Ticks (Acari: Ixodidae) infesting cattle in coastal Kenya harbor a diverse array of tick-borne pathogens

Ticks and the microbes they transmit have emerged in sub-Saharan Africa as a major threat to veterinary and public health. Although progress has been made in detecting and identifying tick-borne pathogens (TBPs) across vast agroecologies of Kenya, comprehensive information on tick species infesting cattle and their associated pathogens in coastal Kenya needs to be updated and expanded. Ticks infesting extensively grazed zebu cattle in 14 villages were sampled and identified based on morphology and molecular methods and tested for the presence of bacterial and protozoan TBPs using PCR with high-resolution melting analysis and gene sequencing. In total, 3,213 adult ticks were collected and identified as Rhipicephalus appendiculatus (15.8%), R. evertsi (12.8%), R. microplus (11.3%), R. pulchellus (0.1%), Amblyomma gemma (24.1%), A. variegatum (35.1%), Hyalomma rufipes (0.6%), and H. albiparmatum (0.2%). Ticks were infected with Rickettsia africae, Ehrlichia ruminantium, E. minasensis, Theileria velifera and T. parva. Coxiella sp. endosymbionts were detected in the Rhipicephalus and Amblyomma ticks. Co-infections with two and three different pathogens were identified in 6.9% (n = 95/1382) and 0.1% (n = 2/1382) of single tick samples, respectively, with the most common co-infection being R. africae and E. ruminantium (7.2%, CI: 4.6 - 10.6). All samples were negative for Coxiella burnetii, Anaplasma spp. and Babesia spp. Our study provides an overview of tick and tick-borne microbial diversities in coastal Kenya.

Proteome Profiling of Mycobacterium tuberculosis Cells Exposed to Nitrosative Stress

Reactive nitrogen species (RNS) are secreted by human cells in response to infection by Mycobacterium tuberculosis (Mtb). Although RNS can kill Mtb under some circumstances, Mtb can adapt and survive in the presence of RNS by a process that involves modulation of gene expression. Previous studies focused primarily on stress-related changes in the Mtb transcriptome. This study unveils changes in the Mtb proteome in response to a sub-lethal dose of nitric oxide (NO) over several hours of exposure. Proteins were identified using liquid chromatography coupled with electrospray ionization mass spectrometry (LC-MS/MS). A total of 2911 Mtb proteins were identified, of which 581 were differentially abundant (DA) after exposure to NO in at least one of the four time points (30 min, 2 h, 6 h, and 20 h). The proteomic response to NO was marked by two phases, with few DA proteins in the early phase and a multitude of DA proteins in the later phase. The efflux pump Rv1687 stood out as being the only protein more abundant at all the time points and might play a role in the early protection of Mtb against nitrosative stress. These changes appeared to be compensatory in nature, contributing to iron homeostasis, energy metabolism, and other stress responses. This study thereby provides new insights into the response of Mtb to NO at the level of proteomics.

The developmentally dynamic microRNA transcriptome of Glossina pallidipes tsetse flies, vectors of animal trypanosomiasis

Summary

MicroRNAs (miRNAs) are single stranded gene regulators of 18-25 bp in length. They play a crucial role in regulating several biological processes in insects. However, the functions of miRNA in Glossina pallidipes, one of the biological vectors of African animal trypanosomosis in sub-Saharan Africa, remain poorly characterized. We used a combination of both molecular biology and bioinformatics techniques to identify miRNA genes at different developmental stages (larvae, pupae, teneral and reproductive unmated adults, gravid females) and sexes of G. pallidipes. We identified 157 mature miRNA genes, including 12 novel miRNAs unique to G. pallidipes. Moreover, we identified 93 miRNA genes that were differentially expressed by sex and/or in specific developmental stages. By combining both miRanda and RNAhybrid algorithms, we identified 5550 of their target genes. Further analyses with the Gene Ontology term and KEGG pathways for these predicted target genes suggested that the miRNAs may be involved in key developmental biological processes. Our results provide the first repository of G. pallidipes miRNAs across developmental stages, some of which appear to play crucial roles in tsetse fly development. Hence, our findings provide a better understanding of tsetse biology and a baseline for exploring miRNA genes in tsetse flies.

