Objectives: The study aims to explore the presence, or absence, of virulence genes and the phylogeny of a multidecade United Kingdom collection of clinical and reference Fusobacterium necrophorum isolates. Methods: Three hundred and eighty-five F. necrophorum strains (1982-2019) were recovered from storage (-80 degrees C). Illumina whole genome sequencing was undertaken with 374/385 genomes available for examination after quality checking. Sequences were analysed, using BioNumerics (bioMerieux; v 8.1), for the presence of known virulence genes. Strain phylogeny was investigated using a bespoke Fusobacterium spp. whole genome multilocus sequence typing (wgMLST) method and single nucleotide polymorphism (SNP) analysis. Results: F. necrophorum ssp. necrophorum and F. necrophorum ssp. funduliforme phylogeny showed a clear separation of the two subspecies and clustering of F. necrophorum ssp. funduliforme into three distinct clades. Congruence between SNP and wgMLST analysis was high (99.3%) and indistinguishable clusters were observed with wgMLST (n = 3) and SNP (n = 1) analysis of isolates derived from different students attending the same education setting. There was no grouping of strains by disease state or decade of isolation. No association was demonstrated with specific virulence gene detection although conspicuous virulence gene patterns were seen among the different subspecies and clades. Discussion: There was no evidence that the pathogenesis of F. necrophorum infection was associated with the presence of the virulence determinants investigated. Host-pathogen interactions should, therefore, be a focus of future research. Person-to-person transmission is a feature of this important pathogen. (c) 2025 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.

Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV) can lead to long-term sequelae in males and females; however, global prevalence data vary between geographical regions, as these sexually transmitted infections are not included in routine screening. The objective of this study was to use the cobas® TV/MG assay to assess the point prevalence of TV and MG in specimens from men and women over a broad European geographical area. Urine, vaginal, endocervical, and rectal samples were collected from patients aged ≥ 18 years receiving Chlamydia trachomatis (CT) and/or Neisseria gonorrhoeae (NG) screening as per local standard of care at sites in Belgium, Germany, Spain, and the UK (Wales). Remnant samples were assessed using the cobas TV/MG assay. Analysis of 2795 samples showed that MG prevalence varied slightly across female sample types (range: 1.7–5.8

OBJECTIVES:The objective of the study was to explore antimicrobial resistance gene determinant, and phenotypic antibiotic susceptibility, data for Fusobacterium necrophorum from a collection of UK strains. Antimicrobial resistance genes detected in publicly available assembled whole genome sequences were investigated for comparison. METHODS:Three hundred and eighty five F. necrophorum strains (1982-2019) were revived from cryovials (Prolab). Subsequent to sequencing (Illumina) and quality checking, 374 whole genomes were available for analysis. Genomes were interrogated, using BioNumerics (bioMérieux; v 8.1), for the presence of known antimicrobial resistance genes (ARGs). Agar dilution susceptibility results for 313 F. necrophorum isolates (2016-2021) were also examined. RESULTS:The phenotypic data for the 313 contemporary strains demonstrated potential resistance to penicillin in three isolates, using EUCAST v 11.0 breakpoints, and 73 (23%) strains using v 13.0 analysis. All strains were susceptible to multiple agents using v 11.0 guidance other than clindamycin (n = 2). Employing v 13.0 breakpoints, metronidazole (n = 3) and meropenem (n = 13) resistance were also detected. The tet(O), tet(M), tet(40), aph(3')-III, ant(6)-la and blaOXA-85 ARGs were present in publicly available genomes. tet(M), tet(32), erm(A) and erm(B) were found within the UK strains, with correspondingly raised clindamycin and tetracycline minimum inhibitory concentrations. CONCLUSIONS:Susceptibility to antibiotics recommended for the treatment of F. necrophorum infections should not be assumed. With evidence of potential ARG transmission from oral bacteria, and the detection of a transposon-mediated beta-lactamase resistance determinant in F. necrophorum, surveillance of both phenotypic and genotypic antimicrobial susceptibility trends must continue, and increase.

