Web Resources; Summary Tables, references (23 p PDF)

Brayton Web Resources + PhenoJargon 

Find your mice + health surveillance info at 

1. Charles River (Crl) http://www.criver.com/en‐ 

US/ProdServ/ByType/ResModOver/ResMod/Pages/ResModels.aspx 

2. Harlan (Hsd, Ola) http://www.harlan.com/products_and_services/research_models_and_services 

3. JAX (J) http://jaxmice.jax.org/query/f?p=205:1:6402492945594701 

4. NCI Frederick (N, Cr) 

http://ncifrederick.cancer.gov/Programs/Science/App/StrainInformation/Default.aspx 

5. Taconic (Tac) http://www.taconic.com/wmspage.cfm?parm1=579 

Find GEM at 

1. Deltagen and Lexicon Knockout Mice and Phenotypic Data 

http://www.nih.gov/science/models/mouse/deltagenlexicon/list.html 

2. IKMC International Knockout Mouse Consortium http://knockoutmouse.org 

3. Jax IMSR (Induced Mutant Strain Resource) http://www.findmice.org/ 

4. KOMP Knockout mouse projecthttp://www.knockoutmouse.org/ 

5. MMRRC http://www.mmrrc.org/ e.g. Apoa 

International Knockout & Phenotyping resources 

1. IKMC International Knockout Mouse Consortium http://knockoutmouse.org 

2. IMPC http://www.mousephenotype.org/ International mouse phenotype consortium 

3. IMPRESS http://www.mousephenotype.org/impress International Mouse Phenotyping Resource of 

Standardised Screens – link to Protocols 

EuroPhenome http://www.europhenome.org/ for phenotype data 

Cbrayton@jhmi.edu Rev July 2013 Page 1 of 9


More Resources on line 

1. Brain Atlas Projects 

High Resolution Mouse Brain Atlas http://www.hms.harvard.edu/research/brain/intro.html 

MBL (Mouse Brain Library) http://www.mbl.org/ 

2. Complex Trait Consortium http://www.complextrait.org/ Collaborative Cross information 

3. Edinburgh Mouse Atlas Project (EMAP, EMAGE) http://www.emouseatlas.org/emap/home.html 

4. Jax online resources 

A Color Atlas of Neoplastic and Non Neoplastic Lesions in Aging Mice Frith & Ward 1988 

http://www.informatics.jax.org/frithbook/ 

Anatomy of the laboratory mouse – Cook http://www.informatics.jax.org/cookbook/ 

THE COAT COLOURS OF MICE (Silvers 1979) http://www.informatics.jax.org/wksilvers/ 

IMSR – Find Mice ‐‐ http://www.findmice.org/index.jsp 

Jax – Es Cell list ftp://ftp.informatics.jax.org/pub/reports/ES_CellLine.rpt 

MGI http://www.informatics.jax.org/ 

Michael Festings list & description of mouse strains 

http://www.informatics.jax.org/external/festing/rat/STRAINS.shtml 

Nomenclature home page http://phenome.jax.org/ LAB CODE 

MOUSE GENETICS by Lee Silver (Silver 1995) http://www.informatics.jax.org/silver/ 

MPD http://phenome.jax.org/ (prioritized strains, protocols, data, more) 

MTB (Mouse Tumor Biology) Database http://tumor.informatics.jax.org/mtbwi/index.do 

Tumor frequency grid at http://tumor.informatics.jax.org/mtbwi/tumorFrequencyGrid.do 

Origins of inbred Mice – MORSE http://www.informatics.jax.org/morsebook/ 

WELFARE AND REPORTING GUIDANCE 

1. ARRIVE GUIDELINES (Animals in Research: Reporting In Vivo Experiments) 

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000412 

Kilkenny, C., W. J. Browne, et al. (2010). "Improving bioscience research reporting: the ARRIVE guidelines for 

reporting animal research." PLoS Biol 8(6): e1000412. 

2. Workman, P., E. O. Aboagye, et al. (2010). "Guidelines for the welfare and use of animals in cancer 

research." Br J Cancer 102(11): 1555‐1577. 

http://www.nature.com/bjc/journal/v102/n11/full/6605642a.html 

3. 2011 (US) National Academy of Sciences (NAS) NAS Guidance for reporting animal research 

http://dels.nas.edu/Report/Guidance‐Description‐Animal/13241 

PATHOLOGY NOMENCLATURE – Terminology & Diagnostic Criteria 

1. MMHCC mouse models of human cancer consortium http://emice.nci.nih.gov/mouse_models/ 

consensus papers 

2. Pathbase European Mutant Mouse Pathology Database http://www.pathbase.net/ 

3. RENI / INHAND http://www.toxpath.org/nomen/index.htm 

Toxpath RENI http://www.eurotoxpath.org/nomenclature/index.php trimming guidelines too 



MORE PATHOLOGY RESOURCES 

1. A Color Atlas of Neoplastic and Non Neoplastic Lesions in Aging Mice Frith & Ward 1988 

http://www.informatics.jax.org/frithbook/ + Print on Demand From http://store.cldavis.org/ 

2. Aperio hosted digital slides corresponding to Treuting P, Dintzis S. Comparative Anatomy and Histology: A 

Mouse and Human Atlas London: Elsevier (Academic Press); 2012. http://repository.aperio.com/c/201/2/ 

3. Cancer Images Database http://emice.nci.nih.gov/caimage 

4. Deltagen Mouse Histology Atlas 

5. JOVE (Charles River Laboratories) 

http://www.criver.com/en‐US/NewsEvents/WhatsNew/Pages/Gross_Examination_JoVE_Video.aspx 

http://www.criver.com/en‐US/NewsEvents/WhatsNew/Pages/Ecto_Endoparasites_JoVE_video.aspx 

6. MTB (Mouse Tumor Biology) Database http://tumor.informatics.jax.org/mtbwi/index.do 

Tumor frequency grid at http://tumor.informatics.jax.org/mtbwi/tumorFrequencyGrid.do 

7. NIAID Veterinary Pathology 

http://www.niaid.nih.gov/labsandresources/labs/aboutlabs/cmb/infectiousdiseasepathogenesissection/vet 

pathology/Pages/VeterinaryPathology.aspx 

8. NIEHS LEP Clinical Pathology 

9. NTP study results for control Data http://ntp.niehs.nih.gov/ 

10. Skinbase mutant mouse skin pathology http://eulep.pdn.cam.ac.uk/~skinbase/index.php 

11. UC Davis MMHCC Image Archive 

12. UC Davis Visible Mouse 

13. UC Davis Virtual mouse Necropsy 

14. UC Davis Genomic Pathology Course Online http://ctrgenpath.net/main 



US based GEM & Phenotyping initiatives (since ~ 1998) 

MMRRC (Mutant Mouse regional resource centers) originally funded ~ 1998 by NIH NCRR to archive and 

distribute (not characterize) genetically engineered mouse stocks and ES cell lines ‐ ‘serving the world‐wide 

genetics and biomedical research community for the benefit of human health’ http://www.mmrrc.org/ 

MMRRC at The Jackson Laboratory mmrrc@jax.org www.jax.org/mmrrc/ 

MMRRC at Univ. of California, Davis mmrrc@ucdavis.edu mmrrc.compmed.ucdavis.edu 

MMRRC at Univ. of Missouri mmrrc@missouri.edu www.mmrrc.missouri.edu 

MMRRC at Univ. of North Carolina, Chapel Hill mmrrc@med.unc.edu 

MMHCC mouse models of human cancer consortium repository is based at NCI. 25 MMHCC Principal 

