Prevalence of enteropathogens and endoparasites in cats at an animal shelter in Ontario

Abstract

Objective

To determine the prevalence of fecal microorganisms and parasites in a population of sheltered cats, and to identify specific animal factors associated with infection.

Animals

A total of 79 sheltered cats and kittens in Guelph, Ontario.

Procedure

A fecal sample was collected from each animal upon shelter entry. A second sample was collected following deworming treatment. Microorganism and parasite prevalence was assessed by PCR assays. A linear mixed model was used to determine the relationships between animal factors (intake source, age, sex, body condition score, time between deworming and sample collection, and fecal consistency) and fecal microorganisms and parasites, as well as to compare samples taken before and after deworming.

Results

Clostridium perfringens alpha toxin gene and feline coronavirus (FCoV) DNA were the most common abnormalities identified. Giardia spp., C. perfringens enterotoxin, and Campylobacter jejuni were rare. Clostridium perfringens prevalence was negatively associated with increasing age (P = 0.04) and FCoV prevalence was positively associated with softer stool (P = 0.02). Hookworms, roundworms, and tapeworms were uncommon, and prevalence was not affected by any animal factor. Parasite prevalence decreased after deworming (P = 0.04).

Conclusion and clinical relevance

There do not appear to be durable relationships between C. perfringens and FCoV prevalence and animal factors in cats. A larger population of cats is required to identify potential relationships between microorganism and parasite prevalence and animal-specific demographic factors.

INTRODUCTION

Diarrhea in cats can be challenging to diagnose and treat owing to its numerous etiologies, including dietary, infectious (bacterial, viral, parasitic), inflammatory, metabolic, and neoplastic causes, as well as stress and dysbiosis (1–3). Cats housed in shelters are especially susceptible to infectious diseases (4). Pathogens that are transmissible to humans or other animals in the shelter may require more intensive housing and management strategies. However, whereas some shelters are well-equipped with medical and financial resources, others have fewer resources at their disposal and may elect to pursue lower-cost diagnostic testing. Alternatively, shelters may attempt empirical treatment in lieu of testing; e.g., administering deworming medication or antimicrobials to cats presenting with diarrhea.

In sheltered cats, diarrhea has an additional consequence of decreasing adoptability and increasing a cat’s length of stay. Longer shelter stays have animal welfare implications due to the higher risk of disease and increased frequency of negative behaviors associated with longer durations spent in a shelter environment (5,6). It is therefore imperative to resolve diarrhea as soon as possible in sheltered cats, to maximize adoptability and decrease length of stay.

The first objective of this research was to determine the prevalence of potentially pathogenic fecal microorganisms and parasites in a population of sheltered cats, both upon entry to a shelter and after anthelmintic treatment was administered. The second was to determine if relationships exist between the presence of these organisms and any demographic factors of the sheltered cats.

MATERIALS AND METHODS

All cats and kittens entering an open-admission Humane Society in Guelph, Ontario between June and August 2018 were eligible for this study, with the exceptions of cats with short-term stays prior to foster home placement and cats transferred from another shelter. All cats were examined by trained shelter staff upon entry. Age was estimated using dentition if not provided by owners upon surrender, except for cats that could not be safely examined. Body condition score (BCS) was determined using a published 9-point scale (7).

This study did not preclude provision of standard care measures for cats, including spaying or neutering of intact animals, dental extractions, and vaccination (typically within 72 h of entry to shelter) against rabies and FVRCP (feline viral rhinotracheitis, calicivirus, and panleukopenia virus) for all cats requiring vaccination or with unknown vaccination status. Feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) statuses were determined using a commercial ELISA assay (SNAP FIV/FeLV Combo; IDEXX Laboratories, Markham, Ontario). Cats without known special dietary requirements were fed a combination of commercial canned and kibble diets (Royal Canin Adult Instinctive Loaf in Sauce Canned Cat Food and Royal Canin Professional Feline Indoor Adult Dry Cat Food, respectively; Royal Canin SAS, Puslinch, Ontario) 2×/d, with kittens receiving the equivalent kitten formulations of these diets. Cats were dewormed (typically within 72 h of entry to the shelter) using a commercial oral anthelmintic containing milbemycin oxime and praziquantel (Milbemax; Elanco, Guelph, Ontario).

