Human Serum is a Potent Chemoattractant for Enterobacteriaceae Species Associated with Gastrointestinal Bleeding

Reviewer #1 (Public Review):

Summary:

Glenn et al. present solid evidence that both lab and clinical Enterobacteriaceae strains rapidly migrate towards human serum using an exciting approach that combines microfluidics, structural biology, and genotypic analysis. The authors succeed in bringing to light a novel context for the role of serine as a bacterial chemoattractant as well as documenting what is likely to be a key step in bloodstream entry for some of the main sepsis-associated pathogens during gastrointestinal bleeding. They aim to expand their conclusions from a single lab serovar of Salmonella enterica to a range of clinical serovars and other species within the Enterobacteriaceae family. This is a powerful approach that greatly increases the scope of their findings but I find that some of their conclusions here are not always supported by strong evidence.

I would also like to note that, while I enjoyed the interdisciplinary scope of this study, I am personally not well positioned to review the protein structural aspects of this work.

Strengths:
- The authors first characterise migration towards serum in detail using a well-characterised lab strain but one of the main strengths of this study is that they then expand their scope to observe equivalent behaviours in several clinical serovars. This strongly supports the clinical relevance of the key behaviours that they document.

- The interdisciplinary nature of this study is a real strength and greatly increases the scope of the conclusions presented. Working from a structural understanding of chemoreceptor-ligand binding through to a larger-scale genetic analysis of chemoreceptor phylogeny allows the authors to draw important (although I find not always definitive) conclusions about bacterial migration towards human serum across a wide range of bacterial species (including many important pathogens). This is a very exciting approach and I was particularly interested to see the authors follow this up with observations of migration in C. koseri (a clinical isolate with little known about its chemotactic capabilities).

- The authors use experiments that compete migrating strains against each other and these offer an exciting glimpse into how bacterial movement and navigation could play out in multi-species environments like the human gut.

- The authors successfully identify a single component of human serum (i.e. serine) as one specific attractant driving the bacterial migration response seen here. Teasing apart the response of bacteria to complex stimuli like human serum is an important step here.

Weaknesses:
There are several issues that I would personally like to see addressed in this study:

1. The authors refer to human serum as a chemoattractant numerous times throughout the study (including in the title). As the authors acknowledge, human serum is a complex mixture and different components of it may act as chemoattractants, chemo-repellents (particularly those with bactericidal activities), or may elicit other changes in motility (e.g. chemokinesis). The authors present convincing evidence that cells are attracted to serine within human serum - which is already a well-known bacterial chemoattractant. Indeed, their ability to elucidate specific elements of serum that influence bacterial motility is a real strength of the study. However, human serum itself is not a chemoattractant and this claim should be re-phrased - bacteria migrate towards human serum, driven at least in part by chemotaxis towards serine.

2. Linked to the previous point, several bacterial species (including E. coli - one of the bacterial species investigated here) are capable of osmotaxis (moving up or down gradients in osmolality). Whilst chemotaxis to serine is important here, could movement up the osmotic gradient generated by serum injection play a more general role? It could be interesting to measure the osmolality of the injected serum and test whether other solutions with similar osmolality elicit a similar migratory response. Another important control here would be to treat human serum with serine racemase and observe how this impacts bacterial migration.

3. The inference of the authors' genetic analysis combined with the migratory response of E. coli and C. koseri to human serum shown in Fig. 6 is that Tsr drives movement towards human serum across a range of Enterobacteriaceae species. The evidence for the importance of Tsr here is currently correlative - more causal evidence could be presented by either studying the response of tsr mutants in these two species (certainly these should be readily available for E. coli) or by studying the response of these two species to serine gradients.

4. The migratory response of E. coli looks striking when quantified (Fig. 6C), but is really unclear from looking at Panel B - it would be more convincing if an explanation was offered for why these images look so much less striking than analogous images for other species (E.g. Fig. 6A).

5. It is unclear why the fold-change in bacterial distribution shows an approximately Gaussian shape with a peak at a radial distance of between 50 -100 um from the source (see for example Fig. 2H). Initially, I thought that maybe this was due to the presence of the microcapillary needle at the source, but the CheY distribution looks completely flat (Fig. 3I). Is this an artifact of how the fold-change is being calculated? Certainly, it doesn't seem to support the authors' claim that cells increase in density to a point of saturation at the source. Furthermore, it also seems inappropriate to apply a linear fit to these non-linear distributions (as is done in Fig. 2H and in the many analogous figures throughout the manuscript).

6. The authors present several experiments where strains/ serovars competed against each other in these chemotaxis assays. As mentioned, these are a real strength of the study - however, their utility is not always clear. These experiments are useful for studying the effects of competition between bacteria with different abilities to climb gradients. However, to meaningfully interpret these effects, it is first necessary to understand how the different bacteria climb gradients in monoculture. As such, it would be instructive to provide monoculture data alongside these co-culture competition experiments.

