Molecular characterization of Brucella species from Zimbabwe

Seroprevalence and assessment of public awareness of Brucella spp., Toxoplasma gondii and Chlamydia abortus in small ruminants from selected smallholder commercial farms of Zimbabwe

Brucella spp., Toxoplasma gondii, and Chlamydia abortus have long been recognized as zoonoses and significant causes of reproductive failure in small ruminants globally. A cross-sectional study was conducted in August 2020 to determine the seroprevalences of Brucella spp., Toxoplasma gondii and Chlamydia abortus in 398 small ruminants from four districts of Zimbabwe (Chivi, Makoni, Zvimba, and Goromonzi) using Indirect-ELISAs. A structured questionnaire was used to assess the knowledge, attitudes, and practices of 103 smallholder farmers towards small ruminant abortions, Brucella spp., T. gondii and C. abortus, and to obtain a general overview of the significance of small ruminant reproductive failure(s) on their livelihoods. The overall seroprevalences were: 9.1% (95% CI: 6.4-12.3) for Brucella spp., 6.8% (95% CI: 4.5-9.7) for T. gondii and 2.0% (95% CI: 0.9-3.9) for C. abortus. Location, age, parity, and abortion history were associated with Brucella spp. seropositivity. Location was also associated with both T. gondii and C. abortus seropositivity. The questionnaire survey established that 44% of respondents had recently faced reproductive disease challenges within their flocks, with 34% correctly identifying abortion causes and only 10%, 6% and 4% having specific knowledge of Brucella spp., C. abortus and T. gondii, respectively. This study provides the first serological evidence of Brucella spp. in small ruminants since 1996 and builds the evidence on small ruminant toxoplasmosis and chlamydiosis in Zimbabwe. Evidence of these zoonoses in small ruminants and the paucity of knowledge shows the need for a coordinated One Health approach to increase public awareness of these diseases, and to establish effective surveillance and control measures. Further studies are required to establish the role these diseases play in small ruminant reproductive failure(s), to identify the Brucella spp. detected here to species/subspecies level, and to assess the socio-economic impact of reproductive failure in livestock among marginalised rural communities.

Seroprevalence, and molecular detection of Brucella abortus in cattle tissues from an abattoir in Namibia

Brucellosis is a worldwide zoonosis that is endemic in Namibia. This study estimated seroprevalence of brucellosis, and determined the presence of Brucella infection in slaughtered cattle using the genus-specific 16-23S rRNA interspacer PCR (ITS-PCR), and the species-specific AMOS-PCR. Between December 2018 and May 2019, sera (n = 304), pooled lymph nodes (n = 304), and individual spleen (n = 304) were collected from slaughtered cattle from 52 farms. Sera were tested for anti-Brucella antibodies using the Rose Bengal test (RBT), and the complement fixation test (CFT). Seroprevalence was 2.3% (7/304) (RBT) and 1.6% (5/304) (CFT). Prevalence of positive herds was 9.6% (5/52). Lymph node (n = 200) and spleen (n = 200) samples from seronegative cattle tested negative for Brucella spp. DNA on ITS-PCR, but Brucella spp. DNA was detected in lymph nodes (85.7%, 6/7) and spleen (85.7%, 6/7) from RBT positive cattle. ITS-PCR confirmed isolates from lymph node (51.4%, 4/7) and spleen (85.7%, 6/7) as Brucella spp.; while AMOS-PCR and Brucella abortus species specific (BaSS) PCR confirmed the isolates as Brucella abortus, and field strains, respectively. Provision of adequate protective gear, and the promotion of brucellosis awareness among abattoir workers is recommended to prevent zoonotic infection.

