The authors would like to thank Ms. A. De Paoli and Ms. Georgie Wray-McCann for technical assistance. The authors acknowledge use of the facilities and technical assistance of Monash Histology Platform, Department of Anatomy and Developmental Biology, Monash University. The laboratory is supported by funding from the National Health and Medical Research Council (NHMRC) to RLF (APP1079930, APP1107930). RLF is supported by a Senior Research Fellowship from the NHMRC (APP1079904). KD and MC are both supported by Monash Graduate Scholarships. KD is also supported by the Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, while MC has an International Postgraduate Scholarship from the Faculty of Medicine, Nursing and Health Sciences, Monash University. Research at the Hudson Institute of Medical Research is supported by the Victorian Government&#8217;s Operational Infrastructure Support Program.

<ol>
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G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lack+of+genetic+influence+on+the+innate+inflammatory+response+to+helicobacter+infection+of+the+gastric+mucosa.">Lack of genetic influence on the innate inflammatory response to helicobacter infection of the gastric mucosa.</a> Frontiers in Immunology. 3, 181 (2012).</li><li>Cai, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Helicobacter+felis+eradication+restores+normal+architecture+and+inhibits+gastric+cancer+progression+in+C57BL/6+mice.">Helicobacter felis eradication restores normal architecture and inhibits gastric cancer progression in C57BL/6 mice.</a> Gastroenterology. 128 (7), 1937-1952 (2005).</li><li>Ferrero, R. L., Labigne, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cloning,+expression+and+sequencing+of+Helicobacter+felis+urease+genes.">Cloning, expression and sequencing of Helicobacter felis urease genes.</a> Molecular Microbiology. 9 (2), 323-333 (1993).</li><li>Stevenson, T. H., Castillo, A., Lucia, L. M., Acuff, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growth+of+Helicobacter+pylori+in+various+liquid+and+plating+media.">Growth of Helicobacter pylori in various liquid and plating media.</a> Letters in Applied Microbiology. 30 (3), 192-196 (2000).</li><li>Uotani, T., Graham, D. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diagnosis+of+Helicobacter+pylori+using+the+rapid+urease+test.">Diagnosis of Helicobacter pylori using the rapid urease test.</a> Annals of Translational Medicine. 3 (1), 9 (2015).</li><li>Riley, L. K., Franklin, C. L., Hook, R. R., Besch-Williford, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+murine+helicobacters+by+PCR+and+restriction+enzyme+analyses.">Identification of murine helicobacters by PCR and restriction enzyme analyses.</a> Journal of Clinical Microbiology. 34 (4), 942-946 (1996).</li><li>Chaouche-Drider, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+commensal+Helicobacter+sp.+of+the+rodent+intestinal+flora+activates+TLR2+and+NOD1+responses+in+epithelial+cells.">A commensal Helicobacter sp. of the rodent intestinal flora activates TLR2 and NOD1 responses in epithelial cells.</a> PLoS One. 4 (4), e5396 (2009).</li><li>Fox, J. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Helicobacter+bilis:+bacterial+provocateur+orchestrates+host+immune+responses+to+commensal+flora+in+a+model+of+inflammatory+bowel+disease.">Helicobacter bilis: bacterial provocateur orchestrates host immune responses to commensal flora in a model of inflammatory bowel disease.</a> Gut. 56 (7), 898-900 (2007).</li><li>McGee, D. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cholesterol+enhances+Helicobacter+pylori+resistance+to+antibiotics+and+LL-37.">Cholesterol enhances Helicobacter pylori resistance to antibiotics and LL-37.</a> Antimicrobial Agents and Chemotherapy. 55 (6), 2897-2904 (2011).</li><li>Viala, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nod1+responds+to+peptidoglycan+delivered+by+the+Helicobacter+pylori+cag+pathogenicity+island.">Nod1 responds to peptidoglycan delivered by the Helicobacter pylori cag pathogenicity island.</a> Nature Immunology. 5 (11), 1166-1174 (2004).</li><li>Kong, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+sensitive+and+specific+PCR+method+to+detect+Helicobacter+felis+in+a+conventional+mouse+model.">A sensitive and specific PCR method to detect Helicobacter felis in a conventional mouse model.</a> Clinical and Vaccine Immunology. 3 (1), 73-78 (1996).</li><li>Ng, G., Every, A., McGuckin, M., Sutton, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Increased+Helicobacter+felis+colonization+in+male+129/Sv+mice+fails+to+suppress+gastritis.">Increased Helicobacter felis colonization in male 129/Sv mice fails to suppress gastritis.</a> Gut Microbes. 2 (6), 358-360 (2011).</li><li>Ferrero, R. L., Ave, P., Radcliff, F. J., Labigne, A., Huerre, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Outbred+mice+with+long-term+Helicobacter+felis+infection+develop+both+gastric+lymphoid+tissue+and+glandular+hyperplastic+lesions.">Outbred mice with long-term Helicobacter felis infection develop both gastric lymphoid tissue and glandular hyperplastic lesions.</a> The Journal of Pathology. 191 (3), 333-340 (2000).</li></ol>

The authors have nothing to disclose.

