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We report sequences of the complete linear chromosome and five linear plasmids of the relapsing fever spirochete “ Candidatus Borrelia fainii” Qtaro. The chromosome sequence of 951,861 bp and the 243,291 bp of plasmid sequences were predicted to contain 852 and 239 protein-coding genes, respectively. The predicted total GC content was 28.4%.

Increased antimicrobial resistance (AMR) has been reported for pathogenic and commensal

Pigs have been shown to be a reservoir for recently emerging livestock-associated

The presence of antimicrobial-resistant Enterococci in poultry is a growing public health concern worldwide due to its potential for transmission to humans. The aim of this study was to determine the prevalence and patterns of antimicrobial resistance and to detect drug-resistant genes in Enterococcus faecalis and E. faecium in poultry from four districts in Zambia. Identification of Enterococci was conducted using phenotypic methods. Antimicrobial resistance was determined using the disc diffusion method and antimicrobial resistance genes were detected using polymerase chain reaction and gene-specific primers. The overall prevalence of Enterococci was 31.1% (153/492, 95% CI: 27.1–35.4). Enterococcus faecalis had a significantly higher prevalence at 37.9% (58/153, 95% CI: 30.3–46.1) compared with E. faecium, which had a prevalence of 10.5% (16/153, 95% CI: 6.3–16.7). Most of the E. faecalis and E. faecium isolates were resistant to tetracycline (66/74, 89.2%) and ampicillin and erythromycin (51/74, 68.9%). The majority of isolates were susceptible to vancomycin (72/74, 97.3%). The results show that poultry are a potential source of multidrug-resistant E. faecalis and E. faecium strains, which can be transmitted to humans. Resistance genes in the Enterococcus species can also be transmitted to pathogenic bacteria if they colonize the same poultry, thus threatening the safety of poultry production, leading to significant public health concerns.

Water is a global need for the health and survival of all life forms and a habitat to some. However, approximately one billion people in developing countries do not have access to safe drinking water in which Namibia is not an exception. Rural communities of Ohangwena and Omusati regions of Namibia construct hand-dug wells as a source of water. However, these hand-dug wells are not monitored for water quality and are generally poorly constructed. In addition, these hand-dug wells are easily accessed by both humans and animals making them a potential reservoir for zoonotic bacteria partly known to aid antimicrobial resistance development, a global health concern. A metagenomics analysis targeting the 16S rRNA gene was used to detect the bacterial communities in a total of 40 hand-dug well water samples, with 20 being from the wet season and the rest from the dry season. A total of 57 bacterial pathogens were detected with a diverse of zoonotic assemblage. Analysis revealed significant differences in diversity and evenness, and no significant difference in richness of zoonotic bacterial pathogens in hand-dug wells between the wet and dry seasons (P < 0.05) with the dry season having a higher diversity and evenness compared to the wet season. The analysis showed that the hand-dug well water was not definitely safe for human and livestock consumption and their exposure to zoonotic pathogens was pronounced in the dry season.

Namibia is a large country with a population slightly above 2 million of which 73% live in rural areas. It is the driest country in sub-Saharan Africa with unpredictable rainfall patterns which occur between October and May. The Cuvelai Etosha Basin is a rural setting in which most people depend on groundwater to circumvent water scarcity by the construction of hand-dug wells. Communities consume hand-dug well water throughout the year without; knowledge of its safety, and treatment prior to use. Hence, this study aimed at evaluating the seasonal safety and quality of hand-dug well water for human consumption. A 16S rRNA metagenomics study was conducted to explore the influence of season on the human pathogenic bacterial species richness, diversity, evenness and abundance in the hand-dug wells. Bacterial pathogens were identified and analysis revealed no significant difference in species richness and diversity, and a significant difference in species evenness and abundance between the wet and dry seasons. Hence, seasonality had an influence on human bacterial pathogens evenness and abundance but had no influence on species richness and diversity. In addition, the water in hand-dug wells of the Cuvelai Etosha Basin is not safe for consumption and domestic use unless sanitized. It is recommended that efforts should be made to treat the water prior to use, and hand-dug wells should be properly constructed to reduce contamination.