Fecal consistency was monitored daily by shelter staff and presence of diarrhea recorded for all cats. An existing fecal consistency scale (8) was used to score stool consistency. In brief, feces were scored as follows: 1 (liquid, unformed), 2 (wet but not liquid, unformed), 3 (soft, formed), 4 (dry, formed), or 5 (dry, hard, crumbly fecal balls). If multiple stools were present during the day (unit of observation) and represented > 1 score, the lowest score was recorded. The first available stool from each eligible cat was collected from the cat’s litter box upon shelter entry. Deworming was done at times convenient for shelter staff, resulting in some cats having their initial stool sample collected before deworming and others within 3 d after, depending on the timing of both events. If individual stools could not be collected from cats housed in pairs, 1 fecal sample was collected and randomly assigned by coin flip to 1 cat in the cage. If the cat was present in the shelter at least 5 d following deworming, a second stool sample was collected from the dewormed cat.

Samples were stored in sealed plastic bags and refrigerated at 4°C for up to 4 d, until they were transferred to individual sterile plastic containers and delivered to a commercial diagnostic laboratory (IDEXX Laboratories). Upon receipt, samples were stored at 4°C for up to 2 d before analysis.

Samples were analyzed using real-time PCR for Clostridium perfringens alpha toxin gene, C. perfringens enterotoxin gene, Campylobacter coli, Campylobacter jejuni, Cryptosporidium spp., feline coronavirus (FCoV), Giardia spp., feline panleukopenia virus, Salmonella spp., Toxoplasma gondii, and Tritrichomonas foetus. The assay was conducted as previously described (9), with the following differences: total nucleic acid extraction was completed using proprietary lysis buffer and Kingfisher Flex Magnetic Particle Processor (Thermo Fisher Scientific Canada, Toronto, Ontario), and a Salmonella enrichment protocol was not conducted (IDEXX Laboratories, Markham, Ontario; personal communication, 2022). A PCR assay for fecal parasites was conducted using proprietary methods to target DNA of hookworms (Ancylostoma spp., Uncinaria spp. with species-level determination of U. stenocephala given a positive genus-level result), roundworms (Toxocara spp. with species-level determination for T. canis, T. cati, and T. malaysiensis given a positive genus-level result), tapeworms (Diphyllobothrium latum, Dipylidium caninum, Echinococcus spp. with species-level determination for E. canadensis and E. multilocularis given a positive genus-level result, Spirometra mansonoides, Taenia spp. with species-level determination for T. taeniaeformis and T. pisiformis given a positive genus-level result), and whipworms (Trichuris spp.) (IDEXX Laboratories; personal communication, 2022).

All PCR assays were run with 6 quality controls, including extraction controls, spike-in internal positive controls, pan-bacterial 16s rRNA, reagent blank, and positive and negative controls. All proprietary assays were designed to conform to give a limit of detection at 10 molecules per reaction, as determined using synthetic positive controls. Specifically, the Echinococcus PCR assays have a limit of detection at 1 to 2 eggs/g feces and 100% specificity, according to in silico analysis and cross-reactivity study using materials containing known parasites, including T. taeniaeformis and T. pisiformis (10) (IDEXX Laboratories; personal communication, 2022).

