Shigella flexneri can invade zebrafish cells, escape from the phagosome and induce septin caging at 28°C

The infection cycle of Shigella in human cells is well understood. After internalization, Shigella escape from the phagocytic vacuole to the cytosol where they may be recognized by septin cages and autophagy [14], [15]. As Shigella is not a natural pathogen of fish and grows optimally at 37°C, initial experiments sought to determine whether the hallmarks of the Shigella infection cycle - invasion, phagosome escape and cytoskeleton reorganization- could be reproduced at 28°C, the optimal growth temperature of zebrafish. To test this, we first established a zebrafish fibroblast-like cell line (ZF-AB; see Material and Methods) that we could infect in vitro. The septins are a family of proteins required for the autophagy of Shigella in human cells, and SEPT7 in particular is essential for mammalian septin function [17]. Pan et al. reported a sept7 orthologue in zebrafish [37], and our own search of the most recent zebrafish genome assembly (zv9, www.ensembl.org) and EST databases identified three genes encoding proteins highly similar to the human protein (Fig. S1A), with predicted molecular weights of 48–49 kDa. This close similarity indicated that an antibody raised against human SEPT7 was likely to cross-react with the zebrafish proteins. Indeed, using a human SEPT7 antibody, Western blotting of zebrafish lysates revealed proteins at 49 and 44 kDa (Fig. 1A and S1B), and immunofluorescent labeling of ZF-AB cells revealed septin filaments partially overlapping with the actin cytoskeleton (Fig. 1B), in agreement with what is known in mammalian cells [38], [39]. We then infected ZF-AB cells with S. flexneri M90T. As observed with the human epithelial cell line HeLa infected at 28°C (Fig. S1C) and at 37°C [14], [15], Shigella invaded ZF-AB cells and induced the formation of septin cages (Fig. 1B), demonstrating that Shigella can enter the cytosol of zebrafish cells and be targeted to autophagy. These results strongly suggest that the virulence factors required for Shigella invasion, escape from the phagocytic vacuole and replication in the cytosol can be expressed and are functional at 28°C, the most commonly used temperature for zebrafish rearing.

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Figure 1. Characterization of zebrafish cells and infection with Shigella.

A. Western blots of larval extracts, using antibodies against SEPT7 or elongation factor 1-α (EF1α). See Fig. S1B for complete lane of SEPT7 blot and antibody specificity. B. Immunofluoresence microscopy of ZF-AB cells. F-actin (green), SEPT7 (red), DAPI (blue). Top: uninfected cell; note colocalization of actin and SEPT7 filaments (arrows). Bottom: Shigella-infected cell; note septin cage-like structure surrounding DAPI-labeled Shigella (arrow). Scale bar, 4 µm. C. Scheme of a 72 hpf larva (length ∼3.5 mm), showing the duct of Cuvier (the wide vessel flowing over the yolk; black arrowhead), also called common cardinal vein, and the iv injection site (red arrowhead) in the tail vein just caudal to the urogenital opening (ugo). D. Survival curves of 72 hpf larvae injected with various doses of S. flexneri and incubated at 28°C for 48 hpi. The effective inoculum, quantified a posteriori, was classified as low (<10³ CFU, open circles; effective range: 1.5–9.9×10² CFU), medium (∼4×10³ CFU, open triangles; effective range: 1.3–6.0×10³ CFU) or high (∼10⁴ CFU, open squares; effective range: 7.8–34.2×10³ CFU). Mean±SEM of n = 10–24 larvae per group from 3 or more independent experiments per inoculum class. E. Enumeration of live bacteria in homogenates from individual larvae at various times post infection measured by plating onto LB. Low dose inoculum = open circles. Medium or high dose inoculum = open squares. Of note, dead larvae at 24 or 48 hpi (overwhelmed with bacteria, as determined by fluorescence stereomicroscopy) were not included here, and only larvae having survived the infection (thus far) were included here (and in this case, statistics are in grey). Mean±SEM also shown (horizontal bars). Significance testing performed by Student's t test. ns, P>0.05; ***, P<0.001. F. Distribution of bacteria (GFP-Shigella) determined by live imaging using a fluorescence stereomicroscope at various times post injection of a low, medium or high dose inoculum. Overlay of transmission image (grey) and GFP fluorescence (green).

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Zebrafish larvae are susceptible to intravenous S. flexneri infection

We next sought to establish whether S. flexneri could cause disease in zebrafish swimming larvae. Larvae aged 72 h post fertilization (hpf) were microinjected intravenously (iv) near the cloaca (ugo) with a range of doses of wild-type S. flexneri (Fig. 1C), and their survival at 28°C was assessed by regular observation with a stereomicroscope. For Shigella doses 10³ CFU or less, there was 100% survival of the infected larvae; in contrast, a typical inoculum of 4×10³ Shigella resulted in the death of most larvae within 48 hours post infection (hpi) (Fig. 1D). Of note, larvae injected with a comparable (or even higher) inoculum of type III secretion system (T3SS) deficient (T3SS−) Shigella (ΔmxiD strain; Fig. S1D) or the closely related, but non-pathogenic, E. coli K12 (data not shown and [26]) always survived for the entire time of observation.

We followed the progression of infection using two approaches. First, to monitor the replication of bacteria in the host, we measured the amount of viable bacteria within larvae at various time points by plating serial dilutions of homogenates of euthanized animals onto bacterial culture dishes. As shown in Fig. 1E, the survival of the larvae was closely associated with the clearance of the inoculated bacteria. Larvae inoculated with a low dose (<10³ CFU) progressively cleared bacteria, with a burden reduced by >90% within 48 hrs. In contrast, in larvae inoculated with a high dose, S. flexneri numbers increased ∼30fold in the first 24 h; by 48 hpi, most larvae were dead, although in a minority of survivors the bacterial load declined. During infections using comparable or higher inocula of T3SS− Shigella (Fig. S1E) or E. coli (data not shown and [26]), bacterial numbers always decreased over time, with only a few viable bacteria able to persist for 48 h at highest doses.

