A faecal egg count with nothing found: what a negative result does not rule out

A faecal egg count counts eggs, not worms

In the laboratory a weighed amount of dung is suspended in a fluid in which worm eggs float to the top. What appears in a counting chamber under the microscope is counted, and the result is given as eggs per gram of dung. What is measured is egg output at one moment, not the number of worms in the animal. A 2023 review puts this unusually bluntly: egg counts cannot estimate the host's worm burden, because they relate neither to the number of small strongyles nor to the number of tapeworms.

The reason is biological. Only sexually mature females lay eggs, and they do so in the gut lumen. A large share of the small strongyles, however, sits as an encysted larva in the gut wall. Development work on a serological test cites a figure taken from earlier studies of up to 90 per cent of the total burden, with several million larvae reported in individual horses. These stages lay no eggs and do not appear under the microscope, however carefully the counting is done.

So does a result with no eggs mean worm free?

No. It means that at the time of sampling no eggs were found in the amount of dung examined. Whether a horse carries no worms, a few, or many larvae in its gut wall, the method does not tell apart. The same review notes that most horses carry low burdens with no signs of disease.

The counting technique shapes the result

How many eggs are found depends on the method. In a laboratory experiment, dung samples were spiked with known egg counts, from five to a thousand eggs per gram, and counted in triplicate. Against that known figure, the Mini-FLOTAC technique recovered on average about 65 per cent of the eggs, an automated smartphone system about 33 per cent and the modified McMaster technique about 22 per cent. An Australian review describes that same McMaster technique as the routine method in practice. A result therefore does not state the number of eggs in the dung, but the share of them that the chosen method makes visible.

A comparison on the same samples shows the same dependency from the other side. In a Portuguese study, 32 dung samples were processed in parallel by three techniques. The detection rate was 93 per cent for Mini-FLOTAC, 89 per cent for FLOTAC and 85 per cent for McMaster, a difference that was not statistically secure. Something else stood out: the technique with the lowest detection rate was the one that reported the highest egg counts. The values from the three methods were closely related but did not coincide.

Same horse, another week, another value

Even with the technique held constant, the value varies. An analysis of 2,637 dung samples from 303 naturally infected horses examined how stable a single animal's egg output stays over time. The authors conclude that high shedders can be identified and treated selectively. The same figure says a second thing: on the definition the authors used, about half the spread of all values was due to differences between horses. The other half was not. A single sample therefore places a horse with noticeable blur.

The values were also more spread out than a simple random distribution would lead one to expect: a few horses shed a great deal, many shed little. In everyday terms, a value just below a threshold and one just above lie closer together than the split into treated and untreated suggests.

What the faecal egg count never sees

Some parasites escape the method not because of their numbers but because of their biology. The tapeworm Anoplocephala perfoliata sheds its eggs irregularly. In an Italian survey of 173 horses on 35 holdings, tapeworm eggs were found in five dung samples, that is in just under 3 per cent. A blood test on the same animals placed about one horse in five at or above its treatment threshold.

For the large redworm the gap lies with the migrating stages. In a Swedish survey of 529 dung samples from 106 holdings, 28 per cent of the horses and 61 per cent of the holdings carried this parasite. Among the low shedders, that is 150 eggs per gram or fewer, the share was 25 per cent. The level of shedding was not linked to detection, and holdings that treated on egg counts alone carried the parasite about three times as often as holdings that also set up larval cultures or treated routinely.

How far apart microscope and indirect methods can lie is shown by a German study of 620 clinic horses. Faecal examination found strongyle eggs in 41.8 per cent, genetic detection found the large redworm in 1.1 per cent, the blood test in 32.3 per cent, and for the tapeworm in 10.7 per cent. Which of these pictures comes closest to reality, none of the methods settles on its own.

Where the threshold comes from

Selective worming treats not every horse but the animals above a set egg count. In a survey of 183 Swiss Army horses that value was set at 200 eggs per gram. The same work shows how differently one threshold strikes two populations: the army's own riding horses shed on average 111 eggs per gram, the privately kept train horses 539. Small strongyles were found in 60.4 and 71.5 per cent of the animals respectively, although both groups share the same pastures on duty.