Context Some populations of introduced species cause significant undesirable impacts but can also act as reservoirs for genetic diversity. Sambar deer (Cervus unicolor) are ‘Vulnerable’ in their native range and invasive in Australia and New Zealand. Genetic data can be used to determine whether these introduced populations might serve as genetic reservoirs for declining native populations and to identify spatial units for management. Aims We aimed to identify the provenance of sambar deer in Australia and New Zealand, and to characterise their genetic diversity and population structure. Methods We used mitochondrial control region sequences and 18 nuclear microsatellite loci of 24 New Zealand and 63 Australian sambar deer collected across continuous habitat in each location. We estimated genetic diversity and population differentiation by using pairwise FST, AMOVA, and Structure analyses. We compared our data with 27 previously published native and invasive range sequences to identify phylogenetic relationships. Key results Sambar deer in Australia and New Zealand are genetically more similar to those in the west of the native range (South and Central Highlands of India, and Sri Lanka), than to those in the east (eastern India, and throughout Southeast Asia). Nuclear genetic diversity was lower than in the native range; only one mitochondrial haplotype was found in each introduced population. Australian and New Zealand sambar deer were genetically distinct but there was no population structure within either population. Conclusions The genetic differences we identified between these two introduced populations at putatively neutral loci indicate that there also may be underlying diversity at functional loci. The lack of population genetic structure that we found within introduced populations suggests that individuals within these populations do not experience barriers to dispersal across the areas sampled. Implications Although genetic diversity is reduced in the introduced range compared with the native range, sambar deer in Australia and New Zealand harbour unique genetic variants that could be used to strengthen genetic diversity in populations under threat in the native range. The apparent high levels of gene flow across the areas we sampled suggest that localised control is unlikely to be effective in Australia and New Zealand.

Introduction. A retrospective data analysis of 34 months (spanning 2016???2020) of 961573 diagnostic results obtained before and after nucleic acid amplification testing (NAAT) implementation, across the Public Health Wales microbiology network. Hypothesis / Gap Statement. This is the first network -wide analysis of the implementation of enteric NAAT in diagnostic microbiology. Aim. To assess the outcome of replacing microscopy and bacterial culture with NAAT as the primary test in the diagnosis of: Campylobacter spp., Salmonella sp., Shigella spp., Shiga toxin-producing Escherichia coli (STEC), Cryptosporidium spp. and Giardia duodenalis infections. Methodology. Following NAAT introduction, bacterial culture was performed as a secondary test, to provide further information from NAAT positive samples for epidemiological purposes. Primary detection rates and overall bacterial culture rates were calculated for each target pathogen using both testing regimes (Stage I) including a comparison of in-patient and out-patient diagnoses (Stage II). Results. Stage I analysis showed that the primary detection rate significantly increased for Campylobacter spp. (P<0.0001), Salmonella sp. (P=0.0151), Shigella spp. (P<0.0001), STEC (P<0.0001), Cryptosporidium spp. (P<0.0001) and Giardia duodenalis (P<0.0001) when using NAAT compared to microscopy or bacterial culture. A significant decrease was seen in the overall rate of Campylobacter spp. isolation by bacterial culture (P<0.0001), whilst other targets remained unaffected. Stage II analysis showed that NAAT positive out-patient samples were more likely to be supplemented by a positive bacterial culture than NAAT positive in-patient samples for Campylobacter spp. (P<0.0001), Salmonella sp. (P=0.0004) and STEC (P=0.0039). However, Shigella spp. was more frequently isolated from NAAT positive in-patient samples (P=0.0005). A notable increase was seen for G. duodenalis detection from in-patient samples (P=0.0002). Reference laboratory data showed the NAAT assay can detect at least 53 serotypes of STEC but may not be able to detect some of the rarer species of Cryptosporidium seen in human infections. Conclusion. The implementation of NAAT has significantly increased the primary detection rate of all target enteric pathogens in Wales and information gleaned previously from direct culture is largely unaffected.

Objectives: To assess the differences in antimicrobial susceptibility of UK Bacteroides species across two distinct cohorts from 2000 to 2016. Methods: Strain identification was performed using matrix-assisted laser-desorption ionisation time of flight mass spectrometry (MALDI-TOF MS) or by partial 16S rRNA sequencing. Minimum inhibitory concentrations (MICs) were determined using agar dilution, following CLSI guidelines (CLSI, 2012; 2017). Results: 224 isolates were included from 2000 to 168 from 2016. Bacteroides fragilis was the most common species, comprising 68% of the 2000 cohort, and 77% in 2016. For all antimicrobials tested, there was an overall increase in the rates of non-susceptible isolates between the cohorts. Conclusions: The antibiogram of Bacteroides species in the UK is no longer predictable. Multi-drug resistant isolates although rare, are on the rise, and require testing to guide therapy. The monitoring and surveillance of resistance trends is imperative, as is the development of standardised, robust and accessible antimicrobial susceptibility testing methodology for clinical laboratories. Crown Copyright (c) 2021 Published by Elsevier Ltd. All rights reserved.