This protocol describes the use of an in vivo mouse model for Helicobacter infection. The critical steps of the procedure are the: 1) preparation of Helicobacter inocula containing viable and motile bacteria; 2) delivery of the appropriate numbers of bacteria to the mouse via intragastric gavage; 3) detection of bacterial infection by colony counting and/or PCR; and 4) processing of gastric tissues to enable the assessment of histopathology in infected stomachs. Further suggestions for modifications, troubleshooting and technical considerations are discussed below.
The method of growing Helicobacter spp. using Blood Agar Base no. 2 supplemented with horse blood has been well established in our laboratory. However, alternate agar bases such as Brucella agar and Columbia blood agar can also be used22. It is important to ensure that only sterile glassware that is free of detergent is used to prepare the growth medium. Furthermore, to obtain optimal growth, H. pylori bacteria should be routinely subcultured on agar plates that have residual moisture and are not dry. When preparing Helicobacter spp. inocula for infection, it is vital to subculture H.&#160;pylori and H. felis strains every 1&#8211;1.5 or 2 days, respectively, to ensure bacterial viability. At every subculture, bacteria should be assessed for their viability and motility by phase contrast microscopy. A urease assay can also be routinely employed to discriminate between gastric Helicobacter spp. and other bacteria23, however, it is important to realize that this assay detects both viable and non-viable Helicobacter bacteria. Following inoculation of animals, viable counts on Helicobacter suspensions must be performed to quantitate numbers of viable bacteria used for infection. As H. felis does not reproducibly form isolated colonies on agar medium15, estimation of bacterial numbers is performed using phase contrast microscopy. Quantification of bacterial numbers by optical density measurement (A600) alone is inaccurate as this method does not discriminate between viable and non-viable bacteria. This method should not be used in Helicobacter research without rigorous optimization, as described above (Section 1.5).
When performing Helicobacter infection studies, it is crucial to consider the optimal mouse and Helicobacter strain, as well as the length of infection, to suit the purpose of the experiment. It is also essential to regularly confirm that the animals used for experimentation are indeed Helicobacter-free using genus-specific PCR primers24. The presence of other enteric Helicobacter species, such as Helicobacter bilis, Helicobacter hepaticus or Helicobacter muridarum, may alter the disease susceptibility of mice and introduce confounding factors into in vivo studies25,26. It is also advisable to include a mock treatment control group of animals (i.e., fed broth only) in initial screening experiments to investigate the effects of the normal microbiota on Helicobacter colonization and pathogenesis.
Post-euthanasia, H. pylori colonization in murine stomachs can be measured by viable counting. HBA plates used for colony counts should be supplemented with bacitracin and naladixic acid in addition to the modified Skirrow&#8217;s selective supplement, to restrict the growth of bacterial species from the normal gastric microbiota and hence prevent contamination27. H. felis does not always form colonies, but instead tends to form swarming growth on agar plates15,28. Therefore, PCR and qPCR are normally employed to determine the presence and levels of H. felis, respectively29,30. In section 4.2, we introduced a simple and quick PCR method to confirm colonization by H. felis in the murine stomach using a pair of primers, which have been validated to target a 325 bp region of H. felis and H.&#160;pylori ureB genes. Using the PCR conditions described above, it is possible to discriminate between infection by these gastric Helicobacter spp. and urease-producing enterohepatic Helicobacters. Other genes that have been validated for PCR detection of gastric Helicobacter infection include the 16s rRNA and flagellin B (flaB) genes15,29,30.
Finally, we have described the use of two powerful staining techniques: H&#38;E staining, to assess histopathological changes in the stomach post-infection; and Giemsa staining, to detect H. felis infection. To obtain optimal staining, it is essential to ensure that tissues have been preserved, processed and embedded in the correct orientation. Additionally, only freshly prepared solutions and filtered stains must be used during this process. Tissue sections can be stored indefinitely and utilized for more specific analysis of gastric pathology via immunofluorescence or immunohistochemistry. Some other common measures of gastric inflammation and disease include: immune cell recruitment (anti-CD45 staining); mucosal thickening/destruction (Periodic Acid Schiff/Alcian blue staining); epithelial cell proliferation (proliferating cell nuclear antigen, PCNA/Bromodeoxyuridine, BrDU staining); or cellular apoptosis (TUNEL staining). The lymphoid follicles observed in the H&#38;E-stained tissues of H. felis-infected mice can be confirmed by immunohistochemistry, using antibodies directed against B (B220+) and T cell (CD3+) antigens31.
In summary, animal models of bacterial disease provide valuable tools in the field of infection biology. The protocols of intragastric gavage and processing of stomach tissues provided here may be adapted to mouse infection models involving other enteric pathogens.

Helicobacter pylori is a spiral-shaped, Gram-negative, human gastric pathogen present in all populations across the world, with infection rates in developing countries estimated to be in the order of 80%1. Although most H. pylori-infected individuals are asymptomatic, some develop more severe diseases, ranging from peptic ulceration to gastric cancer2. H. pylori-associated cancers are broadly characterized either by malignant changes in epithelial cells (GECs) or by the formation of extra-nodal lymphoid tissues in the stomach, resulting in gastric adenocarcinoma or mucosa-associated lymphoid tissue (MALT) lymphoma, respectively. H. pylori is highly adapted to survive in the harsh ecological niche of the stomach due to the presence of various virulence factors and mechanisms facilitating its adherence, growth and metabolism in this niche. In particular, virulent strains of H. pylori possess the 40 kb cag Pathogenicity Island (cagPAI) that encodes approximately 30 genes required for the production of a Type 4 secretion system (T4SS)3,4. cagPAI-positive H. pylori strains are associated with the induction of higher levels of chronic inflammation in the host, which has been implicated as an essential precursor of gastric adenocarcinoma5.
In vivo animal models, particularly mice, have been highly informative by allowing researchers to investigate the relative contributions of host, bacterial and environmental factors on H. pylori infection and disease outcome6. Studies have previously demonstrated that prolonged H. pylori infection of mice on the C57BL/6 genetic background results in the development of chronic gastritis and gland atrophy, both hallmarks of H. pylori infection7. Furthermore, infection with the related feline/canine bacterial species, H. felis, has been shown to induce MALT formation in mice with similar pathology and disease progression as seen in human MALT lymphoma8,9. The most commonly used H. pylori isolate in mouse colonization studies is the &#8220;Sydney Strain 1&#8221; (SS1) strain10, which is cagPAI+ but has a non-functional T4SS (T4SS&#8722;)11. Other widely used strains include H. pylori B128 7.13 (cagPAI+/T4SS+)12 and X47-2AL (cagPAI-/T4SS&#8722;)13. For H. felis infections, the strain CS1 (&#8220;Cat Spiral 1&#8221;, cagPAI-/T4SS&#8722;) is generally used14.
Herein, we provide a protocol describing the preparation of Helicobacter inocula for in vivo infection, the procedure for intragastric gavage of mice, as well as methods for the processing of tissues for the study of histopathological changes in the stomach. In particular, this article will focus on the histological methods used to visualize bacterial colonization and assess histopathological changes, including MALT formation, in the gastric mucosa of infected mice. Some of the methods described here may be adapted to the study of other gut pathogens such as S. Typhimurium or C. rodentium.