Where such a value comes from is harder to answer than the report suggests. An Australian review of 51 publications spanning almost seven decades states expressly that the egg count above which treatment should be given remains disputed. The threshold is therefore not a measurement but an agreement, and it separates horses by their shedding, not by their risk of disease.

Why treat on egg counts at all, then?

Because the strategy pursues a different aim from a diagnosis. It is meant to keep small the share of the worm population that meets an active substance at all, and so to reduce the selection pressure towards resistant worms. Whether that calculation works out is tested by none of the studies assessed here; the Swedish survey names a possible price for the large redworm.

The check after two weeks measures something else

A treatment is often followed by a second dung sample after about two weeks. This check does not test whether a horse is healthy, but whether the active substance still works on the holding. An international methods recommendation from 2023 has recast the rules and departs from the earlier ones on four points: the same animals are compared before and after treatment rather than two groups; what now counts is the total number of eggs actually counted rather than a mean value per gram; group size is set by the expected egg count; and the assessment thresholds are matched to animal species, active substance and parasite.

The most important sentence in that recommendation lies between the lines. It describes a procedure that measures efficacy at group level, and it says nothing about what a single sample from a single horse can show. It exists in a more demanding version for research and a simpler one for practice.

A low reduction value also does not necessarily mean that the worms have become insensitive. In an Argentinian experiment on naturally infected horses, the same active substance given by mouth worked at 100 per cent against the small strongyles, but only at 36 to 64 per cent after injection into the muscle, even though blood levels were higher after injection. What is measured is always the whole arrangement: active substance, route, host and worms together.

Eggs gone does not mean worms gone

The most instructive experiment compared two active substances against an untreated group in 36 young grazing horses, then counted the worms in the gut. Two weeks after treatment the adult worms had almost entirely gone, at 99.9 and 99.7 per cent. Five weeks later the same values stood at 88.3 and 57.6 per cent, and by then neither active substance was working against the larval stages in the gut lumen. For only one of the two were the encysted larvae counted as well: 18.1 per cent against the early stages after two weeks and 8.0 per cent after five, 60.4 and 21.2 per cent against the later stages in the mucosa. Those figures are missing for the other substance, so no comparison is possible.

A second experiment in 18 young horses shows the same decoupling from the other side. A multi-day fenbendazole regime lowered egg counts by only 44.6 per cent but removed 71.2 per cent of the late larval stages in the mucosa: the egg count did not reflect the effect on larvae, it markedly understated it. With moxidectin both values were high, 99.9 per cent for the eggs and 85.2 per cent for those same stages, although the larval counts in that group did not differ securely from the untreated animals.

The time until eggs reappear is therefore readily read as an early warning. A systematic review of 54 studies across five decades found eight different definitions of that measure. Among the studies with a comparable definition, twenty report shortened periods, 35 days for moxidectin and 28 days for ivermectin. The authors leave expressly open what lies behind it: resistance, or a biological factor in the horse, the worm species or the environment.

How little a single check reveals is shown by a study of 82 treated mares. Fourteen days after treatment the egg reduction was 99.9 per cent in one group and 41.9 per cent in the other. After 45 days the second group was already above its starting values, while the first stayed below them for more than 90 days. A value at two weeks describes a moment, not a duration.

What the test delivers, and what does not follow from it

That this question burns at all is down to the resistance situation. A synthesis of 60 studies from 1994 to 2022 covering 11,835 animals found the lowest efficacies for the macrocyclic lactones against roundworms, about 68 per cent, and for the benzimidazoles against strongyles, about 70 per cent. Resistance to benzimidazoles is documented on all six continents. The authors' passing remark is worth noting: across the period no secure trend emerged.

Whether genetic methods close the gap is open. A systematic review of 54 molecular studies notes that these techniques so far mainly separate species that the microscope cannot tell apart. The review reports no comparative assessment of their accuracy against faecal examination. None of these methods is therefore established for routine use.