Investigators & research groups ivolved more than fifty institutions in the U.S. and abroad. 

http://emice.nci.nih.gov/ NIH funded ~2000‐2012 

Cancer Images Database http://emice.nci.nih.gov/caimage 

KOMP Knock Out Mouse Project Repository is a ‘trans‐NIH initiative to generate, together with the other 

members of the International Knockout Mouse Consortium (IKMC), a public resource of mouse embryonic stem 

(ES) cells containing a null mutation in every gene in the mouse genome ~2010‐2020 

Thus NIH participates in IKMC thru KOMP http://www.knockoutmouse.org/aboutkomp#komp‐network and 

began participation in high throughput IMPC phenotyping c2012 through KOMP2. 

http://commonfund.nih.gov/KOMP2/ 

KOMP 

KOMP production Centers KOMP Data Coordination center KOMP repository 

1. CSD (CHORI, WTSI, UCDavis) 

2. Regeneron 

Jackson Laboratory 

UCDavis, CHORI 

http://www.komp.org/ 

KOMP2 

Knockout Mouse Phenotyping 

(U54) RFA‐RM‐10‐011: 

1. UCD‐TCP‐CHORI consortium 

2. Jackson Laboratory 

3. BASH Consortium (Baylor 

Sanger Harwell) 

Knockout Mouse Phenotyping 

Project Database 

(U54) RFA‐RM‐10‐012: 

EMBL 

Knockout Mouse Production and 

Cryopreservation 

(U42) RFA‐RM‐10‐013: 

1. DTC consortium 

2. Jackson Laboratory 

3. BASH Consortium 


EU and international GEM & Phenotyping initiatives (since ~ 2002) 


EUMORPHIA was the initial EU initiative (2002‐2006) that created EMPRESS EUMODIC EUROPHENOME 

EUMODICs (European Mouse Disease Clinics) used EMPRESS (European Mouse Phenotyping Resource of 

Standardised Screens) Pipelines developed in the EUMORPHIA initiatives, but now (2013) use IMPC Pipelines – 

details at IMPRESS (International Mouse Phenotyping Resource of Standardised Screens). 

GEM & phenotype resources have proved to be highly bioinformatics dependent and driven, resulting in: 

CASIMIR (Coordination and Sustainability of International Mouse Informatics Resources) . Phenotype data from 

IMREPSS (formerly EMPRESS) pipelines feed into the EUroPhenome Database (also into MPD), using a 

standardized vocabulary /ontology 

MA = Mouse Anatomy ontology (the Anatomical Dictionary for the Adult Mouse, 

http://www.informatics.jax.org/searches/anatdict_form.shtml )., annotates tissue/entity) , 

MP = Mammalian Phenotype ontology (http://www.informatics.jax.org/searches/MP_form.shtml 

(annotates normal/abnormal, present/absent, enlarged/small) 

MPATH annotates pathology process terms (e.g. necrosis), and diagnostic terms (e.g. carcinoma) 

PATO Phenotype and Trait Ontology (PATO) http://code.google.com/p/pato annotates 

distribution/size/shape/consistency/color/quantity) 

(Pathbase http://www.pathbase.net/ ) 

EUCOMM is the European Conditional Mouse Mutagenesis Program which aims to generate archive & 

distribute up to 13.000 conditional mutations across the mouse genome in C57BL/6N ES cells 

Mutant ES cells & targeting vectors are distributed by European Mouse Mutant Cell Repository (EuMMCR) 

Mutant mice distributed by the European Mouse Mutant Archive (EMMA) 

‘coordinates’ with KOMP (&TIGM) in US & NorCoMM in Canada 

Infrafrontier is an EU initiative aiming to organize infrastructure networks for large‐scale phenotyping and 

archiving of mouse models serving the European genetics and biomedical research community. Infrafrontier 

builds on existing infrastructures from EMMA and EUMODIC to form a coalition with funding agencies to 

develop a common European infrastructure, Using 15 European laboratories. 

International Knockout Mouse Consortium (IKMC) http://www.knockoutmouse.org/ aims to mutate all 

protein‐coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse 

embryonic stem (ES) cells. IKMC includes the following programs: 

1. Knockout Mouse Project (KOMP) (USA) (CSD, Regeneron; Jax) 

2. European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) 

3. North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) 

4. Texas A&M Institute for Genomic Medicine (TIGM) (USA) 

International Mouse Phenotyping Consortium (IMPC) http://www.mousephenotype.org/ aims to provide 

systematic genome‐wide phenotyping of knockout mice generated from IKMC. As of 2013 there are 13 

participating sites in 10 countries 

Europe/UK North America AustralAsia 

1. DE, GMC Germany 

2. FR, ICS Strasbourg 

3. IT, CNR EMBL Monterotondo 

4. UK, MRC Harwell 

5. UK ,WTSI Sanger 

6. CA, TCP Toronto 

7. US, BASH Baylor, + Sanger, Harwell 

8. US, DTC ‐ UCDavis, CHORI, Charles 

River Laboratories + TCP 

9. US, Jackson Laboratories 

10. AU, APN 

11. CH, MARC 

12. JA, RIKEN 

13. KR, KMPC 



Jargonomics for Mouse Genomics ‐ Glossary for Mousers 

Location 

Acronym, term or part of Definition, URL, comments 

speech 

APN AU Australian Phenomics Network http://www.australianphenomics.org.au/ 

BASH consortium INT 1 BaSH consortium, Baylor College of Medicine (BCM), Houston, Texas, the 

Wellcome Trust Sanger Institute Mouse Genetics Programme, Hinxton, 

United Kingdom, and the Medical Research Council Harwell, (Mammalian 

Genetics Unit and Mary Lyon Centre), United Kingdom, KOMP2 consortium 

for mouse production and cryopreservation and phenotyping 

http://commonfund.nih.gov/pdf/justice.pdf 

CASIMIR 

EU EC 

Coordination and Sustainability of International Mouse Informatics 

Resources http://www.casimir.org.uk/ 

CARD 

JA 

Center for Animal Resources and Development 

http://card.medic.kumamoto‐u.ac.jp/card/english/index.html 

CHORI US Children's Hospital Oakland Research Institute 

CIBERDEM ES 

Centro de Investigación Biomédica en Red de Diabetes y Enfermedades 

Metabólicas Asociadas 

CMC CA Canadian Mouse Consortium http://www.mousecanada.ca/ 

CMHD 

CA 

Centre for Modeling Human Disease at Toronto Centre for Phenogenomics 

(TCP) http://www.cmhd.ca/ 

CMMR CA Canadian Mutant Mouse Repository http://www.cmmr.ca/ 

Collaborative cross INT 

Panel of r multiparental recombinant inbred (RI) mouse lines derived from 

8 genetically diverse inbred strains—A/J, C57BL/6J, 129S1/SvlmJ, 

NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/ Ph, and WSB/EiJ aiming to mode 

aiming to model complexity of the human genome 

http://compgen.unc.edu/wp/?page_id=99 

Collaborative team (KOMP awardee) at Children's Hospital Oakland 

CSD 

US Research Institute (CHORI), the Wellcome Trust Sanger Institute (WTSI) and 

UK the University of California at Davis (UCD) School of Veterinary Medicine , 

more at http://www.knockoutmouse.org/about 

DTC consortium INT 

UC Davis, Toronto Centre for Phenogenomics (TCP), and Charles River 

Laboratories KOMP2 consortium for mouse production and 

cryopreservation http://www.komp.org/ 

Dysmorphology noun 

First Pub med Citation 1966, D.W. Smith 102 author’s definition: The study of, 

or general subject of, abnormal development of tissue form; since used in 

reference to human (and more recently non human) teratology and 

malformations, abnormalities 

EMBL 

EU 

http://www.embl.it/index.php European Molecular Biology Laboratory – 

Grenoble Hamburg Heidelberg Hinxton Monterotondo 

EMBL Monterotondo is north of Rome, shared with Italian national research 

groups (IBC‐CNR) and the headquarters of the European Mouse Mutant 

Archive (EMMA). 