<table>
	<tbody>
		<tr>
			<td>Bacteriological reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Oxoid Blood Agar Base No.2</td>
			<td>Thermo Fischer Scientific</td>
			<td>CM0271B</td>
			<td>Dissolve in deinonized water prior to sterilization</td>
		</tr>
		<tr>
			<td>Premium Defibrinated Horse blood</td>
			<td>Australian Ethical Biologicals</td>
			<td>PDHB100</td>
			<td></td>
		</tr>
		<tr>
			<td>Bacto Brain Heart Infusion Broth</td>
			<td>BD Bioscience</td>
			<td>237500</td>
			<td>Dissolve in deinonized water prior to sterilization</td>
		</tr>
		<tr>
			<td>CampyGen gas packs</td>
			<td>Thermo Fischer Scientific</td>
			<td>CN0035A/CN0025A</td>
			<td></td>
		</tr>
		<tr>
			<td>Histological reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Formalin, neutral buffered, 10%</td>
			<td>Sigma Aldrich</td>
			<td>HT501128</td>
			<td></td>
		</tr>
		<tr>
			<td>Absolute alcohol, 100% Denatured</td>
			<td>ChemSupply</td>
			<td>AL048-20L-P</td>
			<td></td>
		</tr>
		<tr>
			<td>Isopropanol (2-propanol)</td>
			<td>Merck</td>
			<td>100995</td>
			<td></td>
		</tr>
		<tr>
			<td>Xylene (sulphur free)</td>
			<td>ChemSupply</td>
			<td>XT003-20L</td>
			<td></td>
		</tr>
		<tr>
			<td>Mayer&#39;s Haematoxylin</td>
			<td>Amber Scientific</td>
			<td>&#160;MH-1L</td>
			<td>Filter before use</td>
		</tr>
		<tr>
			<td>Eosin, Aqueous Stain</td>
			<td>Amber Scientific</td>
			<td>EOCA-1L</td>
			<td>Filter before use</td>
		</tr>
		<tr>
			<td>Wright-Giemsa Stain, modified</td>
			<td>Sigma Aldrich</td>
			<td>WG80-2.5L</td>
			<td>Dilute before use (20% Giemsa, 80% deionized water)</td>
		</tr>
		<tr>
			<td>Histolene</td>
			<td>Grale Scientific</td>
			<td>11031/5</td>
			<td></td>
		</tr>
		<tr>
			<td>DPX mounting medium</td>
			<td>VWR</td>
			<td>1.00579.0500</td>
			<td></td>
		</tr>
		<tr>
			<td>Molecular biology reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Qubit dsDNA BR Assay Kit</td>
			<td>Thermo Fischer Scientific</td>
			<td>Q32850</td>
			<td></td>
		</tr>
		<tr>
			<td>Oligonucleotides</td>
			<td>Sigma Aldrich</td>
			<td></td>
			<td>The annealing temperature of ureB primers used in this study is 61&#176;C</td>
		</tr>
		<tr>
			<td>GoTaq Flexi DNA Polymerase</td>
			<td>Promega</td>
			<td>&#160;M8291</td>
			<td>Kit includes 10X PCR buffer and Magnesium Chloride</td>
		</tr>
		<tr>
			<td>dNTPs</td>
			<td>Bioline</td>
			<td>BIO-39028</td>
			<td>Dilute to 10mM in sterile nuclease free water before use</td>
		</tr>
		<tr>
			<td>Molecular Grade Agarose</td>
			<td>Bioline</td>
			<td>BIO-41025</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Hydrogen Carbonate</td>
			<td>Univar (Ajax Fine Chemicals)</td>
			<td>A475-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium Sulphate Heptahydrate</td>
			<td>Chem-Supply</td>
			<td>MA048-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Antibiotics</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Vancomycin</td>
			<td>Sigma Aldrich</td>
			<td>V2002-1G</td>
			<td>Dissolve in deionized water</td>
		</tr>
		<tr>
			<td>Polymyxin B</td>
			<td>Sigma Aldrich</td>
			<td>P4932-5MU</td>
			<td>Dissolve in deionized water</td>
		</tr>
		<tr>
			<td>Trimethoprim (&#8805;98% HPLC)</td>
			<td>Sigma Aldrich</td>
			<td>T7883</td>
			<td>Dissolve in 100% (absolute) Ethanol</td>
		</tr>
		<tr>
			<td>Amphotericin</td>
			<td>Amresco (Astral Scientific)</td>
			<td>E437-100MG</td>
			<td>Dissolve in deionized water</td>
		</tr>
		<tr>
			<td>Bacitracin from Bacillus licheniformis</td>
			<td>Sigma Aldrich</td>
			<td>B0125</td>
			<td>Dissolve in deionized water</td>
		</tr>
		<tr>
			<td>Naladixic acid</td>
			<td>Sigma Aldrich</td>
			<td>N8878</td>
			<td>Dissolve in deionized water</td>
		</tr>
		<tr>
			<td>Other reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Methoxyflurane (Pentrhox)</td>
			<td>Medical Developments International</td>
			<td>Not applicable</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraffin Wax</td>
			<td>Paraplast Plus, Leica Biosystems</td>
			<td>39601006</td>
			<td></td>
		</tr>
		<tr>
			<td>Equipment and plasticware</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Oxoid Anaerobic Jars</td>
			<td>Thermo Fischer Scientific</td>
			<td>HP0011/HP0031</td>
			<td></td>
		</tr>
		<tr>
			<td>COPAN Pasteur Pipettes</td>
			<td>Interpath Services</td>
			<td>200CS01</td>
			<td></td>
		</tr>
		<tr>
			<td>Eppendorf 5810R centrifuge</td>
			<td></td>
			<td></td>
			<td>Collect bacterial pellets by centrifugation at 2,200 rpm for 10 mins at 4&#176;C</td>
		</tr>
		<tr>
			<td>23g precision glide needle</td>
			<td>BD Bioscience</td>
			<td>301805</td>
			<td></td>
		</tr>
		<tr>
			<td>Parafilm M</td>
			<td>Bemis, VWR</td>
			<td>PM996</td>
			<td></td>
		</tr>
		<tr>
			<td>Portex fine bore polythene tubing</td>
			<td>Smiths Medical</td>
			<td>800/100/200</td>
			<td></td>
		</tr>
		<tr>
			<td>Plastic feeding catheters</td>
			<td>Instech&#160; Laboratories</td>
			<td>FTP20-30</td>
			<td></td>
		</tr>
		<tr>
			<td>1 ml tuberculin luer slip disposable syringes</td>
			<td>BD Bioscience</td>
			<td>302100</td>
			<td></td>
		</tr>
		<tr>
			<td>Eppendorf micropestle for 1.2 - 2 mL tubes</td>
			<td>Sigma Aldrich</td>
			<td>Z317314</td>
			<td>Autoclavable polypropylene pestles used for stomach homogenization</td>
		</tr>
		<tr>
			<td>GentleMACs Dissociator</td>
			<td>Miltenyi Biotec</td>
			<td>130-093-235</td>
			<td>Use a pre-set gentleMACS Programs for mouse stomach tissue</td>
		</tr>
		<tr>
			<td>M Tubes (orange cap)</td>
			<td>Miltenyi Biotec</td>
			<td>30-093-236</td>
			<td></td>
		</tr>
		<tr>
			<td>&#160;Qubit Fluorometer</td>
			<td>Thermo Fischer Scientific</td>
			<td>Q33216</td>
			<td></td>
		</tr>
		<tr>
			<td>Sterile plastic loop</td>
			<td>LabServ</td>
			<td>LBSLP7202</td>
			<td></td>
		</tr>
		<tr>
			<td>Cold Plate, Leica EG1160 Embedding System</td>
			<td>Leica Biosystems</td>
			<td>Not applicable</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue-Tek Base Mould System, Base Mold 38 x 25 x 6</td>
			<td>Sakura, Alphen aan den Rijn</td>
			<td>4124</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue-Tek III Uni-Casette System</td>
			<td>Sakura, Alphen aan den Rijn</td>
			<td>4170</td>
			<td></td>
		</tr>
		<tr>
			<td>Microtome, Leica RM2235</td>
			<td>Leica Biosystems</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Charged SuperFrost Plus glass slides</td>
			<td>Menzel Glaser, Thermo Fischer Scientific</td>
			<td>4951PLUS4</td>
			<td></td>
		</tr>
	</tbody>
</table>