As a second approach to follow the progression of infection, larvae were infected with sublethal or lethal inocula of fluorescent S. flexneri M90T, i.e. GFP-Shigella, and were analyzed by fluorescence microscopy. Large clusters (∼10² bacteria or more) were detectable using a fluorescence stereomicroscope (Fig. 1F, see also Fig. 2 below), while smaller groups and single bacteria could be viewed at higher magnifications using widefield or confocal fluorescence microscopy (see below e.g., Fig. 3, 4). At 4 hpi with a sublethal inoculum of S. flexneri, bacterial aggregates, probably associated to phagocytes [26], [40], were observed mostly in the caudal hematopoietic tissue (CHT) near the injection site, as well as in the more distant common cardinal vein over the yolk sac; the majority of the bacteria were cleared from the blood (Fig. 1F, see also Fig. S2 below). The situation was relatively similar in larvae inoculated with a lethal inoculum at 4 hpi, except for the higher number of bacterial foci observed in the CHT and over the yolk sac (Fig. 1F see also Fig. S2 below). However, the infection course by 24 hpi was radically different between the sublethal and lethal inocula. At this time point, larvae that received a sublethal inoculum had almost all cleared the infection, showing few foci of Shigella mainly located near the injection point in the caudal part of the larvae. In contrast, larvae that received a lethal inoculum showed a massive infection at 24 hpi, with Shigella abundant in the blood (i.e., bacteremia) and in the tissues near the site of injection (Fig. 1F, see also Fig. S2 below).

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Figure 2. Macrophage and neutrophil depletion upon Shigella infection.

A. mpeg1:G/U:mCherry (red macrophages) and lyz:dsRed (red neutrophils) 3 dpf larvae were infected with sublethal or lethal GFP-Shigella inocula, fixed 4 and 24 hpi and leukocyte and bacteria labeled using anti-dsRed (red) and anti-GFP (green) antibodies. 4 and 24 hpi uninfected (CTRL), sublethal and lethal inoculated mpeg1:G/U:mCherry and lyz:dsRed fish are shown. Fixed, labeled whole larvae were imaged using a fluorescent stereomicroscope. Overlay of green and red fluorescence. B. Macrophage (left) and neutrophil (right) counts in uninfected (control, C) or upon sublethal (S) or lethal (L) Shigella injections. Macrophages and neutrophils were counted from images using ImageJ and plotted as specified in Material and Methods. Mean±SEM also shown (horizontal bars). Significance testing performed by ANOVA with Bonferroni posttest. ns, P>0.05; ***, P<0.001.

https://doi.org/10.1371/journal.ppat.1003588.g002

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Figure 3. In vivo Shigella-phagocyte interactions.

A–E: Frames extracted from in vivo time-lapse confocal imaging sessions of 3 dpf larvae injected in the bloodstream and in the adjacent mesenchyme with sublethal inocula of GFP-Shigella. Caudal area, rostral to bottom right, dorsal to top right. Overlay of green (Shigella) and red (macrophages or neutrophils) fluorescence; transmission image (grey) is also overlaid on the first frame in A, B and E as an anatomical guide. Scale bars: A–B, 50 µm; C–E, 10 µm. A. mpeg1:G/U:mCherry larva (red macrophages); first frame at 20 mpi. By 20 mpi, Shigella have already adhered to or have been engulfed by macrophages (red cells, white arrows). They persist in macrophages over time (last frame at 2h30pi). Note that neutrophils (highlighted in green by the engulfed GFP-Shigella, #1,2,3 yellow arrows), that have engulfed bacteria in the mesenchyme have a similar bacterial load to that of macrophages, and efficiently kill the engulfed bacteria (as indicated by the diffuse GFP staining over time in these neutrophils). Maximum intensity projection from 25 planes every 2 µm. See also Video S1. B. lyz:dsRed larva (red neutrophils), first frame at 20 mpi. Neutrophils are rapidly recruited to engulf and degrade GFP-Shigella in the mesenchyme. By contrast, note the macrophage that remains strongly decorated by GFP-Shigella over time (white arrow), highlighting bacterial persistence inside macrophages. Maximum intensity projection from 25 planes every 2 µm. See also Video S4. C. mpeg1:G/U:mCherry larva, first frame at 20 mpi. A red macrophage harboring GFP-Shigella over time (white arrow) eventually undergoes cell death (loss of red label). Note in the bottom right corner of the field a group of neutrophils that have engulfed the bacteria in the mesenchyme and appear engorged by them, is able to control the engulfed GFP-Shigella over time (diffuse and decreasing in intensity GFP signal). Maximum intensity projection of 6 planes every 2 µm. See also Video S5. D. lyz:dsRed larva, first frame at 4h30pi. Neutrophils collect dying infected macrophages. GFP-Shigella proliferate inside a macrophage (white arrow), which then undergoes cell death, and is quickly engulfed by dsRed+ neutrophils (yellow arrows). Single confocal plane. See also Video S6. E. lyz:dsRed larva, first frame at 7 hpi. Shigella are able to invade other cell types and replicate in the cytoplasm, causing their death, and subsequent engulfment by neutrophils. The white line delineates a muscle fiber invaded by GFP-Shigella. Shortly before 6 h of time-lapse, the muscle cell bursts and is engulfed by red neutrophils (yellow arrows). Maximum intensity projection of 4 planes every 2 µm. See also Video S7.

https://doi.org/10.1371/journal.ppat.1003588.g003

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Figure 4. Shigella escape to the cytosol and induce septin caging and autophagy in zebrafish larvae in vivo.

