Biosecurity measures designed to reduce the risk of the infectious disease’s introduction in dairy farms by employees and visitors.
\r\n\tIn this book, the different factors of liquefaction, the field methods and laboratory tests to identify a potentially liquefiable soil aim to be reviewed; in addition with history cases (ground behavior during the occurrence of an earthquake, state of stress, deformation, shear strength, flow, etc.).
\r\n\tA very important aspect of this topic is the presentation of the different constructive techniques used to ground improvement (vibrocompaction, dynamic compaction, jet grouting, chemical injection, replacement, etc.), placing special emphasis on those constructive methods used to solve problems on structures already located in areas of low relative density with liquefaction potential, where the installation of monitoring and control equipment is also required (tiltmeters, piezometers, topographic points, seismographs, pressure cells, etc.).
Quantitative analysis using liquid chromatography/mass spectrometry (LC/MS) is widespread, especially in drug metabolism and pharmacokinetics studies, and in many laboratories label-free LC/MS analyses are carried out, i.e., without using isotope labeling techniques. However, even if the analytical method is well validated, an unexpected change in matrix concentrations in biological samples may cause matrix effects such as ion suppression or ion enhancement. When ion suppression occurs, for example, the ionization efficiency of an analyte molecule decreases, and the ion intensity of the analyte decreases from the expected intensity (Tang et al., 2004, Buhrman et al., 1996). Then the linear relationship between the sample amount and the ion intensity is lost, as shown in Figure 1.
\n\t\t\tWhen ion suppression occurs, the linear relationship between the ion intensity and the sample amount is lost, as shown by an arrow, and thus, label-free quantitative analysis becomes difficult.
The effects of ion suppression can be overcome by using stable-isotope labeling techniques such as 12C/13C and 14N/15N labeling, since an isotope-labeled molecule, used as an internal standard, exhibits chemical properties or effects of ion suppression almost identical to those of the unlabeled one. Eventually, though, label-free LC/MS analyses have to be carried out when we cannot employ isotope labeling techniques, which are rather laborious and expensive.
\n\t\t\tIon suppression occurs in LC/MS interfaces such as electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI), which are used to analyze less volatile and volatile molecules, respectively. Because ESI is the more widely used technique, ion suppression in ESI is mainly described here, although that in APCI is also discussed later.
\n\t\t\tBecause the effect of ion suppression depends on the chemical properties of the analyte molecule in ESI, it is difficult to correct for decreased intensity, so quantitative analysis becomes difficult. The potential occurrence of ion suppression can be reduced by desalting and fractionating the sample, reducing the sample volume, and the effect of ion suppression can be reduced by using a structural analog. Nevertheless, ion suppression may occur, and correcting for the decreased intensity remains difficult. Several sample preparation protocols for specific analytes have been proposed to reduce the effect of ion suppression by using internal standards (Matuszewski et al., 1998, Bonfiglio et al., 1999), but they are not widely used in label-free LC/MS.
\n\t\t\tWe have developed a simple technique for detecting potential ion suppression in ESI (Hirabayashi et al., 2007, 2009). In this technique, a specific concentration of a probe molecule, which is sensitive to the occurrence of ion suppression, is added to an LC mobile phase, and the intensity of the protonated probe molecule is monitored. When ion suppression occurs, the intensity of the protonated probe is expected to decrease more than those of other protonated molecules, [M+H]+.
\n\t\tIn this section, a brief explanation for why ion suppression occurs in ESI is presented, based on ion formation mechanisms of less volatile analyte molecules than solvent molecules, before explaining the technique for detecting potential ion suppression.
\n\t\t\tIn ESI and other spray ionizations, an LC effluent in a capillary is sprayed from the capillary tip. Then, charged droplets are formed, from which gaseous ions are produced. Figure 2 shows a schematic view of a positively charged droplet. The droplet initially produced has a diameter of the order of 1 μm, and the diameter decreases as the solvent molecules evaporate. In the droplet, positive ions are concentrated near the inside of the droplet surface because of a Coulomb repulsive force. As solvent molecules evaporate, the gaseous ions are produced from the liquid-phase ions inside the droplet surface through ion evaporation (Iribarne & Thomson, 1976, de la Mora, 2000) or charged residue mechanisms (Dole et al., 1968). Therefore, most ions analyzed in a mass spectrometer originate from the liquid-phase ones near the inside of the charged droplet surface. In the charged droplet, the liquid-phase chemistry, ignoring the effect of the surface, is not necessarily valid but is a good approximation (Hirabayashi 1993).
\n\t\t\tIon suppression occurs in the ionization processes when a component eluted from an LC column affects the ionization of coeluted analytes. In the droplet surface, the analyte molecules are charged in accordance with their chemical properties when the number of charges is much higher than that of analyte molecules. Then the ionization efficiency for each analyte molecule remains constant. Under these conditions, label-free quantitative analysis is readily performed. On the contrary, when the number of charges in the droplet is comparable to, or less than, that of analyte molecules, charge competition occurs among the analyte molecules. Because the decrease in the number of charges can be regarded as an increase in pH, the protonation for acidic molecules, for example, is likely to be reduced to a greater extent than that for neutral and basic ones. Of these molecules, those weakly dissociated near the surface tend to lose their charge in the competition, and their ionization efficiencies decrease, leading to ion suppression. Thus, in molecules with low ionization efficiencies, the ionization efficiencies tend to decrease further when ion suppression occurs. In contrast, when the number of charges in the droplet increases, the ionization efficiencies of some molecules increase. This leads to ion enhancement. The ionization efficiencies of molecules with low ionization efficiencies are expected to increase when ion enhancement occurs.
\n\t\tCross-sectional view of a positively charged droplet. The ionization processes of acidic molecules with low ionization efficiencies are shown: most of the molecules are deprotonated and concentrated in the central region of the droplet, but some do not undergo deprotonation because of their dissociation equilibrium. These neutral molecules with a low surface accessibility mostly remain in the droplet, but only a small part of the molecules can reach the droplet surface (1). Then, the protonated molecules may form near the surface (2). Gaseous ions are formed from the liquid-phase ions inside the droplet surface by ion evaporation or charge residue mechanisms.