Higher diversity of Brucella canis in Latin America, according to an MLVA_13 Bc analysis

Brucella canis is the main causative agent of canine brucellosis, which affects domestic and wild canids and leads to clinical signs and symptoms of the reproductive and locomotor systems. Owing to the scarce information on this pathogen, here we addressed the genetic diversity of the circulating strains of this species in Argentina by following an MVLA_13 Bc scheme. The analyzed sample set consisted of 101 strains of B. canis isolates collected between 2006 and 2020 from canines of the Autonomous City of Buenos Aires (CABA) and other regions of Argentina, as well as 235 isolates from North America. . The analysis yielded 336 variants (Hunter-Gaston Diversity Index, HGDI equal to 1.0) showing high diversity on a global scale. The analysis of the six most variable markers also reveled high diversity and allowed further analysis regarding variant relationships. Although the diversity obtained using both schemes (all or the 6 most variable markers) was higher for the Latin American than for the North American strains, we cannot discard that this was due to biases in the sampling methodology or to the different health policies employed in these regions regarding the management of infected individuals. Altogether, the Argentine circulating strains are genetically diverse, but with no apparent geographical association. The markers used in the MLVA_13 Bc are variable and highly useful for the evaluation of outbreaks. Furthermore, the reduced panel of 6 markers (MLVA_6 Bc) proposed in this study is convenient for the study of B. canis strain diversity.

Original and introduced lineages co-driving the persistence of Brucella abortus circulating in West Africa

Introduction

Brucellosis, a serious public health issue affecting animals and humans, is neglected in West Africa (WA).

Methods

In the present study, bio-typing, multi-locus sequence typing (MLST), multiple-locus variable-number tandem repeat analysis (MLVA), and whole genome sequencing single-nucleotide polymorphism (WGS-SNP) analysis were used to characterize the Brucella abortus (B. abortus) strains from WA.

Results

All of the 309 strains analyzed in this study were extracted and downloaded from the international MLVA bank and were from 10 hosts (cattle, humans, ovine, buffalo, dromedaries, horse, sheep, zebu, dog, and cat) distributed in 17 countries in WA. Based on the bio-typing, three biovars, dominated by B. abortus bv.3, were observed and reported across seven decades (1958–2019). With MLST, 129 B. abortus strains from the present study were sorted into 14 STs, with ST34 as the predicted founder. These 14 STs clustered into the global MLST data into three clone complexes (C I–C III) with the majority of strains clustering in C I, while C II forms an independent branch, and C III harbors three STs shared by different continents. These data revealed that most cases were caused by strains from native lineages. According to the MLVA-11 comparison, 309 strains were divided into 22 MLVA-11 genotypes, 15 of which were unique to WA and the remaining seven had a global distribution. MLVA-16 analysis showed that there were no epidemiological links among these strains. Based on the MLVA data, B. abortus strains from WA have high genetic diversity, and predominated genotypes were descended from a native lineage. While the MLVA-16 globally highlights that the dominant native and few introduced lineages (from Brazil, the USA, South Korea, Argentina, India, Italy, Portugal, the UK, Costa Rica, and China) co-driving the B. abortus ongoing prevalence in WA. The high-resolution SNP analysis implied the existence of introduced B. abortus lineages, which may be reasonably explained by the movement and trade of dominant hosts (cattle) and/or their products.

Discussion

Our results indicated that B. abortus strains in WA consist of native and introduced strains that necessitate control such as vaccination, testing, slaughtering, and movement control by the relevant country authorities to reduce brucellosis in livestock.

Comparison of BP26, Omp25 and Omp31 and a Multiepitope-Based Fusion Protein in the Serological Detection of Canine Brucellosis

Background

Brucellosis is one of the most important zoonotic diseases in the world. Canine brucellosis, caused mainly by Brucella canis, is seriously neglected, and there is a lack of accurate diagnostic tools.

Methods

In this study, to compare BP26, Omp25, Omp31 and a multiepitope-based fusion protein in the serological detection of canine brucellosis, using 34 brucellosis-positive dog sera and 62 negative control sera, the Brucella outer membrane proteins Omp31, BP26, Omp25 and a multiepitope-based fusion protein were evaluated by iELISA for their potential use as antigens in the serological diagnosis of canine brucellosis.

Results

The results showed that the multiepitope-based fusion protein performed best in distinguishing brucellosis-positive and brucellosis-negative dog sera, with a positive predictive value (PPV) of 100% and a negative predictive value (NPV) of 98.41%. BP26 and Omp31 showed excellent sensitivity in detecting brucellosis-positive dog sera, but their cross reaction to sera infected with Vibrio parahaemolyticus and Listeria monocytogenes may hinder their application as diagnostic reagents. Omp25 lacked sufficient sensitivity and showed limited ability in distinguishing positive and negative dog sera.