EMMA 

EU EC 

European Mouse Mutant Archive http://www.emmanet.org/ 

See EMBL Monterotondo 

1 INT – international 



Acronym, term 

Location 

or part of Definition, URL, comments 

speech 

EMPRESS 

EU EC 

European Mouse Phenotyping Resource of Standardised Screens database 

of SOPs, from the EUMORPHIA consortium, ‐ NOW IMPRESS 

http://www.empress.har.mrc.ac.uk/ 

EUCOMM EU EC 

European Conditional Mouse Mutagenesis project which (with KOMP & 

NorCOMM) aims to produce conditional mutations in 20,000 mouse genes, 

in C57BL/6N ES cells EUMODIC will use these ES cells in the null 

configuration http://www.eucomm.org/ consortium of 9 participants in 4 EU 

countries 

EUMODIC EU EC 

http://www.eumodic.org/ European MOuse DIsease Clinics assess mouse 

phenotypes using EMPReSS SOPs. Consortium of 18 laboratories in Europe. 

Eumorphia EU EC 

The initial EU functional genomics effort (2002‐2006) from which derive 

EMPRESS EUMODIC EUROPHENOME 

Europhenome EU EC 

http://www.europhenome.org/ database to hold phenome data obtained 

from EMPReSS now IMPRESS 

FIMRE INT Federation of International Mouse Researchers http://www.fimre.org/ 

GEM, GMM, GMO 

Genetically Engineered Mice; Genetically Modified Mice; Genetically 

Modified Organisms 

GO 

Gene Ontology http://www.geneontology.org 

IEG 

FRG 

Institute for Experimental Genetics at Helmholz Munich – download 

MausDB LMIMS from http://jupiter.helmholtz‐muenchen.de/ 

IGTC INT International Gene Trap Consortium http://www.genetrap.org/ 

IKMC 

INT 

International Knockout Mouse Consortium (IKMC) aims to mutate all 

protein‐coding genes in mouse using gene trapping & targeting in C57BL/6 

ES cells: EUCoMM KOMP NorCoMM TIGM http://www.knockoutmouse.org/ 

IMGS / IMGC INT 

International Mammalian (formerly Mouse) Genome Society – holds IMGC 

meetings; publishes Mammalian Genome, publishes mouse and gene 

nomenclature recommendations http://imgs.org/ 

IMPC INT International mouse phenotype consortium 

http://www.mousephenotype.org/ I 

IMPRESS 

INT 

International Mouse Phenotyping Resource of Standardised Screens 

http://www.mousephenotype.org/impress link to Protocols 

INFRAFRONTIER EU UK CA 

Infrafrontier Project aims to establish research infrastructure for systemic 

phenotyping, archiving and distribution of mouse models, with partners in 

12 European countries and Canada http://www.infrafrontier.eu/ 

INHAND 

INT 

International Harmonization of Nomenclature and Diagnostic Criteria for 

Lesions in Rats and Mice (INHAND) project 

(http://www.toxpath.org/nomen/) 

InterPhenome INT 

Integration of Mouse Phenome Data Resources / Mouse Phenotype 

Database Integration Consortium http://interphenome.org/ 

IPGTT 

Intraperitoneal glucose tolerance test 

JMC JA Japan Mouse Clinic – see RIKEN 



Acronym, term 

Location 


speech 

KOMP 

US NIH 

Knock Out Mouse Project ‐ trans‐NIH initiative (2006‐2011) to generate, with 

the other members of the IKMC, a public resource of mouse embryonic stem 

(ES) cells containing a null mutation in every gene in the mouse genome. 

http://public.nhlbi.nih.gov/GeneticsGenomics/home/komp.aspx 

http://www.genome.gov/17515708 

http://www.komp.org/ KOMP repository at UCD 

KOMP2 

US NIH 

2010 NIH Common Fund program that aims to build on KOMP knockout 

mouse resource by initiatives to characterize (phenotype) IKMC mutant lines 

http://grants.nih.gov/grants/guide/rfa‐files/RFA‐RM‐10‐011.html 

http://commonfund.nih.gov/KOMP2/ 

MARC 

CN 

Model Animal Research Center of Nanjing University, China 

Houses China’s National Resource for Mutant Mice (NRCMM)/ 

http://www.en.nicemice.cn/ 

MMHCC 

US NIH 

Mouse Models of human Cancer consortium, an initiative of NCI, more at 

http://emice.nci.nih.gov/ 

MMRRC 

US NIH 

mutant mouse regional research resource centres supported by NCRR NIH 

http://www.mmrrc.org/ 

MGI 

US JAX NIH 

Mouse Genome Informatics – LOOK UP GENES NOMENCLATURE 

HOMOLOGIES ALLELES REFRENCES http://www.informatics.jax.org/ 

MGP UK See WTSI MGP Wellcome Trust Sanger Institute Mouse Genetics Programme 

MODIS 

US 

Mouse Disease Information System (MoDIS) database tools for recording 

mouse pathology diagnoses/phenotypes 

http://research.jax.org/faculty/sundberg/index.html 

MRB EU GR Mouse Resource Browser http://bioit.fleming.gr/mrb/ 

MPD US JAX NIH MOUSE PHENOME DATABASE 2 http://phenome.jax.org/ 

MUGEN MMDB EU GR 

MUGEN Mouse Database (MMdb) of murine models of immune processes 

and immunological diseases, developed by MUGEN consortium of 21 

institutes and universities http://bioit.fleming.gr/mugen/mde.jsp 

Muromics Noun The science and study of mice; first pub med citation 2002 S.W. Barthold 33 

MTB 

US JAX NIH 

Mouse Tumor Biology Database 

http://www.informatics.jax.org/mtbwi/index.do 

MMPC US NIH Mouse Metabolic Phenotyping Consortium http://www.mmpc.org/ 

NorIMM EU Nordic Infrastructure for Mouse Models 

NFGN FRG Nationales Genomforschungsnetz Deutschland 

Pathbase UK European mutant mouse pathology database http://eulep.pdn.cam.ac.uk/ 

PATO 

PRIME 

Phenobabelomics 

Phenogenomics 

EU EC 

Noun 

Noun 

Phenotype and Trait Ontology http://code.google.com/p/pato 

Priorities for Mouse Functional Genomic Research across Europe. 

http://www.prime‐eu.org/ 

First pub med citation 2008, J Hancock and A‐M. Mallon 66 in reference to 

phenotyping terms and the challenge for bioinformatics 

Science or study of the relationships between phenome and genome of an 

organism; frst pub med citation, 2001 J Rossant and C McKerlie 104 



Acronym, term 

Location 


speech 

Phenome 

Noun 

Originally: the sum total of the constituents of a cell exclusive of its genetic 

material (rare). Now more widely: the phenotypic counterpart or expression 

of the genome; the complete set of phenotypic characteristics of an 

organism. From Oxford English dictionary at http://www.oed.com/ accessed 

8/23/2010 Attributed to 1964 Soulé Systematic Zool. 113 114/2 … phenome 

(the phenotypic analog of the genome) 

Phenotype Noun 

The sum total of the observable characteristics of an individual, regarded as 

the consequence of the interaction of the individual's genotype with the 

environment; a variety of an organism distinguished by observable 

characteristics rather than underlying genetic features. From Oxford English 

dictionary at http://www.oed.com/ accessed 8/23/2010. Attributed to W. 