mouse models of helicobacter infection and gastric pathologies

Helicobacter pylori is a gastric pathogen that is present in half of the global population and is a significant cause of morbidity and mortality in humans. Several mouse models of gastric Helicobacter infection have been developed to study the molecular and cellular mechanisms whereby H. pylori bacteria colonize the stomach of human hosts and cause disease. Herein, we describe protocols to: 1) prepare bacterial suspensions for the in vivo infection of mice via intragastric gavage; 2) determine bacterial colonization levels in mouse gastric tissues, by polymerase chain reaction (PCR) and viable counting; and 3) assess pathological changes, by histology. To establish Helicobacter infection in mice, specific pathogen-free (SPF) animals are first inoculated with suspensions (containing &#8805;105 colony-forming units, CFUs) of mouse-colonizing strains of either Helicobacter pylori or other gastric Helicobacter spp. from animals, such as Helicobacter felis. At the appropriate time-points post-infection, stomachs are excised and dissected sagittally into two equal tissue fragments, each comprising the antrum and body regions. One of these fragments is then used for either viable counting or DNA extraction, while the other is subjected to histological processing. Bacterial colonization and histopathological changes in the stomach may be assessed routinely in gastric tissue sections stained with Warthin-Starry, Giemsa or Haematoxylin and Eosin (H&#38;E) stains, as appropriate. Additional immunological analyses may also be undertaken by immunohistochemistry or immunofluorescence on mouse gastric tissue sections. The protocols described below are specifically designed to enable the assessment in mice of gastric pathologies resembling those in human-related H. pylori diseases, including inflammation, gland atrophy and lymphoid follicle formation. The inoculum preparation and intragastric gavage protocols may also be adapted to study the pathogenesis of other enteric human pathogens that colonize mice, such as Salmonella Typhimurium or Citrobacter rodentium.