A. Zebrafish larvae were infected in the tail muscle with GFP-Shigella for 4 (medium dose) or 24 h (low dose), fixed, labeled with antibodies against SEPT7 (red) and to GFP (green) and imaged by confocal microscopy. Scale bar, 5 µm. B. GFP-Lc3 zebrafish larvae were infected with mCherry-Shigella for 4 (medium dose), fixed, labeled with antibodies against mCherry (red) and to GFP (green) and imaged by confocal microscopy. Scale bar, 5 µm. Shown here is an example of a GFP-Lc3 positive cell controlling bacterial replication (better than its neighbouring cells) 4 hpi. See also Video S8 for live imaging observations of GFP-Lc3 recruitment to Shigella. C. Cytosolic Shigella are sequestered in autophagosomes in vivo. Zebrafish larvae were infected in the tail muscle with GFP-Shigella for 4 h (medium dose) and fixed for electron microscopy. C2 is an expanded region of boxed region in C1 (i.e., autophagosome sequestering bacteria), C3 is an expanded region of boxed region in C2 (i.e., double membrane, a hallmark of autophagosomes). Scale bar, 1 µm (C1) or 0.25 µm (C2). See also Video S9 for a tilt series of Shigella autophagosomes in vivo.

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We observed that larvae that controlled the bacterial proliferation within 24 hpi usually survived. By comparison, inoculation of fluorescent T3SS− Shigella or E. coli yielded an initial distribution of bacteria (at 4 hpi) very similar to that of wildtype Shigella. However, neither T3SS− Shigella (data not shown) nor E. coli (data not shown and [26]) were proliferating and bacterial numbers always decreased over time (in agreement with CFU enumeration, Fig. S1E). These data strongly suggest that virulence factors required for Shigella pathogenesis are expressed during infection of zebrafish larvae at 28°C. Actin tail and septin cage formation are critically dependent upon expression of Shigella virulence factors icsA (T3SS independent) and icsB (T3SS dependent) [14], [15]. By extracting RNA from zebrafish larvae infected with Shigella, the expression of icsA and icsB were clearly detected at 4, 12 and 24 hpi (Fig. S1F). In agreement with observations from survival assays (Fig. 1D), CFU enumerations (Fig. 1E) and live confocal fluorescence microscopy (see below, e.g., Video S1, S3, S5), these data indicate that Shigella virulence factors are expressed at 28°C during infection of zebrafish larvae. They also show that zebrafish larvae are susceptible to S. flexneri, suggesting their applicability to study the innate immune response to Shigella infection.

Macrophage and neutrophil behaviour upon Shigella infection

To analyse macrophage and neutrophil behaviour in vivo upon Shigella infection, transgenic zebrafish larvae (3 dpf) harboring red macrophages (Tg(mpeg1:Gal4-FF)^gl25/Tg(UAS-E1b:nfsB.mCherry)^c264, herein referred as mpeg1:G/U:mCherry) or red neutrophils (Tg(lyz:dsRed)^nz50, herein referred to as lyz:dsRed) were inoculated with sublethal or lethal inocula of GFP-Shigella, and macrophages and neutrophils upon Shigella infection were followed in vivo using widefield fluorescence microscopy. Strikingly, the number of both macrophages and neutrophils appeared to decrease strongly in larvae unable to control Shigella proliferation, and leukocyte depletion was associated with bacteremia preceding larval death (Fig. 2A, S2). To more precisely quantify macrophages and neutrophils, we fixed larvae at 4 or 24 hpi, stained them with anti-dsRed and anti-GFP antibodies to label leukocytes and GFP-Shigella respectively, and counted the number of labeled macrophages and neutrophils per larva (Fig. 2B). Macrophage counts significantly decreased both in lethally (P<0.001) and sublethally (P<0.001) infected animals, suggesting that macrophages undergo cell death in vivo following Shigella ingestion. The number of neutrophils also significantly declined in lethally inoculated larvae (P<0.001), with an almost total neutrophil depletion by 24 hpi. In contrast, larvae controlling Shigella infection did not show a decrease in neutrophil number (P>0.05).

A scavenger role for neutrophils during Shigella infection

To analyse in detail Shigella-phagocyte interactions in vivo, transgenic 3 dpf zebrafish larvae harboring red macrophages (mpeg1:G/U:mCherry) or red neutrophils (lyz:dsRed) were inoculated with sublethal doses of GFP-Shigella, and Shigella-phagocyte interactions were captured immediately thereafter using high resolution fluorescence confocal microscopy. Although only one of the two phagocyte populations was labelled in each of these experiments, non-labelled cells containing pooled GFP-Shigella could generally be assigned to the other phagocyte population in a non-ambiguous manner, based on their localization and motility [24], [26]. As soon as 20 min post infection (the earliest possible time point in our experimental setup), we observed that most blood borne bacteria were stuck on, or were already engulfed by, macrophages and few interacted with neutrophils (Fig. 3A, Video S1, data not shown), as previously observed using non-pathogenic E. coli [26] or Listeria [24]. However, unlike T3SS- Shigella (Fig. S3A, Video S2) or E. coli [26] which is degraded inside macrophages, we observed that wildtype Shigella were able to survive in macrophages and then the infected macrophages would burst (Fig. 3A, Fig. S3B, Video S1; see also Video S3). By contrast, neutrophils having phagocytosed similar amounts of Shigella quickly degraded the engulfed bacteria, as indicated by the diffuse GFP staining that transiently accumulated in these cells (Fig. 3B, Video S4; see also Fig. 3A, Video S1).