7. Linked to the above point, it would be especially instructive to test a tsr mutant's response in monoculture. Comparing the bottom row of Fig. 3G to Fig. 3I suggests that when in co-culture with a cheY mutant, the tsr mutant shows a higher fold-change in radial distribution than the WT strain. Fig. 4G shows that a tsr mutant can chemotax towards aspartate at a similar, but reduced rate to WT. This could imply that (like the trg mutant), a tsr mutant has a more general motility defect (e.g. a speed defect), which could explain why it loses out when in competition with the WT in gradients of human serum, but actually seems to migrate strongly to human serum when in co-culture with a cheY mutant. This should be resolved by studying the response of a tsr mutant in monoculture.

8. In Fig. 4, the response of the three clinical serovars to serine gradients appears stronger than the lab serovar, whilst in Fig. 1, the response to human serum gradients shows the opposite trend with the lab serovar apparently showing the strongest response. Can the authors offer a possible explanation for these slightly confusing trends?

9. In Fig. S2, it seems important to present quantification of the effect of serine racemase and the reported lack of response to NE and DHMA - the single time-point images shown here are not easy to interpret.

10. Importantly, the authors detail how they controlled for the effects of pH and fluid flow (Line 133-136). Did the authors carry out similar controls for the dual-species experiments where fluorescent imaging could have significantly heated the fluid droplet driving stronger flow forces?

Reviewer #2 (Public Review):

Summary:
This manuscript characterizes a chemoattractant response to human serum by pathogenic bacteria, focusing on pathogenic strains of Salmonella enterica (Se). The researchers conducted the chemotaxis assays using a micropipette injection method that allows real-time tracking of bacterial population densities. They found that clinical isolates of several Se strains present a chemoattractant response to human serum. The specific chemoattractant within the serum is identified as L-serine, a highly characterized and ubiquitous chemoattractant, that is sensed by the Tsr receptor. They further show that chemoattraction to serum is impaired with a mutant strain devoid of Tsr. X-ray crystallography is then used to determine the structure of L-serine in the Se Tsr ligand binding domain, which differs slightly from a previously determined structure of a homologous domain. They went on to identify other pathogens that have a Tsr domain through a bioinformatics approach and show that these identified species also present a chemoattractant response to serum.

Strengths and Weaknesses:
This study is well executed and the experiments are clearly presented. These novel chemotaxis assays provide advantages in terms of temporal resolution and the ability to detect responses from small concentrations. That said, it is perhaps not surprising these bacteria respond to serum as it is known to contain high levels of known chemoattractants, serine certainly, but also aspartate. In fact, the bacteria are shown to respond to aspartate and the tsr mutant is still chemotactic. The authors do not adequately support their decision to focus exclusively on the Tsr receptor. Tsr is one of the chemoreceptors responsible for observed attraction to serum, but perhaps, not the receptor. Furthermore, the verification of chemotaxis to serum is a useful finding, but the work does not establish the physiological relevance of the behavior or associate it with any type of disease progression. I would expect that a majority of chemotactic bacteria would be attracted to it under some conditions. Hence the impact of this finding on the chemotaxis or medical fields is uncertain.

The authors also state that "Our inability to substantiate a structure-function relationship for NE/DHMA signaling indicates these neurotransmitters are not ligands of Tsr." Both norepinephrine (NE) and DHMA have been shown previously by other groups to be strong chemoattractants for E. coli (Ec), and this behavior was mediated by Tsr (e.g. single residue changes in the Tsr binding pocket block the response). Given the 82% sequence identity between the Se and Ec Tsr, this finding is unexpected (and potentially quite interesting). To validate this contradictory result the authors should test E. coli chemotaxis to DHMA in their assay. It may be possible that Ec responds to NE and DHMA and Se doesn't. However, currently, the data is not strong enough to rule out Tsr as a receptor to these ligands in all cases. At the very least the supporting data for Tsr being a receptor for NE/DHMA needs to be discussed.

The authors also determine a crystal structure of the Se Tsr periplasmic ligand binding domain bound to L-Ser and note that the orientation of the ligand is different than that modeled in a previously determined structure of lower resolution. I agree that the SeTsr ligand binding mode in the new structure is well-defined and unambiguous, but I think it is too strong to imply that the pose of the ligand in the previous structure is wrong. The two conformations are in fact quite similar to one another and the resolution of the older structure, is, in my view, insufficient to distinguish them. It is possible that there are real differences between the two structures. The domains do have different sequences and, moreover, the crystal forms and cryo-cooling conditions are different in each case. It's become increasingly apparent that temperature, as manifested in differential cooling conditions here, can affect ligand binding modes. It's also notable that full-length MCPs show negative cooperativity in binding ligands, which is typically lost in the isolated periplasmic domains. Hence ligand binding is sensitive to the environment of a given domain. In short, the current data is not convincing enough to say that a previous "misconception" is being corrected.

Author Response

We are delighted that the reviewers found our work to have merit and we are thankful for their careful reviews and suggestions for experiments and changes to the text to further improve this study.