An initial census of layer farms in Khartoum State, Sudan, was carried out in late 2007 and early 2008 and found that there were 252 layer farms with a total population of 2 221 800 birds. This paper reports the findings of the census. Based on this information, a structured questionnaire survey of 92 farms was then conducted in the state in April 2008 to collect data on antibiotic usage, demographic data and public health awareness. Ninety-eight per cent of participating farms comprised open-sided houses. It was found that 49% of the farms surveyed were on antibiotic treatment when the survey was conducted, whilst 59% of the farms had used antibiotics within the last 3 months. The study found that farmers and producers had a lack of knowledge about antimicrobial residues, their withdrawal periods and the risk posed by the consumption of these residues. The study also concluded that traditional farming systems in Sudan relied heavily on antimicrobial medication to control disease and almost half of the farms surveyed were treating their flocks with antimicrobials. In addition to this, there was a lack of disease control programmes which probably resulted in a massive use of antibiotics to control endemic diseases. This was further compounded by the absence of governmental supervision and control on the use of drugs.

An initial census of layer farms in Khartoum State, Sudan, was carried out in late 2007 and early 2008 and found that there were 252 layer farms with a total population of 2 221 800 birds. This paper reports the findings of the census. Based on this information, a structured questionnaire survey of 92 farms was then conducted in the state in April 2008 to collect data on antibiotic usage, demographic data and public health awareness. Ninety-eight per cent of participating farms comprised open-sided houses. It was found that 49% of the farms surveyed were on antibiotic treatment when the survey was conducted, whilst 59% of the farms had used antibiotics within the last 3 months. The study found that farmers and producers had a lack of knowledge about antimicrobial residues, their withdrawal periods and the risk posed by the consumption of these residues. The study also concluded that traditional farming systems in Sudan relied heavily on antimicrobial medication to control disease and almost half of the farms surveyed were treating their flocks with antimicrobials. In addition to this, there was a lack of disease control programmes which probably resulted in a massive use of antibiotics to control endemic diseases. This was further compounded by the absence of governmental supervision and control on the use of drugs.

A cross-sectional study was conducted between September and October 2010 in five states of South Sudan that were selected on the basis of the perceived risk of tick-borne diseases. The purpose was to investigate epidemiological parameters of tick-borne diseases in South Sudan and their uses in future control strategies. A total of 805 calves were assessed by clinical, microscopic and serological examination and tick counts. The indirect Enzyme-Linked Immuno-Sorbent Assay (ELISA) was used to detect antibodies to Theileria parva, Theileria mutans, Anaplasma marginale and Babesian bigemina. Sero-conversion risks for T. parva and T. mutans were 27.3% and 31.3% respectively, whilst the risk was 57.6% and 52.8% for A. marginale and B. bigemina, respectively. Major tick species identified include Rhipicephalus appendiculatus, Rhipicephalus decoloratus, Rhipicephalus microplus, Amblyomma variegatum, and Rhipicephalus evertsi. There was great variation (P ≤ 0.001) in the number of all these ticks, both between herds in a state and between calves in an individual herd. The low and intermediate sero-conversion risks observed in the study states suggest that immunisation against East Coast fever (ECF) is justified. Fortunately, three major genotypes that were identified by applying Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCRRFLP) analysis on the p104 to the blood samples and T. parva Muguga, matched very well with T. parva Kiambu 5 and T. parva Muguga; therefore the Muguga cocktail can be used for the immunisation of cattle in South Sudan. However, prospective studies are required to develop optimal control measures for tick-borne diseases under different ecological and husbandry practices in South Sudan.