Objectives: To determine the impact of the 2018 introduction of nucleic acid amplification tests (NAATs) for C. difficile detection on the laboratory diagnosis of C. difficile infection (CDI), and the distribution of C. difficile ribotypes. Methods: A retrospective analysis of five years (2015-2019) of C. difficile diagnostic laboratory and PCR ribotyping test results. Results: A total of 255,104 diagnostic results, from 136,353 patients were analysed: 199,794 samples where glutamate dehydrogenase (GDH) was used as the primary screen; and 55,310 where NAATs were employed. An overall decrease in frontline positivity from 2015 to 2019 (10.3% [n = 5017] to 6% [n = 3190] - p < 0.0001) was observed, despite an increase in the number of samples tested (48,778 to 52,839). NAAT positivity was lower than GDH (p < 0.0001) for the two years where it was implemented. The variance was accounted for by increased overall C. difficile isolation and reduced toxin negative strain culture from NAAT positive samples (p < 0.0001). Ribotype distribution (6546 samples) remained stable with decreasing RT27 isolation in each year except 2017 (p < 0.0001). RT78 was associated with toxin A/B EIA positivity (p < 0.0001). Conclusions: Use of NAAT for the detection of C. difficile, as part of a 2-step algorithm, has not led to an increase in CDI laboratory diagnostic test positivity. In spite of ribotype distribution being comparable for screening in toxin A/B positive samples, there is a significantly greater correlation between NAAT positivity and culture of toxigenic strains compared to GDH. Crown Copyright (C) 2020 Published by Elsevier Ltd. All rights reserved.

An inability to standardize the bioinformatic data produced by whole-genome sequencing (WGS) has been a barrier to its widespread use in tuberculosis phylogenetics. The aim of this study was to carry out a phylogenetic analysis of tuberculosis in Wales, United Kingdom, using Ridom SeqSphere software for core genome multilocus sequence typing (cgMLST) analysis of whole-genome sequencing data. The phylogenetics of tuberculosis in Wales have not previously been studied. Sixty-six Mycobacterium tuberculosis isolates (including 42 outbreak-associated isolates) from south Wales were sequenced using an Illumina platform. Isolates were assigned to principal genetic groups, single nucleotide polymorphism (SNP) cluster groups, lineages, and sublineages using SNP-calling protocols. WGS data were submitted to the Ridom SeqSphere software for cgMLST analysis and analyzed alongside 179 previously lineage-defined isolates. The data set was dominated by the Euro-American lineage, with the sublineage composition being dominated by T, X, and Haarlem family strains. The cgMLST analysis successfully assigned 58 isolates to major lineages, and the results were consistent with those obtained by traditional SNP mapping methods. In addition, the cgMLST scheme was used to resolve an outbreak of tuberculosis occurring in the region. This study supports the use of a cgMLST method for standardized phylogenetic assignment of tuberculosis isolates and for outbreak resolution and provides the first insight into Welsh tuberculosis phylogenetics, identifying the presence of the Haarlem sublineage commonly associated with virulent traits.

The air transportation system has a broad and deep value chain. Some of the stakeholders are directly part of the air transportation system and use real-time flight, airport and air traffic control data as part of their operations. Other stakeholders are several layers removed and do not have access to system status even though it impacts their business. For these stakeholders it may be outside their core competency or cost prohibitive to purchase access to a data feed and the required hardware/software infrastructure to support real-time status alerting. In many cases, the need for status alerting is only temporary (e.g. seasonal, during period of construction, or transition to new gate leasing arrangement). This paper describes a low-cost software application that can be deployed to provide real-time alerts to stakeholders whose operations are directly impacted by flight and system status changes, but cannot afford to maintain their own status alerting system. The flight status alerting system described in this paper can be configured over the web and transmits alerts via email or text messages to the cell phones of employees. Case studies are provided for: (1) alerts to adjust staffing at an airport food concession for forecast irregular operations (to generate an estimated $46K to $121K in additional annual profit), (2) alerts to investigate excessive taxiin times and gate utilization compliance. Implications and limitations of the system are discussed.