What remains is a test with a clearly bounded use. It identifies the horses that shed many eggs and so load the pasture most, and it measures on a holding whether an active substance still works. It is not information on whether an individual horse carries worms, and it is no measure of that horse's risk of disease. The feared form, larval cyathostominosis, carries a case fatality of around 50 per cent in the literature, and it arises precisely from the stages that are missing under the microscope.

What shows up in a faecal egg count and what does not, stage by stage

Original analysis

Limitations and uncertainty

• None of the studies assessed here measures how reliably a single dung sample indicates the actual worm burden of a living horse. The post-mortem studies count worms after treatment; they test the effect of an active substance, not the quality of the test. A reference measure in the living animal is missing in this field.
• The two post-mortem experiments cover 36 and 18 horses, that is six animals per group and time point, and the larval counts are extraordinarily variable. The authors of the second experiment note that the larval counts in the moxidectin group did not differ statistically from the untreated animals, and that the interval between treatment and post-mortem remains an unresolved confounder.
• The method comparisons have no independent yardstick: the Portuguese work compares 32 samples of unknown worm burden, and the laboratory work uses artificially spiked samples from a single laboratory with few operators. Both say how far methods differ, not which one delivers the true value.
• The thresholds of the two blood tests come from the manufacturer, and in both studies that use them co-authors are employed by that manufacturer. No independent check of these thresholds appears in the publications assessed here.
• The data are scattered geographically: Australia, Portugal, Sweden, Italy, Germany, Argentina and the United States. The only Swiss dataset comes from a military population with particular husbandry conditions and does not transfer to leisure horses.
• The resistance synthesis combines studies from almost three decades with very different test protocols, most of them older than today's assessment criteria. Positive findings are also published more often, which tends to overstate the share of resistant populations.

Open questions

• From which egg count does an individual horse's risk of disease rise measurably, and can such a threshold be determined empirically at all rather than agreed?
• Where does the shortened time to egg reappearance come from: resistance, features of the individual horse, the species composition or the environment?
• Do serological or molecular methods achieve independently checked accuracy for the larval burden, and how do they compare with the faecal egg count in the same animal?
• Does a treatment strategy geared to egg counts actually reduce the share of resistant worms, and at what price among the parasites the faecal egg count does not see?

Frequently asked questions

The faecal egg count was negative. Does my horse now have no worms?

That cannot be concluded from this result. What was measured is that no eggs were found in the amount of dung examined at that time. Only sexually mature females lay eggs, in the gut lumen, while the encysted larvae in the gut wall can make up as much as 90 per cent of the total burden according to older work and shed no eggs at all. A 2023 review therefore notes that egg counts cannot estimate a horse's worm burden. The same work recalls that most horses carry low burdens with no signs of disease. What follows from a result is decided by the attending practice.

How reliable is a faecal egg count in the horse anyway?

As a count of eggs it is usable; as a picture of the worm burden it is not. Two quantities limit it. First the method: against samples with a known egg count, the Mini-FLOTAC technique recovered about 65 per cent of the eggs and the modified McMaster technique about 22 per cent. Second the variation within the same animal: across 2,637 counts from 303 horses, only about half the spread was due to differences between horses. For the task of identifying high shedders that is enough in the authors' judgement; for the question of whether a particular horse carries worms, it is not.

Does the faecal egg count pick up tapeworms as well?

Only unreliably, because this tapeworm sheds its eggs in waves. In an Italian survey of 173 horses on 35 holdings, tapeworm eggs were found in five dung samples, that is in just under 3 per cent, while a blood test on the same animals placed about one horse in five at or above its treatment threshold. One caveat goes with that blood test: its thresholds come from the manufacturer, which employs several co-authors of the study, and they were not independently checked there. All that is certain is that the two methods give very different pictures on the same day.

What does the figure in eggs per gram on my report mean?

It states how many eggs per gram of dung the chosen method made visible in that sample. It is not a measure of the number of worms and not a measure of a risk of disease. Treatment thresholds such as 200 eggs per gram, used for instance in a survey of 183 Swiss Army horses, are agreements: an Australian review of 51 publications states expressly that the value above which treatment should be given remains disputed. The figure places a horse within a group; it does not describe its condition.