Conclusion

The multiepitope-based fusion protein can be used as an ideal antigen for serologically diagnosing canine brucellosis currently prevalent worldwide.

Characterization of Brucella spp. and other abortigenic pathogens from aborted tissues of cattle and goats in Rwanda

Background

Abortions cause tremendous economic losses in food‐producing animals and may lead to food insecurity.

Objectives

This study aimed to characterize Brucella spp. and other abortigenic pathogens from aborted tissues of cattle.

Methods

For cattle, aborted tissues (n = 19) were cultured, and Brucella spp. were detected using the genus‐specific 16S‐23S ribosomal DNA interspacer region (ITS) assay and speciated using Brucella abortus, Brucella melitensis, Brucella ovis, and Brucella suis (AMOS) and Bruce‐ladder PCR assays. Brucella negative samples were screened using the eight abortigenic pathogens PCR panel. Samples from an abortion outbreak that occurred within a goat tribe were included in this investigation. Sera of females (n = 8) and males (n = 2) were analyzed using the Rose Bengal Test (RBT) and indirect enzyme‐linked immunosorbent assay (i‐ELISA), while vaginal swabs (n = 3) and aborted tissues (n = 1) were cultured and characterized.

Results

The ITS‐PCR detected Brucella DNA in cultures from two aborted tissues of cattle (10.5%, [2/19]), which were identified as B. melitensis (n = 1), and B. abortus (n = 1) using AMOS and Bruce‐ladder PCR assays. Campylobacter fetus (n = 7) and Leptospira spp. (n = 4) including co‐infections (n = 2) of C. fetus and Leptospira spp. were identified from the Brucella negative samples of cattle. Goats (100.0%, 10/10) were brucellosis seropositive on RBT and i‐ELISA. Mixed infections caused by B. melitensis and B. abortus were isolated from the vaginal swabs (n = 3) and aborted tissues (n = 1).

Discussion and conclusions

This is the first identification of abortion‐associated pathogens in aborted cattle indicating the enormous financial losses and a threat to public health. It is therefore essential to include these identified pathogens in the surveillance scheme of veterinary and human services.

Brucella melitensis, a latent "travel bacterium," continual spread and expansion from Northern to Southern China and its relationship to worldwide lineages

Brucellosis caused by Brucella melitensis is considered to be one of the most important zoonotic diseases in China. In this study, Conventional bio-typing, MLVA (multiple locus variable-number tandem repeat analysis), and WGS (whole-genome sequencing)-SNP (single nucleotide polymorphism) were used to study the genetic similarity of B. melitensis in northern and southern China and analyze its relationship with worldwide lineages. Currently, the distribution of species/biovars of B. melitensis has obviously changed, and B. melitensis has become the dominant species in southern regions of China. Strains from the southern had a common geographic origin with strains from the northern. Many MLVA-16 events were shared in the genotypes of the southern and northern strains, suggest that genotypic movement occurred from north to south. Based on WGS-SNP analysis, strains from different provinces were closely related and may have descended from one common ancestor, suggests that the southern strains originated from northern China. These data indicate that B. melitensis is a latent “travel bacterium” that spread and expanded from North China to South China. Moreover, B. melitensis strains from China are also genetically related to strains from other Asian regions (Kazakhstan, Russia, Mongolia, and India). The movement of infected sheep and their products requires control.

Investigation of Genetic Relatedness of Brucella Strains in Countries Along the Silk Road

