Genetic Diversity, Phylogenetic Structure, and Assessment of the Zoonotic Potential of Coxiella burnetii Strains Circulating in Africa

1. Introduction

Coxiella burnetii, the pathogen responsible for Q fever, is an obligate intracellular bacterium belonging to the class Gammaproteobacteria. It exhibits high environmental resilience and the ability to infect a wide range of hosts, including domestic ruminants, wildlife, numerous tick species, and humans. This ecological diversity explains its widespread global distribution and its growing importance in veterinary and public health [1]. The primary reservoirs are domestic ruminants, cattle, sheep, and goats. During parturition or abortion, infected females excrete large quantities of the bacterium into the external environment. Humans are primarily infected by inhaling contaminated aerosols from livestock farms or infected biological materials; transmission through the consumption of raw milk remains rare or secondary [2]. Molecular studies, specifically Multispacer Sequence Typing (MST) and Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA), have provided insights into the genetic diversity of C. burnetii. These approaches have demonstrated that the bacterium does not constitute a homogeneous group, but rather a population of lineages that differ in terms of virulence and zoonotic potential. Recent pan-genomic analyses also indicate an open pan-genome, rich in accessory genes, reflecting active evolutionary dynamics despite the bacterium’s ability to live intracellularly [3]. Africa has been largely overlooked in phylogenetic research on C. burnetii, not because of low prevalence of the microorganism, but rather due to insufficient molecular surveillance, inadequate diagnostic infrastructure, and a focus on other zoonotic diseases. However, several reviews have shown that C. burnetii circulates widely across the continent in cattle, sheep, goats, camelids, dogs, rodents, and ticks, with prevalence rates that are sometimes high depending on the region

Africa therefore likely represents an ancient and still under-explored reservoir of genetic diversity. [4]. Africa therefore likely represents an ancient and still under-explored reservoir of genetic diversity. Several African studies have begun to document this diversity. In East Africa, research conducted in Ethiopia has identified a new MST genotype proposed ST52, as well as several novel MLVA profiles in ticks of the genus Amblyomma, revealing the existence of local lineages distinct from those described in Europe or the Americas. These results marked a turning point by demonstrating that African populations of C. burnetii possess unique genetic signatures [5].

However, data from West Africa and, even more so, from Guinea regarding the genetic diversity of C. burnetiid strains are insufficient. This review highlights the genetic diversity and phylogenetic structure of C. burnetii strains and underscores the gaps in research on C. burnetii infection with a view to improving epidemiological management.

2. Life Cycle and Pathophysiology of C. burnetii Infection

2.1. Morphology

C. burnetii is a strictly intracellular, aerobic bacterium measuring 0.2 to 0.4 μm in width and 0.4 to 1 μm in length. Although it exhibits characteristics of Gram-negative bacteria, it is difficult to detect by Gram staining and is classified within the Proteobacteria group based on its 16S ribosomal RNA sequence [6]. This bacterium is pleomorphic, allowing it to survive and persist in both the host and the environment in various forms [7]. As a strictly intracellular bacterium, it evades phagolysosomal degradation to survive and replicate [8,9]. In macrophages, virulent strains of C. burnetii reside and multiply within compartments also known as phagolysosome-like vacuoles. These vacuoles share characteristics common to late endosomes and lysosomes. These compartments contain neither lysosomal enzymes nor the small GTPase RAB7, but are acidic and express lysosome-associated membrane protein 1 (LAMP-1) [10,11]

2.2. Life Cycle of C. burnetii Infection

The bacterium C. burnetii exhibits a biphasic life cycle characterised by the alternation of two forms: a small dormant form (the small cell variant, or SCV), which enables this obligate intracellular bacterium to persist for long periods outside host cells and to withstand environmental conditions that would be lethal to most prokaryotes, and which constitutes the primary infectious stage encountered by eukaryotic hosts [12]. Conversely, a large, metabolically active morphotype (the large-cell variant, or LCV) enables the pathogen to replicate within the acidified parasitophorous vacuoles (PVs) of a host cell. The marked physiological changes, differential gene expression, and the regulatory and structural components involved in Coxiella morphogenesis, from LCV to SCV and then back to LCV, are fascinating characteristics of this pathogen. The LCV form is pleomorphic and can grow to over 1 µm in length, with a relatively sparse periplasmic space and dispersed DNA [13]. As for the SCV form, it is stable in the external environment and resistant to physical and chemical stresses [14].

The primary mode of transmission of the infection in humans is through the inhalation of contaminated aerosols. C. burnetii virulence factors primarily target mononuclear phagocytes to initiate its biphasic intracellular life cycle. After internalisation, C. burnetii establishes a specialised, membrane-bound replicative niche known as a Coxiella-containing vacuole (CCV). Research conducted by Shepherd et al. in 2023 demonstrated that SCVs are characterised by equidistant stacks of inner membrane, which likely facilitate the transition to LCV; this transition is coupled with the expression of the Dot/Icm type IVB secretion system (T4BSS) [15]. A class of T4BSS particles has been observed, associated with extracellular clusters that may be involved in host infection. Furthermore, SCVs contain multilayered spherical membrane structures of varying sizes and locations, suggesting that they are not associated with sporulation [12]. In infected Vero cells, a homogeneous population of SCVs is observed after 21–28 days of incubation. Research has shown that, in axenic culture, the acidified citrate–cysteine medium of the second generation (ACCM-2) allows these transitions to be accurately reproduced while maintaining bacterial viability. However, ACCM-1 medium promotes the conversion of SCVs to LCVs, as well as the reverse transformation of LCVs to SCVs after prolonged incubation [16]. The bacterium then adopts an altered appearance, characterised by condensed chromatin associated with a loss of cytoplasmic content [17,18]. Both of these cellular variants are infectious in vitro and in vivo; however, the lack of resistance in LCVs indicates that only SCVs play a role in transmission, while LCVs are responsible for the dissemination of the bacterium within the infected host [19].