Why does the vet have a second sample examined after worming?

Because that second sample answers a different question: does the active substance still work on the holding? An international methods recommendation from 2023 describes this procedure expressly as a measurement at group level, comparing the same animals before and after treatment and using thresholds matched to animal species, active substance and parasite. About the condition of an individual horse the result says nothing. A value at two weeks says nothing about duration either: in a study of 82 mares, one group was already above its starting values after 45 days.

How often should I have a faecal egg count done?

This text deliberately does not answer that, because it depends on the holding, the age of the horses, pasture management and the resistance situation, and it belongs with the attending practice. What the studies contribute is the order of magnitude of the uncertainty: a single value places a horse only loosely, since about half the spread is not due to differences between animals. And a Swedish survey found the large redworm in 25 per cent of the low-shedding horses, that is precisely in those that a strategy based on egg counts alone passes over.

Sources

1. Matthews JB, Peczak N, Lightbody KL. The Use of Innovative Diagnostics to Inform Sustainable Control of Equine Helminth Infections. Pathogens, 2023 (Other | Horse)DOI 10.3390/pathogens12101233
   Narrative review of diagnostics: egg counts cannot estimate the host's worm burden, as they relate neither to the number of small strongyles nor to that of Anoplocephala perfoliata, which is why the authors call for antibody-based methods; three co-authors are employed by the manufacturer of the tests discussed.
2. Tzelos T, Geyer KK, Mitchell MC, McWilliam HEG. Characterisation of serum IgG(T) responses to potential diagnostic antigens for equine cyathostominosis. International Journal for Parasitology, 2020 (Laboratory study | Horse)DOI 10.1016/j.ijpara.2020.01.004
   Development work on a serological test that selects an antigen combination and takes as its starting point that egg counts do not relate to the worm burden; the figures of up to 90 per cent encysted larvae and of several million larvae in individual animals are taken from earlier work.
3. Scare JA, Slusarewicz P, Noel ML, Wielgus KM. Evaluation of accuracy and precision of a smartphone based automated parasite egg counting system in comparison to the McMaster and Mini-FLOTAC methods. Veterinary Parasitology, 2017 (Laboratory study | Horse)DOI 10.1016/j.vetpar.2017.10.005
   Against samples with known egg counts from 5 to 1,000 eggs per gram, Mini-FLOTAC reached a mean accuracy of 64.51 per cent, the smartphone system 32.53 per cent and the modified McMaster technique 21.67 per cent, with Mini-FLOTAC significantly more accurate than the other two methods.
4. Varandas M, Lozano J, Agricola R, Gomes L. Comparing the Performance of McMaster, FLOTAC and Mini-FLOTAC Techniques in the Diagnosis of Strongylid Infections in Two Horse Populations in Portugal. Pathogens, 2025 (Laboratory study | Horse)DOI 10.3390/pathogens14111075
   On the same 32 dung samples the detection rates were 93 per cent for Mini-FLOTAC, 89 per cent for FLOTAC and 85 per cent for McMaster with no secure difference, while McMaster of all methods reported significantly higher egg output and agreement between the techniques was substantial rather than complete.
5. Scheuerle MC, Stear MJ, Honeder A, Becher AM. Repeatability of strongyle egg counts in naturally infected horses. Veterinary Parasitology, 2016 (Cohort study | Horse)DOI 10.1016/j.vetpar.2016.08.021
   From 2,637 counts in 303 horses the repeatability came to 0.52, which the authors read as output stable enough to identify high shedders selectively; the same value means that about half the spread is not due to differences between horses.
6. Buono F, Castaldo E, Scarcelli S, Piantedosi D. A study on the prevalence of cyathostomin and Anoplocephala perfoliata infections in Italian horses: diagnostic testing and analysis of factors affecting infection risk. Journal of Equine Veterinary Science, 2025 (Cross-sectional study | Horse)DOI 10.1016/j.jevs.2025.105763