Statistical analyses were conducted using SAS 9.4 software (SAS/STAT 9.4; SAS Institute, Cary, North Carolina, USA). The relationships between positive assay results at shelter entry and demographic information of this population of cats were evaluated individually for the 2 most-commonly identified microorganisms, C. perfringens alpha toxin and FCoV, and for fecal parasites. Total number of fecal parasites was treated as a binary outcome for organisms identified in the population of cats, whereas organisms that were not present in the study population were excluded from the model. Each statistical analysis was conducted using a GLMMIX procedure (with a binary distribution specified where appropriate). Each statistical model included the main effects of entry route (stray versus surrender), BCS, age, sex, fecal consistency score of initial stool sample, and number of days between deworming and initial sample collection. Interactions of these effects were included in each model. For cats with 2 fecal samples collected (an initial sample and a sample collected after deworming), individual statistical analyses were conducted as above to evaluate demographic factors associated with positive C. perfringens alpha toxin gene, FCoV, and fecal parasite status. These statistical models additionally included the random effect of cat, the effect of time (entry sample versus after-deworming sample), and changes in rates of positivity after deworming. Statistical results are presented as simplified models with nonsignificant variables removed.

Results are reported as P-values, odds ratios (OR), and 95% confidence intervals (CI95). Statistical significance was set at P < 0.05. Descriptive data are presented as median, interquartile range (IQR; Q3 to Q1), and range. Demographic data and prevalence of individual pathogens and parasites are presented as percentages of the total number of cats from which samples were obtained.

RESULTS

Fecal samples were collected from 79 cats upon shelter entry, and 49 subsequent fecal samples were obtained from the cats that received a deworming treatment. Four samples at entry were obtained from cages of cats housed in littermate pairs for which individual samples could not be collected. The after-deworming samples for 2 littermate pairs were excluded from analysis, as it could not be determined if the same cat was sampled each time. Thus, data for 47 cats following deworming are presented (Table 1).

TABLE 1.

Demographic information for 79 shelter cats, of which 47 cats were sampled again after deworming.

	All cats		Cats after deworming		Cats with positive entry assay results
	n	%	n	%	n	%
Total	79	—	47	—	52	—
Age
Kitten (< 1 y)	16	20	7	15	14	27
Adult (1 to 6 y)	46	58	33	70	33	63
Senior (≥ 7 y)	15	19	7	15	5	10
Unknown	2	3	0	0	0	0
Sex
Male	43	54	28	60	28	54
Female	36	46	19	40	24	46
Breed
Domestic shorthair	68	86	40	85	46	88
Domestic medium-hair	1	1	1	2	1	2
Domestic long-hair	10	13	6	13	5	10
Intake
Stray/Outdoor	50	63	31	66	39	7
Surrender	29	37	16	34	13	25
Fecal consistency score (/5)
Soft (1 to 2)	12	15	8	17	10	19
Formed (3 to 4)	41	52	31	66	27	52
Hard (5)	26	33	7	15	15	29
Unknown	0	0	1	2	0	0
Body condition score (/9)
Underconditioned (1 to 3)	9	11	5	11	5	10
Ideal (4 to 5)	45	57	27	57	35	67
Overconditioned (6 to 7)	9	11	4	9	3	6
Obese (8 to 9)	8	10	7	15	4	8
Unknown	8	10	4	9	5	10

At shelter entry, median age was 1.5 y (range: 2 mo to 11 y, IQR: 3 y), median BCS was 4/9 (range: 1 to 9, IQR: 1), and median fecal consistency was 3/5 (range: 1 to 5, IQR: 2). Cats were housed in the shelter for a median of 2 d (range: 0 to 5 d, IQR: 1 d) at the time of initial fecal sample collection. Cats were dewormed a median of 1 d after entry (range: 0 to 13 d, IQR: 3 d); and 88% (68/79) of all cats entering the shelter received anthelmintic treatment after shelter entry, whereas 12% (11/79) did not (e.g., returned to owner shortly after shelter entry). As this study was designed to have minimal effect on shelter operations, cats were dewormed according to shelter protocols, independently of fecal sample collection time points. Because of this, the initial fecal sample was collected before deworming in 49% (33/68) of cats and after deworming in 51% (35/68) of cats (Table 2).

TABLE 2.

Positive enteropathogen and parasite assay results at shelter entry for 68 sheltered cats that received anthelmintic treatment, according to timing of defecation and administration of anthelmintic treatment.