Availability and implementation

Raw sequence data are available from NCBI Sequence Read Archives (SRA) under Bioproject accession number PRJNA590626.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

Prevalence of Trypanosome Species in Cattle Near Ruma National Park, Lambwe Valley, Kenya: An Update From the Historical Focus for African Trypanosomosis

The effective control of diseases in areas shared with wildlife depends on the validity of the epidemiologic parameters that guide interventions. Epidemiologic data on animal trypanosomosis in Lambwe valley are decades old, and the recent suspected outbreaks of the disease in the valley necessitate the urgent bridging of this data gap. This cross-sectional study estimated the prevalence of bovine trypanosomosis, identified risk factors, and investigated the occurrence of species with zoonotic potential in Lambwe valley. The area is ~324 km², of which 120 km² is the Ruma National Park. Blood was sampled from the jugular and marginal ear veins of 952 zebu cattle between December 2018 and February 2019 and tested for trypanosomes using the Buffy Coat Technique (BCT) and PCR-High-Resolution Melting (HRM) analysis of the 18S RNA locus. Risk factors for the disease were determined using logistic regression. The overall trypanosome prevalence was 11.0% by BCT [95% confidence interval (CI): 9.0–13.0] and 27.9% by PCR-HRM (95% CI: 25.1–30.8). With PCR-HRM as a reference, four species of trypanosomes were detected at prevalences of 12.7% for T. congolense savannah (95% CI: 10.6–14.8), 7.7% for T. brucei brucei (CI: 6.0–9.4), 8.7% for T. vivax (CI: 6.9–10.5), and 1.3% for T. theileri (CI: 0.6–2.0). About 2.4% of cattle had mixed infections (CI: 1.4–3.41). No human-infective trypanosomes were found. Infections clustered across villages but were not associated with animal age, sex, herd size, and distance from the park. Approximately 85% of infections occurred within 2 km of the park. These findings add to evidence that previous interventions eliminated human trypanosomosis but not bovine trypanosomosis. Risk-tailored intervention within 2 km of Ruma Park, especially in the north and south ends, coupled with stringent screening with molecular tools, could significantly reduce bovine trypanosomosis.

Tsetse Bloodmeal Analyses Incriminate the Common Warthog Phacochoerus africanus as an Important Cryptic Host of Animal Trypanosomes in Smallholder Cattle Farming Communities in Shimba Hills, Kenya

Trypanosomes are endemic and retard cattle health in Shimba Hills, Kenya. Wildlife in the area act as reservoirs of the parasites. However, wild animal species that harbor and expose cattle to tsetse-borne trypanosomes are not well known in Shimba Hills. Using xeno-monitoring surveillance to investigate wild animal reservoirs and sources of trypanosomes in Shimba Hills, we screened 696 trypanosome-infected and uninfected tsetse flies for vertebrate DNA using multiple-gene PCR-High Resolution Melting analysis and amplicon sequencing. Results revealed that tsetse flies fed on 13 mammalian species, preferentially Phacochoerus africanus (warthogs) (17.39%, 95% CI: 14.56–20.21) and Bos taurus (cattle) (11.35%, 95% CI: 8.99–13.71). Some tsetse flies showed positive cases of bloodmeals from multiple hosts (3.45%, 95% CI: 2.09–4.81), including warthog and cattle (0.57%, 95% CI: 0.01–1.14). Importantly, tsetse flies that took bloodmeals from warthog had significant risk of infections with Trypanosoma vivax (5.79%, 95% CI: 1.57–10.00), T. congolense (7.44%, 95% CI: 2.70–12.18), and T. brucei sl (2.48%, 95% CI: −0.33–5.29). These findings implicate warthogs as important reservoirs of tsetse-borne trypanosomes affecting cattle in Shimba Hills and provide valuable epidemiological insights to underpin the parasites targeted management in Nagana vector control programs in the area.