A cross-sectional study was conducted between September and October 2010 in five states of South Sudan that were selected on the basis of the perceived risk of tick-borne diseases. The purpose was to investigate epidemiological parameters of tick-borne diseases in South Sudan and their uses in future control strategies. A total of 805 calves were assessed by clinical, microscopic and serological examination and tick counts. The indirect Enzyme-Linked Immuno-Sorbent Assay (ELISA) was used to detect antibodies to<em> Theileria parva</em>, <em>Theileria mutans</em>, <em>Anaplasma marginale</em> and <em>Babesian bigemina</em>. Sero-conversion risks for <em>T. parva</em> and <em>T. mutans</em> were 27.3% and 31.3% respectively, whilst the risk was 57.6% and 52.8% for <em>A. marginale</em> and <em>B. bigemina</em>, respectively. Major tick species identified include <em>Rhipicephalus appendiculatus</em>, <em>Rhipicephalus decoloratus</em>, <em>Rhipicephalus microplus</em>, <em>Amblyomma variegatum</em>, and <em>Rhipicephalus evertsi</em>. There was great variation (<em>P</em> ≤ 0.001) in the number of all these ticks, both between herds in a state and between calves in an individual herd. The low and intermediate sero-conversion risks observed in the study states suggest that immunisation against East Coast fever (ECF) is justified. Fortunately, three major genotypes that were identified by applying Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCRRFLP) analysis on the p104 to the blood samples and T. parva Muguga, matched very well with <em>T. parva</em> Kiambu 5 and <em>T. parva</em> Muguga; therefore the Muguga cocktail can be used for the immunisation of cattle in South Sudan. However, prospective studies are required to develop optimal control measures for tick-borne diseases under different ecological and husbandry practices in South Sudan.

Four hand-reared, naïve roan antelope, 4 months of age, were exposed to naturally infected pasture on a game farm in Mpumalanga Province, South Africa, where roan are known to die from theileriosis. Various clinical parameters were recorded during this period. The predominant ticks parasitising these animals at the time (January to February), were Rhipicephalus appendiculatus and Rhipicephalus evertsi evertsi adults. After a period of 5 weeks the animals developed signs of clinical theileriosis and were treated with buparvaquone to prevent mortality. Primary hyperplasia of the local draining lymph nodes (Lnn. anorectales) near the feeding site of adult R. evertsi evertsi indicated possible transmission of Theileria sp. (sable) by this tick species. After recovery from theileriosis, these animals were confirmed carriers of Theileria sp. (sable) by PCR (polymerase chain reaction) and DNA probe analysis. Laboratory-bred larvae and nymphs of R. evertsi evertsi and R. appendiculatus respectively, were fed on the ears of these roan antelope. Salivary glands from moulted and prefed adult ticks of each species were dissected and stained for Theileria spp., and the PCR and DNA probe applied to a representative batch of dissected glands. R. appendiculatus adults collected from grass in infected camps were also dissected after prefeeding them on rabbits. Salivary glands of both tick species showed infected acini on staining and were also positive for Theileria sp. (sable) only, on multiprotozoal PCR-screening analysis. There was no statistical significant difference between the infection rate and the intensity of infection between the two tick species. R. appendiculatus ticks collected from grass were also PCR-positive for Theileria sp. (sable).

Four hand-reared, naïve roan antelope, 4 months of age, were exposed to naturally infected pasture on a game farm in Mpumalanga Province, South Africa, where roan are known to die from theileriosis. Various clinical parameters were recorded during this period. The predominant ticks parasitising these animals at the time (January to February), were Rhipicephalus appendiculatus and Rhipicephalus evertsi evertsi adults. After a period of 5 weeks the animals developed signs of clinical theileriosis and were treated with buparvaquone to prevent mortality. Primary hyperplasia of the local draining lymph nodes (Lnn. anorectales) near the feeding site of adult R. evertsi evertsi indicated possible transmission of Theileria sp. (sable) by this tick species. After recovery from theileriosis, these animals were confirmed carriers of Theileria sp. (sable) by PCR (polymerase chain reaction) and DNA probe analysis. Laboratory-bred larvae and nymphs of R. evertsi evertsi and R. appendiculatus respectively, were fed on the ears of these roan antelope. Salivary glands from moulted and prefed adult ticks of each species were dissected and stained for Theileria spp., and the PCR and DNA probe applied to a representative batch of dissected glands. R. appendiculatus adults collected from grass in infected camps were also dissected after prefeeding them on rabbits. Salivary glands of both tick species showed infected acini on staining and were also positive for Theileria sp. (sable) only, on multiprotozoal PCR-screening analysis. There was no statistical significant difference between the infection rate and the intensity of infection between the two tick species. R. appendiculatus ticks collected from grass were also PCR-positive for Theileria sp. (sable).

