Accuracy of qPCR and bacterial culture for the diagnosis of bovine intramammary infections and teat skin colonisation with Streptococcus agalactiae and Staphylococcus aureus using Bayesian analysis

Pathogen Detection via Quantitative PCR in Milk of Healthy Cows Collected Using Different Sampling Protocols

In this study we evaluated the prevalence of pathogens detected via quantitative PCR (qPCR) in milk from apparently healthy cows to identify the most common etiological agents present in Italian dairy farms. Milk samples were collected using a sterile protocol at quarter-level (3239 samples, 822 cows) and a conventional protocol at udder level as composite milk from the functional quarters of each cow (5464 samples, 5464 cows). The qPCR commercial kit detected Mycoplasma bovis, Mycoplasma spp., Staphylococcus aureus, coagulase-negative staphylococci (CNS), Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus uberis, Prototheca spp., Escherichia coli, Klebsiella spp., Enterococcus spp. and Lactococcus lactis ssp. lactis as well as DNA from the penicillin resistance β-lactamase gene from staphylococci. The prevalence of specific DNA was calculated based on its presence or absence in the samples, factoring in both the sampling protocols and herds. Regardless of the sampling protocol used, the most frequently detected pathogens were CNS (26.6% in sterile and 13.9% in conventional protocol) and Streptococcus uberis (9.6% and 16.5%, respectively). These results underscore the necessity for pathogen-specific interventions at the farm level to enhance the udder health of dairy cows via management recommendations.

Bayesian estimation of sensitivity and specificity of a rapid mastitis test kit, bacterial culture, and PCR for detection of Staphylococcus aureus, Streptococcus species, and coliforms in bovine milk samples

Our objectives were to evaluate the diagnostic accuracy of a rapid and novel immunochromatography-based mastitis kit that includes 3 independent tests to detect coliforms (Escherichia coli or Klebsiella pneumoniae), Streptococcus spp., and Staphylococcus aureus. The kit was developed to facilitate diagnostic-based mastitis treatment. Validation of the kit was based on 154 aseptically collected mastitis samples from 2 clinical herds (clinical population) and 120 milk samples from 3 nonclinical herds (nonclinical population) without clinical cases at the time of enrollment. One herd sampled at different times was common to both populations. A 3-test in 2-population Bayesian latent class model with uniform priors for all test parameters except specificity of culture, which was modeled informatively, was used to estimate sensitivity (Se) and specificity (Sp) of the test kit, culture, and PCR at the cow level. The mastitis test kit's 96.9% Sp for Streptococcus spp. had a low false positive percentage (3.1%), which, together with the kit's rapid turnaround time for results, makes it a suitable initial screening test that producers can use to identify clinical cows to treat based on Streptococcus spp. mastitis in kit-positive results. Due to the 60.4% kit Se, producers should follow up on Streptococcus spp. kit-negative cows using a confirmatory test such as PCR (Sp of 98.4%) or culture (Sp of 99.6%). In contrast, aerobic culture had Se of 76.5% and Sp of 99.6% for Streptococcus spp. Similarly, the Sp of the kit (98.2%) and culture (99.8%) for Staph. aureus were particularly high, and even though the kit's Se (61.0%) was lower than culture (88.4%; posterior probability of difference 98%), the kit could be beneficial before use of a confirmatory test for kit-negative samples due to its ease and rapid turnaround time. Mostly, quantitative real-time (q)PCR outperformed the kit's Se (37.7%) and Sp (92.9%) for coliforms, as well as the kit's Se (60.4%) for Streptococcus spp. However, qPCR may require more technical skills and turnaround time for final results. Use of the on-farm mastitis test kit evaluated in the present study could enhance sustainable antimicrobial drug use by rapidly identifying Streptococcus mastitis for targeted treatment. Furthermore, the kit may be used in a Staph. aureus outbreak where cows can be rapidly screened to identify cases for segregation or culling during an outbreak and kit-negative cows further confirmed by milk culture or qPCR. However, the cost-effectiveness of such an approach has not been investigated.