Lineage-Specific Proteomic Signatures in the Mycobacterium tuberculosis Complex Reveal Differential Abundance of Proteins Involved in Virulence, DNA Repair, CRISPR-Cas, Bioenergetics and Lipid Metabolism

Despite the discovery of the tubercle bacillus more than 130 years ago, its physiology and the mechanisms of virulence are still not fully understood. A comprehensive analysis of the proteomes of members of the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages 3, 4, 5, and 7 was conducted to better understand the evolution of virulence and other physiological characteristics. Unique and shared proteomic signatures in these modern, pre-modern and ancient MTBC lineages, as deduced from quantitative bioinformatics analyses of high-resolution mass spectrometry data, were delineated. The main proteomic findings were verified by using immunoblotting. In addition, analysis of multiple genome alignment of members of the same lineages was performed. Label-free peptide quantification of whole cells from MTBC lineages 3, 4, 5, and 7 yielded a total of 38,346 unique peptides derived from 3092 proteins, representing 77% coverage of the predicted proteome. MTBC lineage-specific differential expression was observed for 539 proteins. Lineage 7 exhibited a markedly reduced abundance of proteins involved in DNA repair, type VII ESX-3 and ESX-1 secretion systems, lipid metabolism and inorganic phosphate uptake, and an increased abundance of proteins involved in alternative pathways of the TCA cycle and the CRISPR-Cas system as compared to the other lineages. Lineages 3 and 4 exhibited a higher abundance of proteins involved in virulence, DNA repair, drug resistance and other metabolic pathways. The high throughput analysis of the MTBC proteome by super-resolution mass spectrometry provided an insight into the differential expression of proteins between MTBC lineages 3, 4, 5, and 7 that may explain the slow growth and reduced virulence, metabolic flexibility, and the ability to survive under adverse growth conditions of lineage 7.

The helicase DinG responds to stress due to DNA double strand breaks

Neisseria meningitidis (Nm) is a Gram-negative nasopharyngeal commensal that can cause septicaemia and meningitis. The neisserial DNA damage-inducible protein DinG is a helicase related to the mammalian helicases XPD and FANCJ. These helicases belong to superfamily 2, are ATP dependent and exert 5′ → 3′ directionality. To better understand the role of DinG in neisserial genome maintenance, the Nm DinG (DinG_Nm) enzymatic activities were assessed in vitro and phenotypical characterization of a dinG null mutant (NmΔdinG) was performed. Like its homologues, DinG_Nm possesses 5′ → 3′ directionality and prefers DNA substrates containing a 5′-overhang. ATPase activity of DinG_Nm is strictly DNA-dependent and DNA unwinding activity requires nucleoside triphosphate and divalent metal cations. DinG_Nm directly binds SSB_Nm with a K_d of 313 nM. Genotoxic stress analysis demonstrated that NmΔdinG was more sensitive to double-strand DNA breaks (DSB) induced by mitomycin C (MMC) than the Nm wildtype, defining the role of neisserial DinG in DSB repair. Notably, when NmΔdinG cells grown under MMC stress assessed by quantitative mass spectrometry, 134 proteins were shown to be differentially abundant (DA) compared to unstressed NmΔdinG cells. Among the DNA replication, repair and recombination proteins affected, polymerase III subunits and recombinational repair proteins RuvA, RuvB, RecB and RecD were significantly down regulated while TopA and SSB were upregulated under stress condition. Most of the other DA proteins detected are involved in metabolic functions. The present study shows that the helicase DinG is probably involved in regulating metabolic pathways as well as in genome maintenance.