It is known that in vitro human macrophages infected by Shigella undergo cell death [41]. We also observed this phenomenon in zebrafish macrophages in vivo (Fig. 3C, Video S5; see also Video S4). To further investigate cell death induced upon Shigella infection, we performed TUNEL labeling of infected larvae and detected host cell DNA damage, a hallmark of cell death. Infected leukocytes were clearly labeled by TUNEL (Fig. S3C). Strikingly, we found that macrophages dead from Shigella infection were frequently engulfed by patrolling neutrophils, suggesting a newfound scavenger role for neutrophils during Shigella infection (Fig. 3D, Video S6; see also Video S4). In support of our live imaging studies, analysis by electron microscopy also highlighted that membrane and DNA from infected, dead cells are engulfed by leukocytes in vivo (Fig. S3D, S3E).

It is also well known that Shigella are able to actively invade non-immune cell types such as epithelial cells [42]. In zebrafish, invasion of some muscle fibers near the point of inoculation was observable from 5hpi (Fig. 3E, Video S7). We observed that Shigella were able to replicate within non-immune cells, which died after a few hours, releasing debris and bacteria that were quickly cleared by neutrophils (Fig. 3E, Video S7). We never observed bacterial invasion and/or replication in vivo with T3SS- Shigella (data not shown) nor E. coli (data not shown and [26]).

Collectively, these results demonstrate that, in vivo, Shigella is able to survive and replicate in macrophages and in some non-immune cells, ultimately leading to their death. Our results also highlight a scavenger role for neutrophils in engulfing and eliminating infected macrophages and non-immune cell types that have failed to control Shigella infection.

Shigella escape to the cytosol and induce septin caging and autophagy in zebrafish larvae in vivo

We observed that in some cells (e.g., such as the macrophage or the muscle fiber displayed in Fig. 3D or 3E) Shigella seemed to occupy the entire cell (rather than a compartmentalized vacuole) strongly suggesting bacterial invasion of the cytosol. Because this cannot be fully ascertained from these live images, we fixed and labeled infected larvae for confocal microscopy to investigate the recruitment of septin cages to GFP-Shigella, a hallmark of cytosolic invasion [15]. In every larva infected (at 4 or 24 hpi), some GFP-Shigella were surrounded by SEPT7 cage-like structures. Confocal microscopy and deconvolution was used to obtain a high-resolution image of fluorescently-labeled assemblies and showed that septin structures assembled into cages around individual Shigella (Fig. 4A), in complete agreement with dimensions obtained from Shigella-septin cages measured in human cells [15]. Thus, in vivo, Shigella are able to invade the cytosol where they may be directed to autophagy by septin caging.

In mammalian cells, ATG8/LC3 is the marker widely used to define autophagosomes [43], [44]. Zebrafish Lc3 is an ATG8 homologue, and to confirm the targeting of bacteria to autophagy in zebrafish we infected transgenic GFP-Lc3 zebrafish larvae with Shigella. GFP-Lc3 was clearly recruited to intracellular Shigella in vivo (Fig. 4B, Video S8). Ultrastructural analysis of Shigella-infected zebrafish by electron microscopy confirmed the sequestration of cytosolic bacteria by autophagosomes (Fig. 4C, Video S9), classically observed as a double membrane structure [43], [44]. We also observed the in vivo recruitment of septin cages (Fig. S4A) and GFP-Lc3 (Fig. S4B, Video S10) to intracellular M. marinum, a natural fish pathogen previously shown in vitro to be recognized septin caging and autophagy [14], [15]. Taken together, the recruitment of autophagy markers to intracellular bacteria suggest the applicability of zebrafish larvae to study the manipulation of anti-bacterial autophagy.

The autophagy receptor p62 is crucial for anti-Shigella defense in vivo

Though autophagy is considered a crucial aspect of innate immunity to Shigella, this has not yet been tested in vivo [12], [13]. We proceeded to test the role of autophagy in the zebrafish response to Shigella infection. p62 is an autophagy receptor critical for autophagic recognition of bacteria in vitro, and is required for septin caging [14], [15]. Our analysis of the zebrafish genome revealed a single orthologue of p62/sqstm1 (Fig. S5A). We thus designed a morpholino to knockdown p62 in zebrafish larvae (Fig. 5A). Fish depleted of p62 developed until 72 hpf with a survival rate similar to controls (∼80%), although we observed a slight developmental delay (data not shown). We then injected p62 morphants (i.e., zebrafish larvae injected with p62 morpholino oligonucleotides) with a sublethal inoculum of Shigella and observed that p62 knockdown significantly reduced host survival upon Shigella infection (P = 0.01; Fig. 5B). To understand the cause of increased death in p62 morphants, we examined the bacterial burden in these fish. CFU counts clearly showed that p62 knockdown during Shigella infection prevents bacterial clearance (Fig. 5C).

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Figure 5. In vivo perturbation of bacterial autophagy via p62 depletion.