This protocol describes an oral gavage technique to achieve intragastric infection with H. pylori or H. felis in murine mouse models (Figure 1). Following euthanasia, stomachs are removed, weighed and divided into 2 equal halves comprising the antrum, body and non-glandular regions of gastric tissues (Figure 2). The non-glandular region is removed prior to performing any analyses.
Successful colonization of animals is typically confirmed by performing viable counting on H. pylori-infected gastric homogenates, and subsequently enumerating individual colonies on HBA plates (Figure 3). Alternatively, PCR is employed to verify infection with H. felis using specific, validated primers directed at a 325 bp region of the H. felis and H.&#160;pylori ureB genes (Figure 4).
Gastric tissues are processed, embedded and sectioned for downstream histological applications. The H&#38;E staining technique is used to assess the histopathology in Helicobacter-infected mice. In the current example, WT C57BL/6 mice display moderate signs of inflammation, including hyperplasia (enlarged mucosa) and gland atrophy at 6 months&#8217; post-infection with H. felis. The presence of cellular infiltrates can also be observed in the sub-mucosa. Interestingly, however, more severe inflammation is observed in KO mice at the same time point, with the additional presence of lymphoid follicles located in close proximity to cellular infiltrates (Figure 5). Finally, H. felis bacteria are observed in Giemsa-stained sections of infected mouse stomachs (Figure 6).
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/56985/56985fig1.jpg" /> 
Figure 1: Image demonstrating the oral gavage technique. A disposable 1 mL syringe and flexible catheter are used to deliver &#8805;105 CFU of bacterial inocula to a mouse via the intragastric route. The mouse was anesthetized using methoxyflurane and held in a firm grip at the neck, allowing for access of the catheter to the stomach via the esophagus.
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/56985/56985fig2.jpg" /> 
Figure 2: Harvesting of mouse spleens and stomachs post-infection. Mouse stomachs were harvested post-euthanasia and their contents removed by scraping with a scalpel and washing in sterile PBS. The tissues were then weighed and flattened on a cotton sheet to reveal 2 equal halves, each comprising the gastric antrum, body and non-glandular regions; Scale bar = 10 mm.
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/56985/56985fig3.jpg" /> 
Figure 3: Viable counts on H.&#160;pylori-infected mouse stomachs. Mice on the C57BL/6 background were inoculated with 107 CFU of H. pylori SS1 and left for 8 weeks. (A) Dilutions of each gastric homogenate are plated onto a half (or third) of an HBA plate and bacterial loads assessed by enumerating 10-100 individual colonies. The left half of the plate shows a pure culture of H. pylori bacteria. (B) The presence of contaminating bacteria from the mouse gastric microbiota (left) or large numbers of H. pylori colonies (right) can complicate the enumeration of H. pylori CFUs. (C) Common examples of contaminating bacteria in gastric homogenate samples. Scale bar = 1.7 cm. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/56985/56985fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/56985/56985fig4.jpg" /> 
Figure 4: PCR detection of H. felis infection in gastric biopsies using oligonucleotides targeting the ureB gene. A specific oligonucleotide pair was designed to recognize and bind to homologous sequences in both H. felis and H. pylori ureB genes. These primers were validated using genomic DNA from H. pylori SS1 (lane 2) or H. felis (lane 3). Deionized water was included as a negative control (lane 1).
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/56985/56985fig5v2.jpg" /> 
Figure 5: Representative images of H&#38;E-stained stomach sections from WT and KO mice at 6 months&#8217; post-infection with H. felis. Paraffin-embedded tissue sections were stained with H&#38;E. WT mice receiving BHI broth alone (control) had a normal gastric epithelium and no significant inflammation. In contrast, WT animals with chronic H. felis infection displayed moderate levels of inflammation and mucosal thickening which was further exacerbated in H. felis-infected KO animals. Tissue sections from H. felis-infected KO mice exhibited the presence of mucosal lymphoid follicles (*), cellular infiltrates (&#8594;), gland atrophy (&#9654;) and hyperplasia. Scale bar = 100 &#956;m. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/56985/56985fig5v2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/56985/56985fig6.jpg" /> 
Figure 6: Representative images of Giemsa-stained gastric sections from C57BL/6 WT mice at 3 months&#8217; post-infection with H. felis. Paraffin-embedded tissue sections were stained with Giemsa. Arrows indicate the presence of H. felis in the gastric glands. Scale bar = 200 &#956;m.

Watch this Scientific Journal Video about Mouse Models Of Helicobacter Infection And Gastric Pathologies at JoVE.com

Mouse Models Of Helicobacter Infection And Gastric Pathologies

Mice represent an invaluable in vivo model to study infection and diseases caused by gastrointestinal microorganisms. Here, we describe the methods used to study bacterial colonization and histopathological changes in mouse models of Helicobacter pylori-related disease.

Mouse Models Of Helicobacter Infection And Gastric Pathologies

Helicobacter pylori is a gastric pathogen that is present in half of the global population and is a significant cause of morbidity and mortality in ...

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19.4K Views.  Hudson Institute of Medical Research. Mice represent an invaluable in vivo model to study infection and diseases caused by gastrointestinal microorganisms. Here, we describe the methods used to study bacterial colonization and histopathological changes in mouse models of Helicobacter pylori-related disease.

Video: Mouse Models Of Helicobacter Infection And Gastric Pathologies

Transurethral Induction of Mouse Urinary Tract Infection

Uropathogenic bacterial strains of interest are grown on agar. Generally, uropathogenic E. coli (UPEC) and other strains can be grown overnight on Luria-Bertani (LB) agar at 37&deg;C in ambient air. UPEC strains grow as yellowish-white translucent colonies on LB agar. Following confirmation of appropriate colony morphology, single colonies are then picked to be cultured in broth. LB broth can be used for most uropathogenic bacterial strains. Two serial, overnight LB broth cultures can be employed to enhance expression of type I pili, a well-defined virulence factor for uropathogenic bacteria. Broth cultures are diluted to the desired concentration in phosphate buffered saline (PBS). Eight to 12 week old female mice are placed under isoflurane anesthesia and transurethrally inoculated with bacteria using polyethylene tubing-covered 30 gauge syringes. Typical inocula, which must be empirically determined for each bacterial/mouse strain combination, are 106 to 108 cfu per mouse in 10 to 50 microliters of PBS. After the desired infection period (one day to several weeks), urine samples and the bladder and both kidneys are harvested. Each organ is minced, placed in PBS, and homogenized in a Blue Bullet homogenizer. Urine and tissue homogenates are serially diluted in PBS and cultured on appropriate agar. The following day, colony forming units are counted.

