Genomic adaptations of Campylobacter jejuni to long-term human colonization

Campylobacter is a genus of bacteria that has been isolated from the gastrointestinal tract of humans and other animals around the world [1], and from the environments these animals inhabit [2]. Some Campylobacter species are host generalists, colonizing a wide range of host species [3], others are host-specific [4], and some are pathogenic to the animals they colonize [5]. Population genomics and animal studies have demonstrated that Campylobacter adapts to hosts by changing its gene content and expression [6, 7]. As long-term Campylobacter colonization in humans is rare, few studies have investigated Campylobacter adaption to human hosts [8, 9].

Previously, a patient in New Zealand was identified that had been excreting the same strain of Campylobacter, C. jejuni sequence type (ST) 45, for over a decade [8]. The patient had been diagnosed with common variable immune deficiency (CVID) and had suffered from daily diarrhea that varied in severity. Previous genomic analysis and antimicrobial susceptibility testing of Campylobacter isolates collected from the patient determined that the patient was consistently colonized with Campylobacter over this time period, and that the Campylobacter had developed resistance to the antimicrobial agents the patient was prescribed. However, it was unclear to what extent the Campylobacter was contributing to the patient’s diarrhea. In this study we compared the genomes of ST45 isolates collected from the patient to those collected from other sources, including another patient from the United Kingdom with long-term colonization, to investigate how Campylobacter had adapted to human hosts, and used 16S rRNA metabarcoding and biochemical markers to investigate changes in microbial communities and biochemical markers over the period of long-term Campylobacter colonization.

Long-term colonization of human patients places selective pressure on Campylobacter. Non-synonymous SNPs and frameshifts were found in multiple genes from Campylobacter isolates collected from the New Zealand and United Kingdom patients, especially in genes involved in motility and signal transduction mechanisms. Two genes were found that had more than five of these mutations in both patients: the porA gene that encodes the major outer membrane protein (MOMP) and the ccmL gene that encodes the multi-ligand binding chemoreceptor (CcmL). Previous work on isolates from the New Zealand patient demonstrated that they varied in motility, possibly to evade phagocytes [8]; whilst studies on Campylobacter collected from the same patients within 24-h demonstrated variation in motility and chemotaxis genes [14, 15]. This suggests that long-term colonization is selecting for changes in Campylobacter motility, signal transduction (particularly chemotaxis) and membrane proteins, possibly to evade host defenses.

Populations of bacteria are continuously accumulating mutations: canonically, if they are beneficial then those containing them will thrive and the mutation will increase in frequency, whilst if they are deleterious those containing them will struggle and the mutation will eventually disappear. However, Ramiro et al. [16] investigated Escherichia coli colonizing the gut of mice over 190 days and found that beneficial mutations increased in frequency but were not fixed in the population, and slightly deleterious mutations remained in the population for extended periods of time, possibly by the variable mouse gut buffering their deleterious effects. In this study, mutations were observed that were stably-inherited within the Campylobacter populations of the long-term patients, especially in those involved in cell motility and signal transduction. These Campylobacter were collected over longer time periods than Ramiro et al. experiments, possibly allowing these beneficial mutations to be fixed within the population or the Campylobacter were exposed to larger selective sweeps than the E. coli. However, a large number of mutations were observed in isolates that were not fixed within the Campylobacter population, suggesting that the human gastrointestinal tract allows for variation in many Campylobacter genes, but over time selective sweeps select for specific genetic variants. Nevertheless, we cannot rule out the possibility that many of the stably-inherited mutations were the result of “genetic hitchhiking” [17].

The isolates collected from the New Zealand and United Kingdom patients both belonged to ST45. However, within this sequence type the isolates from each patient were distantly related, allowing us to identify mutations specific to long-term colonization by comparing isolates from these patients to ST45 from other sources. Genetic comparisons identified one mutation associated with long-term patient colonization, T86I in the gyrA gene. This mutation is the most common cause of quinolone resistance in C. jejuni [11], and the New Zealand patient [8] and likely the United Kingdom patient [9] were prescribed quinolones, selecting for this mutation. A large number of other genes contained mutations in the New Zealand and United Kingdom patient isolates. However, the mutations either differed between isolates from each patient or were found in multiple other ST45 isolates. This suggests that apart from quinolone resistance, long-term human colonization selected for changes in particular genes, but not specific mutations.