In the following we consider the ionization processes of molecules with low ionization efficiencies in a charge droplet. In the droplet, the neutral or negatively charged molecules remain deep, as shown in Fig. 2. To be protonated, these molecules have to access the surface. Then, near the inside of the droplet surface, they are protonated in accordance with their isoelectric point, or dissociation constant. Therefore, the major factors determining the ionization efficiency are (1) surface accessibility (or hydrophobicity) and (2) isoelectric point (or dissociation constant) of the analyte molecule. Hydrophobic and basic molecules are expected to be insensitive to ion suppression, and their ionization efficiencies are rather high. On the contrary, the ionization efficiencies of quite hydrophilic and acidic molecules are much lower than those of the above molecules. However, these molecules would be quite sensitive to the occurrence of ion suppression and can potentially be used as probes for detecting ion suppression in the analysis of positive ions (protonated molecules).
\n\t\t\tHydrophobicity (Black & Mould, 1991) and isoelectric point (Linde, 1995) for 20 amino acids.
In developing the probe, a convenient technique is to synthesize a quite hydrophilic and acidic peptide, which has an amino-acid sequence including a hydrophilic and neutral amino acid as well as an acidic one, as the probe for detecting ion suppression. Figure 3 compares 20 amino acids in terms of their hydrophobicity and isoelectric points (pI). Among the amino acids, serine (S), asparagine (N), and glutamine (Q) are very hydrophilic and neutral. On the other hand, aspartic acid (D) and glutamic acid (E) are very acidic, with a pKR of 3.65 and 4.25, respectively (Linde, 1995a), where pKR is the pK for the side chain of the amino acid. Then, as a probe for ion-suppression detection, we synthesized a peptide, DSSSSS, the isoelectric point of which is calculated to be 3.80 (Gasteiger et al., 2005). This probe is so acidic that no multiply protonated molecule of the probe is detected; only singly protonated ones can be detected at m/z 569.3 in a mass spectrometer. The molecular weight of the probe can be modified by altering the number of hydrophilic and neutral amino acids such as S. As mentioned above, the ionization efficiency of the probe is relatively low, whereas the probe concentration in the LC mobile phase should preferably be low, so as not to cause ion suppression. More acidic molecules than DSSSSS, for example, DDSSSS or DDDSSS with respective isoelectric points of 3.56 and 3.42, would be more sensitive to the occurrence of ion suppression, and could also be used as the probes. However, because of their higher acidities, their concentration should be higher than that of DSSSSS to be detected clearly in a mass spectrometer. Since the probe is rather insensitive to the occurrence of ion suppression of more acidic molecules than the probe, it is difficult to detect potential ion suppression for such acidic molecules if they are there. Note that the probe should be used to detect potential ion suppression for protonated molecules, not for cations and cationized molecules such as [M]+ and [M+Na]+.
\n\t\t\tFor a probe used in negative-ion analysis, on the other hand, quite hydrophilic and basic peptides should be synthesized by using a very basic amino acid of R or K with a pKR of 12.48 and 10.53, respectively (Linde, 1995) and the very hydrophilic ones. Then ion suppression of ions with the form of [M-H]- can be detected by monitoring the intensity of the deprotonated molecule of the probe.
\n\t\t\tIn the following, the usability of the probe is examined. In most LC/MS analyses, the pH of the mobile phase ranges from 2 to 6, and the concentration of the organic solvent such as acetonitrile and methanol is below 90%. Figure 4 (a) plots the intensity of the protonated probe as a function of the acetonitrile concentration of the mobile phase under several pH conditions. The intensity appears to be almost independent of the mobile-phase pH. On the other hand, the intensity increases with an increase in the acetonitrile concentration. The increase in the ion intensity (or the ion formation efficiency of the probe) can be ascribed to the enhanced solvent evaporation of the charged droplets, since the surface accessibility (or hydrophobicity) of the probe has been confirmed to be almost independent of the organic solvent concentration by comparing the probe with a much more hydrophobic peptide of FDFSF (Hirabayashi, 2009). Furthermore, the number of charges in the droplet is likely to be almost independent of the organic solvent concentration. This is because the ion current, which is the current for all of the ions and charged droplets produced by ESI, is almost unchanged, as shown in Fig. 4 (b), and this trend is independent of the organic solvent such as acetonitrile and methanol. Thus, the probe is expected to be much less surface-accessible and quite acidic under the conditions used in LC/MS analyses.
\n\t\tAs mentioned earlier, the effect of ion suppression depends on the sample amount. Therefore, different sample amounts of fractionated human plasma, as a typically crude sample, were analyzed with a nanoLC/TOF-MS system to detect the occurrence of ion suppression. An aqueous solution of the probe is added to the LC mobile phase at a gradient mixer-pump unit of the nanoLC system just before being introduced into a separation column. Then, a linear gradient of acetonitrile concentration from 7 to 50% is run at a flow rate of 50nL/min. Since the probe is very hydrophilic, it can pass through the reverse-phase separation column without adsorption when the organic solvent concentration of the LC mobile phase is above 4%. Then the protonated probe is detected in the mass spectrometer during the LC/MS analysis.
\n\t\t\ta) Intensity of the protonated probe molecule and (b) current for all the ions and charged droplets produced by ESI as a function of the acetonitrile (ACN) concentration of the mobile phase under several pH conditions.
a) Total ion current chromatograms obtained from human plasma with injection amounts of 0.005, 0.05, and 0.5 μg, and (b) corresponding mass chromatograms of the protonated probe.
\n\t\t\t\tFigure 5 compares (a) chromatograms of the total ion current and (b) mass chromatograms of the protonated probe. For an injected amount of 0.005 μg, the mass chromatogram, shown in blue, is rather flat, except for the moment of sample injection using a manual injector. Thus, no ion suppression is likely to occur. However, for 0.05-μg injection, the intensity for the protonated probe, shown in yellow, decreases appreciably at a retention time above 50 min. For 0.5-μg injection, shown in red, a significant decrease in intensity is detected at a retention time above 40 min. For example, at 60 min (indicated by the vertical dashed line) the ion intensity for the 0.05-μg injection decreases by about 20%, and the decrease is above our experimental error of 10%. This means that potential ion suppression occurs and its maximum effect on ion intensity is 20%. Therefore, if an uncertainty of 20% is accepted, quantitative analysis is readily performed at the retention time. On the other hand, for the 0.5-μg injection, the effect of ion suppression is serious, and quantitative analysis would be difficult.