Aquatic systems are affected by a variety of anthropogenic activities that decrease water quality through the introduction of organic and inorganic pollutants. To investigate the relationship between fish parasite communities and water quality, metazoan parasites were examined in 140 specimens of the Mozambique tilapia (Oreochromis mossambicus) sampled in three lakes in the Limpopo Province, namely the Luphephe–Nwanedi Dams (regarded as unpolluted), the Flag Boshielo Dam (regarded as moderately polluted) and a return water dam on a mine site (regarded as polluted). The monogenean parasites Cichlidogyrus halli, digenean larval stages of Clinostomum and Diplostomum spp. and a gryporynchid cestode were found in or on O. mossambicus in all the sampled sites. The distribution of monogeneans (Cichlidogyrus sclerosus, Cichlidogyrus dossoui, Cichlidogyrus tilapiae, Scutogyrus longicornis and three Enterogyrus spp.), metacercarial stages of two digeneans (Neascus and Acanthostomum spp.) and nematodes (an unidentified nematode, Contracaecum sp., Paracamallanus cyathopharynx and Procamallanus laevionchus) was limited to the unpolluted and moderately polluted lakes. Larval stages of Diplostomum sp. were present in O. mossambicus collected from the unpolluted and polluted sites. The variability of the calculated infection indices (prevalence, mean abundance and mean intensity) and the parameters of species richness and diversity suggest that the structure of parasite communities are affected by the pollution levels of the water. The unpolluted reference site had the highest species richness and the highest overall parasite abundance values.

Aquatic systems are affected by a variety of anthropogenic activities that decrease water quality through the introduction of organic and inorganic pollutants. To investigate the relationship between fish parasite communities and water quality, metazoan parasites were examined in 140 specimens of the Mozambique tilapia (Oreochromis mossambicus) sampled in three lakes in the Limpopo Province, namely the Luphephe–Nwanedi Dams (regarded as unpolluted), the Flag Boshielo Dam (regarded as moderately polluted) and a return water dam on a mine site (regarded as polluted). The monogenean parasites Cichlidogyrus halli, digenean larval stages of Clinostomum and Diplostomum spp. and a gryporynchid cestode were found in or on O. mossambicus in all the sampled sites. The distribution of monogeneans (Cichlidogyrus sclerosus, Cichlidogyrus dossoui, Cichlidogyrus tilapiae, Scutogyrus longicornis and three Enterogyrus spp.), metacercarial stages of two digeneans (Neascus and Acanthostomum spp.) and nematodes (an unidentified nematode, Contracaecum sp., Paracamallanus cyathopharynx and Procamallanus laevionchus) was limited to the unpolluted and moderately polluted lakes. Larval stages of Diplostomum sp. were present in O. mossambicus collected from the unpolluted and polluted sites. The variability of the calculated infection indices (prevalence, mean abundance and mean intensity) and the parameters of species richness and diversity suggest that the structure of parasite communities are affected by the pollution levels of the water. The unpolluted reference site had the highest species richness and the highest overall parasite abundance values.