Timing of initial fecal sample collection	No. (%) of cats dewormed	No. (% of group) of cats with positive results
		Any positive result	Microorganisms	Parasites
Prior to deworming	33 (49)	24 (73)	21 (64)	8 (24)
< 24 h prior	11	9	7	5
> 24 h prior	22	15	14	3
Following deworming	35 (51)	23 (66)	20 (57)	6 (17)
24 h later	24	16	13	5
48 h later	8	6	6	0
72 h later	3	1	1	1

The prevalence of fecal microorganisms and parasites at entry and following deworming is reported in Table 3. At shelter entry, 58% (46/79) of cats tested positive for 1 microorganism, 15% (12/79) tested positive for 2 microorganisms, and no cats tested positive for > 2 microorganisms. Nineteen percent (15/79) of cats tested positive for at least 1 parasite at shelter entry, though each cat with positive fecal parasite results tested positive for only a single family of parasite (i.e., hookworms, roundworms, or tapeworms). Eleven percent (9/79) of cats tested positive for at least 1 microorganism and at least 1 parasite, concurrently. The following were not identified: feline panleukopenia virus, C. coli, Cryptosporidium spp., Salmonella spp., T. foetus, Echinococcus spp., S. mansonoides, Taenia spp., and Trichuris spp.

TABLE 3.

Fecal microorganisms and parasites identified in 79 cats upon shelter entry, a subset of which (n = 47) were sampled again following anthelmintic treatment.

	Positive results: All cats, entry sample	Positive results: Cats with paired samples
	No. (%) at entry	No. (%) at entry	No. (%) after deworming	No. (%) positive both times
Microorganisms
Clostridium perfringens alpha toxin	25 (32)	14 (30)	13 (28)	6 (13)
Clostridium perfringens enterotoxin	4 (5)	2 (4)	1 (2)	0 (0)
Campylobacter jejuni	3 (4)	2 (4)	2 (4)	1 (2)
Feline coronavirus	22 (28)	12 (26)	11 (23)	10 (21)
Giardia spp.	4 (5)	2 (4)	2 (4)	1 (2)
Toxoplasma gondii	0 (0)	0 (0)	1 (2)	0 (0)
Parasites
Hookworms	3 (4)	3 (6)	0 (0)	0 (0)
Ancylostoma spp.	3 (4)	3 (6)	0 (0)	0 (0)
Uncinaria spp. (U. stenocephala)	2 (3)	2 (4)	0 (0)	0 (0)
Roundworms	6 (8)	3 (6)	0 (0)	0 (0)
Toxocara spp.	6 (8)	3 (6)	0 (0)	0 (0)
T. canis	4 (5)	2 (4)	0 (0)	0 (0)
T. cati	3 (4)	1 (2)	0 (0)	0 (0)
T. malaysiensis	3 (4)	1 (2)	0 (0)	0 (0)
Tapeworms	6 (8)	4 (9)	1 (2)	0 (0)
Diphyllobothrium latum	4 (5)	3 (6)	0 (0)	0 (0)
Dipylidium caninum	5 (6)	3 (6)	1 (2)	0 (0)

After deworming, 45% (21/47) of cats tested positive for 1 fecal microorganism, 6% (3/47) tested positive for 2 microorganisms, and 2% (1/47) for 3 microorganisms. Two percent (1/47) of cats tested positive for 1 parasite. This positive parasite result was a new infection (Dipylidium caninum). No cat tested positive for ≥ 2 parasites. Potentially persistent microorganism infections after deworming were seen in 36% (17/47) of cats, with persistence of the same single organism in 34% (16/47) and the same 2 organisms in 2% (1/47) of cats. Forty-seven percent (22/47) of cats had a change in microorganism status between fecal samples collected at entry and after deworming; of these, 21% (10/47) developed a new infection, and 28% (13/47) tested negative for a microorganism that was identified at entry. There was no potentially persistent fecal parasite infection.