\n\t\t\tPeak areas for the m/z 639.91 and 558.93 ions as a function of the injected sample amount. Broken lines with a slope of 1 are shown as a visual aid. Error bars show the decrease in intensity of the protonated probe.
The probe is expected to be so sensitive to the occurrence of ion suppression that the decrease in intensity for the protonated probe is stronger than those for other protonated molecules. Figure 6 shows the experimental results for protonated molecules chosen randomly. The red line shows the intensity or the peak area for a protonated molecule with m/z 636.97 detected at a retention time of about 60 min, as a function of the sample injection amount. As the injection amount increases, the difference between the observed intensity and the expected one, shown as a dashed line, increases, and this shows the effect of ion suppression. Another protonated molecule detected at m/z 558.93 is also shown in blue. Ion suppression for this ion is detected for the 0.5-μg injection, but the decrease in intensity of this ion is weaker than that for the protonated molecule with m/z 636.97. Furthermore, the error bars in the figure show the decrease in intensity for the protonated probe at 60 min. The decrease is actually stronger than those for the ion with m/z 636.97. Therefore, the results are consistent with the above expectation. For the 0.05-μg injection, ion suppression may occur for some ions but the intensities of the two ions with m/z 636.97 and 558.93 are not decreased.
\n\t\t\tExperimental setup for LC/MS/MS. An aqueous solution of the probe, pumped by a syringe pump, is mixed with the LC effluent at post-column with a tee.
For semi-micro or conventional LC/MS, the liquid flow rate is so high that the probe solution can be added to the LC mobile phase at post-column through a tee, since the band width of a component separated by the LC column is not expected to be degraded by using a tee with a small dead volume. A typical experimental setup is shown in Figure 7. An aqueous solution of the probe pumped at 5 μL/min is mixed with the LC mobile phase (0.01M-CH3COONH4/CH3CN/CH3COOH, 600/400/0.15; isocratic) in the tee, and the mixed solution is introduced into a triple-quadrupole mass spectrometer operated in selected reaction monitoring (SRM) mode.
\n\t\t\tMass chromatograms of a fragment ion of the protonated probe for blank and plasma samples.
Before analyzing plasma samples, reference data are obtained using a blank sample such as water. In Figure 8, the mass chromatogram for a fragment (m/z 359.0) of the protonated probe obtained from the blank sample is shown in blue, and that from a plasma sample is shown in red, where the injection amount is about an order of magnitude higher than usual. It is clear that ion suppression is detected just after the sample injection until the retention time of 4 min. In particular, at a retention time of 0.6 min corresponding to the sample injection, the decrease in intensity for the plasma sample is much more significant than that for the reference data. This can be ascribed to an elution of very hydrophilic compounds in the plasma sample.
\n\t\t\tMass chromatograms of a fragment ion of the protonated probe for blank and plasma samples, and that of the protonated analyte (Omeprazole).
\n\t\t\t\tFigure 9 shows an example of ion-suppression detection obtained under our usual experimental conditions, in which no ion suppression is expected to occur. Omeprazole, a proton-pump inhibitor, is added to human plasma (4.5 μL). At a retention time ranging from 1.1 to 1.8 min, the fragment of the protonated Omeprazole is detected at m/z 198.1, but the intensity of the protonated probe (fragment) at 1.4 min decreases by 11%, which is beyond our experimental error of about 2%. This means that potential ion suppression occurs, and the intensity of the fragment of the protonated Omeprazole may be suppressed by less than 11% at 1.4 min since the decrease in the intensity of the protonated probe is expected to be stronger than that of other protonated molecules, as described earlier. On the other hand, the dependence of the peak area (intensity) of the fragment of the protonated Omeprazole on the amount of plasma is shown in Figure 10. The results are obtained under the condition that the injected amount of Omeprazole is constant. The figure shows that the peak area at 4.5 μL was 12% lower than those at 0 and 0.45 μL. This 12% decrease in peak area can be ascribed to the decrease in intensity of the protonated probe ranging from 8 to 22%, as shown in Fig. 9 (b). Thus, the decrease in peak area shown in Fig. 10 is almost consistent with the decrease (11%) in intensity of the protonated probe (fragment) at the retention time corresponding to the peak intensity for the protonated Omeprazole. Then, if the error of 11% obtained from the decrease in intensity of the protonated probe at the chromatogram peak is acceptable, the data can be readily analyzed quantitatively. If not, we may have to desalt the sample, reduce the injection amount, enhance the fractionation, or modify our LC separation conditions.
\n\t\t\tPeak area (intensity) of the fragment of the protonated Omeprazole as a function of the injected plasma amount.
The detection of ion suppression has been described. As mentioned earlier, ion suppression occurs when the number of charges in the droplet is comparable to, or less than, those of analyte molecules. However, when the number of charges in the droplet increases, ion enhancement occurs. Then, intensities of the protonated molecules increase in accordance with the molecules’ chemical properties. Since the increase in charge number can be regarded as a decrease in liquid pH, the protonation for acidic molecules is likely to be enhanced to greater degree than those for neutral and basic ones. This means that intensities of the protonated acidic molecules would increase more than those of other analyte molecules. Thus, when ion enhancement occurs, the intensity of the protonated probe is expected to increase more than those of other analyte molecules. An example of ion enhancement detection is shown in Figure 11. The reference mass chromatogram for the protonated probe, shown in blue, is compared with the mass chromatogram obtained from the plasma sample, shown in red. Ion enhancement is detected at a retention time of about 1.5 min. Furthermore, at 0.5-1.3 min ion suppression is also detected. Because complex matrix effects occur in this case, quantitative analysis of the data is difficult.