Haemophilus parasuis is the etiological agent of Glässer’s disease, which is characterised by fibrinous polyserositis, meningitis and polyarthritis, causing severe economic losses to the swine industry. In this study, a loop-mediated isothermal amplification (LAMP) test was developed to improve the specificity, facility and speed of diagnosis of H. parasuis isolates. The LAMP assay rapidly amplified the target gene within 50 min incubation at 63 °C in a laboratory water bath. The LAMP amplicon could be visualised directly in the reaction tubes following the addition of SYBR Green I dye. The detection limit of this LAMP method was 10 CFU/mL, which was 10 times more sensitive than the earlier 16S rRNA polymerase chain reaction (PCR) test conducted by Oliveira, Galina and Pijoan (2001), and no cross-reactivity was observed from other non-H. parasuis strains. This LAMP test was evaluated further on 187 clinical specimens from pigs suspected of being infected with H. parasuis. Forty-three were found positive by bacterial isolation of H. parasuis, as well as by the 16S rRNA PCR and LAMP tests. The 43 H. parasuis isolates were classified into 9 serovars and had 37 genetic patterns when analysed by pulsed-field gel electrophoresis (PFGE). This displayed that various H. parasuis serovars and genotypes were widely distributed in South China. Therefore, the speed, specificity and sensitivity of the LAMP test, the lack of a need for expensive equipment, and the visual readout showed great potential for a correct clinical diagnosis of H. parasuis in favour of controlling Glässer’s disease.

Haemophilus parasuis is the etiological agent of Glässer’s disease, which is characterised by fibrinous polyserositis, meningitis and polyarthritis, causing severe economic losses to the swine industry. In this study, a loop-mediated isothermal amplification (LAMP) test was developed to improve the specificity, facility and speed of diagnosis of H. parasuis isolates. The LAMP assay rapidly amplified the target gene within 50 min incubation at 63 °C in a laboratory water bath. The LAMP amplicon could be visualised directly in the reaction tubes following the addition of SYBR Green I dye. The detection limit of this LAMP method was 10 CFU/mL, which was 10 times more sensitive than the earlier 16S rRNA polymerase chain reaction (PCR) test conducted by Oliveira, Galina and Pijoan (2001), and no cross-reactivity was observed from other non-H. parasuis strains. This LAMP test was evaluated further on 187 clinical specimens from pigs suspected of being infected with H. parasuis. Forty-three were found positive by bacterial isolation of H. parasuis, as well as by the 16S rRNA PCR and LAMP tests. The 43 H. parasuis isolates were classified into 9 serovars and had 37 genetic patterns when analysed by pulsed-field gel electrophoresis (PFGE). This displayed that various H. parasuis serovars and genotypes were widely distributed in South China. Therefore, the speed, specificity and sensitivity of the LAMP test, the lack of a need for expensive equipment, and the visual readout showed great potential for a correct clinical diagnosis of H. parasuis in favour of controlling Glässer’s disease.

This study was aimed at determining the prevalence of Cryptosporidium spp. and Giardia duodenalis in pigs which were being raised in intensive management systems. Faecal samples were collected from pigs of all age groups from three different piggery units. Samples were collected directly from the rectum for piglets and weaners and from the floor within 2 min – 5 min of excretion for sows and boars. At the time of collection, faecal consistency was noted as being normal, pasty or diarrhoeic. Samples were analysed further using the Merifluor® Cryptosporidium/Giardia immunofluorescence assay. All piggeries had at least one pig infected with either parasite. From a total 217 samples collected, 96 (44.2%; confidence interval [CI] = 37.6% – 50.9%) were positive for Cryptosporidium spp., whilst 26 (12%; CI = 7.6% – 16.3%) had G. duodenalis parasites. Of all the pigs, 6.9% (15/217) harboured both parasites. With regard to Cryptosporidium spp. infection, statistically significant differences were observed amongst the three units (p = 0.001), whereas no significant differences were observed for G. duodenalis infection (p = 0.13). Prevalence was higher in weaners as compared to other pig classes for both parasites, with significant differences being observed for G. duodenalis infection (p = 0.013). There was, however, no difference in infection between male and female pigs for both parasites. Furthermore, most infections were asymptomatic. From the study results it was clear that Cryptosporidium spp. and G. duodenalis infections were prevalent amongst pigs in the piggeries evaluated and, as such, may act as a source of infection for persons who come into contact with them.