The prevalence of Clostridium perfringens alpha toxin gene identification at shelter entry was 32% (25/79) and was not affected by age (P = 0.13, OR: 0.87, CI95: 0.73 to 1.04), sex (P = 0.76, OR: 1.15, CI95: 0.44 to 3.03), intake source (P = 0.20, OR: 1.76, CI95: 0.52 to 5.92), BCS (P = 0.15, OR: 0.80, CI95: 0.58 to 1.08), or fecal consistency (P = 0.32, OR: 0.73, CI95: 1.12 to 8.47). In cats with both an initial and an after-deworming fecal sample obtained, there was a positive association between age and C. perfringens alpha toxin gene prevalence (P = 0.04, OR: 0.8, CI95: 0.61 to 0.98), in which every year’s increase in age had an associated 25% decreased prevalence of C. perfringens alpha toxin gene detection. There was no change in C. perfringens alpha toxin gene prevalence after deworming (P = 0.91, OR: 0.94, CI95: 0.31 to 2.86) and no relationships with sex (P = 0.06, OR: 3.53, CI95: −0.95 to 13.07), intake source (P = 0.58, OR: 0.67, CI95: −0.16–2.84), BCS (P = 0.20, OR: 0.80, CI95: 0.56 to 1.13), time from deworming to fecal sample collection (P = 0.97, OR: 1.08, CI95: 0.51 to 0.82), or fecal consistency (P = 0.15, OR: 0.88, CI95: 0.50 to 1.31).

Feline coronavirus prevalence at shelter entry was 28% (22/79) and was significantly associated with BCS (P = 0.02) and fecal consistency (P = 0.01), but not with age (P = 0.07, OR: 0.84, CI95: 0.69 to 1.03), sex (P = 0.26, OR: 0.99, CI95: 0.36 to 2.71), intake source (P = 0.15, OR: 1.8, CI95: 0.60 to 5.38), or time between sample collection and deworming (P = 0.15, OR: 0.92, CI95: 0.80 to 1.05). However, when nonsignificant variables were removed from the model, the effect of BCS became nonsignificant (P = 0.79, OR: 1.03, CI95; −0.78 to 1.36) and the effect of fecal consistency remained statistically significant (P = 0.02, OR: 0.63, CI95: 0.40 to 0.99): softer stool was associated with increasing FCoV prevalence. In cats with both an initial and an after-deworming fecal sample obtained, there was no change in FCoV prevalence after deworming (P = 0.28, OR: 1.13, CI95: 0.61 to 2.88) and no relationships with age (P = 0.49, OR: 0.72, CI95: 0.29 to 1.82), sex (P = 0.94, OR: 0.04, CI95: 0.001 to 773.47), time from deworming to fecal sample collection (P = 0.15, OR: 1.21, CI95: 0.92 to 1.6), or fecal consistency (P = 0.34, OR: 0.59, CI95: 0.20 to 1.75).

Fecal parasite prevalence upon shelter entry was not associated with age (P = 0.1, OR: 0.79, CI95: −0.59 to 1.05), intake source (P = 0.15, OR: 2.37, CI95: −0.68 to 10.89), BCS (P = 0.13, OR: 0.74, CI95: 0.49 to 1.09), time between deworming and initial defecation (P = 0.68, OR: 1.02, CI95: 0.93 to 1.11), sex (P = 0.63, OR: 0.76, CI95: 0.24 to 2.41), or fecal consistency (P = 0.29, OR: 0.77, CI95: 0.47 to 1.26). In cats with both an initial and an after-deworming fecal sample obtained, there was a significant decrease in parasite prevalence after deworming (P = 0.02, OR: 0.08, CI95: 0.01 to 0.70). There was no difference in parasite prevalence based on intake source (P = 0.26, OR: 2.75, CI95: −0.51 to 14.94), BCS (P = 0.79, OR: 0.96, CI95: 0.69 to 1.34), time from deworming to sample collection (P = 0.42, OR: 0.85, CI95: 0.59 to 1.24), age (P = 0.29, OR: 0.84, CI95: 0.61 to 1.17), sex (P = 0.76, OR: 0.80, CI95: 0.19 to 3.28), or fecal consistency (P = 0.65, OR: 0.87, CI95: 0.47 to 1.59).