Background The food industry is increasingly becoming more scrutinized, given the frequency and intensity with which zoonotic diseases are being reported. Pathogen tracking has become more applicable with regards food safety. It is in this regard that the present study was formulated to track Listeria species. in freshly slaughtered cattle carcasses by utilizing standard and molecular biological techniques. Methods A cross-sectional study design was conducted from March to December 2020 with 200 samples being equally collected in the rainy and dry seasons. A total of 180 and 20 swabs were aseptically collected from carcasses and the environment respectively. Samples were first subjected to pre-enrichment in half-strength Fraser broth followed by enrichment in full strength Fraser broth and subsequent plating on Listeria agar. Listeria growth characteristics were identified up to species level based on their morphological and biochemical characteristics. Further, molecular detection and phylogenetic analysis was conducted. Quantitative proportionate survey data were analyzed using Stata Version 15 software to estimate crude prevalence taking into account complex design at abattoir level. Factors associated with contamination were characterized using logistic regression. Sequences were analyzed using, Genetyyx version 12 and phylogenetic Mega. Results Of the 200 samples, 19 were positive for Listeria species identified as L.innocua 14/19 (73.7%) and L. monocytogenes 5/19 (26.3%). All isolates were from freshly slaughtered carcasses, and none from environment. Siginificant differences in contamination levels were observed based on season: rainy season yielded 14 (73.6%) whilst the dry season 5 (26.3%). The L. monocytogenes strains showed a high degree of homogeneity on phylogenetic analysis and clustered based on abattoir. Seasonality was identified as a major determinant influencing contamination based on the final logistic regression model. Conclusion This study found evidence of L. monocytogenes contamination on traditionally raised beef carcasses across various abattoirs surveyed. The failure to find Listeria contamination on the abattoir environment may to a greater extent intimate cattle carccases as primary sources of contamination. However, a more comprerehnsive study incorporating different geographical regions is needed to conclusively ascertain these present findings.

Pigs have been shown to be a reservoir for recently emerging livestock-associated Staphylococcus aureus (LA-SA), including methicillin resistant strains in many countries worldwide. However, there is sparse information about LA-SA strains circulating in Zambia. This study investigated the prevalence, phenotypic and genotypic characteristics of S. aureus from pigs and workers at farms and abattoirs handling pigs in Lusaka Province of Zambia. A total of 492 nasal pig swabs, 53 hand and 53 nasal human swabs were collected from farms and abattoirs in selected districts. Standard microbiological methods were used to isolate and determine antimicrobial susceptibility patterns of S. aureus. Polymerase Chain Reaction was used to confirm the species identity and detect antimicrobial resistance and virulence genes of isolates, whereas genetic diversity was evaluated using spa typing. Overall prevalence of S. aureus was 33.1%, 37.8% for pigs and 11.8% for humans. The isolates were resistant to several antibiotics with resistance ranging from 18% to 98% but were all susceptible to vancomycin. Typical LA-SA spa types were detected. The presence of plasmid mediated resistance genes such as tetM (12.8%), other resistance determinants and immune evasion cluster genes among the isolates is of great public health concern. Thus, continuous surveillance of S. aureus using a “One health” approach is warranted to monitor S.aureus infections and spread of antimicrobial resistance.