Johannsen c 1910. 

Phenotype Verb 

To allocate to a phenotype. From Oxford English dictionary at 

http://www.oed.com/ accessed 8/23/2010. Attributed to W. Johannsen c 

1910. 

RENI 

Registry Nomenclature Information System 

http://www.goreni.org/ 

RIKEN (RBRC) JA 

Riken Bioresource Center http://www.brc.riken.jp/lab/animal/en/ 

Houses Japan Mouse Clinic JMC 

http://www.brc.riken.jp/lab/jmc/mouse_clinic/en/ 

SHIRPA 

UK 

Qualitative morphological, clinical behavioral screening method for 

abnormal phenotypes in the mouse – Acronym for 

SmithKline Beecham Pharmaceuticals 

Harwell, MRC Mouse Genome Centre and Mammalian Genetics Unit 

Imperial College School of Medicine at St Mary's 

Royal London Hospital, St Bartholomew's and the Royal London School of 

Medicine 

Phenotype 

Assessment 

SweIMP EU Swedish Infrastructure for Mouse Phenotyping 

TIGM US Texas Institute for Genomic Medicine http://tigm.org/ participant in IKMC 

UCD‐TCP‐CHORI 

consortium 

WTSI MGP 

UK 

Mouse Biology Program at U. California Davis (UCD), the Toronto Center for 

Phenogenomics (TCP), and Children's Hospital of Oakland Research 

Institution (CHORI). A KOMP2 phenotyping consortium 

http://www.komp.org/ 

Wellcome Trust Sanger Institute Mouse Genetics Program 

http://www.sanger.ac.uk/mouseportal/ 


Mouse Diseases Common Conditions (phenotypes) and Infectious Diseases TABLES only 

TABLES ‐ Table number corresponds to section in TEXT 

Table Ia Common conditions by age Page 2 

Table Ib Common conditions or phenotypes by strain 

Table Ic Some immune relevant genotypes (in common strains) 

Table Id Immunodeficient mice: Properties of important genes & mutations Page 5 

Table Ie Immunodeficient mice: Effects of Background strain on phenotypes 

Table If Immunodeficient mice: Primary T cell deficient options 

Table Ig Immunodeficient mice: MORE nude options 

Table Ih Immunodeficient mice: MORE scid options 

Table Ii Immunodeficient mice: MORE options 

Table II Infectious Agents by site/system Page 9 

Table IV Viruses – Test methods, prevalence 

Table V Bacteria – Test methods, prevalence 

Table VI Eukaryotes – Test methods, prevalence 

Table VIa Protozoa by site 

Table VIb Fur mite comparison 

Table VIc Pinworm comparison 

WEB Resources Page 14 

References 

I 

II 

III 

IV 

V 

VI 

TEXT SECTIONS see also [1] 

Common disease conditions – Spontaneous or Non infectious 

Common diseases – Infectious by system 

Infectious agents, diagnostic methods 

Infectious agents, Viruses 

1. Comments by agent (alphabetical order) 

Infectious agents, Bacteria 

1. Comments by agent (alphabetical order) 

Infectious agents, Eukaryotes 

1. Fungi – inc Protista – Comments by agent (alphabetical order) 

2. Protozoa – Comments by agent (alphabetical order) 

Metazoa ‐ Comments by agent (alphabetical order) 

a) Arthropods Comments by agent (alphabetical order) 

b) Helminths Comments by agent (alphabetical order) 

cbrayton@jhmi.edu 2013 Page 1 of 14


Table Ia: Non infectious CLINICAL conditions in mice at different ages [2] [3] [4] 

Life threatening 

Usually not life 

threatening 

Usually young mice 

Hydrocephalus 

Malocclusion 

Microphthalmia 

Usually adult, 

various ages 

Dermatitis and wounds 

Abdominal enlargement (e.g. 

hydrometra, 

hydronephrosis, urinary 

obstruction, ascites). 

‘Neurologic’ signs (e.g. paresisparalysis, 

seizures, vestibular 

signs) 

Alopecia due to barbering 

Blind / deaf 

Usually older mice 

Neoplasia (tumors) 

Wasting due to chronic 

progressive 

conditions (e.g. 

amyloidosis, 

nephropathy, 

neoplasia) 

Obesity 

Table Ib. Non infectious conditions and neoplasms in common mouse strains [2] [3] [4] [5] 

129 strains Acallosity‐hypocallosity; acidophilic macrophage pneumonia, hyalinosis 

Lung tumors (testicular teratomas) 

A/J 

Congenital anomalies; amyloidosis; muscular dystrophy 

Lung tumors, rhabdomyosarcoma [6] 

AKR 

Thymic lymphoma 

BALB/c 

BALB/cBy 

C3H 

C57BL/6 

DBA 

FVB/N 

NOD 

SJL/J 

Swiss 

Not inbred 

BLIND rd1 

DEAF 

Acallosity‐hypocallosity; conspecific (male) aggression; cardiac calcinosis; cardiac thrombi; 

vaginal septa 

Lung tumors; Harderian gland tumors; myoepithelioma; rhabdomyosarcoma, 

induced plasmacytoma 

Blind (rd1/rd1); cardiac calcinosis, soft tissue mineralization 

Mammary tumors in females; liver tumors in males 

Hydrocephalus; microphthalmia; ulcerative dermatitis; amyloidosis; acidophilic macrophage 

pneumonia, hyalinosis 

Lymphoma; histiocytic sarcoma 

dba, Cardiac calcinosis, soft tissue mineralization; seizures; deafness; glaucoma 

Blind (rd1/rd1); seizures; mammary hyperplasia 

Lung tumors 

Diabetes; immune alterations 

Lymphoma 

Blind (rd1/rd1); conspecific (male) aggression; muscular dystrophy 

Radioresistant 

Lymphoma 

Strain stock variations in: blind due to rd1/rd1; acidophilic macrophage pneumonia; 

amyloidosis; nephropathy; urinary syndrome 

Lymphomas; lung tumors; liver tumors; skin tumors 

C3H, CBA, FVB, SJL, SWR etc 

C57BL/6, BALB, DBA, etc 

Re tumor frequency – see also http://tumor.informatics.jax.org/mtbwi/index.do 



Table Ic: Some immune relevant genotype variations (in common strains) [7] 

Gene Gene /Locus name Chrom Allele Allele name Mutation Strains 

symbol 

Symbol 

H2 

Major 

17 a H2a * A (A/HeJ, A/J, AWySnJ) 

Histocompatibility 

Complex (MHC) H2 

haplotypes 

H2 MHC H2 haplotype 17 b H2b C57BL/6, C57BL/10 

129 ‐ all? 

