat-shock resistance and affects the expression of catalases and superoxide dismutases (Klancnik et al., 2009). Our analysis revealed that 336 genes are differentially regulated upon exposure to Fraquil. C. jejuni uses amino acids, and to a lesser extent, short chain fatty acids as carbon and energy sources (Stahl et al., 2012). Since Fraquil is devoid of these nutrients, expression of transporters and enzymes involved in their catabolism should be repressed. Indeed, the amino acid transporters pebA and pebC, as well as the aspartate ammonia-lyase aspA and the gamma glutamyltransferase ggt required for the utilization of aspartate, glutamate and glutamine were repressed in Fraquil (Table 3). The serine ammonia-lyase sdaA followed a similar expression pattern (Table 3). In contrast, genes involved in the biosynthesis of various amino acids were induced in Fraquil (Figure 4). Genes involved in the catabolism of short-chain fatty acid, such as acs and lctP were also repressed following exposure to Fraquil (Table 3); however, fabH and fabF involved in the biosynthesis of fatty acids were induced.

Costly biosynthetic processes such as glycosylation (pglJ) and production of the flagellum (flaG, fliS, flgG, flgI) were repressed in Fraquil (Table 3). Repression of flagella genes was expected since C. jejuni is known to repress them in the post-exponential phase of growth, when nutrients are limiting and waste accumulates (Wright et al., 2009). Adhesins used during infection, including cadF and jlpA were strongly repressed in Fraquil.

The need to repress costly metabolic systems in water is supported by recent analyses of the survival of L. pneumophila in water (Li et al., 2015). L. pneumophila is transmitted to humans by inhalation of contaminated aerosols (Mittal et al., 2013). Transcriptomic profiling revealed that L. pneumophila represses most systems in Fraquil, including transcription, translation, flagellum synthesis, and virulence factors (Li et al., 2015). In L. pneumophila, this is mediated by the stringent response and the sigma factor RpoS (Trigui et al., 2015a). C. jejuni does not possess RpoS and only codes three sigma factors (RpoD, FliA, and RpoN) within its genome (Parkhill et al., 2000). RpoD is the housekeeping sigma factor, while FliA and RpoN regulated flagella synthesis and defense against various stresses, respectively (Hwang et al., 2011). The stringent response is initiated by the production of guanosine tetraphosphate (ppGpp), a cellular alarmone signaling starvation (Mittenhuber, 2001). In general, Gram-negative bacteria employ two enzymes to regulate cellular levels of ppGpp; RelA which synthesizes the alarmone and the dual acting SpoT which has low synthase and high hydrolase activities (Mittenhuber, 2001; Gaynor et al., 2005). However, ppGpp levels in C. jejuni are regulated solely by SpoT. Deletion of spoT affects multiple phenotypes in C. jejuni, including interaction with host cells, resistance to rifampicin and oxygen, and survival in the stationary phase (Gaynor et al., 2005). C. jejuni survives poorly in stationary phase compared to model bacteria, presumably because it lacks an rpoS homolog, the stationary phase sigma factor (Kelly et al., 2001). It is likely that survival of C. jejuni in water is mediated mainly by the stringent response. Transcriptomic analysis of the spoT mutant at different growth phases in rich broth revealed that 30 genes are regulated by the stringent response in C. jejuni (Gaynor et al., 2005). The transcriptome of 81116 in Fraquil showed limited similarities to the spoT mutant in broth, which suggests that, in Fraquil, only a few genes are under the control of the stringent response. For example, clpB is repressed in Fraquil, but induced in the spoT mutant, while and the putative ferredoxin napH was induced in Fraquil, but repressed in the spoT mutant. Attempts at deleting spoT in 81116 in order to confirm the role of the stringent response in water was unsuccessful. Additional studies are required to fully appreciate the role of the stringent response in the survival of C. jejuni in water.