In this study, MLVA (multiple-locus variable-number tandem repeat analysis) genotype data of Brucella strains from 11 countries along the Silk Road were downloaded from the MLVAbank. MLVA data of strains were applied to the constructed Minimum Spanning Tree to explore the species/biovars distribution, geographic origins, and genetic relationships of the strains analyzed. Moreover, whole-genome sequencing–single-nucleotide polymorphism (WGS-SNP) phylogenetic analysis of the genome of Brucella melitensis strains from GenBank was performed to discriminate the relatedness of strains further and investigate the transmission pattern of B. melitensis brucellosis. A total of 1,503 Brucella strains were analyzed in this study: 431 Brucella abortus strains (29.8%), 1,009 B. melitensis strains (65.7%), and 63 Brucella suis strains (4.5%). B. melitensis biovar 3 was the dominant species and was shown to be widespread in all of the examined regions, suggesting that the prevention and surveillance of the B. melitensis population are a main challenge in these countries. A wide host spectrum was observed for this Brucella population; many animal reservoirs are a potential reason for the continuous brucellosis circulation in these countries. Although the B. abortus strains from the examined regions had common geographic origins, only a few shared genotypes were observed in different countries. These data revealed that the majority of B. abortus strains were spreading within the national borders. However, the B. melitensis strains from Italy originated from a Western Mediterranean lineage; strains from the other 10 countries originated from Eastern Mediterranean lineage, and this lineage was shared by strains from three to nine different countries, suggesting that the introduction and reintroduction of the disease in the 10 countries might have occurred in the past. Furthermore, the most shared MLVA-16 genotypes were formed in the B. melitensis strains from China, Kazakhstan, and Turkey, suggesting that the introduction and trade in sheep and goats have occurred frequently in these countries. WGS-SNP analysis showed that the B. melitensis in this study originated from the Malta (Italy) region. According to their territorial affiliation between four clade strains from these countries in genotype B, the absence of a clear differentiation suggests that strains continuously expand and spread in countries along with Silk Road. Active exchange and trade of animals (sheep and goats) among these countries are reasonable explanations. B. suis strains from different nations showed unique geographic origins and epidemiological characteristics. Therefore, there is an urgent need for the control of transfer and trade of infected sheep (goats) in countries along the Silk Road, namely, the strengthening of the entry–exit quarantine of sheep and goats and improvements in the diagnosis of animal brucellosis.

Brucella canis Group 2 isolated in Argentina

The aim of this study was to estimate the diversity and prevalence of both groups of Brucella canis 1 and 2 with and without deletion respectively in different areas of Argentina. A total of 104 bacterial cultures were typed as B. canis strains using the classical biotyping method. Two PCR assays were performed to confirm that all isolates were B. canis and not Brucella suis. The differentiation between groups 1 and 2 was achieved using another PCR assay and the diversity of B. canis isolates was assessed with four MLVA_16 markers. All strains belonged to Group 2. Bruce 09 marker (MLVA_16 assay) showed the greatest diversity. Only Group 2 of B. canis was identified among the strains evaluated. The markers chosen from the MLVA_16 allowed us to detect genetic diversity among the strains of B. canis studied.

The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake

Next generation sequencing technologies are becoming more accessible and affordable over the years, with entire genome sequences of several pathogens being deciphered in few hours. However, there is the need to analyze multiple genomes within a short time, in order to provide critical information about a pathogen of interest such as drug resistance, mutations and genetic relationship of isolates in an outbreak setting. Many pipelines that currently do this are stand-alone workflows and require huge computational requirements to analyze multiple genomes. We present an automated and scalable pipeline called BAGEP for monomorphic bacteria that performs quality control on FASTQ paired end files, scan reads for contaminants using a taxonomic classifier, maps reads to a reference genome of choice for variant detection, detects antimicrobial resistant (AMR) genes, constructs a phylogenetic tree from core genome alignments and provide interactive short nucleotide polymorphism (SNP) visualization across core genomes in the data set. The objective of our research was to create an easy-to-use pipeline from existing bioinformatics tools that can be deployed on a personal computer. The pipeline was built on the Snakemake framework and utilizes existing tools for each processing step: fastp for quality trimming, snippy for variant calling, Centrifuge for taxonomic classification, Abricate for AMR gene detection, snippy-core for generating whole and core genome alignments, IQ-TREE for phylogenetic tree construction and vcfR for an interactive heatmap visualization which shows SNPs at specific locations across the genomes. BAGEP was successfully tested and validated with Mycobacterium tuberculosis (n = 20) and Salmonella enterica serovar Typhi (n = 20) genomes which are about 4.4 million and 4.8 million base pairs, respectively. Running these test data on a 8 GB RAM, 2.5 GHz quad core laptop took 122 and 61 minutes on respective data sets to complete the analysis. BAGEP is a fast, calls accurate SNPs and an easy to run pipeline that can be executed on a mid-range laptop; it is freely available on: https://github.com/idolawoye/BAGEP.