Effect of enhanced hygiene on transmission of Staphylococcus aureus, Streptococcus agalactiae, and Streptococcus dysgalactiae in dairy herds with automatic milking systems

The objective of the study was to evaluate the effect of hygiene measures in automatic milking units on the transmission of 3 mastitis pathogens considered to be mainly or partly transmitted from cow to cow during milking events. Two studies were conducted as within-herd experimental trials in 2 Danish commercial dairy herds (A and B) with automatic milking systems. Interventions to enhance hygiene were implemented on the automatic milking units. The 2 studies evaluated separate interventions. In herd A, the hygiene interventions were manual wash with the Lely foam unit and adjustments on the brush-mediated teat cleaning procedure. In herd B, the hygiene intervention included automatic disinfection spray on the upper surface of the brush motor and daily change of brushes. Composite milk samples were collected longitudinally at 3- or 4-wk intervals from all lactating cows. Additional milk samples were taken from cows entering or leaving the study groups. Milk samples were analyzed with quantitative PCR. A hidden Markov model implemented within a Bayesian framework was used to estimate the transmission probability. For analysis, 701 samples from 156 cows were used for herd A, and 1,349 samples from 390 cows were used for herd B. In the intervention group in herd B, transmission of Streptococcus agalactiae was reduced to 19% (95% posterior credibility interval: 0.00-64%) of the transmission in the control group, whereas transmission of Streptococcus dysgalactiae was reduced to 17% (95% posterior credibility interval: 0.00-85%) of transmission in the control group. This suggests that automatic spray on the upper surface of the brush motor with disinfectant along with daily change of brushes collectively reduced transmission of Strep. agalactiae and Strep. dysgalactiae. Results on Staphylococcus aureus in herd B and results on manual foam cleaning and brush-mediated teat cleaning adjustments in herd A were inconclusive.

Differences in the coinfective process of Staphylococcus aureus and Streptococcus agalactiae in bovine mammary epithelial cells infected by Mycobacterium avium subsp. paratuberculosis

The interactions between Mycobacterium avium subsp. paratuberculosis (MAP) and the causative agents of bovine mastitis are still relatively unknown. Still, it is suspected that they may contribute to the worsening and persistence of mastitis within the mammary epithelial cells. Considering the growing economic implications of paratuberculosis and subclinical mastitis in dairy herds, this study aimed to determine the coinfection interaction between MAP and S. aureus or S. agalactiae in bovine mammary epithelial cells (MAC-T) in an ex-vivo model. For this purpose, internalisation tests of MAP + S. aureus or MAP + S. agalactiae were performed in MAC-T cells for 10, 30 and 120 min. The qPCR was performed to quantify internalised MAP at the time of exposure. Colony-forming units were counted on BHI agar medium for internalised subclinical mastitis bacteria at each time of infection. Viability tests of MAC-T cells, using the lactate dehydrogenase assay, were performed. The results showed that in the MAC-T cells previously infected by MAP and subsequently by S. aureus, there was a rapid internalisation in the first 10 min, maintaining a higher number of internalised bacteria during all exposure times. Regarding MAP + S. agalactiae, there were no changes in the internalisation patterns. The amount of MAP remained constant at all times evaluated, and there was no compromise in the viability of MAC-T cells during the tests. Thus, the results demonstrate the existence of an interaction between MAP + S. aureus, favouring internalisation and being able to contribute to the persistence of subclinical mastitis in dairy herds.

Visual detection of microRNA146a by using RNA-functionalized gold nanoparticles

Gold nanoparticles of different sizes have been synthesized and surface-functionalized with selected RNA probes in order to develop a rapid, low-cost and sensitive method for detection of microRNA146a (miR146a). The strategy is based on the change of colour that can be observed visually after aggregation of the RNA modified-gold nanoparticles (AuNPs) in presence of miR146a. Experimental conditions have been carefully selected in order to obtain a good sensitivity that allows to perform visual detection of microRNA at the nM level, achieving a detection limit of 5 nM. Good repeatability and selectivity versus other sequences that only differ from miR146a in 3 bases was achieved. miR146a has been described as one of the main microRNA involved in the immune response of bovine mastitis, being expressed in tissue, blood and milk samples. The method was successfully applied to the detection of miR146a in raw cow milk samples. The present scheme constitutes a rapid and low-cost alternative to perform highly sensitive detection of microRNA without the need of instrumentation and amplification steps for the early detection of bovine mastitis in the agrofood industry. Graphical abstract Schematic representation of the assay based on aggregation of RNA-modified gold nanoparticles (blue) in presence of microRNA146a generating a dark blue spot onto a solid support, versus a pink spot observed in absence of miR146a due to dispersed gold nanoparticles (red).