This study was aimed at determining the prevalence of <em>Cryptosporidium</em> spp. and <em>Giardia duodenalis</em> in pigs which were being raised in intensive management systems. Faecal samples were collected from pigs of all age groups from three different piggery units. Samples were collected directly from the rectum for piglets and weaners and from the floor within 2 min – 5 min of excretion for sows and boars. At the time of collection, faecal consistency was noted as being normal, pasty or diarrhoeic. Samples were analysed further using the Merifluor® <em>Cryptosporidium</em>/<em>Giardia</em> immunofluorescence assay. All piggeries had at least one pig infected with either parasite. From a total 217 samples collected, 96 (44.2%; confidence interval [CI] = 37.6% – 50.9%) were positive for <em>Cryptosporidium</em> spp., whilst 26 (12%; CI = 7.6% – 16.3%) had <em>G. duodenalis</em> parasites. Of all the pigs, 6.9% (15/217) harboured both parasites. With regard to <em>Cryptosporidium</em> spp. infection, statistically significant differences were observed amongst the three units (<em>p</em> = 0.001), whereas no significant differences were observed for <em>G. duodenalis</em> infection (<em>p</em> = 0.13). Prevalence was higher in weaners as compared to other pig classes for both parasites, with significant differences being observed for <em>G. duodenalis</em> infection (<em>p</em> = 0.013). There was, however, no difference in infection between male and female pigs for both parasites. Furthermore, most infections were asymptomatic. From the study results it was clear that <em>Cryptosporidium</em> spp. and <em>G. duodenalis</em> infections were prevalent amongst pigs in the piggeries evaluated and, as such, may act as a source of infection for persons who come into contact with them.

Tsetse-transmitted trypanosomosis (nagana) has been the cause of stock losses in the recent past and still presents a major problem to livestock owners in certain areas of KwaZulu- Natal, South Africa. Over 10 000 cattle mortalities were reported in the 1990 nagana outbreak. Although information on the distribution and abundance of the tsetse flies Glossina brevipalpis and Glossina austeni in KwaZulu-Natal exists, data on their vector competence are lacking. This study aimed to determine the rate of natural Trypanosoma congolense infection by field-collected as well as colony-reared flies of these species. A total of 442 field-collected G. brevipalpis and 40 G. austeni flies were dissected immediately after collection to determine their infection rates, whilst 699 G. brevipalpis and 49 G. austeni flies were fed on susceptible animals in 10 and four batches, respectively, for use in xenodiagnosis experiments. Teneral colony flies were fed on infected animals and dissected 21 days post infection to confirm their infectivity testing. Glossina austeni harboured 8% immature and mature infections. In G. brevipalpis, the infection with the immature stages was lower (1%) and no mature infections were observed. Although all four batches of G. austeni transmitted T. congolense to four susceptible animals, no transmission resulted from 10 batches of G. brevipalpis fed on susceptible cattle. Colony-derived G. austeni (534) and G. brevipalpis (882) were fed on four bovines infected with different T. congolense isolates. Both G. austeni and G. brevipalpis acquired trypanosome infection from the bovines, with immature infection ranges of 20% – 33% and 1% – 4%, respectively. Parasites, however, only matured in G. austeni (average = 4%). Glossina austeni plays a larger role in the epidemiology of animal trypanosomosis in KwaZulu-Natal than G. brevipalpis and therefore more focus should be aimed at the former when control measures are implemented.

Tsetse-transmitted trypanosomosis (nagana) has been the cause of stock losses in the recent past and still presents a major problem to livestock owners in certain areas of KwaZulu- Natal, South Africa. Over 10 000 cattle mortalities were reported in the 1990 nagana outbreak. Although information on the distribution and abundance of the tsetse flies Glossina brevipalpis and Glossina austeni in KwaZulu-Natal exists, data on their vector competence are lacking. This study aimed to determine the rate of natural Trypanosoma congolense infection by field-collected as well as colony-reared flies of these species. A total of 442 field-collected G. brevipalpis and 40 G. austeni flies were dissected immediately after collection to determine their infection rates, whilst 699 G. brevipalpis and 49 G. austeni flies were fed on susceptible animals in 10 and four batches, respectively, for use in xenodiagnosis experiments. Teneral colony flies were fed on infected animals and dissected 21 days post infection to confirm their infectivity testing. Glossina austeni harboured 8% immature and mature infections. In G. brevipalpis, the infection with the immature stages was lower (1%) and no mature infections were observed. Although all four batches of G. austeni transmitted T. congolense to four susceptible animals, no transmission resulted from 10 batches of G. brevipalpis fed on susceptible cattle. Colony-derived G. austeni (534) and G. brevipalpis (882) were fed on four bovines infected with different T. congolense isolates. Both G. austeni and G. brevipalpis acquired trypanosome infection from the bovines, with immature infection ranges of 20% – 33% and 1% – 4%, respectively. Parasites, however, only matured in G. austeni (average = 4%). Glossina austeni plays a larger role in the epidemiology of animal trypanosomosis in KwaZulu-Natal than G. brevipalpis and therefore more focus should be aimed at the former when control measures are implemented.