A. Western blots of extracts of larvae injected with control (CTRL) or p62 morpholinos (mo), using antibodies against elongation factor 1-α (EF1α; control) or p62. Representative blots using lysates from AB fish; p62 depletion has also been observed in p62 morpholino-treated mpeg:G/U:mCherry and lyz:dsRed fish (data not shown). B. Survival curves of zebrafish larvae treated with control (CTRL) or p62 morpholinos and infected with a sublethal dose of S. flexneri (+M90T) or not infected (no bact). Representative experiment of at least 3 independent ones; n = 12 or more larvae per group. Significance testing performed by Log Rank test. **, P = 0.01. C. Bacterial counts in zebrafish larvae treated with control (CTRL) or p62 morpholinos and infected with a sublethal dose of S. flexneri. Enumeration of live bacteria in homogenates from individual larvae at various times postinfection measured by plating onto LB. CTRL larvae = open circles. p62-depleted larvae = open squares. One representative experiment of at least 3 independent ones; 3 larvae per condition. Of note, dead larvae at 24 or 48 hpi (overwhelmed with bacteria, as determined by fluorescence stereomicroscopy) were not included here, and only larvae having survived the infection (thus far) were included here (and in this case, statistics are in grey). Mean±SEM also shown (horizontal bars). Significance testing performed by Student's t test. ns, P>0.05; **, P<0.01; ***, P<0.001. D. Leukocyte behaviour and infection progression upon Shigella inoculation in p62 knockdown larvae over time. lyz:dsRed p62-depleted 3 dpf larva inoculated with GFP-Shigella and live imaged from 20 mpi to 40 hpi. Maximum intensity projection of 35 sections spaced by 2 µm. Frames extracted at various time points (20 mpi, 5h30mpi, 16 hpi, 24 hpi, 32 hpi and 40 hpi) suggest that neutrophils are unable to restrict bacterial proliferation. The infected larva is progressively depleted in neutrophils and overwhelmed with Shigella. Scale bar, 50 µm. E. Zebrafish larvae treated with either control (CTRL; left image) or p62 (right image) morpholinos were infected with GFP-Shigella for 4 (medium dose), fixed, labeled with antibodies against SEPT7 (red) and to GFP (green), and imaged by confocal microscopy. Arrows highlight some examples of Shigella entrapped in septin cages (CTRL) or not (p62 depleted) a 4 hpi. Scale bar, 5 µm.

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T3SS- Shigella and E. coli may not escape to the cytosol of cells that have engulfed it, and are not expected to be targeted to autophagic degradation in vivo. Thus, as a control, we infected p62 morphants with T3SS- Shigella or E. coli. In contrast to infection using wildtype Shigella, we observed that the knockdown of p62 had no impact on growth of T3SS- Shigella nor E. coli, nor did it impact zebrafish survival (Fig. S5B–S5E). These data suggest that p62-mediated autophagy is critical for the control of bacteria able to escape to the cytosol.

We tested whether the inflammatory cytokine response to Shigella was modulated by p62 knockdown. Experiments suggested that the inflammatory response was stronger in p62 morphants inoculated with Shigella (data not shown), yet these results may reflect the increased bacterial burden of p62 morphants compared to controls. Using confocal microscopy, we observed that in the absence of p62, initial bacterial engulfment by phagocytes (macrophages and neutrophils) was not affected; yet uncontrolled Shigella proliferation ensued, accompanied by the ultimate lysis of leukocytes and death of the infected larvae (Fig. 5D). These observations indicated that, as compared to control fish, p62 morphants are not able to restrict Shigella proliferation and, as a result, they are more susceptible to Shigella infection. We evaluated septin caging in p62 morphants. In every larva infected (at 4 or 24 hpi), septin recruitment to Shigella was clearly reduced (Fig. 5E), in agreement with previous in vitro work showing that septin cage assembly is more efficient once the process of autophagy has been initiated [14], [15]. Together, these results strongly suggest that p62-mediated autophagy is a critical component of anti-Shigella defense in vivo.

Autophagy stimulation by rapamycin does not protect fish from Shigella infection

Rapamycin is an inhibitor of mTOR, a serine/threonine protein kinase that regulates a wide range of cellular responses and is a suppressor of autophagy [45]. Autophagy is classically activated in vitro by treating cells with rapamycin, and in agreement with previous work [46], [47], we observed that critical autophagy components in zebrafish larvae can respond to rapamycin, i.e., p62 is degraded and LC3-II accumulates (data not shown). Importantly, we saw no effect of rapamycin (at the dose we applied throughout this study) on the development of uninfected larvae, in agreement with a previously published study showing that rapamycin has no discernible effect on zebrafish development past 76 hpf [48].

The stimulation of autophagy by rapamycin is generally viewed as helping to clear bacterial infection [2], [49]. To test this in vivo, we infected zebrafish larvae with a sublethal dose of Shigella and immediately after infection, treated these fish with rapamycin. Surprisingly, rapamycin treatment in zebrafish during Shigella infection significantly reduced host survival (P = 0.001; Fig. 6A), albeit at a slower rate than observed for p62 morphants (Fig. 5B). To understand the cause of increased death due to rapamycin treatment, we examined the bacterial burden in these fish. CFU counts showed that rapamycin treatment in zebrafish during Shigella infection may result in more bacterial growth (Fig. 6B). Using fluorescence stereomicroscopy, we confirmed that dying larvae were overwhelmed with GFP-Shigella (data not shown). We tested if an impairment of the inflammatory response could explain the enhanced susceptibility of rapamycin-treated fish; however, il1b induction was not found to be modulated by rapamycin in vivo (Fig. 6C). Moreover, rapamycin treatment of the T3SS- Shigella- or E. coli-infected larvae did not affect zebrafish survival nor bacterial load (Fig. S6A–S6D), indicating that rapamycin-treated fish are still able to mount an innate immune response.

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Figure 6. In vivo perturbation of autophagy via rapamycin stimulation.