Bacteria can adapt to environments by both gene loss and gene acquisition. Gene loss may increase the fitness of the bacteria by decreasing resource expenditure on unnecessary cellular processes [18], whilst gene acquisition may allow the bacteria to gain cellular processes to thrive in the environment [19]. Previous studies on long-term Pseudomonas aeruginosa cystic fibrosis (CF) [20] and Salmonella enterica [21] infections found that gene loss outweighed gene acquisition over the course of these infections. However, Bayjaynov et al. [22] investigated long-term colonizing E. faecium strains and found similar amounts of gene loss and gene acquisition. In our study, several genes were identified that were stably-lost over the course of colonization in the New Zealand and United Kingdom patients, and there was some evidence of the total number of genes decreasing over time. However, no functional group was overrepresented in the accessory genome, suggesting that genome reduction is not the main way Campylobacter adapts to long-term colonization. Gene loss could have occurred between acquisition and isolation of the first isolate, but there was no evidence that the long-term patients had smaller number of genes compared to the other human ST45 isolates. This is a similar observation to long-term E. faecium colonization rather than to P. aeruginosa or S. enterica infections, namely evidence of similar amounts of gene loss and gene gain. Further research is required to determine if this is due to the different biology of these bacteria, different environments, or different types of infection.

In the New Zealand patient, we identified two genetically distinct clades or subpopulations of Campylobacter. In CF infections, divergence of P. aeruginosa subpopulations has been reported prior to infection [23] and within the host [24]. Analysis of long-term E. faecium colonization has demonstrated the presence of multiple lineages within the gastrointestinal tract of humans, but these lineages diverged prior to colonization [22]. Phylogenetic analysis suggests that the two Campylobacter subpopulations diverged between 2009 and 2011, after the first isolate was collected from the patient in 2006, indicating that the subpopulations diverged within the host. There is evidence of multiple subpopulations coexisting prior to this divergence in the New Zealand patient, and in the isolates collected from the United Kingdom patient, but these patients were not sampled frequently during these time periods, preventing further analysis of these subpopulations.

The competitive exclusion principle states that no two species can occupy the same niche [25]. Accordingly, the subpopulations of Campylobacter found within the patient are likely to have distinct niches. In CF patients, the presence of multiple subpopulations has been attributed to the bacterium accumulating mutations and phenotypically adapting to different environments within the human lung [26]. There is evidence of this when looking at the genetic differences between the two Campylobacter lineages found within the human host, specifically the dcuB gene that encodes a fumarate/succinate active antiporter under low oxygen conditions that can also import aspartate [27]. Succinate concentrations in the gastrointestinal tract have been shown to increase during gut dysbiosis [28] and inflammation [29], but it remains to be determined if these conditions affect fumarate or aspartate concentrations. The New Zealand patient’s gastrointestinal tract showed a large amount of variation in inflammation plus variation in the microbiota composition and these may be influencing the concentration of succinate and possibly other metabolites. The concentration of calprotectin was negatively associated with the proportion of isolates made up of the lineage missing dcuB, suggesting that the two lineages could have emerged in response to the variation in gastrointestinal inflammation and microbiota disruptions. The dcuA gene is a fumarate/aspartate:H⁺ symporter and 90% of isolates from the dcuB-negative clade contained the L212F mutation in the dcuA gene, whilst all isolates belonging to the dcuB-containing clade contained the S148F mutation in this gene. However, it is unclear how these mutations affect the function of this transporter. DcuA and DcuB work in close association with the cytoplasmic-facing fumarate reductase FrdABC, but no mutations were found in the frdA, frdB or frdC genes [30]. Nevertheless, the absence of DcuB would prevent correct stoichiometric exchange of succinate and fumarate that allow FrdABC to function. Campylobacter also has a unidirectional fumarate reductase that cannot oxidize succinate, MfrABE, that operates independently of DcuA and DcuB, as it is periplasm-facing [31]. For the clade with an intact dcuB gene, three out eighteen of the isolates contained a truncated mfrA gene due to a frameshift. It has been shown that FrdABC is the major contributor to fumarate reduction but that MfrABE is required for full fitness when the bacteria rely on fumarate respiration to conserve energy [31]. Taken together, these observations suggest that different clades will have distinct contributions of Dcu/Frd versus Mfr mediated fumarate respiration during colonization. The role of DcuA and DcuB in aspartate uptake in low oxygen intestinal niches may also be physiologically important. Further work on the concentrations of gastrointestinal aspartate, succinate and fumarate in the patient and how this relates to the different lineages is required to determine if gastrointestinal inflammation is creating distinct niches where certain metabolites are not required. However, multiple other mutations were found amongst the two lineages and we cannot rule out the possibility that the mutations associated with dcuB were genetic hitchhikers.

C. jejuni ST45 is one of the most frequently isolated strains of Campylobacter collected from humans, domestic animals and the environment [32‐34]. It is regarded as a ‘generalist’ strain, as it has been isolated from multiple host species and environments [35, 36], and has demonstrated frequent host switching [37]. We found clades of ST45 that consisted of isolates collected from different sources, supporting ST45 as a generalist strain, but also found some clades that only consisted of isolates from single sources and many clades that only consisted of a single non-human source. Further analysis of non-human ST45 isolates is required to determine the extent that ST45 is a “generalist” strain.