Newcastle disease (ND) is regarded as a highly contagious and economically important disease in poultry and has a worldwide distribution. Viral determinants for Newcastle disease virus (NDV) virulence are not completely understood and viruses of different pathotypes can be found at live-bird markets in different geographical areas. The prevalence of Newcastle disease in village poultry in Mozambique is not well documented and strains of NDV involved in yearly outbreaks are unknown. The fusion (F) protein is an important determinant of pathogenicity of the virus and is used commonly for phylogenetic analysis. Newcastle disease viruses from various geographical regions of Mozambique were sequenced and compared genetically to published sequences obtained from GenBank. Samples were collected in three different areas of Mozambique and NDV was isolated by infection of embryonated chicken eggs. Sequence analysis of the F-protein encoding gene was used to classify 28 isolates from Mozambique into genotypes and compare these genotypes phylogenetically with existing genotypes found in GenBank. The isolates obtained from Mozambique grouped mainly into two clades. In the first clade, 12 isolates grouped together with sequences of isolates representing genotypes from Mozambique that were previously described. In the second clade, 16 isolates group together with sequences obtained from GenBank originating from Australia, China, South Africa and the USA. Eleven of these isolates showed a high similarity with sequences from South Africa. The number of samples sequenced (n = 28), as well as the relatively small geographical collection area used in this study, are too small to be a representation of the circulating viruses in Mozambique in 2005. Viruses characterised in this study belonged to lineage 5b, a similar finding of a previous study 10 years ago. From this data, it merely can be concluded that no new introduction of the virus occurred from 1995 to 2005 in Mozambique.

Newcastle disease (ND) is regarded as a highly contagious and economically important disease in poultry and has a worldwide distribution. Viral determinants for Newcastle disease virus (NDV) virulence are not completely understood and viruses of different pathotypes can be found at live-bird markets in different geographical areas. The prevalence of Newcastle disease in village poultry in Mozambique is not well documented and strains of NDV involved in yearly outbreaks are unknown. The fusion (F) protein is an important determinant of pathogenicity of the virus and is used commonly for phylogenetic analysis. Newcastle disease viruses from various geographical regions of Mozambique were sequenced and compared genetically to published sequences obtained from GenBank. Samples were collected in three different areas of Mozambique and NDV was isolated by infection of embryonated chicken eggs. Sequence analysis of the F-protein encoding gene was used to classify 28 isolates from Mozambique into genotypes and compare these genotypes phylogenetically with existing genotypes found in GenBank. The isolates obtained from Mozambique grouped mainly into two clades. In the first clade, 12 isolates grouped together with sequences of isolates representing genotypes from Mozambique that were previously described. In the second clade, 16 isolates group together with sequences obtained from GenBank originating from Australia, China, South Africa and the USA. Eleven of these isolates showed a high similarity with sequences from South Africa. The number of samples sequenced (<em>n</em> = 28), as well as the relatively small geographical collection area used in this study, are too small to be a representation of the circulating viruses in Mozambique in 2005. Viruses characterised in this study belonged to lineage 5b, a similar finding of a previous study 10 years ago. From this data, it merely can be concluded that no new introduction of the virus occurred from 1995 to 2005 in Mozambique.