\n\t\t\tThe probe can be used for optimizing the sample preparation protocol and analytical conditions as well as for analyzing label-free samples in LC/MS. Furthermore, by monitoring the intensity of the protonated probe, we can detect degradation or pollution of the LC/MS component clearly. Figure 12 compares the mass chromatograms of the protonated probe for the reference data obtained on different days. At about 0.6 min a decrease in intensity is observed in the green result. This decrease can be ascribed to ion suppression caused by contamination at the injection valve. Thus, when the decrease becomes serious, cleaning the valve is recommended.
\n\t\t\tTypical example of detection of ion enhancement as well as ion suppression. Also, mass chromatogram for a fragment (m/z 294.2) of the protonated analyte (Aminopterin) is shown in a lower figure.
Comparison of mass chromatograms for a fragment ion of the protonated probe. They were obtained from the blank sample on different days.
As described above, the potential occurrence of ion suppression and ion enhancement is detected with the probe when the intensity of the protonated probe molecule changes. However, there are some cases where the probe is not always useful for quantitative analysis. Even when neither ion suppression nor ion enhancement is detected with the probe, the intensity of the protonated analyte molecule may possibly have increased. The increase in intensity of the protonated analyte molecule can be ascribed to proton-transfer reactions in the gas-phase with other protonated molecules produced by ESI, not to the matrix effects. Such an increase in intensity occurs only when 1) the analyte such as Aminopterin has a proton affinity much higher than that of the probe and 2) molecules with proton affinities between those of the analyte and the probe are co-eluted with the analyte from LC with high concentrations.
\n\t\tIn APCI, volatile analyte molecules vaporized from an LC effluent by a nebulizer are introduced into a corona discharge plasma, which is generated under atmosphere. In the plasma, protonated solvent molecules such as H3O+ and their hydrated clusters are produced as major reagent ions for chemical ionization in positive ion analysis. In negative ion analysis, on the other hand, anions such as O2\n\t\t\t\t- and OH- and their hydrated clusters are major reagent ions. In the plasma, positive and negative charges are balanced. Then, the analyte molecules are ionized by gas-phase ion/molecule reactions such as a proton-transfer reaction and an electron-transfer reaction with the reagent ions in the plasma, as shown below.
\n\t\t\tH3O+ + M → H2O + [M+H]+ (proton-transfer reaction)
\n\t\t\tO2\n\t\t\t\t- + M → O2 + M- (electron-transfer reaction)
\n\t\t\tHere, M is an analyte, and hydrated clusters are omitted for simplicity. The protonated analyte molecule [M+H]+ is produced by the proton-transfer reaction when the analyte has a proton affinity higher than that of H2O. Thus, the major factor determining the ionization efficiency for the protonated analyte molecule is the proton affinity of the analyte (Hunter& Lias, 1998). The negatively charged analyte molecule M-, on the other hand, is produced by an electron-transfer reaction when the analyte has an electron affinity higher than that of O2. Thus, the major factor determining the ionization efficiency for the negatively charged analyte molecule is the electron affinity of the analyte (Linde, 1995b). Although the ion/molecule reactions at atmospheric pressure are expected to be almost in equilibrium state, the density of the ion produced by APCI is proportional to that of the reagent ion for the ion/molecule reaction. That means that ion suppression occurs when the density of the reagent ions decreases appreciably. This situation is caused, for example, when the density of co-eluted molecules with proton affinities higher than that of the reagent molecule becomes significant.
\n\t\t\tIn APCI, several kinds of ion/molecule reactions in the gas phase occur such as a proton-transfer reaction, electron-transfer reaction, anion-transfer reaction, and anion-attachment reaction (Moini, 2007). Therefore, it is important to identify the reagent ion for the ion/molecule reaction of the analyte molecule before the analysis. Then, the occurrence of ion suppression can be detected by monitoring the intensity of the reagent ion for the analyte molecule. Before analyzing biological samples, reference data should be obtained using a blank sample. Potential ion suppression is detected when the intensity of the reagent ion for a biological sample becomes lower than that for the reference sample. In the analysis of protonated analyte molecules, for example, ion suppression can be detected by monitoring the intensity of the protonated solvent molecule such as H3O+ or its hydrated cluster. In the analysis of negatively charged analyte molecules, it can be detected by monitoring the intensity of the anions such as O2\n\t\t\t\t- and OH-. In APCI, however, ion suppression occurs less frequently than in ESI probably because charges or the current for the reagent ions, produced in the corona discharge plasma, are much higher than the charges produced by ESI.
\n\t\tIn ESI as an interface in LC/MS, a technique to detect ion suppression or enhancement using a probe has been developed. In positive-ion analysis, the probe should be more hydrophilic and acidic than analyte molecules. In negative-ion analysis, it should be more hydrophilic and basic than analyte molecules. When ion suppression occurs in positive-ion analysis, for example, the intensity of the protonated molecule of the probe is expected to decrease more than those of other analytes. Furthermore, potential error for the intensity of the protonated analyte can be estimated from the decrease in the intensity of the protonated probe.
\n\t\t\tIn preparing a stock solution of the probe, the probe powder is readily dissolved in pure water by adding a small amount of ammonia or trifluoroacetic acid (TFA) to adjust the solution’s pH. In an organic-solvent/water solution, however, the very hydrophilic probe might be aggregated in several ten minutes. Thus, the aqueous solution of the probe should be mixed with the LC mobile phase just before the analysis, as shown in Fig. 7.
\n\t\t\tDirections for the use of the probe are summarized as follows:
\n\t\t\tAdd the probe in the LC mobile phase.
Obtain reference LC/MS data with a blank sample.
Obtain LC/MS data with a biological sample.
Compare mass chromatogram for the protonated probe with that in the reference data.
Measure potential error from the decrease in intensity for the protonated probe.
The probe can also be used to detect the occurrence of ion enhancement. When ion enhancement occurs, the intensity of the protonated molecule of the probe is expected to increase more than those of other analytes. When neither ion suppression nor ion enhancement occurs, the probe can be used as an internal standard in quantitative LC/MS analysis. Unlike isotope labeling techniques, however, it cannot be used as an internal standard in sample preparation.