This video will demonstrate methods to transurethrally induce mouse urinary tract infections and quantify the extent of resulting infections.

Uropathogenic bacterial strains of interest are grown on agar. Generally, uropathogenic E. coli (UPEC) and other strains can be grown overnight on ...

Diagnosis of Ecto- and Endoparasites in Laboratory Rats and Mice

Internal and external parasites remain a significant concern in laboratory rodent facilities, and many research facilities harbor some parasitized animals. Before embarking on an examination of animals for parasites, two things should be considered. One: what use will be made of the information collected, and two: which test is the most appropriate. Knowing that animals are parasitized may be something that the facility accepts, but there is often a need to treat animals and then to determine the efficacy of treatment. Parasites may be detected in animals through various techniques, including samples taken from live or euthanized animals. Historically, the tests with the greatest diagnostic sensitivity required euthanasia of the animal, although PCR has allowed high-sensitivity testing for several types of parasite. This article demonstrates procedures for the detection of endo- and ectoparasites in mice and rats. The same procedures are applicable to other rodents, although the species of parasites found will differ.

This article describes various procedures for screening rats and mice to detect endo- or ectoparasitism. Several diagnostic assays will be demonstrated, both those suitable for use on live animals and those used after euthanasia of the animal. Photographs to aid in identification of rat and mouse parasites will be included.

Internal and external parasites remain a significant concern in laboratory rodent facilities, and many research facilities harbor some parasitized ...

Bioluminescence Imaging of NADPH Oxidase Activity in Different Animal Models

NADPH oxidase is a critical enzyme that mediates antibacterial and antifungal host defense. In addition to its role in antimicrobial host defense, NADPH oxidase has critical signaling functions that modulate the inflammatory response 1. Thus, the development of a method to measure in "real-time" the kinetics of NADPH oxidase-derived ROS generation is expected to be a valuable research tool to understand mechanisms relevant to host defense, inflammation, and injury.
Chronic granulomatous disease (CGD) is an inherited disorder of the NADPH oxidase characterized by severe infections and excessive inflammation. Activation of the phagocyte NADPH oxidase requires translocation of its cytosolic subunits (p47phox, p67phox, and p40phox) and Rac to a membrane-bound flavocytochrome (composed of a gp91phox and p22phox heterodimer). Loss of function mutations in any of these NADPH oxidase components result in CGD. Similar to patients with CGD, gp91phox -deficient mice and p47phox-deficient mice have defective phagocyte NADPH oxidase activity and impaired host defense 2, 13. In addition to phagocytes, which contain the NADPH oxidase components described above, a variety of other cell types express different isoforms of NADPH oxidase.
Here, we describe a method to quantify ROS production in living mice and to delineate the contribution of NADPH oxidase to ROS generation in models of inflammation and injury. This method is based on ROS reacting with L-012 (an analogue of luminol) to emit luminescence that is recorded by a charge-coupled device (CCD). In the original description of the L-012 probe, L-012-dependent chemiluminescence was completely abolished by superoxide dismutase, indicating that the main ROS detected in this reaction was superoxide anion 14. Subsequent studies have shown that L-012 can detect other free radicals, including reactive nitrogen species 15, 16. Kielland et al. 16 showed that topical application of phorbol myristate acetate, a potent activator of NADPH oxidase, led to NADPH oxidase-dependent ROS generation that could be detected in mice using the luminescent probe L-012. In this model, they showed that L-012-dependent luminescence was abolished in p47phox-deficient mice.
We compared ROS generation in wildtype mice and NADPH oxidase-deficient p47phox-/- mice 2 in the following three models: 1) intratracheal administration of zymosan, a pro-inflammatory fungal cell wall-derived product that can activate NADPH oxidase; 2) cecal ligation and puncture (CLP), a model of intra-abdominal sepsis with secondary acute lung inflammation and injury; and 3) oral carbon tetrachloride (CCl4), a model of ROS-dependent hepatic injury. These models were specifically selected to evaluate NADPH oxidase-dependent ROS generation in the context of non-infectious inflammation, polymicrobial sepsis, and toxin-induced organ injury, respectively. Comparing bioluminescence in wildtype mice to p47phox-/- mice enables us to delineate the specific contribution of ROS generated by p47phox-containing NADPH oxidase to the bioluminescent signal in these models.
Bioluminescence imaging results that demonstrated increased ROS levels in wildtype mice compared to p47phox-/- mice indicated that NADPH oxidase is the major source of ROS generation in response to inflammatory stimuli. This method provides a minimally invasive approach for "real-time" monitoring of ROS generation during inflammation in vivo.

NADPH oxidase is the major source of reactive oxygen species (ROS) in phagocytes. Because of the ephemeral nature of ROS, it is difficult to measure and monitor ROS levels in living animals. A minimally invasive method for serial quantification of ROS in living mice is described.

NADPH oxidase is a critical enzyme that mediates antibacterial and antifungal host defense. In addition to its role in antimicrobial host defense, NADPH ...