H2 MHC H2 haplotype 17 b2 H2b2 NZB 

H2 MHC H2 haplotype 17 d H2d DBA/2 

BALB/c, BALB/cBy, 

H2 MHC H2 haplotype 17 g7 H2g7 NOD 

H2 MHC H2 haplotype 17 k H2k AKR, 

C3H, CBA, MRL 

H2 MHC H2 haplotype 17 P H2p P 

H2 MHC H2 haplotype 17 q H2q DBA/1, FVB/N, Nu/J 

H2 MHC H2 haplotype 17 r H2r RIII 

H2 MHC H2 haplotype 17 s, s2 H2s,s2 SJL, SJL/J 

H2 MHC H2 haplotype 17 z H2z NZW, NZN, NZO 

Hc 

Hemolytic 

complement (c5) 

2 0 

(Hc 0 ) 

Tlr4 Toll like receptor 4 4 Lps‐d 

(Tlr4 Lsp‐d ) 

Rmcf MCF sensitive 5 s 

(Rmcf s ) 

Rmcf MCF sensitive 5 R 

(Rmcf r ) 

Ceacam1 carcinoembryonic 7 Hc2‐r 

antigen‐related cell 

(Ceacam1 

adhesion molecule 

Hv2‐r ) 

1 

Klra1 

(Ly49a) 

killer cell lectin‐like 

receptor, subfamily 

A1 (aka Ly49A) 

6 Klra1 

C57BL/6 

etc 

Klra2 Aka Ly49B 6 Klra2 

C57BL/6 

etc 

Klra3 Aka Ly49C 6 Klra3 

C57BL/6 

Klra5,6,9,1 

5,17,19, 

20,21,22 

Aka Ly49E,F,I,O, 

Q,S,T,V 

0 = deficient 2 base "TA" 

deletion 

d = defective 

lipopolysaccharide 

response 

s = sensitive to mcf 

forming leukemia viruses 

C to A 

substitution 

in 3 rd exon 

recessive 

A/HeJ, AKR/J, DBA/2J, 

FVB/N; NZB/B1NJ, 

SWR/J, B10.D2/SnJ 

C3H/HeJ 

AKR/J, C57BL/6, 

BALB/c, CBA/J, NFS, 

NZB, 129/J. 

DBA/1, DBA/2, and 

CBA/Ca 

SJL/J 

Resistant to mcf forming 

leukemia viruses 

Dominant 

allele 

r = resistance to Mouse Deletion 

hepatitis virus (MHV‐4) 23 aa 

substitution 

recessive 

Inhibit killing activity [8] Various B6, NOD, 129, BALB/c 

Inhibit killing activity [8] Various B6, 129, BALB/c 

Inhibit killing activity [8] Various B6, NOD, BALB/c 

etc 

6 Inhibit killing activity [8] Various Various 

* See also http://jaxmice.jax.org/literature/catalog/mhc_h2_haplotypes.pdf 

http://www.imgt.org/IMGTrepertoireMHC/Polymorphism/haplotypes/mouse/MHC/Mu_haplotypes.html 



Gene 

symbol 

Klra4,8, 

13,14,16, 

18,21,23, 

25,28,30 

Mx1 

Mx1 

Mx1 

Tcrb‐V8 

Tcrb‐V8 

Nlrp1a 

Nlrp1a 

Slc11a1 

(Nramp1) 

Slc11a1 

(Nramp1) 

Gene /Locus name Chrom Allele 

Symbol 

Allele name Mutation Strains 

Aka Ly4D,H,M, 6 Activate NK etc [8] Various Various 

N,P,R,U,W 

myxovirus 

(influenza virus) 

resistance 1 

myxovirus 

resistance 1 

myxovirus 

resistance 1 

T cell receptor beta, 

variable 8 

T cell receptor beta, 

variable 8 

NOD‐like receptor 

(NLR) 1a 

NOD‐like receptor 

(NLRs) 1a 

solute carrier family 

11 member 1; host 

resistance 

solute carrier family 

11 member 1; 

pathogen 

susceptibility 

16 Mx1 r r = resistance to 

Myxovirus (etc 

intranuclear virus ) [9] 

Wild type A2G, SL/NiA, CAST/Ei 

16 Mx1 s1 s1 = susceptibility 1 [10] deletion Most common strains 

C57BL/6J, C3H/HeJ, 

BALB/cJ,etc 

16 Mx1 s2 s2 = susceptibility 2 [10] Point CBA/J, CE/J, I/LnJ, 

mutation 

PERA/Ei 

6 Tcrb‐V8 a A = wild type Wild type A/J, AKR/J, BALB/cJ, 

C3H/HeJ, C57BL/10J, 

C57BL/6J, MRL 

6 Tcrb‐V8 c deletion C57L/J, SJL/J 

11 Nlrp1a R/R Resistance to anthrax LT 

lethal toxin [11] NLRs = 

inflammasome 

components 

11 Nlrp1a s/s Sensitivity to anthrax LT 

lethal toxin [11] 

1 Slc11a1 r r = resistance to certain 

agents – some 

Mycobacterium sp, 

S. typhimurium, 

L donovani [12] 

1 Slc11a1 s s = susceptibility to 

certain agents – some 

Mycobacterium sp, 

S. typhimurium, 

L donovani [12] 

dominant 

allele 

(wild type?) 

G to A 

point 

mutation 

recessive 

C57BL/6J, A/J, I/LnJ, 

SPRET/EiJ, PWK/PhJ, 

PWD/PhJ, AKR/J, 

NOD/LtJ, DBA/2J 

129S1/SvlmJ, Balb/cJ, 

FVB/NJ, SWR/J, 

CAST/EiJ, C57/LJ 

A; C3H; CBA; DBA [12] 

C3H/HeJ, 129/Sv 

BALB/c; C57BL [12] 

Search for gene/locus/allele updates at http://www.informatics.jax.org/ 

Search for mice at http://www.findmice.org/index.jsp 



Table Id: Immunodeficient mice: properties of important genes & mutations 

Gene 

B2m 

beta‐2 

microglobulin 

Foxn1 

forkhead box N1, 

formerly Hfh11 

Il2rg 

interleukin 2 

receptor, gamma 

chain 

Myd88 

myeloid 

differentiation 

primary response 

gene 88 

Prf1 

perforin 1 

(pore‐forming 

protein) 

Prkdc 

protein kinase, 

DNA‐activated, 

catalytic 

polypeptide 

Rag1 

recombination 

activating gene 1 

Ticam1 

Trif 

PROPERTIES 

Required for normal expression of major histocompatibility class I proteins (displaying viral and self 

antigens to potentially responsive T cells) and for 

CD8+ T cell maturation and NK cell development 

Tm Deficiency NK cell development/activity, CD8+ T cell activity 

nu mutation known as nude. 

nu/nu are ‘hypothymic’ – ‘athymic’ T cell deficient; respond poorly to thymus‐dependent antigens, 

should accept allogeneic and xenogeneic grafts(but may have NK activity & be leaky) 

Greatly increased susceptibility to infection. 

Necessary for IL2, IL4, IL7, IL9, IL15, IL21 high affinity binding & signaling. 

Role in mediating susceptibility to thymic lymphomas in mice 

Tm Deficiency NO NK development +other defects in innate immunity. 

NO thymic lymphomas on susceptible background 

Myd88 is an adapter protein used by all TLRs (except TLR 3) to activate transcription factor NF-κB in 

innate immunity 

Tm Deficiency innate responses – neutrophils, macrophages, 

hematopoietic, molecular signaling, and apoptotic abnormalities 

Essential in lytic pathway by which NK and CD8+ lymphocytes kill targeted cells. 

Tm Deficiency NK cell activity, CD8+ T cell activity 

Involved in repairing double‐stranded DNA breaks and in recombining the variable (V), diversity (D), and 

joining (J) segments of immunoglobulin and T‐cell receptor genes. 

scid mutation/allele ‘severe combined immunodeficient’ 

scid/scid no mature T and B cells, cannot mount cell mediated or humoral adaptive immune 

responses, do not reject allogeneic and xenogeneic grafts, useful cancer research models. 