   In 173 horses on 35 holdings, strongyle eggs were found in 80.9 per cent and tapeworm eggs in 2.9 per cent of dung samples, while the serological test placed 21.4 per cent of the animals at or above the treatment threshold; the thresholds come from the manufacturer, which employs four co-authors.
7. Tyden E, Enemark HL, Franko MA, Hoglund J. Prevalence of Strongylus vulgaris in horses after ten years of prescription usage of anthelmintics in Sweden. Veterinary Parasitology: X, 2019 (Cross-sectional study | Horse)DOI 10.1016/j.vpoa.2019.100013
   In 529 samples from 106 holdings the prevalence of Strongylus vulgaris was 28 per cent of horses and 61 per cent of holdings, and 25 per cent among low-shedding horses; holdings treating on egg counts alone carried about a threefold higher risk than those with additional larval cultures or routine treatment.
8. Gehlen H, Wulke N, Ertelt A, Nielsen MK. Comparative Analysis of Intestinal Helminth Infections in Colic and Non-Colic Control Equine Patients. Animals, 2020 (Case-control study | Horse)DOI 10.3390/ani10101916
   In 620 clinic horses faecal examination found strongyle eggs in 41.8 per cent, genetic detection found Strongylus vulgaris in 1.1 per cent and serology in 32.3 per cent, and for Anoplocephala perfoliata in 10.7 per cent; no serological status was linked to colic status.
9. Bellaw JL, Nielsen MK. Meta-analysis of cyathostomin species-specific prevalence and relative abundance in domestic horses from 1975-2020: emphasis on geographical region and specimen collection method. Parasites & Vectors, 2020 (Meta-analysis | Horse)DOI 10.1186/s13071-020-04396-5
   The synthesis of 37 studies shows that the collection method shifts the species picture: gathering worms from the dung after treatment overstates the prevalence of rare species and understates their relative abundance compared with post-mortem work, and infection with ten or more species per horse is the rule.
10. Spieler N, Schnyder M. Helminths and their management in Swiss Army horses: differences between riding horses and pack horses evidence the need of improvement. Schweizer Archiv für Tierheilkunde, 2022 (Cross-sectional study | Horse)DOI 10.17236/sat00355
    In 183 Swiss Army horses selective worming was applied with a threshold of 200 eggs per gram; the riding horses shed on average 111 eggs per gram and the privately kept train horses 539, which leads the authors to see room for improvement in the care of the train horses.
11. Saeed MA, Beveridge I, Abbas G, Beasley A. Systematic review of gastrointestinal nematodes of horses from Australia. Parasites & Vectors, 2019 (Systematic review | Horse)DOI 10.1186/s13071-019-3445-4
    The review of 51 studies from 1950 to 2018 notes that routine diagnosis still rests on the McMaster technique and that the egg count above which treatment should be given remains expressly disputed.
12. Kaplan RM, Denwood MJ, Nielsen MK, Thamsborg SM. World Association for the Advancement of Veterinary Parasitology (W.A.A.V.P.) guideline for diagnosing anthelmintic resistance using the faecal egg count reduction test in ruminants, horses and swine. Veterinary Parasitology, 2023 (Professional guideline | Multiple species)DOI 10.1016/j.vetpar.2023.109936
    The recommendation recasts the egg count reduction test on four points: paired comparison of the same animals rather than two groups, a minimum number of eggs actually counted rather than a mean value per gram, flexible group size, and thresholds matched to host, active substance and parasite; it measures efficacy at group level, not the diagnostic validity of a single sample.
13. Saumell C, Lifschitz A, Baroni R, Fuse L. The route of administration drastically affects ivermectin activity against small strongyles in horses. Veterinary Parasitology, 2017 (Randomised trial | Horse)DOI 10.1016/j.vetpar.2017.01.025
    In two experiments on naturally infected horses, efficacy against small strongyles was 100 per cent after oral dosing and 36 to 64 per cent after intramuscular injection, although blood levels were higher there: what decides is the exposure of the worms in the gut lumen, not the plasma concentration.