Purpose. Conventional laboratory detection methods for gastrointestinal parasites are time consuming, require considerable technical expertise and may suffer from poor analytical sensitivity. This study sought to evaluate the automated BD MAX Enteric Parasite Panel (EPP) for the detection of Cryptosporidium parvum/hominis, Entamoeba histolytica and Giardia duodenalis.Methodolgy. A total of 104 known positive samples (43 Cryptosporidium parvum/hominis and 61 G. duodenalis), 15 simulated samples (E. histolytica and other Entamoeba species) and 745 patient stool samples, submitted for enteric pathogen culture and microscopy, were inoculated into BD MAX EPP sample buffer tubes (SBTs). All specimens were blinded and tested within 7 days of SBT inoculation using the BD MAX EPP assay with results compared to those generated by microscopy.Results/Key findings. Combining the results from the known positive samples and anonymously tested patient samples, the sensitivity of the BD MAX EPP assay was 100% for both Cryptosporidium spp. and G. duodenalis. Specificities of 99.7 and 98.9% were calculated for the detection of Cryptosporidium spp. and G. duodenalis respectively. Insufficient clinical specimen data was available to determine the performance of the assay for E. histolytica detection.Conclusions. The findings of this study indicate that the BD MAX EPP is suitable for the detection of Cryptosporidium parvum/hominis and G. duodenalis from clinical specimens with reduced hands-on time and complexity compared to microscopy. Results for the detection of E. histolytica were promising although further work is required to evaluate the assay for the detection of this pathogen.

Invasive aspergillosis is a significant cause of morbidity and mortality within at-risk groups. Directed antifungal chemotherapy, guided by effective screening algorithms that incorporate reliable and validated molecular assays, reduces the morbidity associated with empirical administration and allows earlier diagnosis. The efficient extraction of nucleic acid from Aspergillus fumigatus is the main limiting factor for-successful Aspergillus PCR from clinical specimens. With the integration of automated extraction platforms, assessment of the suitability of these platforms for specific targets is of paramount importance. In this study, four extraction robots (Applied Biosystenns MagMAX, bioMerieux easyMAG, Qiagen EZ1 and Roche MagNA Pure LC) were evaluated for their ability to extract clinically significant levels of A. fumigatus from blood. All of the platforms could detect 10(1) c.f.u. ml(-1) from EDTA whole blood, although only the easyMAG, EZ1 and MagNA Pure had 100% reproducibility at this level. Despite good analytical sensitivity, contamination associated with the easyMAG platform excluded its use for diagnostic Aspergillus PCR. The EZ1 and MagNA Pure platforms demonstrated equivalent high sensitivity and negative predictive values (97.4-100%), essential for screening assays.

Infectious gastrointestinal disease is caused by a diverse array of pathogens, and is a challenging syndrome to correctly diagnose and manage. Conventional laboratory diagnostic methods are often time-consuming and frequently suffer from low detection rates. Two commercial multiplex nucleic acid amplification tests [Luminex xTAG Gastrointestinal Pathogen Panel (GPP) and Savyon Diagnostics Gastrointestinal Infection Panel (GIP)] were applied to 1000 stored diarrhoea] clinical stool samples. The Luminex xTAG GPP and Savyon GIP detected Campylobacter in 42/44 and 44/44 culture-positive samples, Salmonella in 4/4 and 3/4 culture-positive samples, Shigella in 1/1 culture-positive sample, Clostridium difficile toxin in 32/35 ELISA-positive samples, and Giardia in 6/6 wet-preparation-microscopy-positive samples, respectively. When the Luminex GPP assay was used concurrently with conventional methods for 472 clinical samples, it detected Campylobacter in 22/22 culture-positive samples, Salmonella in 1/1 culture-positive sample, Clostridium difficile toxin in 14/14 ELISA-positive samples and Giardia in 4/4 wet-preparationmicroscopy-positive samples. The pathogen/toxin detection rate for conventional methods in both sample sets was <10%. The Luminex xTAG GPP detection rate was 24.8% in the stored samples and 32.6% in the concurrently tested samples. The Savyon GIP detection rate was 22.5%. From stored samples, 2.4% of Luminex xTAG GPP detections and 3.1% of Savyon GIP detections could not be confirmed using alternative nucleic acid amplification tests. Enhanced detection rates resulted from increased detection of pathogens routinely sought using conventional methods and were also due to ascertainment of micro-organisms that current testing strategies do not diagnose. Use of multiplex nucleic acid amplification tests will allow clinical laboratories to diagnose infectious gastroenteritis in more patients with diarrhoeal disease by increasing the sensitivity of pathogen detection and by reducing the selective bias of current strategies. The clinical and economic impact of these results warrants further investigation.