BUT leakiness some functional B and T cells as they age. 

leakiness in non‐SPF conditions, 

leakiness C57BL/6J, BALB/cByJ backgrounds > C3H/HeSnJSmn > NOD/LtSzJ background 

++ radiosensitive cannot be as thoroughly irradiated as other immunodeficient models before 

being engrafted 

renders NOD mice diabetes‐free useful for adoptive transfer of diabetes by T cells. 

Essential for V(D)J gene rearrangements necessary functional antigen receptors in T & B cells. 

Deficient tm1Mom mutants no mature, functional T and B cells. 

Renders NOD mice diabetes‐free. 

+ B cell lymphomas in NOD.129S7(B6)‐Rag1tm1Mom/J 

Toll-like receptor adaptor molecule 1 (formerly uses TIR-domain–containing adapter-inducing interferon-b 

(TRIF)). adapter protein used by TLR 3 to activate transcription factor NF-κB in innate immunity 

Tm Deficiency innate responses – esp when combined with Myd88 Tm 

Tm = targeted mutation (knockout) 



Table Ie: Immunodeficient mice: Effects of Background strain on phenotypes 

adapted from Jaxnotes #501, 2006 [13] http://jaxmice.jax.org/jaxnotes/archive/501.pdf etc 

Back ground 

BALB 

Substrains 

C57BL/6J 

Innate 

NK etc 

Leaky H2 Examples 

‘common name’ 

Normal Yes T d CByJ.Cg‐Foxn1 nu /J 

‘BALB/c Nude’ 

Normal High d CBySmn.CB17‐ 

Prkdc scid /J 

‘BALB/c scid’ 

Normal 

 

Normal 

 

NO b B6.129S7‐ 

Rag1 tm1Mom /J 

‘B6 Rag’ 

High b B6.CB17‐ 

Prkdc scid /SzJ 

‘B6 scid’ 

NOD Low NO g7 NOD/ShiLtJ 

‘NOD’ 

Low NO g7 NOD.129S7(B6)‐ 

Rag1 tm1Mom /J 

‘NOD Rag’ 

Low NO g7 NOD.Cg‐Rag1 tm1Mom 

Prf1 tm1Sdz /SzJ 

‘NOD Rag Prf’ 

Low Low g7 NOD.CB17‐ 

Prkdc scid /J 

Low Low g7 NOD.Cg‐Prkdc scid 

B2m tm1Unc /J 

‘NOD scid B2m’ 

Low NO g7 NOD.Cg‐Prkdc scid 

Il2rg tm1Wjl /SzJ 

‘NSG’ 

Low NO NOD.Cg‐Prkdc scid 

Il2rg tm1Sug /JicTac 

‘NOG’ 

Characteristics (Phenotypes) 

Normal B cells etc 

Extra thymic T cells with age 

POOR breeders, female fertility nu/+ F x nu/nu M 

NO functional B and T cells 

HIGH NK, complement activity (normal APC function) 

Thymic lymphomas but < NOD.CB17‐Prkdcscid/SzJ 

RadioSensitive 


HIGH NK activity (normal APC, complement c5) 


HIGH NK, complement activity (normal APC function) 

susceptible to immune mediated insulitis + diabetes 

NK, macrophage, APC activity; Hc 0 No c5 

RadioResistant 


Pre‐B cell > Thymic lymphomas ( 10.5mo) 

Somewhat RadioResistant 

NO functional B and T cells, 

NO NK cell activity; Hc 0 No c5 

Thymic lymphomas (short lifespan ~8.5mo) 

RadioResistant: survives up to 8 Gy 


NOD background low NK activity, Hc 0 No c5, 

defects in myeloid development, poor APC functions 


RadioSensitive: tolerates up to 4 Gy 


No MHC 1 expression ~NO NK activity 


Hemochromatosis dt? 

NO lymphocytes; NO NK cell activity 

Lymphoma‐resistant; long‐lived > 16m 

JAX 

NO lymphoctes; NO NK cell activity 

Lymphoma‐resistant; long‐lived > 16m 

TAC 

NIH stock Normal Yes T q NU/J (Foxn1nu) NIH outbred nude stock inbred at TJL 



Table If: Immunodeficient mice: Primary T cell deficient options 

Mutations 

T 

Cells 

B 

Cells 

Innate 

NK 

Leaky 

Tumors 

Foxn1 nu (nude) D N N yes 

Prkdc scid (scid) D D N‐ yes 

Prkdc scid Lyst bg 

(scid‐bg) 

NOD‐Prkdc scid 

(NOD‐scid) 

NOD, Prkdc scid , 

Il2rg tm… (NSG, NOG) 

D = Deficient, N = ‘normal’ 