The human microbiota is affected by disease [38], diet [39] and genetics [40]. Youmans et al. [38] investigated the microbiota of individuals with traveler’s diarrhea and found that regardless of cause, diarrheic samples contained a high Prevotella-to-Bacteroides (P/B) ratio. This observation is supported in this study, where the third diarrheal sample collected from the patient was higher on the Bristol scale (softer) and had a higher P/B ratio. Braun et al. [41] investigated the microbiota of healthy individuals and hospitalized patients suspected of infectious diarrhea, and found diarrhea patients were associated with an increased abundance of Proteobacteria. The first diarrheal sample collected from the patient had the highest Proteobacteria proportion, but this is because it has the highest Campylobacter proportion which made up most of the Proteobacteria in the microbiota of this sample. Zhuang et al. [42] found that diarrhea brought on by irritable bowel syndrome resulted in increased Bacteroidetes and decreased Firmicutes, such as with the first two samples. However, the amount of Prevotella and Proteobacteria in the microbiota is also affected by diet [39, 43]. Further microbiota samples and dietary information from the time of collection are required to investigate the role of disease and diet on the patient’s microbiota.

The sampled ancestor model identified multiple isolates from the United Kingdom patient that represented ancestors to other isolates collected from this patient, but it detected no likely ancestors amongst the New Zealand patient’s isolates. This suggests that the population of Campylobacter was more diverse within the New Zealand patient than within the United Kingdom patient, and therefore sampled isolates were less likely to represent an ancestral state. However, Campylobacter within these patients have likely undergone multiple bottlenecks, especially with antimicrobial therapies [8, 9], and we cannot rule out the possibility that the United Kingdom patient was sampled during several of these bottlenecks when the genetic diversity was smaller, whilst the New Zealand patient was not.

Campylobacter collected from the New Zealand patient had a substitution rate twice that of those collected from the United Kingdom patient, with no overlap between 95% HPD intervals. Multiple differences were found in genes involved in DNA replication and repair between isolates collected from these patients. The mutS gene had the largest number of differences, but knockouts in this gene in the closely related bacterium, Helicobacter pylori, are not associated with increased substitution rates [44]. Mutations in mutY have been associated with faster substitution rates in Campylobacter [45, 46], but isolates collected from the long-term patients had identical mutY genes. Further work is required to determine the effects of other mutations in DNA replication and repair genes on the substitution rate of Campylobacter.

An original objective of this research was to determine if Campylobacter was contributing to the patient’s diarrheal episodes or simply colonizing the patient. The lack of evidence for anti-Campylobacter antibodies suggests that the patient had not mounted an immune response against the Campylobacter. However, most studies on Campylobacter serology have focused on acute infections, rather than the possible chronic infection described here. In addition, most serological tests have a high false-negative rate and for those individuals that do seroconvert the antibody titer quickly decreases after a few months [47, 48]. Studies on acute Guillain-Barré syndrome, a disease often triggered by Campylobacter infections have found up to 80% of cases display serological evidence of Campylobacter, but it is unclear whether the negative cases were triggered by Campylobacter or other infections [49], and false positives have been observed [50]. Regarding the New Zealand patient, this could be explained by a number of scenarios including: the Campylobacter was not the cause of any pathology and had not been presented to the immune system or triggered an immune response; the Campylobacter contributed to the diarrheal episodes but the patient was unable to form an immune response sufficient to remove the bacteria or be detected using the serological method described.

In this study we investigated the genomes of Campylobacter from two patients that were both colonized for over a decade and found that multiple selective pressures were imposed on the Campylobacter. There was some evidence of genome degradation, but more evidence that Campylobacter adapted through the accumulation of non-synonymous SNPs and frameshifts in genes involved in cell motility, signal transduction and the major outer membrane protein, possibly to evade host defenses. However, we also found that the Campylobacter collected from the patients differed in substitution rates and diversity as evidenced by sampled ancestral states, although the reason for these differences remains unclear. Through 16S rRNA metabarcoding and biochemical markers we demonstrated that the New Zealand patient displayed a large amount of variation in their microbiome, inflammation and immunosuppression over five months, and that the Campylobacter collected from the patient could be divided into two subpopulations, the proportion of which correlated with the amount of gastrointestinal inflammation. This suggests that subpopulations of Campylobacter evolve within the gastrointestinal tract to adapt to changing environments. Overall, this study demonstrates how genomics, phylogenetics, 16S rRNA metabarcoding and biochemical markers can provide insight into how Campylobacter adapts to changing environments within human hosts.