Molecular Characteristics of Brucella Isolates Collected From Humans in Hainan Province, China

Brucellosis has been reported in several regions of Hainan Province, but the extent of the disease has not been fully elucidated. Conventional biotyping methods, multiple locus variable number tandem repeats analysis (MLVA), and single-nucleotide polymorphisms (SNPs) from draft genome sequencing were employed to characterize the strains. There were four biovars (Brucella melitensis bv. 1, 2, and 3 and Brucella suis bv. 3) detected, which showed that the biovar diversity of Brucella in Hainan is higher than in other areas of China. Both B. melitensis bv. 3 and B. suis bv. 3 were dominant species and showed epidemiology patterns that were compatible with both southern and northern China. Eight of MLVA-11 genotypes were known (31, 111, 116, 120, 136, 291, 297, and 345), and the remaining seven were novel (HN11-1 to HN11-7); these data showed that Brucella strains in this study had multiple geographic origins and exhibited characteristics of origin and evolution of co-existing imported and Hainan specific lineage. A total of 41 strains were found, belonging to 37 unique genotypes that each represented a single strain, which suggests that these strains were not directly related epidemiologically and indicates that the epidemic characteristics of human brucellosis in Hainan was dominated by sporadic strains. The high HGDI values were observed in MLVA-8, MLVA-11, and MLVA-16 among two species, suggesting considerable genetic diversity among these species. MST is characterized based on MLVA-16 that was found both throughout China and on a global level and showed that strains of this study had significant genetic differences with strains from many parts of the globe and seemingly represent a unique genetic lineage. Whole-genome SNP analysis showed that four B. melitensis were closely related to strains from China's northern provinces, and the source of infection was partly of human brucellosis in this province that may have been from these regions. The B. suis were closely related to strains from the United States, and further investigation of the transportation of animals, such as pigs, is needed to elucidate the origins of these strains.

Seroprevalence of human brucellosis and molecular characteristics of Brucella strains in Inner Mongolia Autonomous region of China, from 2012 to 2016

In the present study, a total of 1102304 serum samples were collected to detected human brucellosis between the years 2012 and 2016 in Inner Mongolia. Overall, an average of 3.79% anti-Brucella positive in Inner Mongolia was presented but the range of positive rates were among 0.90 to 7.07% in 12 regions. Seroprevalence of human brucellosis increased gradually from 2012 to 2016. However, the incidence rate of human brucellosis showed a declining trend. One hundred and seven Brucella strains were isolated and identified as B. melitensis species, and B. melitensis biovar 3 was the predominant biovar. MLVA-11 genotypes 116 was predominant and had crucial epidemiology to the human population. All 107 strains tested were sorted into 75 MLVA-16 genotypes, with 54 single genotypes representing unique isolates. This result revealed that these Brucellosis cases had epidemiologically unrelated and sporadic characteristics. The remaining 21 shared genotypes among two to four strains, confirming the occurrence of cross-infection and multiple outbreaks. Extensive genotype-events were observed between strains from this study and Kazakhstan, Mongolia, and Turkey, these countries were key members of the grassland silk road. Long-time trade in small ruminants (sheep) in these countries has possibly promoted the spread of Brucella spp. in these regions.

Genetic Diversity of Brucella melitensis in Kazakhstan in Relation to World-Wide Diversity

We describe the genetic diversity of 1327 Brucella strains from human patients in Kazakhstan using multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA). All strains were assigned to the Brucella melitensis East Mediterranean group and clustered into 16 MLVA11 genotypes, nine of which are reported for the first time. MLVA11 genotype 116 predominates (86.8%) and is present all over Kazakhstan indicating existence and temporary preservation of a “founder effect” among B. melitensis strains circulating in Central Eurasia. The diversity pattern observed in humans is highly similar to the pattern previously reported in animals. The diversity observed by MLVA suggested that the epidemiological status of brucellosis in Kazakhstan is the result of the introduction of a few lineages, which have subsequently diversified at the most unstable tandem repeat loci. This investigation will allow to select the most relevant strains for testing these hypotheses via whole genome sequencing and to subsequently adjust the genotyping scheme to the Kazakhstan epidemiological situation.