Comparative Proteomic Analysis of Mycobacterium tuberculosis Lineage 7 and Lineage 4 Strains Reveals Differentially Abundant Proteins Linked to Slow Growth and Virulence

In order to decipher the nature of the slowly growing Mycobacterium tuberculosis (M.tuberculosis) lineage 7, the differentially abundant proteins in strains of M. tuberculosis lineage 7 and lineage 4 were defined. Comparative proteomic analysis by mass spectrometry was employed to identify, quantitate and compare the protein profiles of strains from the two M. tuberculosis lineages. Label-free peptide quantification of whole cells from M. tuberculosis lineage 7 and 4 yielded the identification of 2825 and 2541 proteins, respectively. A combined total of 2867 protein groups covering 71% of the predicted M. tuberculosis proteome were identified. The abundance of 125 proteins in M. tuberculosis lineage 7 and 4 strains was significantly altered. Notably, the analysis showed that a number of M. tuberculosis proteins involved in growth and virulence were less abundant in lineage 7 strains compared to lineage 4. Five ABC transporter proteins, three phosphate binding proteins essential for inorganic phosphate uptake, and six components of the type 7 secretion system ESX-3 involved in iron acquisition were less abundant in M. tuberculosis lineage 7. This proteogenomic analysis provided an insight into the lineage 7-specific protein profile which may provide clues to understanding the differential properties of lineage 7 strains in terms of slow growth, survival fitness, and pathogenesis.

Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis

Background

DNA processing chain A (DprA) is a DNA binding protein which is ubiquitous in bacteria, and is required for DNA transformation to various extents among bacterial species. However, the interaction of DprA with competence and recombination proteins is poorly understood. Therefore, the proteomes of whole Neisseria meningitidis (Nm) wildtype and dprA mutant cells were compared. Such a comparative proteomic analysis increases our understanding of the interactions of DprA with other Nm components and may elucidate its potential role beyond DNA processing in transformation.

Results

Using label-free quantitative proteomics, a total of 1057 unique Nm proteins were identified, out of which 100 were quantified as differentially abundant (P ≤ 0.05 and fold change ≥ |2|) in the dprA null mutant. Proteins involved in homologous recombination (RecA, UvrD and HolA), pilus biogenesis (PilG, PilT1, PilT2, PilM, PilO, PilQ, PilF and PilE), cell division, including core energy metabolism, and response to oxidative stress were downregulated in the Nm dprA null mutant. The mass spectrometry data are available via ProteomeXchange with identifier PXD006121. Immunoblotting and co-immunoprecipitation were employed to validate the association of DprA with PilG. The analysis revealed reduced amounts of PilG in the dprA null mutant and reduced amounts of DprA in the Nm pilG null mutant. Moreover, a number of pilus biogenesis proteins were shown to interact with DprA and /or PilG.

Conclusions

DprA interacts with proteins essential for Nm DNA recombination in transformation, pilus biogenesis, and other functions associated with the inner membrane. Inverse downregulation of Nm DprA and PilG expression in the corresponding mutants indicates a link between DNA processing and pilus biogenesis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-1004-8) contains supplementary material, which is available to authorized users.

Characterization of the Neisseria meningitidis Helicase RecG

Neisseria meningitidis (Nm) is a Gram-negative oral commensal that opportunistically can cause septicaemia and/or meningitis. Here, we overexpressed, purified and characterized the Nm DNA repair/recombination helicase RecG (RecG_Nm) and examined its role during genotoxic stress. RecG_Nm possessed ATP-dependent DNA binding and unwinding activities in vitro on a variety of DNA model substrates including a Holliday junction (HJ). Database searching of the Nm genomes identified 49 single nucleotide polymorphisms (SNPs) in the recG_Nm including 37 non-synonymous SNPs (nsSNPs), and 7 of the nsSNPs were located in the codons for conserved active site residues of RecG_Nm. A transient reduction in transformation of DNA was observed in the Nm ΔrecG strain as compared to the wildtype. The gene encoding recG_Nm also contained an unusually high number of the DNA uptake sequence (DUS) that facilitate transformation in neisserial species. The differentially abundant protein profiles of the Nm wildtype and ΔrecG strains suggest that expression of RecG_Nm might be linked to expression of other proteins involved in DNA repair, recombination and replication, pilus biogenesis, glycan biosynthesis and ribosomal activity. This might explain the growth defect that was observed in the Nm ΔrecG null mutant.