Rapid Staphylococcus aureus Detection From Clinical Mastitis Milk by Colloidal Gold Nanoparticle-Based Immunochromatographic Strips

Rapid diagnostic technologies for bovine mastitis caused by Staphylococcus aureus (S. aureus) are urgently needed. In the current study, we generated an anti-ribosomal protein-L7/L12 antibody to detect S. aureus and an anti-ribosomal protein-L7/L12 antibody-coated immune-chromatographic strip (ICS) test. Moreover, we determined the ability of the ICS test to detect S. aureus from milk samples collected from cows with clinical mastitis. The developed ICS reacted to S. aureus in a bacteria load-dependent manner with a detection limit of ~10⁴ CFU/mL. In the evaluation of possible cross-reactivity of the ICS test, six strains of coagulase-negative Staphylococci showed slightly positive reactions, although at a lower level; however, other bacteria were completely negative. Next, we investigated the sensitivity and specificity of the ICS test compared with the bacteriological culture method using milk samples from clinical bovine mastitis. The results of the experiments demonstrated that the ICS test had high sensitivity [100%, 95% confidence interval (CI): 91.3–100%] and specificity (91.9%, CI: 90.5–91.9%) compared with culture tests. In addition, the kappa statistic demonstrated that ICS tests showed substantial agreement (k = 0.77, CI: 0.66–0.87) with culture tests. Positive correlations were observed for the statistical analysis between S. aureus (nuc gene) copy numbers and ICS test scores in mastitic milk infected by S. aureus. Therefore, we assume that this new detection method using ICS may be useful as a highly sensitive S. aureus-screening method for the diagnosis of bovine mastitis. Our findings support the ongoing effort to develop an ICS method for bovine S. aureus-induced mastitis, which can contribute to the rapid diagnosis of this disease.

Comparison of quantitative PCR and MALDI-TOF mass spectrometry assays for identification of bacteria in milk samples from cows with subclinical mastitis

AIMS

The objective of this study was to compare qualitatively and quantitatively the results of identification of the bacteria present in milk samples from cows with subclinical mastitis using multiplex qPCR assay and matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS^® ) after bacteriological growth.

METHODS AND RESULTS

A total of 182 samples were aseptically collected from 119 cows with high somatic cell counts (>2·10⁵ SCC per ml) on 11 farms in Belgium in 2014. The mutiplex qPCR assay was carried out on 350 µl of milk with the PathoProof^® Complete-16kit. Ten microlitre of milk was streaked on Columbia blood agar and three selective agar plates. Growing colonies were identified by MALDI-TOF MS. Of the 182 samples, 90 gave positive results with either or both tests for one or two bacterial species/genera. Total qualitative agreement of the bacteria identified was observed in 41 mono- or bi-bacterial samples (46%) and partial agreement in 19 bi-bacterial samples at both or either tests (21%). The results of both tests on those mono- and bi-bacterial samples were not significantly different (McNemar test; P = 0·395) with a fair agreement (Cohen's kappa test; k = 0·375; P = 0·055). Moreover, quantitative correlation between the qPCR intensity and the numbers of growing colonies was observed in half of the 60 samples with qualitative matching results.

CONCLUSIONS

Both methods give identical qualitative and quantitative results with approximately a half and a quarter of the mono- and bi-bacterial samples respectively. Several reasons can explain the differences. The multiplex qPCR assay only targets the most important mammary gland pathogens and can detect DNA of bacteria both alive and dead. Conversely, bacteria only grow when alive and the MALDI-TOF MS databases do not include all bovine milk-associated bacterial species yet.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study further highlights the limitations and complementarity of the genetic and phenotypic tests for the identification of bacteria present in milk samples.

Bayesian estimation of qPCR and bacterial culture accuracy for detection of bovine coagulase-negative staphylococci from milk and teat apex at different test cut-off points

AIM

To primarily estimate the sensitivity (Se) and specificity (Sp) of the commercially available Mastit4 quantitative PCR (qPCR) assay and bacterial culture (BC) for diagnosis of intramammary infections (IMI) and teat apex colonization (TAC) with coagulase-negative staphylococci (CNS) at different cut-offs for qPCR cycle threshold values using Bayesian latent class analysis. A secondary objective was to evaluate two cut-offs of BC for diagnosis of IMI and TAC with CNS.

METHODS AND RESULTS

We randomly selected 13-20 cows with subclinical mastitis from eight dairy herds. Teat skin samples and aseptically collected foremilk samples were collected from the right hindquarters (n = 149) for BC and qPCR analysis. The Se of qPCR was always higher than BC_Se in diagnosis of IMI, however; the Sp of BC was higher than qPCR_Sp . BC_Se and BC_Sp showed no substantial difference between the tested BC cut-offs. In contrast to IMI, estimates of BC and qPCR in diagnosing TAC were different. BC_Se was higher than qPCR_Se at all tested cut-offs, however; qPCR_Sp was higher than BC_Sp .

CONCLUSION

The overall performance of qPCR is higher than BC in the diagnosis of IMI; however, the performance of BC is better than qPCR in diagnosis of TAC. The qPCR and BC are valid diagnostics for bovine IMI with CNS. However, for TAC, both techniques require further investigation to reduce the uncertainty of the true status of the quarter and teat skin.