\n\t\t\tIn contrast, in APCI the occurrence of ion suppression can be detected by monitoring the intensity of the reagent ion for the analyte.
\n\t\tThe author is grateful to M. Furukawa, M. Umeda, T. Bando, Y. Orii, and T. Mori of Hitachi High-Technologies for their help in the experiments and their contribution to our fruitful discussions. He also thanks M. Ishimaru, N. Manri, T. Yokosuka, and H. Hanzawa of Hitachi for their invaluable assistance.
\n\t\tIn dairy farms, biosecurity, surveillance, resilience/immunity, biocontainment, and control of disease spread within the herd are the pillars that need to be appropriately managed to ensure the healthy herd [1].
\nBiosecurity is focused to reduce and prevent the introduction of diseases or pests of animals on a farm, and to minimize the spread of diseases or pests within a farm. Biosecurity action plans need to be implemented mainly in large dairy farms where the disease agents can be introduced by various sources such as labor, advisers, replacement cattle, supplies, feedstuffs, and vehicles [2].
\nSurveillance programs are developed for early detection of emerging pathogens, to establish disease-free status or the prevalence of a specific disease in a herd [3].
\nRelation resilience immunity is based on the individuals’ resistance to diseases that can be modulated by the ability of animals to adapt to adverse conditions (stress factor) and recover from them [4].
\nBiocontainment and control programs are important backup systems for biosecurity plans that will prevent the emerging disease spreading within the herd or the endemic diseases spreading between animals into the farm [2, 5].
\nThe overall biosecurity of dairy farm uses different levels or shells of actions (national or supranational, regional, and local), linked with the epidemiological profile of the pathogen. For highly contagious infectious agent (e.g., foot-and-mouth disease), the most efficient biosecurity plan is at national or European Union level, while for infectious agents transmitted by close contact between animals (e.g., bovine tuberculosis), the regional biosecurity measures such as movement controls will protect the status of the region [1].
\nBiosecurity practices on livestock farms have been described and prioritized in various ways [1, 2, 5, 6]. In this chapter, we grouped biosecurity measures in the following categories: dairy farm sanitation, facility biosecurity, animal biosecurity, feed biosecurity, and manure biosecurity.
\nSome infectious agents are specific for dairy cattle and others are zoonotic, affecting both bovine and human health. Employees and visitors can contribute to the spread of all these infectious agents on a dairy farm [7]. The transmission of pathogens by humans can be reduced or even stopped by providing on-farm laundry facilities for all protective clothing used on the farm, using only clean overalls during farm visits, providing disposable clean booties for visitors and cleaning of boots with disinfecting solution after scrubbing off any visible dirt at the end of the visit, and washing of hands before and after working with sick or young animals [7, 8, 9].
\nMilking parlor personnel should wear latex gloves while milking to reduce the spreading potential of the contagious mastitis pathogens [9]. Sometimes, these hired personnel can take care of other animals outside the dairy farm and carry pathogens on the farm. Employees should be regularly trained in good practices to prevent the spread of disease (the principles of hygiene and disease security). They need to know that calves are susceptible to diseases carried by adult animals, and daily activities should be organized so that employees work with younger animals before working with older animals. Prevention of the infectious agent’s introduction and spreading from outside and inside sources should also be considered in the education of hired personnel in basic hygiene and disinfection [10]. The main actions included in the biosecurity plan for dairy farms should reduce the risk of infectious diseases to be introduced by employees and visitors (Table 1).
\nBiosecurity measure | \nAction | \n
---|---|
Record in the logbook all farm visitors | \nPlace the visitor logbook at the farm entrance | \n
Restrict the access of visitors to the stable | \nLocking the stable doors | \n
Inform unauthorized persons that they are not allowed to enter the stable | \nPost-warning signs asking visitors not to pass inside stable and several directing signs to the farm offices | \n
The visitors can access the stable only with clean clothes and boots, which they have not used in other farms | \nProvide clean boots and overalls for all visitors | \n
The visitors should use a footbath with disinfectant and clean their boots before entering the stable | \nPlace a disinfectant footbath and brushes outside the stable | \n
The dealer or transporter of the newly arrived animals is not allowed to enter in stable or in contact with the farm animals | \nThe access of the cars is made on a route that avoids contact with the farm animals, directly toward the quarantine area located at a distance from the herd | \n
The livestock renderer access in the stable or the contact with cattle is restricted | \nStore dead animals away from the stable and main roads | \n
Biosecurity measures designed to reduce the risk of the infectious disease’s introduction in dairy farms by employees and visitors.
The access of visitors must be limited and recorded in a logbook; the farm touring must start from younger to older animal groups; barn doors are recommended to be locked and a warning sign must be posted to keep out unauthorized personnel [9].
\nAlso, along the access road of the farm must be displayed signs directing visitors to the administrative area and to the visitor parking, as well as warning signs to limit direct contact of visitors with farm feed and animals [11].
\nEquipment can be contaminated with infectious secretions, excretions, and blood and the movement of equipment between stalls and farms may also transport pathogens [12].
\nAll equipment used on the farm must be regularly cleaned and disinfected [11]. To prevent contamination of equipment, storage containers need to be used for all tools and feeding equipment. Also, all storage containers are regularly cleaned and disinfected. The storage containers must protect equipment from diseases, pests, or weeds [13]. Before use in healthy animals, equipment that has been used on sick animals must be cleaned and disinfected. However, it is better not to use clothing, shoes, and tools dedicated to the compartment of sick animals [14]. Dehorners, ear taggers, hoof knives, clippers, and all shared and hired equipment will be cleaned and disinfected between uses [11, 14].
\nNursing bottles and buckets must be sanitized before each feeding [14], calves kept indoors must have fresh clean dry bedding, and plastic calf hutches will be cleaned and disinfected after use [11].
\nThe equipment used for manure disposal will not be used for transporting or delivering feed [13].
\nDisposable clothing and used veterinary equipment must be removed safely [11].