Objectives Recently marketed nucleic acid amplification tests (NAAT) for the detection of Neisseria gonorrhoeae (NG) have improved specificity over previous generation assays. A study to assess the necessity for confirmation of Roche cobas 4800 NG positive samples was undertaken by the Public Health Wales Microbiology Molecular Diagnostic Unit in Cardiff.Methods Classical NG culture identification was compared to cobas 4800 (DR-9), opacity (opa) gene and porA pseudogene (pap) results. Confirmatory NAATs (opa/pap) were performed prospectively for 120 cobas 4800 NG positive urogenital and extragenital samples. Retrospective supplementary NAAT and sequence analysis of additional cobas 4800 NG positive extragenital samples was also carried out.Results Of the 188 classically identified clinical NG isolates, 184 were identified as NG in all 3 molecular targets. Two isolates were only detected by 2 molecular targets. A further 2 isolates were culture false-positives. Combining the results from prospective and retrospective testing, the sensitivity and negative predictive value for cobas 4800 NG detection for urogenital, rectal and oropharyngeal samples was 100%. Specificity for all sample types was greater than 99.7%. Positive predictive value was 96.0% and 96.4% for urogenital and rectal specimens, respectively, and 88.6% for oropharyngeal samples.Conclusions Molecular tests could be used for culture confirmation where available. Roche cobas 4800 Chlamydia trachomatis/Neisseria gonorrhoeae (CT/NG) CT/NG gonorrhoea diagnosis is superior to culture with urogenital and rectal positives not requiring confirmation. Roche cobas 4800 oropharyngeal NG detection findings warrant further prospective study of routine confirmatory testing accounting for its cost and clinical usefulness.

Infectious gastrointestinal disease is caused by a diverse array of pathogens, and is a challenging syndrome to correctly diagnose and manage. Conventional laboratory diagnostic methods are often time-consuming and frequently suffer from low detection rates. Two commercial multiplex nucleic acid amplification tests [Luminex xTAG Gastrointestinal Pathogen Panel (GPP) and Savyon Diagnostics Gastrointestinal Infection Panel (GIP)] were applied to 1000 stored diarrhoeal clinical stool samples. The Luminex xTAG GPP and Savyon GIP detected Campylobacter in 42/44 and 44/44 culture-positive samples, Salmonella in 4/4 and 3/4 culture-positive samples, Shigella in 1/1 culture-positive sample, Clostridium difficile toxin in 32/35 ELISA-positive samples, and Giardia in 6/6 wet-preparation-microscopy-positive samples, respectively. When the Luminex GPP assay was used concurrently with conventional methods for 472 clinical samples, it detected Campylobacter in 22/22 culture-positive samples, Salmonella in 1/1 culture-positive sample, Clostridium difficile toxin in 14/14 ELISA-positive samples and Giardia in 4/4 wet-preparation-microscopy-positive samples. The pathogen/toxin detection rate for conventional methods in both sample sets was <10%. The Luminex xTAG GPP detection rate was 24.8% in the stored samples and 32.6% in the concurrently tested samples. The Savyon GIP detection rate was 22.5%. From stored samples, 2.4% of Luminex xTAG GPP detections and 3.1% of Savyon GIP detections could not be confirmed using alternative nucleic acid amplification tests. Enhanced detection rates resulted from increased detection of pathogens routinely sought using conventional methods and were also due to ascertainment of micro-organisms that current testing strategies do not diagnose. Use of multiplex nucleic acid amplification tests will allow clinical laboratories to diagnose infectious gastroenteritis in more patients with diarrhoeal disease by increasing the sensitivity of pathogen detection and by reducing the selective bias of current strategies. The clinical and economic impact of these results warrants further investigation.