The Cuvelai Etosha Basin of Namibia is characterised by complex aquifer systems with multi-layered aquifers and various water qualities. Some parts of the basin have been covered with a pipeline system that supplies purified surface water from the Kunene River. Locations that lack a pipeline system utilise hand-dug wells as a source of drinking water. These wells draw water from shallow perched aquifers and are not protected from surface contamination nor is the water quality monitored. Sanitised water supply is relevant for the growth and development of societies and is a priority of the United Nations Millennium Development Goals. A bacteriological water quality study aimed at investigating the presence and seasonal variation of; Citrobacter, Escherichia, Klebsiella, Enterobacter, Proteus, Salmonella, Shigella, and Pseudomonas species was conducted on 44 hand-dug wells in the Ohangwena and Omusati regions of the Cuvelai Etosha Basin. Samples were collected from both the wet and dry seasons. Results disclosed the presence of Salmonella, Shigella, Citrobacter, Escherichia, Klebsiella, Enterobacter, Proteus, and Pseudomonas species. Chi-square confirmed a significant seasonal variation in Salmonella (P 0.05), Escherichia (P > 0.05), Klebsiella (P > 0.05), Enterobacter (P > 0.05), Proteus (P > 0.05) and Pseudomonas (P > 0.05) species. Water from these hand-dug wells is not safe for drinking unless it is subjected to appropriate treatment. It is recommended that hand-dug wells should be properly constructed at safe distances from contaminating structures such a pit latrines and routinely assessed for pathogens, and the water should be sanitized prior to consumption.

Anthrax is caused by Bacillus anthracis, an endospore-forming soil bacterium. The genetic diversity of B. anthracis is known to be low compared with that of Bacillus species. In this study, we performed whole-genome sequencing of Zambian isolates of B. anthracis to understand the genetic diversity between closely related strains. Comparison of genomic sequences revealed that closely related strains were separated into three groups based on single nucleotide polymorphisms distributed throughout the genome. A large genomic deletion was detected in the region containing a bacitracin resistance gene cluster flanked by rRNA operons, resulting in the loss of bacitracin resistance. The structure of the deleted region, which was also conserved among species of the Bacillus cereus group, has the potential for both deletion and amplification and thus might be enabling the species to flexibly control the level of bacitracin resistance for adaptive evolution., Bacillus anthracis is a Gram-positive endospore-forming bacterial species that causes anthrax in both humans and animals. In Zambia, anthrax cases are frequently reported in both livestock and wildlife, with occasional transmission to humans, causing serious public health problems in the country. To understand the genetic diversity of B. anthracis strains in Zambia, we sequenced and compared the genomic DNA of B. anthracis strains isolated across the country. Single nucleotide polymorphisms clustered these strains into three groups. Genome sequence comparisons revealed a large deletion in strains belonging to one of the groups, possibly due to unequal crossing over between a pair of rRNA operons. The deleted genomic region included genes conferring resistance to bacitracin, and the strains with the deletion were confirmed with loss of bacitracin resistance. Similar deletions between rRNA operons were also observed in a few B. anthracis strains phylogenetically distant from Zambian strains. The structure of bacitracin resistance genes flanked by rRNA operons was conserved only in members of the Bacillus cereus group. The diversity and genomic characteristics of B. anthracis strains determined in this study would help in the development of genetic markers and treatment of anthrax in Zambia. IMPORTANCE Anthrax is caused by Bacillus anthracis, an endospore-forming soil bacterium. The genetic diversity of B. anthracis is known to be low compared with that of Bacillus species. In this study, we performed whole-genome sequencing of Zambian isolates of B. anthracis to understand the genetic diversity between closely related strains. Comparison of genomic sequences revealed that closely related strains were separated into three groups based on single nucleotide polymorphisms distributed throughout the genome. A large genomic deletion was detected in the region containing a bacitracin resistance gene cluster flanked by rRNA operons, resulting in the loss of bacitracin resistance. The structure of the deleted region, which was also conserved among species of the Bacillus cereus group, has the potential for both deletion and amplification and thus might be enabling the species to flexibly control the level of bacitracin resistance for adaptive evolution.

To follow-up anthrax in Zambia since the outbreak in 2011, we have collected samples from the environment and the carcasses of anthrax-suspected animals, and have tried to isolate Bacillus anthracis. In the process of identification of B. anthracis, we collected two isolates, of which colonies were similar to B. anthracis; however, from the results of identification using the molecular-based methods, two isolates were genetically related to the highly pathogenic B. cereus, of which clinical manifestation is severe and fatal (e.g., pneumonia). In this study, we showed the existence of bacteria suspected to be highly pathogenic B. cereus in Zambia, indicating the possibility of an outbreak caused by highly pathogenic B. cereus.