A. Survival curves of zebrafish larvae treated with control (CTRL) or rapamycin (RAPA) and infected with a sublethal dose of S. flexneri (+M90T) or not infected (no bact). Representative experiment of at least 3 independent ones; n = 10 or more larvae per group. Significance testing performed by Log Rank test. ***, P = 0.001. B. Bacterial counts in zebrafish larvae treated with control (CTRL) or rapamycin (RAPA) and infected with a sublethal dose of S. flexneri. Enumeration of live bacteria in homogenates from individual larvae at various times postinfection measured by plating onto LB. CTRL larvae = open circles. RAPA-treated larvae = open squares. n = 3 larvae per treatment, pooling of 3 independent experiments. Of note, dead larvae at 24 or 48 hpi (overwhelmed with bacteria, as determined by fluorescence stereomicroscopy) were not included here, and only larvae having survived the infection (thus far) were included here (and in this case, statistics are in grey). Mean±SEM also shown (horizontal bars). Significance testing performed by Student's t test. ns, P>0.05; ***, P<0.001. C. Inflammatory response is not affected in rapamycin-treated larvae. Expression of il1b transcripts at 96 hpf in larvae injected with ∼10³ S. flexneri at 72 hpf (+M90T) or in uninfected controls, treated after infection with rapamycin (RAPA) or vehicle only (DMSO, i.e., CTRL). Il1b/ef1α transcript number ratios, normalized to the mean value in uninfected controls. Results for 5 pools of 3 larvae per group, mean±SEM also shown (horizontal bars).

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Taken together, these results show that rapamycin treatment of bacterial infection can lead to harmful effects in vivo, unlike what may be expected from studies performed in vitro. This suggests possible difficulties in therapeutic modulation of autophagy to resolve bacterial infection, until more specific activators of autophagy are discovered.

Ethics statement

Animal experiments conducted at the Institut Pasteur were performed according to European Union guidelines for handling of laboratory animals (http://ec.europa.eu/environment/chemicals/lab_animals/home_en.htm) and were approved by the Institut Pasteur Animal Care and Use Committee and the Direction Sanitaire et Vétérinaire de Paris under permit #A-75-1061. Animal experiments performed at Imperial College were performed according to the Animals (Scientific Procedures) Act 1986, and were fully approved by the Home Office (Project license: PPL 70/7446).

Zebrafish care and maintenance

Wild-type AB purchased from the Zebrafish International Resource Center (Eugene, OR), and the Tg(lyz:dsRed)^nz50, Tg(mpeg1:Gal4FF)^gl25, Tg(mpeg1:Gal4FF^gl25/UAS:kaede), Tg(UAS-E1b:nfsB.mCherry)^c264, and GFP-Lc3 transgenic zebrafish lines have been previously described [46], [57]–[59]. Eggs were obtained by marble-induced spawning, bleached according to protocols described in The zebrafish book [60], and then kept in Petri dishes containing Volvic source water supplemented with 0.3 µg/ml of methylene blue and, from 24 hours post fertilization (hpf) onwards with 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich) to prevent melanin synthesis. Embryos were reared at 28°C or 24°C according to the desired speed of development; infected larvae were always kept at 28°C. All timings in the text refer to the developmental stage at the reference temperature of 28.5°C [61]. Larvae were anesthetized with 200 µg/ml tricaine (Sigma-Aldrich) during the injection procedure as well as during the in vivo imaging.

Zebrafish fibroblast-like cell line establishment

Fibroblast-like cells were derived from AB zebrafish as follows. After a zebrafish (AB strain) has been sacrificed by overexposure to eugenol, a dorsal slice comprising skin, muscle and the dorsal fin was taken and trypsinised under constant mild shaking for 5 min. The supernatant was collected in modified MacPherson Stoker Eagle's medium (Eurobio) supplemented with 10% fetal calf serum (FCS), 100 IU/mL penicillin and 100 mg/mL streptomycin. The cell suspension was centrifuged for 5 min at 1000 g, and cells were resuspended in culture medium. The rainbow trout fibroblast cell line RTG-2 was then used as feeder, and zebrafish cells were grown on a monolayer of RTG2 for almost one year. At each passage, the co-culture was kept for 1–2/3 weeks at 20°C then put for a few days at 30°C; at this temperature, trout cells died and the remaining zebrafish cells used to seed the next passage over a new RTG-2 monolayer. After one year, ZF-AB cells started to be able to grow without feeder. Once established, fibroblast-like cells derived from AB zebrafish (ZF-AB) cells were cultured in minimum essential medium plus GlutaMAX (Invitrogen) supplemented with 1 mM sodium pyruvate (Invitrogen), 0.1 mM nonessential amino acid solution (Invitrogen), and 10% FCS. Zebrafish cells were grown at 28°C.

Infection of cell lines and microscopy

1–1.5×10⁵ ZF-AB or HeLa cells were plated on glass coverslips in 6-well plates (Techno Plastic Products) and used for experiments 48 h later. Cells on coverslips were fixed for 15 min in 4% paraformaldehyde and then washed with 1× PBS and processed for immunofluorescence (IF). After 10 min of incubation in 50 mm ammonium chloride, cells were permeabilized for 4 min with 0.1% Triton X-100 and then incubated in 1× PBS. Incubation with primary or secondary antibodies was performed in 1× PBS. Vectashield hard set mounting medium with DAPI (Vector Laboratories) or mounting medium for IF (Interchim) was used.

Shigella was added to cells using 400 µl of growth (A_{600 nm} = 0.6) or using 200 µl of overnight growth (A_{600 nm} = 0.6) from single colony, and was diluted in minimum essential medium and added directly to cells for imaging analyses. Bacteria and cells were centrifuged at 700× g for 10 min at 21°C and then placed at 28°C for 30 min, washed with minimum essential medium, and incubated with fresh gentamicin-containing complete medium (50 µg/ml) for 4 h, after which they were washed with 1× PBS and fixed and processed for IF.