DISCUSSION

Clostridium perfringens was the most-commonly identified organism as determined by the presence of alpha toxin gene, which is a marker for C. perfringens due to its presence in all C. perfringens strains. In the present study, C. perfringens alpha toxin gene identification had no relationship with fecal consistency or any demographic factors. This supports the current understanding of alpha toxin as being of low virulence and likely of limited clinical relevance in gastrointestinal disease; similarly, the bacterium is commonly identified in feline gastrointestinal tracts (11) and its relevance in gastrointestinal disease is unclear. In humans, the intestinal microbiome changes with increasing age, due to dysbiosis associated with altered immune function (12). In cats, the prevalence of intestinal C. perfringens may be similarly affected by age-related changes in the gut microbiome.

Feline coronavirus was the second-most common organism. Its prevalence was not affected by any demographic factor, likely due to the virus’s ubiquity in cats. Although FCoV prevalence increased in diarrheic cats in the present study, a clear relationship between FCoV infection and diarrhea has not been demonstrated in sheltered cats (13,14). Our results are similar to those in another study of FCoV prevalence and presence of diarrhea in catteries (15). This study documented a significant association between these factors, but the power of the study was not sufficient to detect causation. Uncommonly identified microorganisms were not statistically evaluated due to sample-size limitations, but the role of these organisms in gastrointestinal disease is similarly unclear. Clostridium perfringens enterotoxin is an enterotoxin produced by some strains of C. perfringens, the role of which in gastrointestinal disease in cats is uncertain but is more likely to be associated with disease in other species (16,17). Campylobacter jejuni can be isolated from both diarrheic and non-diarrheic cats, leading to difficulty in determining the relationship between Campylobacter infection and diarrhea (11). Giardiasis can cause self-limiting to severe diarrhea in cats, though infection is often subclinical. Giardia infection appears to be rare in sheltered cats in Ontario (18).

Fecal parasites were identified in ~20% of cats upon shelter entry. This value is similar to that in a previous survey of parasite prevalence using fecal flotation that also identified a low prevalence of common parasites in Ontario shelter cats (range: 0 to 22.8%) (18). The prevalence of individual species was low and overall parasite prevalence at shelter entry was not related to any demographic factor in this population of cats. Infection with intestinal parasites in cats can be subclinical or mild and may not result in changes to fecal consistency (2). However, interpretation of the present results is limited by low statistical power due to the overall low prevalence of parasites, which may be related to potentially low overall prevalence in this geographical region or may represent poor PCR-assay sensitivity to parasitic organisms. Comparison of results of PCR assays using fecal flotation techniques would be beneficial in future research.

We identified several additional questionable results in this study that call into question the specificity of several assays used in the PCR panel. We identified 2 feline-specific roundworm species (T. cati and T. malaysiensis). We also identified the canine roundworm T. canis in 4 cats, but this likely represented a false-positive result because T. canis infection of cats (aberrant host) is rare and typically results in eosinophilic inflammation and associated tissue injury. To date, T. malaysiensis has only been identified in cats in Malaysia, Vietnam, and China (19–21), and was also likely a false-positive result. Infection with D. caninum is caused by flea ingestion and its identification was not surprising. Diphyllobothrium latum was an unusual finding in cats for this geographical location. Other Diphylloboythrium spp. (D. dendriticum and D. ditremum) infections have been documented in dogs and cats in Canada, possibly suggesting that the assay may not be optimized to distinguish clearly between organisms, resulting in poor specificity. Infection in both dogs and cats occurs from ingestion of raw or undercooked fish infected with the larval parasite (22). Hookworms were less prevalent overall, with Ancylostoma spp. and Uncinaria spp. both identified in low numbers in this study. This is in contrast to previous findings of solely Ancylostoma spp. infections in Canadian animal shelters (18,23).