ABSTRACT Nonculture-based tests are gaining popularity in the diagnosis of invasive fungal disease (IFD), but PCR is excluded from disease-defining criteria because of limited standardization and a lack of commercial assays. Commercial PCR assays may have a standardized methodology while providing quality assurance. The detection of PCR products by a surface-enhanced Raman scattering (SERS) assay potentially provides superior analytical sensitivity and multiplexing capacity compared to that of real-time PCR. Using this approach, the RenDx Fungiplex assay was developed to detect Candida and Aspergillus. Analytical and clinical evaluations of the assay were undertaken using extraction methods according to European Aspergillus PCR Initiative (EAPCRI) recommendations. A total of 195 previously extracted samples (133 plasma, 49 serum, and 13 whole blood) from 112 patients (29 with proven/probable IFD) were tested. The 95% limit of detection of Candida and Aspergillus was 200 copies per reaction, with an overall reproducibility of 92.1% for detecting 20 input copies per PCR, and 89.8% for the nucleic acid extraction–PCR-SERS process for detecting fungal burdens of <20 genome equivalents per sample. A clinical evaluation showed that assay positivity significantly correlated with IFD (P < 0.0001). The sensitivity of the assay was 82.8% and was similar for both Candida (80.0%) and Aspergillus (85.7%). The specificity was 87.5% and was increased (97.5%) by using a multiple (≥2 samples) PCR-positive threshold. In summary, the RenDx Fungiplex assay is a PCR-SERS assay for diagnosing IFD and demonstrates promising clinical performance on a variety of samples. This was a retrospective clinical evaluation, and performance is likely to be enhanced through a prospective analysis of clinical validity and by determining clinical utility.

ABSTRACT Requests for direct molecular diagnosis of mycobacterial disease are increasingly warranted. The Anyplex MTB/NTM assay demonstrates sensitivities, specificities, and positive and negative predictive values of 1.00, 0.96, 0.93, and 1.00 for Mycobacterium tuberculosis complex (MTBC) and 1.00, 0.97, 0.75, and 1.00 for nontuberculous mycobacteria (NTM) detection, respectively, making it a suitable screening test for mycobacterial detection.

Recently marketed nucleic acid amplification tests (NAAT) for the detection of Neisseria gonorrhoeae (NG) have improved specificity over previous generation assays. A study to assess the necessity for confirmation of Roche cobas 4800 NG positive samples was undertaken by the Public Health Wales Microbiology Molecular Diagnostic Unit in Cardiff.Classical NG culture identification was compared to cobas 4800 (DR-9), opacity (opa) gene and porA pseudogene (pap) results. Confirmatory NAATs (opa/pap) were performed prospectively for 120 cobas 4800 NG positive urogenital and extragenital samples. Retrospective supplementary NAAT and sequence analysis of additional cobas 4800 NG positive extragenital samples was also carried out.Of the 188 classically identified clinical NG isolates, 184 were identified as NG in all 3 molecular targets. Two isolates were only detected by 2 molecular targets. A further 2 isolates were culture false-positives. Combining the results from prospective and retrospective testing, the sensitivity and negative predictive value for cobas 4800 NG detection for urogenital, rectal and oropharyngeal samples was 100%. Specificity for all sample types was greater than 99.7%. Positive predictive value was 96.0% and 96.4% for urogenital and rectal specimens, respectively, and 88.6% for oropharyngeal samples.Molecular tests could be used for culture confirmation where available. Roche cobas 4800 Chlamydia trachomatis/Neisseria gonorrhoeae (CT/NG)CT/NG gonorrhoea diagnosis is superior to culture with urogenital and rectal positives not requiring confirmation. Roche cobas 4800 oropharyngeal NG detection findings warrant further prospective study of routine confirmatory testing accounting for its cost and clinical usefulness.

Identifying species occupying an area is essential for many ecological and conservation studies. Faecal DNA is a potentially powerful method for identifying cryptic mammalian species. In New Zealand, 10 species of ungulate (Order: Artiodactyla) have established wild populations and are managed as pests because of their impacts on native ecosystems. However, identifying the ungulate species present within a management area based on pellet morphology is unreliable. We present a method that enables reliable identification of 10 ungulate species (red deer, sika deer, rusa deer, fallow deer, sambar deer, white-tailed deer, Himalayan tahr, Alpine chamois, feral sheep, and feral goat) from swabs of faecal pellets. A high resolution melting (HRM) assay, targeting a fragment of the 12S rRNA gene, was developed. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behaviour for each species. The method was developed using tissue from each of the 10 species, and was validated in blind trials. Our protocol enabled species to be determined for 94% of faecal pellet swabs collected during routine monitoring by the New Zealand Department of Conservation. Our HRM method enables high-throughput and cost-effective species identification from low DNA template samples, and could readily be adapted to discriminate other mammalian species from faecal DNA.