\nVehicles are considered fomites mainly for pathogenic robust organisms that can survive a long time in the environment [1]. Mainly external vehicles that collect milk, calves, and carcasses or deliver feedstuffs, pharmaceuticals, and semen can be involved in the transmission of infectious disease because they travel daily from farm to farm [2, 10]. A high biosecurity risk is associated with carcasses (dead stock) collectors because they are usually in contact with diseased animals [15, 16].
\nTo prevent the introduction of infectious agents, vehicles must be kept clean and should not have access to the zones where the animals are housed [10, 11, 17].
\nExternal vehicles should not be allowed on the farm [18]. If vehicles are necessary on the farm, then ensure that vehicles and trailers are clean when entering the farm and disinfected before and after use [6, 11, 18, 19]. Cleaning and disinfection will cover both the exterior and the interior of the vehicles, with greater attention to areas where dirt may be hidden (e.g., wheel arches and tires) [11]. Because the transport by dealers may pose additional risks of infectious disease transmission between farms, it is recommended that the animal moving will use only farm-owned vehicles [20], with clean and ample bedding to prevent both injuries and disease [14].
\nGuidance indicators and warning and restricting access signs to unauthorized vehicles must be placed at the entrance to the farm road and along the road. The farm must have a designated area for visitors’ vehicles that are at the entrance of the farm and away from the animal and animal stalls [6, 10, 14]. Also, service vehicles should not drive over the routes of feed delivery or manure handling [14].
\nIn a dairy farm, the building’s design can help prevent the spread of pathogens to sick cows, periparturient cows, and newborns [2]. Buildings should have a well-established destination, in correlation with the categories of animals present on the farm. Dairy farms can secure their premises against domestic and wild animals by installing various types of fences (e.g., electric fence) around the buildings. Disinfectant footbaths should be at the entry of livestock housing. All farms should have isolation building (the quarantine facility) where the health status of the newly purchased cows will be observed before they join the rest of the herd [21]. To prevent direct and indirect contact between residents and new animals, the quarantine facility should be located in the farthest possible place on the dairy farm [10]. The farm must have a biosecurity plan that includes building maintenance activities (e.g., check and maintain fences, replace bird netting, and repair holes in buildings), which will reduce the contact of cattle with wild animals and the feed contamination with birds droppings or badger feces [14, 21].
\nThe introduction of new cattle is one of the most important biosecurity risks for dairy farms [10]. In modern dairy farming, the sale and movement of cattle is an intrinsic part of the business as a consequence of the increased herd replacement rate of adult milking cows, the forced culling, and the need to increase the size of the herd [1]. Therefore, keeping a closed herd is the most effective biosecurity measure but is the least practical [6]. To reduce the risk of diseases spreading between farms, the new animals are purchased only from herds with known health status and known vaccination protocols [9, 10].
\nThe best solution to prevent the introduction of diseases through the acquisition of new animals is the hosting of the newly purchased cows in a quarantine facility with trained personnel to handle isolated animals [10, 21]. Quarantine is one of the most important biosecurity tools and consists of the separation of specific groups of animals to prevent the transmission of infectious diseases. Prophylactic quarantine is designed to separate the resident herd from newly acquired animals for 1 month or more. During the 30 days of isolation, the personnel from the quarantine facility will monitor cattle health status and prevent direct and indirect contact between new and resident animals [9, 10]. If the infections have short incubation times, then the animals will develop acute diseases during the quarantine period. In other cases, to prevent the diseases spreading from animals that might be hiding an infectious agent without exhibiting clinical signs to resident animals, the quarantined animals will be tested for various diseases such as bovine tuberculosis, Johne’s disease, brucellosis, leptospirosis, salmonellosis, campylobacteriosis, leucosis, bovine viral diarrhea (BVD), infectious bovine rhinotracheitis (IBR), trichomoniasis, neosporosis, ringworm, liver fluke, lungworm, digital dermatitis, and contagious mastitis pathogens (Streptococcus agalactiae and Staphylococcus aureus) [10, 14]. The testing of animals in the prophylactic quarantine is a valuable biosecurity tool when properly applied.
\nTo prevent the bovine tuberculosis introduction, the biosecurity plan should take into consideration all possibilities of Mycobacterium bovis transmission. Cattle are the main reservoir and spread microbes through aerosols (adults) or manure (calves) to many domestic and wild mammalian species. Sheep, goats, pigs, horses, and dogs are spillover hosts and spread M. bovis spread microbes in various ways (respiratory, digestive, by bites, or scratches). After infection, badgers, brush-tail opossums, wild boars, deer, and other wildlife species become wildlife reservoirs (maintenance host). Humans are susceptible and contract the infection mainly by drinking raw milk and raw milk products. People with pulmonary or urogenital tuberculosis can retransmit the infection to cattle [22].
\nCalves are more susceptible and should be kept in a separate area to minimize their exposure to infectious agents [14]. Calves can carry many infectious diseases without clinical signs and positive results on the laboratory tests (e.g., Johne’s disease). This risk can be reduced by purchasing calves only from herds officially certified as disease-free [1].
\nBecause one of the most common ways of the BVD virus introduction in a free farm is via a pregnant heifer (“Trojan cow”) carrying a persistently infected fetus, all calves from purchased cattle should be tested at birth to detect persistently infected animals with BVD virus [1, 9, 10]. Persistently infected animals are the main route of the BVDV spreading between herds because they cannot be detected by serological tests (immunotolerant calves), but excrete massive amounts of virus [1, 23]. The risk of farm contamination can be reduced by purchasing animals only from herds officially certified as BVDV-free. If the BVDV status in the herd of origin is unknown, then pregnant females should be isolated on arrival (the contact with any animal of breeding age must be restricted), tested for BVD antibody and BVD antigen, and released from isolation only if they are negative results at both tests or antibody positive, antigen-negative, calved, and the calf was tested negative or removed from the herd [1]. To prevent BVDV introduction into a free farm, the following risk factors should be considered: trade with live animals, embryo transfer and semen recipients, return of animals from animal exhibitions, direct contacts between cattle on pasture or over fences, density and activity of arthropod vectors, vaccination, and employee and visitors contact with animals [9, 24].