Using SILAC proteomics to investigate the effect of the mycotoxin, alternariol, in the human H295R steroidogenesis model

The mycotoxin alternariol (AOH) is an important contaminant of fruits and cereal products. The current study sought to address the effect of a non-toxic AOH concentration on the proteome of the steroidogenic H295R cell model. Quantitative proteomics based on stable isotope labeling by amino acids in cell culture (SILAC) coupled to 1D-SDS-PAGE-LC-MS/MS was applied to subcellular-enriched protein samples. Gene ontology (GO) and ingenuity pathway analysis (IPA) were further carried out for functional annotation and identification of protein interaction networks. Furthermore, the effect of AOH on apoptosis and cell cycle distribution was also determined by the use of flow cytometry analysis. This work identified 22 proteins that were regulated significantly. The regulated proteins are those involved in early stages of steroid biosynthesis (SOAT1, NPC1, and ACBD5) and C21-steroid hormone metabolism (CYP21A2 and HSD3B1). In addition, several proteins known to play a role in cellular assembly, organization, protein synthesis, and cell cycle were regulated. These findings provide a new framework for studying the mechanisms by which AOH modulates steroidogenesis in H295R cell model.

An in vitro investigation of endocrine disrupting effects of the mycotoxin alternariol

Alternariol (AOH) is a mycotoxin commonly produced by Alternaria alternata on a wide range of foods. Few studies to date have been performed to evaluate the effects of AOH on endocrine activity. The present study makes use of in vitro mammalian cellular based assays and gene expression to investigate the ability of AOH to act as an endocrine disruptor by various modes of action. Reporter gene assays (RGAs), incorporating natural steroid hormone receptors for oestrogens, androgens, progestagens and glucocorticoids were used to identify endocrine disruption at the level of nuclear receptor transcriptional activity, and the H295R steroidogenesis assay was used to assess endocrine disruption at the level of gene expression and steroid hormone production. AOH exhibited a weak oestrogenic response when tested in the oestrogen responsive RGA and binding of progesterone to the progestagen receptor was shown to be synergistically increased in the presence of AOH. H295R cells when exposed to 0.1-1000ng/ml AOH, did not cause a significant change in testosterone and cortisol hormones but exposure to 1000ng/ml (3.87μM) AOH resulted in a significant increase in estradiol and progesterone production. In the gene expression study following exposure to 1000ng/ml (3.87μM) AOH, only one gene NR0B1 was down-regulated, whereas expression of mRNA for CYP1A1, MC2R, HSD3B2, CYP17, CYP21, CYP11B2 and CYP19 was up-regulated. Expression of the other genes investigated did not change significantly. In conclusion AOH is a weak oestrogenic mycotoxin that also has the ability to interfere with the steroidogenesis pathway.

Prevalence, bacterial causes, and antimicrobial susceptibility profile of mastitis isolates from cows in large-scale dairy farms of Northern Ethiopia