Intranasal Administration of Recombinant Influenza Vaccines in Chimeric Mouse Models to Study Mucosal Immunity

Vaccines are one of the greatest achievements of mankind, and have saved millions of lives over the last century. Paradoxically, little is known about the physiological mechanisms that mediate immune responses to vaccines perhaps due to the overall success of vaccination, which has reduced interest into the molecular and physiological mechanisms of vaccine immunity. However, several important human pathogens including influenza virus still pose a challenge for vaccination, and may benefit from immune-based strategies. 
Although influenza reverse genetics has been successfully applied to the generation of live-attenuated influenza vaccines (LAIVs), the addition of molecular tools in vaccine preparations such as tracer components to follow up the kinetics of vaccination in vivo, has not been addressed. In addition, the recent generation of mouse models that allow specific depletion of leukocytes during kinetic studies has opened a window of opportunity to understand the basic immune mechanisms underlying vaccine-elicited protection. Here, we describe how the combination of reverse genetics and chimeric mouse models may help to provide new insights into how vaccines work at physiological and molecular levels, using as example a recombinant, cold-adapted, live-attenuated influenza vaccine (LAIV). We utilized laboratory-generated LAIVs harboring cell tracers as well as competitive bone marrow chimeras (BMCs) to determine the early kinetics of vaccine immunity and the main physiological mechanisms responsible for the initiation of vaccine-specific adaptive immunity. In addition, we show how this technique may facilitate gene function studies in single animals during immune responses to vaccines. We propose that this technique can be applied to improve current prophylactic strategies against pathogens for which urgent medical countermeasures are needed, for example influenza, HIV, Plasmodium, and hemorrhagic fever viruses such as Ebola virus.

There is an overall lack of knowledge about how vaccines work. Here we propose the combined use of reverse genetics and bone marrow chimeric mice to gain insight into the early host immune responses to vaccines with a special focus on dendritic cells and T cell immunity.

Vaccines are one of the greatest achievements of mankind, and have saved millions of lives over the last century. Paradoxically, little is known about the ...

Organoids as Model for Infectious Diseases: Culture of Human and Murine Stomach Organoids and Microinjection of Helicobacter Pylori

Recently infection biologists have employed stem cell derived cultures to answer the need for new and better models to study host-pathogen interactions. Three cellular sources have been used: Embryonic stem cells (ESC), induced pluripotent stem cells (iPSC) or adult stem cells. Here, culture of mouse and human gastric organoids derived from adult stem cells is described and used for infection with the gastric pathogen Helicobacter pylori. Human gastric glands are isolated from resection material, seeded in a basement matrix and embedded in medium containing growth factors epidermal growth factor (EGF), R-spondin, Noggin, Wnt, fibroblast growth factor (FGF) 10, gastrin and transforming growth factor (TGF) beta inhibitor. In these conditions, gastric glands grow into 3-dimensional organoids containing 4 lineages of the stomach. The organoids expand indefinitely and can be frozen and thawed similarly as cell lines. For infection studies, bacteria are microinjected into the lumen of the organoids. Infected organoids are processed for imaging. The described methods can be adapted to other organoids and infections with other bacteria, viruses or parasites. This allows the study of infection-induced changes in primary cells.

Stem cell derived cultures harbor tremendous potential to model infectious diseases. Here, the culture of mouse and human gastric organoids derived from adult stem cells is described. The organoids are microinjected with the gastric pathogen Helicobacter pylori.

Recently infection biologists have employed stem cell derived cultures to answer the need for new and better models to study host-pathogen interactions. ...

Intra-tracheal Administration of Haemophilus influenzae in Mouse Models to Study Airway Inflammation

Here, we describe a detailed procedure to efficiently and directly deliver Haemophilus influenzae into the lower respiratory tracts of mice. We demonstrate the procedure for preparing H. influenzae inoculum, intra-tracheal instillation of H. influenzae into the lung, collection of broncho-alveolar lavage fluid (BALF), analysis of immune cells in the BALF, and RNA isolation for differential gene expression analysis. This procedure can be used to study the lung inflammatory response to any bacteria, virus or fungi. Direct tracheal instillation is mostly preferred over intranasal or aerosol inhalation procedures because it more efficiently delivers the bacterial inoculum into the lower respiratory tract with less ambiguity.

Intra-tracheal Administration of Haemophilus influenzae in Mouse Models to Study Airway Inflammation

We demonstrate the procedure for intra-tracheal inoculation of Haemophilus influenzae into the lower respiratory tracts of mice. This is a very useful tool to study signaling pathways that regulate airway inflammation in mouse models.

Here, we describe a detailed procedure to efficiently and directly deliver Haemophilus influenzae into the lower respiratory tracts of mice. We ...

One-step Negative Chromatographic Purification of Helicobacter pylori Neutrophil-activating Protein Overexpressed in Escherichia coli in Batch Mode

Helicobacter pylori neutrophil-activating protein (HP-NAP) is a major virulence factor of Helicobacter pylori (H. pylori). It plays a critical role in H. pylori-induced gastric inflammation by activating several innate leukocytes including neutrophils, monocytes, and mast cells. The immunogenic and immunomodulatory properties of HP-NAP make it a potential diagnostic and vaccine candidate for H. pylori and a new drug candidate for cancer therapy. In order to obtain substantial quantities of purified HP-NAP used for its clinical applications, an efficient method to purify this protein with high yield and purity needs to be established.
In this protocol, we have described a method for one-step negative chromatographic purification of recombinant HP-NAP overexpressed in Escherichia coli (E. coli) by using diethylaminoethyl (DEAE) ion-exchange resins (e.g., Sephadex) in batch mode. Recombinant HP-NAP constitutes nearly 70% of the total protein in E. coli and is almost fully recovered in the soluble fraction upon cell lysis at pH 9.0. Under the optimal condition at pH 8.0, the majority of HP-NAP is recovered in the unbound fraction while the endogenous proteins from E. coli are efficiently removed by the resin.
This purification method using negative mode batch chromatography with DEAE ion-exchange resins yields functional HP-NAP from E. coli in its native form with high yield and purity. The purified HP-NAP could be further utilized for the prevention, treatment, and prognosis of H. pylori-associated diseases as well as cancer therapy.