14. Nielsen MK, Steuer AE, Anderson HP, Gavriliuc S. Shortened egg reappearance periods of equine cyathostomins following ivermectin or moxidectin treatment: morphological and molecular investigation of efficacy and species composition. International Journal for Parasitology, 2022 (Randomised trial | Horse)DOI 10.1016/j.ijpara.2022.09.003
    In 36 grazing horses with post-mortem work after two and five weeks, the disappearance of eggs does not mirror the disappearance of the parasites: very high efficacy against adult worms (99.9 and 99.7 per cent after two weeks, 88.3 and 57.6 per cent after five) alongside nil efficacy against luminal larval stages after five weeks; larval counts were reported for moxidectin only.
15. Reinemeyer CR, Prado JC, Nielsen MK. Comparison of the larvicidal efficacies of moxidectin or a five-day regimen of fenbendazole in horses harboring cyathostomin populations resistant to the adulticidal dosage of fenbendazole. Veterinary Parasitology, 2015 (Randomised trial | Horse)DOI 10.1016/j.vetpar.2015.10.003
    In a blinded experiment on 18 young horses with complete worm counts, the five-day fenbendazole regime lowered egg counts by 44.6 per cent but reached 71.2 per cent against late mucosal larvae, while moxidectin reached 99.9 per cent on eggs and 85.2 per cent on those same stages: egg reduction and larval reduction move independently of one another.
16. Mason ME, Voris ND, Ortis HA, Geeding AA. Comparison of a single dose of moxidectin and a five-day course of fenbendazole to reduce and suppress cyathostomin fecal egg counts in a herd of embryo transfer-recipient mares. Journal of the American Veterinary Medical Association, 2014 (Randomised trial | Horse)DOI 10.2460/javma.245.8.944
    In 82 treated mares egg reduction after 14 days was 99.9 per cent against 41.9 per cent, yet after 45 days the second group already exceeded its starting values while the first stayed below them for more than 90 days: a check value at two weeks says nothing about how long the effect lasts.
17. Macdonald SL, Abbas G, Ghafar A, Gauci CG. Egg reappearance periods of anthelmintics against equine cyathostomins: The state of play revisited. International Journal for Parasitology: Drugs and Drug Resistance, 2022 (Systematic review | Horse)DOI 10.1016/j.ijpddr.2022.12.002
    Of 134 studies screened, 54 remained; the review finds eight different definitions of the time to egg reappearance, reports shortened periods of 35 days for moxidectin and 28 days for ivermectin from twenty comparable studies, and expressly leaves open whether resistance or biological factors lie behind them.
18. Cai E, Wu R, Wu Y, Gao Y. A systematic review and meta-analysis on the current status of anthelmintic resistance in equine nematodes: A global perspective. Molecular and Biochemical Parasitology, 2023 (Meta-analysis | Horse)DOI 10.1016/j.molbiopara.2023.111600
    From 60 studies covering 11,835 animals between 1994 and 2022: drug class and active substance influence resistance, whereas formulation, route of administration and dose do not; the lowest efficacies were 67.83 per cent for macrocyclic lactones against roundworms and 69.85 per cent for benzimidazoles against strongyles, and no secure trend emerged across the period.
19. Ghafar A, Abbas G, Beasley A, Bauquier J. Molecular diagnostics for gastrointestinal helminths in equids: Past, present and future. Veterinary Parasitology, 2022 (Systematic review | Horse)DOI 10.1016/j.vetpar.2022.109851
    In 54 studies selected under PRISMA, molecular methods serve above all to separate species that faecal examination cannot tell apart; the review reports neither a comparative assessment of sensitivity and specificity against coproscopy nor validation for routine use.
20. Nielsen MK, Loynachan AT, Jacobsen S, Stewart JC. Local and systemic inflammatory and immunologic reactions to cyathostomin larvicidal therapy in horses. Veterinary Immunology and Immunopathology, 2015 (Randomised trial | Horse)DOI 10.1016/j.vetimm.2015.09.009
    In 18 young horses larvicidal treatment produced only a mild local inflammatory reaction with no systemic response, which the authors rate as of little clinical importance; they recall the case fatality of larval cyathostominosis of around 50 per cent and do not test what egg counts can show.