SIGNIFICANCE AND IMPACT OF THE STUDY

We reported, for the first time, the diagnostic performance of new mastitis technology (Mastit4 PCR) and culture for detection of CNS in milk and nonmilk samples in dairy herds with automatic milking systems. Our findings will improve the interpretation of the test results of culture and qPCR assay and subsequently, will strengthen the control of IMI with CNS in dairy cows.

Composite or aseptic quarter milk samples: Sensitivity and specificity of PCR and bacterial culture of Staphylococcus aureus based on Bayesian latent class evaluation

Bacterial culture (BC) and quantitative polymerase chain reaction (qPCR) are widely used as diagnostic tests for pathogens causing intra-mammary infections (IMI) and it is therefore important to evaluate their performance to optimize pathogen detection. However, with no reference standard, their sensitivity (Se) and specificity (Sp) are unknown. Furthermore, the Se and Sp can differ between quarter samples and composite samples, both of which can be used to test for IMI. Latent class analysis (LCA) offers a method for estimating the Se and Sp of two tests on the same population, but to our knowledge this has not yet been applied to qPCR and BC for the detection of Staph. aureus in both composite and aseptically collected quarter milk samples. This allows for a performance evaluation of not only the two diagnostic methods, but also the two different samples -both cow and quarter level. In this study, we used Bayesian LCA on a dataset from one sampling day at a Danish dairy herd to estimate the Se and Sp for detecting Staph. aureus at cow and quarter level. We used Ct cut-offs of 32 and 37 cycles for the qPCR. When using a cut-off of 37 cycles, the estimated Se and Sp for BC were 62.2% and 90.5% at cow level, and 90.7% and 93.5% at quarter level, respectively. Similarly, the estimated Se and Sp for qPCR at cow level were 82.7% and 84.1%, respectively, and 80.0% and 96.8% at quarter level. Sp was therefore higher for both BC and qPCR at quarter level. Se was also highest for BC at quarter level, but the opposite was true for qPCR. The same pattern was found using a Ct cut-off at 32 cycles, but with different estimates. The results show that qPCR with a Ct cut-off at 37 had a higher Se than BC for composite DHI samples and it is therefore more suitable as a routine screening test for Staph. aureus. However, BC on quarter samples gave the highest Se and Sp and should therefore be used for confirmatory testing.

Expert evaluation of different infection types in dairy cow quarters naturally infected with Staphylococcus aureus or Streptococcus agalactiae

The purpose of this study was to improve the diagnostic recommendations for Staphylococcus aureus and Streptococcus agalactiae control using bacterial culture (BC), polymerase chain reaction (PCR) and somatic cell count (SCC) as diagnostic methods. The study was carried out in three steps: firstly, diagnostic test patterns for naturally infected quarters with Staph. aureus (24 quarters) and Strep. agalactiae (16 quarters) were created by sampling the quarters each day for 21 days and analysing the daily quarter milk samples using BC, PCR and SCC. Secondly, 30 mastitis experts were asked to group and describe the diagnostic test patterns and to establish a diagnosis for each group. The experts' statements regarding the groups they established were subsequently examined using qualitative content analysis to assign "infection types" to the statements. Lastly, the test performance was estimated for BC, PCR and SCC using generalised logistic regression models with the interpreted statements as a reference for infection. The experts mainly identified the Staph. aureus quarter-patterns as persistent infections, while some had more dynamic patterns. Strep. agalactiae quarter-patterns mainly involved persistent infection, yet some appeared hard to diagnose and were assigned to almost all different infection types, while experts did not agree on the interpretation. Estimates of Se for detection of Staph. aureus infection were 95.9% [93.7; 97.3] for BC, 99.5% [98.3; 99.8] for PCR, and 96.1% [94.0; 97.5] for SCC. The corresponding Sp estimates were 74.5% [65.7; 81.7], 66% [57.2; 73.8] and 43.7% [36.2; 51.5] for BC, PCR and SCC, respectively. The Se estimates of BC and PCR for Strep. agalactiae infection were 100% [83.5; 100] and 99.9% [99.6; 100], respectively, whereas the Se of SCC detecting Strep. agalactiae infection was only 34.3% [26.4; 43.3]. This indicated that Strep. agalactiae-positive BC and PCR test results were more important than SCC results to the experts when diagnosing a quarter as infected. The Sp estimates of BC, PCR and SCC for Strep. agalactiae infection were 99% [72.8; 100], 97.7% [62.1; 99.9], and 65.7% [56.7; 73.7], respectively. We conclude that PCR and BC are highly sensitive in the detection of persistent and new infections as defined by the experts, although the Se was not always 100%. An accepted lower Sp suggests that experts place less emphasis on false-positive results. We recommend that efforts are made to develop consistent terminology to characterise intramammary infections over time so that the course of infection can be taken into account at diagnosis.