Strain 81116 induces 187 genes in Fraquil, which may provide useful functions for its survival. Genes involved in the synthesis of the cell envelope were induced in Fraquil (Figure 4), including peptidoglycan synthesis (ddlA, murD, and mraY) and lipopolysaccharide (lipooligosaccharide) synthesis (lpxB, lpxK, waaE, and waaM). Genes involved in iron transport (feoA, feoB, ceuDE, and cfrB), as well as other transport systems and porins were also induced. Some of the genes induced in Fraquil code for hypothetical proteins or proteins with a putative function. The potential contribution of the aforementioned genes to the survival of C. jejuni in water is discussed in the following paragraph.

The peptidoglycan layer plays a role in maintaining the turgor pressure of the cell, and is required for cell growth and division (Egan et al., 2016). C. jejuni cell morphology changes from a rod or spiral shape in the exponential phase to a coccoid form in the stationary phase of growth (Ikeda and Karlyshev, 2012). The amount of peptidoglycan in the coccoid form is about one third of the amount present in the spiral form (Amano and Shibata, 1992). Therefore, C. jejuni modifies the amount of peptidoglycan according to growth conditions. The spiral shape is produced by the action of two peptidoglycan modifying enzymes, Pgp1 and Pgp2 (Frirdich et al., 2012, 2014). Both genes are induced in C. jejuni upon exposure to Fraquil (Table 3). Since C. jejuni does not replicate in Fraquil, the induction of peptidoglycan synthesis and modification genes likely serves an ulterior purpose, such as resistance to hypoosmotic stress or differentiation into the VBNC state. The freshwater medium Fraquil used in this study is hypoosmotic relative to Brucella broth. The latter contains 5 g/L of sodium chloride in addition to other osmolytes. C. jejuni may induce peptidoglycan synthesis in Fraquil to increase the strength of the peptidoglycan mesh, which in turn, resists the influx of water and maintains cell shape. To our knowledge, the hypoosmotic response of C. jejuni has never been studied. Exposure of C. jejuni to moderate hyperosmotic stress results in cell elongation and induces the expression of chaperones, oxidative stress response genes and amino acid synthesis genes (Cameron et al., 2012). The present study and others have shown that exposure of C. jejuni to water triggers differentiation into the VBNC state (Cools et al., 2003; Baffone et al., 2006; Trigui et al., 2015b). In E. coli, the peptidoglycan layer undergoes extensive modification upon entry into VBNC state (Signoretto et al., 2002). Similarly, VBNC Enterococcus faecalis cells contain high level of O-acetylated peptidoglycan (Pfeffer et al., 2006). In addition, VBNC E. faecalis are more resistant to mechanical stress than actively growing cells, likely due to increased peptidoglycan cross-linking (Signoretto et al., 2000). It is tempting to postulate that induction of peptidoglycan-related genes in Fraquil are necessary to modify the cell wall of C. jejuni during differentiation into the VBNC state, protecting cells against stresses, including hypoosmotic stress, encountered in the water environment. The population of C. jejuni cells exposed to Fraquil enters the VBNC state progressively (Figure 1); however, the prerequisite cellular modifications likely occur relatively quickly after exposure to Fraquil, when cells have sufficient energy and supplies to do so.

C. jejuni lipooligosaccharide (LOS) consists of a lipid A moiety, an inner core composed of a conserved trisaccharide and a strain-variable outer core consisting of various sugars (Karlyshev et al., 2005). LOS is similar in structure and function to lipopolysaccharide, but lacks the O-antigen. Modification of LPS is important for many pathogens to evade the host immune defenses (Whitfield and Trent, 2014). Similarly, mutations affecting the length of the outer core of LOS in C. jejuni reduce resistance to complement-mediated killing and colonization of mice (Naito et al., 2010). In addition, abnormal LOS results in increased susceptibility to polymyxin B and sodium dodecyl sulfate, but increase biofilm formation (Naito et al., 2010). The effect of temperature on LOS length is strain-dependent, but growth at 42°C favors the production of a shorter LOS (Semchenko et al., 2010). Induction of LOS synthesis genes in Fraquil suggests that modification of the LOS sheath is important for survival in water and/or for differentiation into the VBNC state.