Decreased intestinal parasite prevalence following deworming can reasonably be attributed to deworming with milbemycin oxime and praziquantel, the combination of which is used to treat infection with hookworms (Ancylostoma spp.), roundworms (Toxocara spp.), and tapeworms (D. caninum, E. multiocularis, Taenia spp.) (24). In the present study, 1 dose of anthelmintic treatment was sufficient to resolve all identified parasitic infections. Repeat dosing is still commonly recommended to resolve infections entirely. One cat with positive D. caninum identification following deworming had a history of infestation with fleas, which act as vectors for infection (22). The infection was thus suspected to be a new infection that developed or was in the prepatent stages when the cat entered the shelter. Interestingly, D. latum and U. stenocephala infections resolved following deworming, despite praziquantel not having a label claim for efficacy or anecdotally requiring a higher dose than the one administered to treat these species. These results support the possibility of poor assay specificity leading to false-positive results at shelter entry, or true infections with these parasites that were effectively treated with the dose of antiparaciticide administered after shelter entry.

Potentially persistent microbial infections were identified in ~1/3 of cats, and almost 50% had microorganism identification patterns change while in the shelter. These major shifts in microorganism identification were unexpected and are difficult to explain. It is possible that assay sensitivity resulted in false-positive results. Transmission of infectious organisms between animals is a known risk in shelter environments (4) and cannot be ruled out. Stress and diet changes may cause alterations in gut microbiota (25,26), and though not assessed in this study, gut microbiome changes may have allowed opportunistic proliferation of potentially pathogenic organisms and identification of new infections upon subsequent analysis. Reinfection with Giardia has been reported in owned cats (27), and infection with FCoV is persistent in some cats whereas others may clear an infection or develop a new infection with time (28). In the present study, 1 case of T. gondii after deworming likely represented a cat that ingested infected prey and entered the shelter during the prepatent period.

Vaccinations and deworming medications were administered shortly after shelter entry for most cats. For many cats, these interventions occurred before initial defecation after shelter entry and subsequent fecal sample collection. Deworming before sample collection did not affect microorganism and parasite prevalence in the fecal samples collected at shelter entry. This may have been due to these organisms’ DNA remaining in the intestinal contents before defecation, and thus identifiable by PCR assay despite organism death. Vaccination before defecation likely had a similarly negligible effect on study results, as no identification of vaccine pathogens occurred.

This study was limited by poor statistical power due to the small number of cats testing positive for any microorganism or parasite. This may have been a factor contributing to the unusual and difficult-to-explain results obtained. Interpretation of these results is therefore limited, and larger studies are required to determine the relevance of demographic factors and fecal consistency for microorganism or parasite prevalence. In addition, identification of canine-specific microorganisms and parasites suggests the possibility of poor assay sensitivity and specificity, and comparison of PCR results with fecal flotation results should be considered in future studies. Assessing the microbiota of sheltered cats is an area of future research that may help to determine risk factors of gastrointestinal disease, including pathogen infection, and potential interventions to promote animal health.

Diagnostic testing of feces using PCR analysis is becoming increasingly available. As we documented in this study, there are many positive results that indicate the presence of microorganisms, but a positive result was not predictive of clinical signs and potential disease. As a result, shelter animal health managers must take care to interpret results in the context of the animal and its clinical signs in order to prevent overtreatment on the sole basis of positive assay results. A shelter’s animal care protocols may require treatment following positive fecal microorganism identification, even in the absence of clinical disease. As awareness grows about antimicrobial and anthelminthic resistance in veterinary species (16,29,30), treatment of fecal microorganisms should be based, at minimum, on the presence of characteristic clinical signs related to a possible pathogenic organism and appropriate veterinary consultation.

Funding Statement

This work was supported by a PetSmart Charities grant.