D D N 

Reduced by 

bg 

D D D Minimal 

D D D No 

Thymic 

lymphoma 

Thymic 

lymphoma 

Thymic 

lymphoma 

Table Ig: Immunodeficient mice: MORE NUDE options 

Source Background Name INbred AKA 

Tac Bom B6N/Tac B6.Cg/NTac‐Foxn1 nu + B6 nude 

BALB/cAnN C.Cg/AnNTac‐Foxn1 nu + BALB/c nude 

BALB/cBom C.Cg/AnBomTac‐Foxn1 nu + BALB/cA nude 

BALB x NIH(S) CrTac:NCr‐Foxn1 nu NIH Nude 

NMRI (S) BomTac:NMRI‐Foxn1 nu Swiss nude 

NIH(S) NTac:NIHS‐Foxn1 nu Swiss Nude 

Crl BALB/cAnN CAnN.Cg‐Foxn1 nu /Crl + BALB/c Nude 

CD1 (S) Crl:CD1‐Foxn1 nu CD1 nude 

NIH Nu Crl:NU‐Foxn1 nu Nu/nu NIH nude 

Hsd Ola NIH Nu Hsd:Athymic Nude‐Foxn1 nu NIH nude 

NMRI (S) HsdCpb:NMRI‐Foxn1 nu Swiss Nude 

CD1 (S) HsdHli:CD1‐Foxn1 nu CD1 nude 

ICR (S) HsdOla:ICRF‐Foxn1 nu Swiss Nude 

MF1 HsdOla:MF1‐Foxn1 nu MF1 nude 

BALB/cOla BALB/OlaHsd‐Foxn1 nu + BALB nude 



Table Ih: Immunodeficient mice: MORE scid options 


Tac Bom C.B17 C.B‐Igh‐1 b /IcrTac‐Prkdc scid + CB17 scid 

IcrTac IcrTac:ICR‐Prkdc scid Scid ‐ Swiss 

C.B‐17 C.B‐Igh‐1b/GbmsTac‐Prkdc scid ‐Lyst bg + scid‐beige 

NOD + NOD/MrkBomTac‐Prkdc scid + NODscid 

NOD NOD.Cg‐Prkdc scid Il2rg tm1Sug /JicTac + CIEA NOG 

Crl C.B17 CB17/Icr‐Prkdc scid /IcrCrl + CB17 scid 

Crl:SHO‐Prkdc scid Hr hr 

Scid hairless outbred 

Hsd Ola BALB/cJ BALB/cJHanHsd‐Prkdc scid + BALB/c Scid 

C.B‐17 C.B‐17/IcrHsd‐Prkdc scid + CB17 scid 

C3H C3H.C‐Prkdc scid /IcrSmnHsd + C3H scid 

ICR (S) HsdIcr:Ha(ICR)‐Prkdc scid Scid 

NOD CB17 NOD.CB17/JHliHsd‐Prkdc scid + NODscid 

Table Ii: Immunodeficient mice: MORE options 


Tac Bom C.B17 C.B‐Igh‐1 b /IcrTac‐Prkdc scid + CB17 scid 

IcrTac IcrTac:ICR‐Prkdc scid Scid ‐ Swiss 

C.B‐17 C.B‐Igh‐1b/GbmsTac‐Prkdc scid ‐Lyst bg + scid‐beige 

NOD + NOD/MrkBomTac‐Prkdc scid + NODscid 

NOD NOD.Cg‐Prkdc scid Il2rg tm1Sug /JicTac + CIEA NOG 

Crl C.B17 CB17/Icr‐Prkdc scid /IcrCrl + CB17 scid 

Crl:SHO‐Prkdc scid Hr hr 

Scid hairless outbred 

Hsd Ola BALB/cJ BALB/cJHanHsd‐Prkdc scid + BALB/c Scid 

C.B‐17 C.B‐17/IcrHsd‐Prkdc scid + CB17 scid 

C3H C3H.C‐Prkdc scid /IcrSmnHsd + C3H scid 

ICR (S) HsdIcr:Ha(ICR)‐Prkdc scid Scid 

NOD CB17 NOD.CB17/JHliHsd‐Prkdc scid + NODscid 



Table II Infectious agents in mice, listed by site or by primary disease phenotype when there are 

pathology findings 

Viruses Bacteria Eukaryotes 

ENTERIC‐HEPATIC 

Calicivirus (MNV) 

Coronavirus (MHV) 

Reovirus 3 (Reo3) 

Rotavirus EDIM 


Gastric yeasts 

RESPIRATORY 

Paramyxovirus (MPV,Sen) 

IMMUNE or MULTISYSTEM 

Adenovirus (MAV1,2) 

Arterivirus (LDV) 

Ectromelia virus (ECT) 

Herpesvirus (MCMV, MTV) 

LCM virus (LCMV) 

LDH virus (LDV) 

Papova (K, MPyV) 

Parvoviruses (MMV, MPV) 


Citrobacter rodentium 

Escherichia coli 

Clostridium piliforme 

Cl difficile, Cl perfringens 

Helicobacters 

Salmonella enterica Ssp typhimurium 

Segmented Filamentous Bacteria (SFB) 

RESPIRATORY 

Bordetella avium, hinzii, etc, 

CAR bacillus 

Klebsiella pneumoniae 

Mycoplasma pulmonis 

Pasteurella pneumotropica 

SKIN (or abscesses) 

Corynebacterium bovis 

Corynebacterium kutscheri 

Staphylococcus aureus 

Staphylococcus species 

Streptobacillus moniliformis 

Eimeria sp. 

Cryptosporidia 

Entamoebae 

Flagellates 

Fungi 

Protozoa 

Nematodes 

Aspiculuris tetraptera 

Syphacia muris 

Syphacia obvelata 

Cestodes 

Cysticercus fasciolaris 

Hymenolepis diminuta 

Rodentolepis microstoma 

Rodentolepis nana 

RESPIRATORY 

Pneumocystis murina 

SKIN/HAIR 

Dermatophytes 

Lice 

Mites – Fur, Follicles 

Fungi 

Fungi 

Arthropods 

CNS 

PicoRNAvirus (TMEV etc) 

OTHER 

Hantavirus (HAN) 

Retrovirus 

Papillomavirus 

Bacteremia, Septicemia 

Klebsiella oxytoca etc spp 

Proteus mirabilis 

Pseudomonas aeruginosa 

Streptococcus, Enterococcus spp. 

OTHER 

Chlamydiae 

Mycobacterium spp 

Mycoplasmas Haemotrophic 

OTHER 

Fungi 

Encephalitozoon cuniculi 

Protozoa 

Klossiella muris 

Sarcocystis muris 

Arthropods 

Mesostigmatid mites 

NON parasitic arthropods 

Psocids 



Table IV Viruses in mice: test methods and results from Pritchett‐Corning, Cosentino, Clifford (2009) [14] 

(see also [15] [16] [17] [18]), and survey results from Carty 2008. [19] The most common agents are in 

boldface. The final column indicates if PCR testing is commercially available on feces (F) or biological 

materials (B) such as serum or cultured cells. 

Agent (common abbreviations) 

Primary 

test [14] 

Confirmatory 

test 

[14] 

cbrayton@jhmi.edu 2013 Page 10 of 14 

%Pos 

Results 

[14] 

%Pos 

inst. [19] 

Comment 

Adenoviridae 

MFIA/ 

Mouse Adenovirus (MAV1, MAV2) ELISA 

IFA 0.02 F B 

Arenaviridae 

MFIA/ 

Lymphocytic choriomeningitis virus 

ELISA 

(LCMV) 

IFA 0.01 Zoonotic B 

Arteriviridae 

Lactate dehydrogenase‐elevating virus Enzyme* PCR Chem B 

(LDHV, LDV) 

Caliciviridae 

MFIA/ 

Murine norovirus (MNV) 

ELISA 

IFA 32.3 F B 

Coronaviridae 

MFIA/ 

Mouse Hepatitis virus (MHV) 

ELISA 

IFA 1.6 >40% F B 

Bunyaviridae 

MFIA/ 

Hantavirus (HAN, HNT) 

ELISA 

IFA 0 Zoonotic B 

Herpesviridae 

MFIA/ 

Mouse Cytomegalovirus (MCMV) 

ELISA 

IFA 0.04 B 

Herpesviridae 

Mouse Thymic virus (MTV, MTLV) 

IFA PCR B 

Paramyxoviridae 

MFIA/ 

Pneumonia virus of mice (PVM) 

ELISA 

IFA, HAI 0.01 B 

Paramyxoviridae 

MFIA/ 

Sendai virus (SEND, SEN) 

ELISA 

IFA, HAI 0 B 

Parvoviridae 

MFIA/ 

Parvovirus (MVM, MMV) 

ELISA 

IFA, HAI 0.3 ~40% F B 

Parvoviridae 

MFIA/ 

Parvovirus (MPV 1,2) 

ELISA 

IFA 1.8 >90% F B 

Picornaviridae (Cardiovirus) 

MFIA/ 

Theiler's murine encephalomyelitis virus 

ELISA 

(TMEV, GD‐VII) 

IFA 0.26 F B 

Polyomaviridae 

MFIA/ 

Mouse Pneumonitis virus (K) 

ELISA 

IFA 0 B 

Polyomaviridae 

MFIA/ 

Polyoma virus (POLY) 

ELISA 

IFA 0.02 B 

Poxviridae (Othopoxvirus) 

MFIA/ 

Ectromelia virus (ECTRO, ECT)) 

ELISA 

IFA 0.02 B 

Reoviridae 

MFIA/ 

Reovirus (REO, REO3) 

ELISA 

IFA, HAI 0.01 B 

Reoviridae 

MFIA/ 

Mouse Rotavirus (EDIM, MRV) 

ELISA 

IFA 0.56 ~30% F B 

Abbreviations in the table – see also section diagnostic methods 

Chem – plasma chemistry test for elevated lactate dehydrogenase activity 

ELISA ‐ Enzyme‐linked immunosorbent assay 

IFA ‐ Indirect immunofluorescence assay 

MFIA ‐ multiplexed fluorometric immunoassay 

HAI ‐ Hemagglutination inhibition assay 

PCR ‐ Polymerase Chain reaction 

PCR?


Table V Bacteria in mice: Test methods and results (expressed as % positive results) from Pritchett‐ 

Corning, Cosentino, Clifford (2009),[14] and survey results from Carty 2008.[19] Agents in boldface were 

detected in > 1% of specimens. Gram positive bacterial agents are shaded. The final column indicates if 

PCR testing is commercially available for specimens from feces, oral or lung swab, or skin/fur swab. 