One-step Negative Chromatographic Purification of Helicobacter pylori Neutrophil-activating Protein Overexpressed in Escherichia coli in Batch Mode

A high yield method for one-step negative purification of recombinant Helicobacter pylori neutrophil-activating protein (HP-NAP) overexpressed in Escherichia coli by using diethylaminoethyl resins in batch mode is described. HP-NAP purified by this method is beneficial for the development of vaccines, drugs, or diagnostics for H. pylori-associated diseases.

Helicobacter pylori neutrophil-activating protein (HP-NAP) is a major virulence factor of Helicobacter pylori (H. pylori). It plays a critical role in H. ...

Influenza A Virus Studies in a Mouse Model of Infection

Influenza viruses cause over 500,000 deaths worldwide1 and are associated with an annual cost of 12 - 14 billion USD in the United States alone considering direct medical and hospitalization expenses and work absenteeism2. Animal models are crucial in Influenza A virus (IAV) studies to evaluate viral pathogenesis, host-pathogen interactions, immune responses, and the efficacy of current and/or novel vaccine approaches as well as antivirals. Mice are an advantageous small animal model because their immune system is evolutionarily similar to that found in humans, they are available from commercial vendors as genetically identical subjects, there are multiple strains that can be exploited to evaluate the genetic basis of infections, and they are relatively inexpensive and easy to manipulate. To recapitulate IAV infection in humans via the airways, mice are first anesthetized prior to intranasal inoculation with infectious IAVs under proper biosafety containment. After infection, the pathogenesis of IAVs is determined by monitoring daily the morbidity (body weight loss) and mortality (survival) rate. In addition, viral pathogenesis can also be evaluated by assessing virus replication in the upper (nasal mucosa) or lower (lungs) respiratory tract of infected mice. Humoral responses upon IAV infection can be rapidly evaluated by non-invasive bleeding and secondary antibody detection assays aimed at detecting the presence of total or neutralizing antibodies. Here, we describe the common methods used to infect mice intranasally (i.n) with IAV and evaluate pathogenesis, humoral immune responses and protection efficacy.

Influenza A viruses (IAVs) are important human respiratory pathogens. To understand the pathogenicity of IAVs and to perform preclinical testing of novel vaccine approaches, animal models mimicking human physiology are required. Here, we describe techniques to evaluate IAV pathogenesis, humoral responses and vaccine efficacy using a mouse model of infection.

Influenza viruses cause over 500,000 deaths worldwide1 and are associated with an annual cost of 12 - 14 billion USD in the United States alone ...

Mouse- and Human-derived Primary Gastric Epithelial Monolayer Culture for the Study of Regeneration

In vitro studies of gastric wound repair typically involves the use of gastric cancer cell lines in a scratch-wound assay of cellular proliferation and migration. One critical limitation of such assays, however, is their homogenous assortment of cellular types. Repair is a complex process which demands the interaction of several cell types. Therefore, to study a culture devoid of cellular subtypes, is a concern that must be overcome if we are to understand the repair process. The gastric organoid model may alleviate this issue whereby the heterogeneous collection of cell types closely reflects that of the gastric epithelium or other native tissues in vivo. Demonstrated here is a novel, in vitro scratch-wound assay derived from human or mouse 3-dimensional organoids which can then be transferred to a gastric epithelial monolayer as either intact organoids or as a single cell suspension of dissociated organoids. The goal of the protocol is to establish organoid-derived gastric epithelial monolayers that can be used in a novel scratch-wound assay system to study gastric regeneration.

Here we describe a protocol for establishing and culturing human- and mouse-derived 3-dimensional (3D) gastric organoids, and the method for the transfer of 3D organoids to a 2-dimensional monolayer. The use of the gastric epithelial monolayer as a novel scratch-wound assay for regeneration studies is also described.

In vitro studies of gastric wound repair typically involves the use of gastric cancer cell lines in a scratch-wound assay of cellular proliferation and ...

Intracranial Subarachnoidal Route of Infection for Investigating Roles of Streptococcus suis Biofilms in Meningitis in a Mouse Infection Model

Streptococcus suis is not only a major bacterial pathogen of pigs worldwide but also an emerging zoonotic agent. In humans and pigs, meningitis is a major manifestation of S. suis infections. A suitable infection model is an essential tool to understand the mechanisms of diseases caused by pathogens. Several routes of infection in mice have been developed to study the pathogenesis of S. suis infection. However, the intraperitoneal, intranasal, and intravenous routes of infection are not suitable for studying the roles of S. suis surface components in meningitis directly in the brain, such as the extracellular matrix from biofilms. Although intracisternal inoculation has been used for S. suis infection, the precise injection site has not been described. Here, the intracranial subarachnoidal route of infection was described in a mouse model to investigate the roles of biofilms in S. suis meningitis. S. suis planktonic cells or biofilm state cells were directly injected into the subarachnoid space of mice through the injection site located 3.5 mm rostral from the bregma. Histopathological analysis and increased mRNA expression of TLR2 and cytokines of the brain tissue from mice injected with biofilm state cells clearly indicated that S. suis biofilm plays definitive roles in S. suis meningitis. This route of infection has obvious advantages over other routes of infection, allowing the study of the host-bacterium interaction. Furthermore, it permits the effect of bacterial components on host immune responses directly in the brain to be assessed, and mimics bacterial entrance into the central nervous system. This route of infection can be extended for investigating the mechanisms of meningitis caused by other bacteria. In addition, it can also be used to test the efficacy of drugs against bacterial meningitis.

Intracranial Subarachnoidal Route of Infection for Investigating Roles of Streptococcus suis Biofilms in Meningitis in a Mouse Infection Model

Here, we describe the intracranial subarachnoidal route of infection in mice to study roles of biofilms in Streptococcus suis meningitis. This infection model is also suitable for studying the pathogenesis of other bacterial meningitis and the efficacy of new drugs against bacterial meningitis.

Streptococcus suis is not only a major bacterial pathogen of pigs worldwide but also an emerging zoonotic agent. In humans and pigs, meningitis is a major ...