\nSick and suspicious animals should be isolated in a specific area and always handled at the end. In the control of contagious mastitis, the latter are milked cows suspected of the disease [9].
\nImplementing effective biosecurity programs will bring long-term economic benefits. Dutch studies have shown that the main benefits of a closed dairy herd with good biosecurity are better fertility and lower slaughter rates. The USA comparative studies in Johne’s disease-positive herds and Johne’s disease-negative herds revealed an economic loss of almost US$ 100 per cow in positive herds. Spread of an infectious disease onto a farm can lead to large economic losses. An outbreak of BVD in an Australian farm with 320 milking cows caused losses of $AUD 144,700 [25].
\nVaccination is another important biosecurity tool designed to protect resident cattle from infectious agents that could have been brought in by the newly purchased cows [26]. In dairy cattle, immunization mainly targets common infectious agents such as BVD virus, IBR virus, parainfluenza-3 (PI3) virus, bovine respiratory syncytial virus (BRSV), leptospirosis, and clostridial infections [27]. Vaccination programs should be established in collaboration with the herd veterinarian and adapted to the risk of the disease spreading on the farm, including infectious agents that evolve in the area [25, 28]. Vaccination should not be considered the primary or single biosecurity tool because no vaccine provides 100% immunity [26, 28].
\nDairy herd vaccination programs are affected by various factors such as age and category of production, disease history, housing, type of vaccine (killed or modified live), and costs [28]. Vaccination programs are designed by age categories and are applied continuously to maximize herd immunity and minimize the spread of the infectious agent [27, 28].
\nVaccination schedule for dairy heifers from birth to 6 months of age can be started with an oral modified live vaccine (MLV) for bovine rotavirus and bovine coronavirus given 30 minutes before the ingestion of colostrum to prevent the inactivation [28]. In the first hour of life, calves must receive 2.8 L of colostrum, and in the next 23 hours, the rest of 2.8 L [27]. Depending on the epidemiological situation, an intranasal vaccination of neonatal calves with respiratory vaccines (IBR/PI-3/BRSV) can be started at 3 days of age or older [28]. At 6 weeks old, dairy heifers can receive an injectable modified-live IBR/PI3/BRSV/BVD vaccine and a seven-way clostridial bacterin-toxoid [27]. The immunity of injectable vaccines is longer than the immunity of intranasal vaccines [28]. Following national and international regulations on brucellosis prophylaxis, at 4–6 months age replacement heifers should receive brucellosis RB51 vaccine. Also, depending on the epidemiological situation, calves can receive the appropriate vaccination for leptospirosis clostridial diseases and/or Histophilus somnus. At 6 months of age, heifers should be revaccinated with modified live IBR/PI3/BRSV/BVD virus vaccine, seven-way clostridial vaccine, and five-way leptospirosis bacterin [27, 28].
\nPre-breeding heifers (10–12 months of age) should be revaccinated with killed or modified live IBR/PI3/BRSV/BVD virus vaccine, five-way leptospirosis bacterin, and seven- or eight-way clostridial bacterin-toxoid [28]. Optionally, it can be done with vibriosis bacterin [27].
\nPre-calving heifers should be revaccinated 40–60 days before calving with killed IBR/PI3/BRSV/BVD virus vaccine, five-way leptospirosis bacterin, killed rotavirus and coronavirus vaccine, and Escherichia coli + Clostridium perfringens types C and D bacterin/toxoid. Three weeks before to calving, heifers should be revaccinated with killed rotavirus and coronavirus vaccine, and Escherichia coli + Clostridium perfringens types C and D bacterin/toxoid [27, 28]. Also, pre-calving heifers should be vaccinated with coliform mastitis bacterin [27].
\nAdult cows should be annually vaccinated, 40–60 days before calving for IBR, PI3, BRSV, and BVDV [27]. Depending on the history of diseases in the region and the associated epidemiological risks, the farm veterinarian should choose vaccines that immunologically protect dairy cows during the lactation period and the dry period for leptospirosis, vibriosis, Rotavirus, Coronavirus, Clostridium perfringens types C and D, and Escherichia coli mastitis. Types of vaccines recommended are killed or bacterin/toxoid and modified-live vaccines (MLV) [27, 28]. Adult dairy cattle should receive a booster vaccination at 3 weeks before calving with killed rotavirus and coronavirus vaccine and Escherichia coli + Clostridium perfringens types C and D bacterin/toxoid vaccine [27]. MLV vaccines should be used with prudence in pregnant cows and only after consultation with the veterinarian [28]. The annual vaccination for vibriosis should be performed in dairy herds where the artificial insemination is not practiced [27].
\nThe annual vaccination of adult dairy cattle for calf scours (rotavirus and coronavirus, Escherichia coli, and Clostridium perfringens types C and D) should be considered in all herds with recent history as a part of the preventative management practices [27].
\nMastitis is one of the most important diseases in dairy cows that affects the welfare, production, and duration of the economic life of the animals [29]. Economic losses are due to direct milk production losses (reduction of quantity, unsalable, or poor quality), culling or removal from the herd of animals with unsatisfactory treatment results, cost of veterinary care, cost of excessive use of antimicrobials and other medicines, and the risk of antibiotic resistance [30].
\nThe main pathogens targeted by mastitis vaccines are Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli [29]. Reduction in the incidence and duration of intramammary infections can be obtained by applying the combination of vaccination with high milking hygiene procedures, treatment of clinical cases, segregation, and culling of known infected cows [29]. The following preventive measures were proved to have a positive result in the management of mastitis in dairy herds: the use of milkers’ gloves, blanket use of dry-cow therapy, washing unclean udders, maintaining cows upright after milking, back-flushing of the milking cluster after milking an animal with clinical mastitis, and application of a treatment protocol [30] Also, to maximize the success of immunization, within 5 days of mastitis vaccines, dairy cows must not receive any other Gram-negative bacterin vaccines (e.g., Escherichia coli, Salmonella spp., Pasteurella spp., Campylobacter sp., and Moraxella bovis) [27].