The study was undertaken to determine the prevalence of bovine mastitis, isolate mastitis causing bacteria, assess the association of some risk factors, and determine the antibiotic resistance pattern of bacterial isolates in cows in large-scale dairy farms of Northern Ethiopia. A total of 305 lactating and nonlactating cows were included in the present study. The overall prevalence of clinical and subclinical mastitis was 3.6 and 33.8 %, respectively. The quarter level prevalence was 15.4 %; from which, 11.9 and 1.1 % were subclinical form and blind teat, respectively, while the remaining 2.4 % were of clinical form. Staphylococcus aureus accounted for 36 % of the isolates followed by Escherichia coli (27.3 %). Risk factors including age (p < 0.001), parity (p < 0.001), and lactation stage (p = 0.02) showed significant association with the occurrence of mastitis. Higher prevalence was observed in both groups of older cows (i.e., 6-9 years (odds ratio (OR) = 4.65, 95 % confidence interval (CI) = 2.74-7.89) and >9 years (OR = 3.63, 95 % CI = 1.42-9.25)), cows with four to seven calves (OR = 3.39, 95 % CI = 2.06-5.60), and cows in late lactation stage (OR = 3.79, 95 % CI = 1.64-8.75). In multivariable logistic regression analysis, age (p = 0.005) and lactation stage (p = 0.027) showed statistically significant association with the occurrence of mastitis. The antimicrobial susceptibility pattern showed high susceptibility of S. aureus to nalidixic acid (82.4 %) followed by chloramphenicol (58.8 %); however, these species were resistant to the rest of the antimicrobials tested. Highest resistance was observed against clindamycin and ampicillin. Coliform bacteria (E. coli and Klebsiella pneumoniae) showed resistance to most of the antimicrobials used. Detailed investigation is needed to identify the interplay of managemental and environmental risk factors to design appropriate control measures.

Effect of Brucella infection on reproduction conditions of female breeding cattle and its public health significance in Western tigray, northern ethiopia

The most common clinical manifestations of brucellosis in livestock are associated with reproduction. This paper reports the result of a cross-sectional study conducted between October, 2007 and April, 2008 in Western Tigray, North Ethiopia, with the objectives of assessing the effect of Brucella infection on reproduction conditions of female breeding bovine and to explore the presence of Brucella seroreactors in vulnerable humans. A total of 1,354 and 246 sera were collected from female cattle and humans, respectively. The sera were screened using Rose Bengal plate test (RBPT), and positive samples were confirmed by complement fixation test (CFT). Reproductive conditions for female cattle and risk to human brucellosis seropositivity were tested by using logistic regression analysis. The result indicated that the overall prevalence in female cattle was 6.1%. The study showed 1.2% prevalence among human risk groups, all of which were herdsmen. Logistic regression identified parity status, calving interval, abortion history, and abortion period were significantly associated with seropositivity. The association was not significant with reproductive status and parity number. Proper hygienic practices and team work between veterinary and health personnel should improve the efforts to combat disease transmission.

Serological evidence of Leishmania donovani infection in apparently healthy dogs using direct agglutination test (DAT) and rk39 dipstick tests in Kafta Humera, north-west Ethiopia

Leishmania (Kinetoplastida: Trypanosomatidae) are protozoan parasites of significant medical and veterinary importance. Over the last decade, visceral leishmaniasis (VL) has emerged as a major opportunistic infection associated with HIV/AIDS in North Western Ethiopia. This paper reports on serological evidence of possible Leishmania donovani (L. donovani) infection in dogs using two serological tests: direct agglutination test (DAT) and Kalazar detect rapid test (KDRT). Two hundred and seventeen asymptomatic local breed dogs were examined for L. donovani antibodies. Performance of the DAT and KDRT was assessed in 162 matching samples of blood collected on filter paper and serum, respectively. Using DAT and KDRT testing in parallel, the overall seroprevalence of L. donovani infection was 27.7% and 14.8%, respectively. The degree of agreement was found to be fair (68.8%, k = 0.234). Univariable logistic regression analysis of some risk factors for L. donovani infection in dogs using DAT indicates that place of residence, sex, age, dog keeping purpose and dog housing condition were not significantly associated with seropositivity. The high proportion of positive dogs suggests the exposure of these animals to L. donovani infection and needs further investigation. Isolation and typing of the parasite aiming at confirming the role of these animals in maintenance and transmission of kala-azar is advocated.