Agent 

Method[14] 

% POS 

Results[14] 

% Pos 

institution[19] 

Bordetella bronchiseptica Culture 0.00 Feces 

Cilia‐associated respiratory bacillus Serology 0.01 Oral/lung 

Citrobacter rodentium Culture 0.00 Feces 

PCR? 

Corynebacterium bovis 

Culture 2 

PCR 9 Skin swab 

Corynebacterium kutscheri Culture 0.00 Feces 

Helicobacter genus (any sp.)* PCR 16.08 ~80% Feces 

‐ Helicobacter hepaticus PCR 12.37 Feces 

‐ Helicobacter bilis PCR 2.17 Feces 

Klebsiella oxytoca Culture 0.38 > 40% Feces 

Klebsiella pneumoniae Culture 0.10 >30% Feces 

Culture 0.00 

Mycoplasma pulmonis 

Serology 0.01 70% Feces 

Other Pasteurella species Culture 0.31 

Any Salmonella species Culture 0.00 Feces 

Staphylococcus aureus Culture 6.07 Feces 

Streptobacillus moniliformis Culture 0.00 Feces 

Streptococcus pneumoniae Culture 0.00 Feces 

Streptococcus sp. – β‐haemolytic, Group B Culture 0.24 Feces 

Streptococcus sp. – β‐haemolytic, Group G Culture 0.00 Feces 



Table VI: Eukaryotes: Test methods and results from Pritchett‐Corning, Cosentino, Clifford (2009),[14] 

and survey results from Carty 2008. [19] The most common agents are in boldface. The final column 

indicates if PCR testing is available for specimens from feces, oral or lung swab, or skin/fur swab. 

Agent 

Method[14] 

%Pos 

Results [14] 

%Pos 

institutions[19] 

Fungi 

Encephalitozoon cuniculi Serology 0.00 

Pneumocystis spp (submissions from 

immunodeficient mice) 

PCR 1 Oral/ lung 

Enteric Protozoa 

Not evaluated 

Chilomastix sp. Wet mount 3.74 

Entamoeba sp. Wet mount 8.08 

Giardia sp. Wet mount 0.00 Feces 

Hexamastix sp. Wet mount 4.45 

Monocercomonoides sp. Wet mount 0.04 

Retortamonas sp. Wet mount 0.03 

Spironucleus sp. Wet mount 0.08 Feces 

Trichomonads Wet mount 8.88 

Metazoa – enteric 

Oxyurids (pinworms) 

>70% 

Aspiculuris tetraptera Direct 0.19 Feces 

Syphacia muris Direct 0.25 Feces 

Syphacia obvelata Direct 0.11 Feces 

Metazoa – Surface, external 

Lice Direct 0.00 

Fur Mites Direct 0.12 ~40% Fur swab 

PCR? 

Table VIa protozoa in mice by type and by site of infection 

Flagellates Coccidia Other 

Stomach 

Cryptosporidium muris 

Duodenum 

Giardia sp. 

Jejunum 

Spironucleus sp. 

Eimeria spp. 

Ileum 

Cryptosporidium parvum 

Large Intestine 

Large Intestine 

Chilomastix sp. 

Entamoeba muris 

Hexamastix sp. 

Monocercomonoides sp. Kidney Kidney / Brain 

Octomitus sp. Klossiella muris [E cuniculi – now a fungus] 

Retortamonas sp. 

Muscle 

Trichomonads 

Sarcocystis muris 

T muris, T diminuta etc Various tissues 

Toxoplasma gondii 



Table VIb Features of common fur mites (oversimplified) [20] 

Body shape 

Distinguishing 

features 

M. musculi 

Elongate body with 

bulges between 

the legs 

1 st pair of legs (tarsi) 

are specialized for 

hair clasping; 

2 nd pair of legs has 

single empodial 

claw 

R affinis 

(formerly M affinis) 

Elongate body with 

bulges between the 

legs 

1 st pair of legs (tarsi) 

are specialized for 

hair clasping; 

2 nd pair of legs has 2 

unequal claws 

M. musculinus 

Rounded‐oval 

3 rd and 4 th pairs of 

legs (tarsi) are 

short thick and 

specialized for hair 

clasping 

Adult size 300‐500u long 300‐500u long Females oval 130x 

350u 

Males rounded < 

200u diameter 

Eggs 

Oval up to 250u long Probably similar to Oval up to 450u long 

Base of hair shaft M musculi 

Distal hair shaft 

Diet 

Feeds on interstitial Probably similar to Feeds on superficial 

fluids 

M musculi 

keratin layer 

Site on mouse 

Deep among hairs 

especially of dorsal 

head neck 

shoulders flank 

Among hairs 

especially of 

inguinal skin and 

ventrum 

T romboutsi 

(formerly 

M romboutsi) 

Rounded‐oval 

3 rd and 4 th pairs of 

legs (tarsi) are 

short thick and 

specialized for hair 

clasping 

Females oval < 300u 

long 

Males rounded < 

200u diameter 

Probably similar to 

M musculinus 

Probably similar to 

M musculinus 

TABLE VIc Comparison of features of Syphacia obvelata and Aspiculuris tetraptera [20] [21] [22] 

Aspiculuris tetraptera Syphacia obvelata S muris 

Prepatent period 

21‐25 days 11–15 days 7‐8 days 

(egg to egg) 

Infectious form Embryonated eggs Embryonated eggs ~ S obvelata 

Larvae hatch from eggs Cecum Cecum ~ S obvelata 

Adult Size 

2‐4mm long, 

< 200u wide 

1‐6mm long, 

(males are shorter) 

< 400u wide 

1‐4mm long, 

(males are shorter) 

< 200u wide 

Adult location Colon lumen Cecum lumen; females 

transit colon to 

deposit eggs at anus 

# eggs 17 per female per day, 350 per female all at 

intermittently 

once 

Eggs 

Not embryonated 

Shed in feces; 

Embryonate in 5‐8days 

~40u wide, 90u long; 

symmetric, 

Unembryonated in fresh 

feces 

Not embryonated; 

On perineum; 

Embryonate within 24hr 

~36u wide`, 134u long; 

crescentic, flattened 

on 1 side, pointed 

ends 

~ S obvelata but eggs 

deposited after 

noon 

all at once in 

afternoon 

Not embryonated; 

On perineum; 

Embryonate within 

few hours 

~30u wide, 75u long; 

flattened on 1 side 



WEB RESOURCES 

1. Frith, C. H. and Ward, J. M. A Color Atlas of Neoplastic and Non Neoplastic Lesions in Aging Mice. 1988. 

http://www.informatics.jax.org/frithbook/ also print on Demand from CL Davis Foundation 

http://store.cldavis.org/ 

2. IMSR ‐ FIND MICE AND ES CELL LINES http://www.findmice.org/index.jsp 

3. Mouse (rat) and Gene NOMENCLATURE & apply for a laboratory code http://www.findmice.org/index.jsp 

4. Mouse Phenome database ‐ mouse data and protocols http://phenome.jax.org/ 

5. Mouse Tumor Biology (MTB) Database & tumor frequency grid 

http://www.informatics.jax.org/mtbwi/index.do 

6. Pathbase: European mutant mouse pathology database http://www.pathbase.net/ 

7. RENI Tissue trimming guide http://reni.item.fraunhofer.de/reni/trimming/index.php 

8. Treuting’s virtual / digital slides corresponding to Treuting & Dintzis 2012. 

http://repository.aperio.com/c/201/2/ 

REFERENCES 

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