\nTo evaluate the effects of mastitis vaccines in dairy cows, the following monitoring parameters are most commonly used:
Clinical and subclinical mastitis incidence and severity
Somatic cell count
Serum and/or milk immunoglobulin G concentrations
Milk bacterial culture or Staphylococcus aureus count in milk
Milk production
Cure or cull rate [29]
Newly acquired dairy herd bulls should be 30–60 days in prophylactic quarantine and tested with negative results for persistent BVDV infection, brucellosis, and tuberculosis. Recommended vaccination schedule for dairy herd bulls is an annual vaccination at the breeding soundness examination with IBR/PI3/BVD killed vaccine, five-way leptospirosis bacterin, and vibriosis bacterin [27].
\nIf there are animal species other than cattle, then the vaccination actions must take into account for these species as well. Farm dogs and cats should be vaccinated at least against rabies to protect humans and other animals [14].
\nAntibiotic overuse can be reduced by using a proper mixture of natural antibacterial peptides, biological response modifiers, prebiotics, probiotics, and correct development of the gut microbiome [31].
\nThe limited use of bacterial culture and sensitivity testing by veterinarians are other causes of the persistence of the multidrug resistance (MDR) isolates in dairy farms. The findings of the last decades highlight the necessity of using antimicrobial susceptibility testing each time before prescribing an antibiotic [32].
\nTo reduce the risk of pathogens spreading in farm animals, dead animals should be disposed of in the shortest time. Depending on the national regulations and farm’s possibilities, the disposal of carcasses can be done by a licensed dead stock collector, burial, or composting [14].
\nStudies designed to investigate what motivates and withholds farmers to implement biosecurity measures placed the carcass storage away from the stables on the second rank for feasibility, but with a lower score for efficacy [33].
\nRendering trucks have a particular risk for farm biosecurity because they are at high risk for carrying animals killed by infectious diseases [26]. To prevent farm contamination, mortality pick-up should be located away from the stable and feed storage bin and silo [34].
\nThe biosecurity of feed and water must start from the source, respectively, from the fields where crops are grown and from the water capture source. Manure used as a natural fertilizer can contaminate the soil, crop, and water used for irrigation and groundwater sources [2]. The quality and potability of water should be tested regularly, and samples from each feedstuff batch or lot should be stored for possible laboratory analyses (e.g., bacteria, toxins, molds, and mycotoxins) until that batch is consumed without incidents [2, 10].
\nTo reduce the risk of the diseases being introduced by contaminated feed, the dairy producer should record and monitor the manure application on its pastures and fields cultivated with feedstuffs [2]. The risk of a feed-related disease outbreak is increased when feedstuffs are purchased from multiple locations or the crops were fertilized with manure from other dairy farms [2, 10].
\nTo prevent feedstuffs to be contaminated through fecal material and urine from rodents, birds, dogs, cats, and any wildlife, dairy farmers should design food storage areas in a way to be inaccessible (e.g., opened bags can be placed into containers with tight lids; barns can have welded wire fence) [2, 14].
\nThe biosecurity plan of the dairy farm should include the frequency of storage areas cleaning, the way of feed bags storage off the floor on pallets, removing and disposing of the not consumed feed within 24 hours, rotation of feed inventory for the purpose to reduce the possible presence of detrimental organisms or toxins in stored feeds, and periodically checking of silos, bins, and bunks to detect and remove as soon as possible moldy or spoiled feedstuff [14].
\nAlthough not recommended, some cattle herds are still using surface water (e.g., lakes, ponds, and rivers) as a water source. Drinking water can be contaminated by animal carcasses (e.g., dead wild animals), manure from other livestock, bird droppings, urine and feces of wildlife, and human waste [2, 10, 14]. Water biosecurity programs should include several measures designed to prevent contamination with toxins and infectious agents such as restriction of the birds and wildlife access to farm water sources, filtration and chemical sterilization of water, and regular testing of water quality and potability [2]. Waterers should be cleaned once a week [14].
\nIn dairy farms, manure is the most problematic waste and should be treated as a biological risk material because it has a huge bacterial load [2]. Manure should be stored in an area inaccessible to cattle [14]. Contact with manure from infected cattle is the main means of spread for rotavirus, coronavirus, Escherichia coli, Salmonellosis, and Johne’s disease to other receptive animals. Manure handling should prevent environmental contamination and should not violate the legislation in force [14].
\nManure is rich in nutrients that could be recycled as fertilizer [35]. However, the use of this natural fertilizer should be done with caution to prevent contamination of crops, pastures, and groundwater sources [2]. Salmonella spp., Escherichia coli, Listeria spp., and Mycobacterium avium subsp. paratuberculosis can be killed by the process of manure composting but the process must be controlled before the use of compost in agriculture [2, 36, 37]. In the process of composting should not be used the manure from the hospital pen, where de infectious agents can be in a high concentration. Also, the temperature and microbial activity should be checked to confirm the complete sterilization [2, 14]. Also, manure can be recycled for bedding and to produce methane [2].
\nManure biosecurity programs should include measures to prevent the manure equipment used to handle feed, the environment infestation with files and intestinal parasites (manure must be removed frequently to prevent the pest life cycles completion), manure run-off or transfer from adults to calves, and feed contamination by manure-covered wheels of farm vehicles [14].
\nManure spreaders and slurry handling equipment are high-risk equipment and should be brought to the farm after proper cleaning or disinfection [1].
\nThe manure cleaning of vehicles and equipment must be done in areas specially designed for this purpose, where water or disinfectants would not splash onto feed or into drinking water. Throughout the entire cleaning and disinfection process, the equipment will be inspected visually to dispel any suspicion of cross-contamination [2].
\nThe development and implementation of biosecurity programs in dairy farms improve cattle health, welfare, and productivity. These programs must be monitored and evaluated continuously to identify new methods of control and new effective critical control points and to further improve the program to prevent the introduction and spread of infectious agents on the farm. The biosecurity program should be focused on the decision and adapted to the specific situations of each dairy farm. Many of the problems encountered can be prevented or minimized with the support of veterinary services. Staff and visitors should be trained on biosecurity measures applied on the farm.
\nThe authors declare no conflict of interest.
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