Genes involved in the acquisition of iron were induced in Fraquil, including the ferrous iron transporters feoAB and the siderophore transporters encoded by ceuDE and cfrB. Presumably, the iron-poor environment of Fraquil leads to induction of genes encoding functions related to iron homeostasis. Oxidative stress resistance genes are repressed by iron in C. jejuni during growth in minimum essential medium (Palyada et al., 2004; Butcher and Stintzi, 2013); however, they are induced during the metabolic switch from acetate production to acetate uptake, and also between the exponential phase and the stationary phase (Wright et al., 2009). Therefore, it was expected that genes involved in the oxidative stress response would also be induced in Fraquil, since it mimicks the low nutrient condition that is found in stationary phase. Unexpectedly, we found that strain 81116 represses three oxidative stress defense genes, sodB, ahpC, and tpx in Fraquil. The absence of nutrient and toxic metabolic waste in Fraquil compared to the stationary phase in broth probably leads to the repression of oxidative stress response genes, which could explain the discrepancies with previous studies. Since iron mediates the formation of reactive oxygen species (ROS) inside cells (Imlay, 2003), it is expected that oxidative stress would be reduced in an iron-limiting condition. This speculation is supported by the findings from Folsom et al. (2014) where several enzymes associated with oxidative stress and ROS in E. coli were down-regulated under iron limitation, including superoxide dismutases (Sod). Nevertheless, despite the down-regulation of these oxidative stress defense genes in Fraquil, strain 81116 is more tolerant to H₂O₂ stress than in rich broth (Figure 2B). Interestingly, strain 81116 induces the expression of ccpA-2, which encodes for a cytochrome peroxidase enzyme (Kim et al., 2015). It has been shown that loss of ccpA-2 in C. jejuni NCTC 11168 resulted in increased sensitivity to H₂O₂ compared to the wild-type (Flint et al., 2014), suggesting that the contribution of ccpA-2 to oxidative stress response is strain-dependent. Strain 81-176 is more sensitive to oxidative stress in Fraquil than 81116, suggesting differential expression of genes involved in resistance to oxidative stress.

A fraction (32 genes, 9.5%) of the differentially expressed genes codes for hypothetical proteins without known or putative functions. Of these, 10 were induced in Fraquil and could encode functions necessary for 81116 to survive in water. In addition, seven genes induced in Fraquil are absent in 81-176 genome, which suggests that they may contribute to 81116’s ability to better survive in water. Therefore, their presence in water-isolated strains, as well as strains isolated from other sources was tested. The presence of the genes was not correlated with the source of the strain (Figure 6) suggesting that the unique genes tested did not contribute significantly to its survival. Alternatively, enhanced survival of 81116 in Fraquil is likely due to the induction of multiple regulatory systems that promote adaptation to water. This is likely due to subtle difference in the regulation of gene expression. Indeed, Dugar et al. (2013) reported that strain-specific transcriptome structure could modulate phenotypic variation among C. jejuni strains. This could be due to acquisition of specific regulators, effectors or organization of the genome.

The transcriptomic profiling of 81116 in water suggest that its ability to survive in water for extended periods of time is due to multiple adaptations that shut down nutrient uptake systems, and costly metabolic pathways, including synthesis of the flagellum. Moreover, the induction of stress response pathways, genes involved in detoxification and cell wall synthesis in response to water enhances the resistance of 81116 to multiple stresses in the aquatic environment. Unique genes do not contribute to its enhanced fitness. Strains with a similar genetic background as 81116 are likely better at transmission via water and more resistant to current disinfection processes.

HT, AT, PF, AL, and SF designed the experiments. HT, KL, and AT performed the experiments. AT, SL, PF, and AL provided strains of C. jejuni. HT, AT, NM, and SF analyzed the data. HT, NM, and SF wrote the manuscript. All authors edited the manuscript and approved the final version.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.