Images were acquired on a fluorescence inverted microscope Axiovert 200 M (Carl Zeiss MicroImaging, Inc.) equipped with a cooled digital charge-coupled device camera (Cool SNAPHQ, Photometrics) driven by Metamorph Imaging System software (Universal Imaging Corp).

Bacteria and bacterial infections

Bacterial strains used in this study were wild-type invasive of S. flexneri serotype 5a (M90T; BUG 2505) [15], M90T expressing green fluorescent protein (GFP) (GFP-Shigella; BUG 1908) [15], dsRed [62] or mCherry (pFPV 25.1 mCherry construct), T3SS− noninvasive variant (ΔmxiD) expressing dsRed [62], E. coli K12 bacteria expressing dsRed [26], and M. marinum M strain expressing GFP or dsRed [15]. In the case of E. coli, infections were performed as previously described [24], [26]. S. flexneri were cultured overnight in trypticase soy, diluted 80× in fresh trypticase soy, and cultured until A_{600 nm} = 0.6. M. marinum M-GFP and M-DsRed were cultured at 30°C in Middlebrook 7H9 (BD Biosciences) supplemented with 0.2% glycerol, 0.05% Tween 80 and 10% ADC Enrichment (Fisher Scientific), diluted 48 h prior to infection in fresh media, and cultured until OD600 nm = 0.6. For injection of zebrafish larvae, bacteria were recovered by centrifugation, washed, resuspended at the desired concentration in PBS. In the case of M. marinum, bacteria were also passaged through a 26 gauge needle to dissociate bacterial clumps and homogenize the bacteria prior to infection. 3 day post-fertilisation (dpf) anesthetized zebrafish larvae were microinjected intravenously (iv) with 0.5–2 nl of bacterial suspension as described previously [24]. The exact inoculum was checked a posteriori by injection in a water drop and plating onto LB agar. Infected larvae were transferred into individual wells (containing 1 ml of Volvic water in 24-well culture plates), incubated at 28°C and regularly observed under a stereomicroscope. Infections with a quantified standard dose were performed at least 3 times per strain of bacteria. Survival curves with graded doses as depicted were repeated at least 3 times.

Measurement of bacterial burden

At the indicated times, animals were anesthetized, rinsed, and collected in 30 µl of sterile water. The animals were lysed in 200 µl of 0.4% Triton X-100 and homogenized through a 26-gauge needle (five up-and-down sequences). Serial dilutions of the homogenates were plated onto LB agar, and CFU were enumerated after 24 h of incubation at 37°C; only colonies with the appropriate morphology and color were scored.

Microscopy of zebrafish (infected or not)

Anesthesized zebrafish larvae were fixed for 2 h at RT or overnight at 4°C in 4% paraformaldehyde with 0.4% triton, then washed with PBS 0.1% tween, and processed for IF. In brief, after 20 additional minutes of PBS 1% triton, larvae were washed 3×5 minutes in PBS 0.4% triton, then incubated in blocking solution: PBS 1× supplemented with 10% sheep serum, 1% DMSO, and 0.1% tween, for 1 hour. Primary antibodies were diluted in blocking solution and were applied to larvae overnight at 4°C. To remove primary antibodies, larvae were washed 4×15 min in PBS +0.1% tween. After washes, larvae were placed in blocking solution for 1 h at RT. Secondary antibodies were diluted in block solution and were applied to larvae overnight at 4°C. To remove secondary antibodies, larvae were washed 4×15 min in PBS 0.1% Tween. Fluorescently labeled larvae were then cleared by progressive transfer to 80% glycerol.

Quantification of macrophages and neutrophils numbers on fixed and labeled transgenic reporter larvae was performed as following. Briefly, brightfield, dsRed and GFP images of whole fixed larvae were taken using a Leica Macrofluo Z16 APOA (zoom 16∶1) equipped with a Leica PlanApo 2.0× lens, and a Photometrics CoolSNAP HQ² camera. Images were captured using the Metavue software version 7.5.6.0 (MDS Analytical Technologies). Then, pictures were analyzed and positive cells for red fluorescence counted using the ImageJ software version 10.2 (developed by the National Institute of Health). Neutrophils numbers were obtained with lyz:dsRed larvae, macrophage numbers with mpeg1:G/U:mCherry larvae. Counts shown in Fig. 2B are numbers of leukocytes per image.

Examination of septin recruitment in vivo was performed using a confocal microscope (Zeiss LSM510). Larvae were infected with GFP-Shigella in the mesenchyme near the caudal vein or in the hindbrain, and fixed and labeled for microscopy 4 or 24 hpi. Z-stacks of infected larvae were acquired for each sample using a 63× or 100× objective and a slice increment of 0.2 µm. These stacks were then deconvoluted (Huygens software) and analysed using ImageJ according to previously established criteria [14], [15], [63].

Live imaging, image processing and analysis

To perform whole-body in vivo imaging, anaesthetized zebrafish larvae were oriented and immobilized in 1% low melting point agarose in 60 mm plastic bottom Petri dishes (up to 9 fish mounted and imaged per dish), then covered with 2 ml Volvic water containing tricaine as described previously [26]. Transmission and fluorescence widefield imaging was done using a Nikon Biostation IM–Q S2 equipped with a DS-Qi camera. Imaging was typically performed at 26°C with a 10× (NA 0,5) dry objective. Multiple-field Z-stacks with a 10 µm Z-step were acquired every 30 minutes.

To perform high resolution confocal live imaging, injected larvae were positioned in 35 mm glass-bottom dishes (Inagaki-Iwaki). To immobilise the larva in the dish a 1% low-melting-point agarose solution covering the entire larva was used. The immobilised larvae were then covered with 2 ml Volvic water containing tricaine. Confocal microscopy was performed at 23–26°C using a Leica SPE inverted microscope and a 40× oil immersion objective (ACS APO 40×1.15 UV) as previously described [26]. A Leica SP8 confocal microscope equipped with two PMT and an Hybrid detector (HyD) and a 20× oil immersion objective (HC PL APO CS2 20×/0.75) was used to live image infected larvae (represented in Figure S4B, Video S8, Video S10).The 4D files generated by the time-lapse acquisitions were processed, cropped, analysed and annotated using the LAS-AF Leica software. Acquired Z-stacks were projected using maximum intensity projection and exported as AVI files. Frames were captured from the AVI files and handled with Photoshop software to mount figures. AVI files were also cropped and annotated with ImageJ software, then compressed and converted into QuickTime movies with the QuickTime Pro software.

Electron microscopy

For standard ultrastructure analyses, as described in [24], [64], anesthetized embryos were fixed in 0.5% glutaraldehyde in 200 mM sodium cacodylate buffer for 2 h, washed in buffer and secondarily fixed in reduced 1% osmium tetroxide, 1.5% potassium ferricyanide for 60 min. The samples were washed in distilled water and stained overnight at 4°C in 0.5% magnesium uranyl acetate, washed in distilled water and dehydrated in graded ethanol, infiltrated with propylene oxide and then graded Epon/PO mixtures until final embedding in full Epon resin in coffin moulds (allowing different orientations) and polymerised at 56°C overnight. Semi-thin survey sections were cut and stained and final ultrathin sections (typically 50–70 nm) and serial sections were collected on Formvar coated slot grids and stained with Reynold's lead citrate and examined in a FEI Tecnai electron microscope with CCD camera image acquisition.

qRT-PCR

RNA was extracted from snap-frozen larvae using Trizol (Invitrogen). cDNA was obtained using M-MLV H- reverse-transcriptase (Promega) with a dT17 primer. Quantitative PCR was then performed on an ABI7300 thermocycler (Applied Biosystems) using SYBR green reaction power mix (Applied Biosystems). The following pairs of primers were used: EF1α (GCTGATCGTTGGAGTCAACA and ACAGACTTGACCTCAGTGGT); IL1b (GAGACAGACGGTGCTGTTTA and GTAAGACGGCACTGAATCCA). Quantifications were performed on triplicate wells, and taking into account the previously measured yield of the reaction as described in [65]. To normalize cDNA amounts, we used the housekeeping gene EF1α transcripts [66].

icsA, icsB expression in vivo

S. flexneri M90T was injected into the hindbrain ventricle of zebrafish larvae and incubated at 28°C for 4 h (high dose), 12 h (medium dose) and 24 h (medium dose). RNA was extracted from 10 snap-frozen larvae per timepoint using Trizol (Invitrogen). cDNA was obtained using QuantiTect Reverse Transcription Kit (Qiagen). PCR was then performed using a PTC-225 Poltier Thermal Cycler (MJ Research) and RedTaq reaction mix (Applied Biosystems). The following pairs of primers were used: icsA (AATCAATAAGGGCACGTTCG and TCGCCATCTGTATCATTCCA); icsB (GCATCGGTACAGCCAAAAAT and GTATGAGTGGCAAGCGTTGA).

Antibodies

Rabbit polyclonal antibodies used were anti-SEPT7 (R170) [15], anti-p62 (Cliniscience, PM045), anti-dsRed (Clontech Laboratoires), anti-elongation factor 1-α (EF1α; GeneTex); to label GFP chicken polyclonal and mouse monoclonal antibodies anti-GFP (Abcam) were used. Secondary antibodies used were Cy3-, Cy5- (Jackson ImmunoResearch Laboratories), Alexa Fluor 488-, or Alexa Fluor 546-conjugated goat anti-rabbit, anti-chicken or goat anti-mouse (Molecular Probes). F-actin was labeled with Alexa Fluor 488-, 546-, or 647-phalloidin (Molecular Probes). Whole-mount immunohistochemistry of infected zebrafish cells was performed using standard protocols [14], [15]. For immunoblotting, total cellular extracts were blotted with the above-mentioned antibodies followed by peroxidase-conjugated goat anti-mouse or anti-rabbit antibodies (Biosys Laboratories). Anti-EF1α was used throughout as a loading control. Proteins were run on 8, 10 or 14% acrylamide gels.

Morpholinos and pharmacological inhibitors

Antisense morpholino oligonucleotides were obtained from GeneTools (www.gene-tools.com). After thawing, morpholinos are heated at 65°C for 10 min to ensure complete dissolution, and diluted to the desired concentration (typically, 250 to 500 µM, for a total injected amount of 4 ng) in morpholino buffer (120 mM KCl, 10 mM Hepes pH 7.2) containing 0.1% phenol red. Injections were performed into 1-cell embryos at 1 nL per embryo. Control (TACCAAAAGCTCTCTTATCGAGGGA, with no known target on the zebrafish genome) and p62-specific (CACTGTCATCGACATCGTAGCGGAA, targeting the start AUG codon) morpholinos were used.

For rapamycin treatment, protocols were adapted from [46]. Larvae were treated with rapamycin (Calbiochem) for 12 h (50 nM), and treatment was continued throughout infection.

Statistical analysis

Significance testing for performed by Log Rank test (survival curves), Student's t test (on log values of CFU counts), or by ANOVA with Bonferroni posttest (leukocyte counts). The level of significance is shown as follows: ns, P>0.05; *, P<0.05; **, P<0.01; ***, P<0.001.