2.3. Pathophysiology of C. burnetii Infection

The innate immune response represents the host’s first line of defence against this pathogen and plays a decisive role in determining whether the infection progresses to mild respiratory symptoms or persists in a chronic form [20]. To survive within macrophages, C. burnetii hijacks the activation pathways of these cells. Research conducted by Conti et al. demonstrated that lipopolysaccharide (LPS) from the virulent strain of C. burnetii interferes with Toll-like receptor-mediated signalling, specifically TLR-4, leading to inhibition of p38α-MAPK pathway activation despite interaction with TLR-4 [21]. For avirulent strains of C. burnetii, LPS from pathogenic strains disrupts this interaction while preventing the transmission of the immune signal necessary for macrophage activation [22] This disruption prevents TLRs from signalling upon recognition of LPS from pathogenic C. burnetii. Inhibition of TLR-2 and TLR-4 is induced by the reorganisation of the macrophage cytoskeleton by C. burnetii LPS [23]. Unlike avirulent variants, whose LPS promotes the functional association between TLR-2 and TLR-4, the LPS of pathogenic strains disrupts this interaction, thereby preventing the transmission of the immune signal necessary for macrophage activation. This phenomenon is associated with a reorganisation of the actin cytoskeleton induced by bacterial LPS. Experimental blockade of this reorganisation restores the TLR-2/TLR-4 association, as well as activation of the p38α-MAPK pathway. This highlights an immune evasion mechanism by which C. burnetii disrupts innate signalling in macrophages, thereby promoting its intracellular persistence and virulence [22] A study has shown that avirulent strains of C. burnetii engage both the CD11b/CD18 and CR3 membrane receptors, whereas virulent strains do not involve CR3. This leads to changes in the exposure of activating epitopes, as well as a reorganisation of the cytoskeleton [24]. Virulent strains of C. burnetii induce early activation of tyrosine kinases, as well as tyrosine phosphorylation in two Src-related kinases, Hck and Lyn. However, avirulent forms do not promote tyrosine kinase activation. These membrane protrusions are induced by the activation of tyrosine kinases by C. burnetii LPS, which reduces the phagocytosis of C. burnetii [21]. The use of tyrosine kinase inhibitors restores the phagocytosis of C. burnetii. However, when the immune response is insufficient or dysfunctional, the bacterium can persist in the body and progress to a chronic infection (primarily endocarditis), particularly in patients with a history of valvular heart disease and, to a lesser extent, in immunocompromised individuals and pregnant women. In animals, this disease is most often asymptomatic but can lead to abortions, metritis, and reproductive disorders, thereby promoting the environmental spread of the bacterium [7,18,19,20].

Immune control of C. burnetii relies on T lymphocytes but does not always result in the complete elimination of the bacterium [27]. In vertebrates, the acute phase of infection is accompanied by the formation of granulomas, leading to a local immune response [28]. Thus, in the chronic form of Q fever, the effectiveness of the immune response is reduced, allowing the bacterium to multiply within macrophages and potentially causing persistent bacteraemia despite high levels of IgG, IgM, and IgA antibodies directed against phases I and II. However, a decrease in lymphocyte numbers and a lower CD4/CD8 ratio are observed [29]. At this stage, biopsies of the liver and heart valves do not reveal the presence of granulomas. Instead, they show large intracellular vacuoles containing C. burnetii [28]. This chronic form of the disease is characterised by the production of interleukin-10 (IL-10), specifically by the monocytes of individuals experiencing a relapse [30]. Experimental studies in animals have identified several host-related factors that influence C. burnetii infection. A protective effect of female hormones, specifically 17β-oestradiol, has been demonstrated and is thought to be responsible for the sex ratio imbalance after puberty [31]. Conversely, pregnant female animals are more likely to develop chronic Q fever and endocarditis because C. burnetii persists in the uterus and mammary glands and can be reactivated by subsequent pregnancies [32].

Immunosuppression is a major factor associated with the severity of acute Q fever and promotes progression to a chronic form of the disease [26,27]. This experimental study showed that immunosuppression leads to reactivation of the infection in animals [35]. The importance of cellular immunity, particularly that mediated by T lymphocytes, is highlighted by the observation that athymic mice consistently develop chronic infection, unlike euthymic mice [29,30]. C. burnetii is highly infectious, as a single bacterium is sufficient to cause infection. [38]. The number of bacteria inoculated and the route of transmission can influence the duration of the incubation period, the severity of the infection, and potentially the clinical presentation of the disease [32,33].

3. Genomic Groups, Genetic Diversity, and Genotyping Tools for C. burnetii Infection

Genomic groups I, II, and III are similar, whereas group V has the highest rate of polymorphisms (SNPs). Group IV is the most distantly related on the phylogenetic tree [41]. In terms of pathogenicity, strains in Group I are more aggressive than those in Groups II and III. Strains in Groups IV and V are intermediate in virulence, and those in Group VI have no effect. [42]. Regarding geographic distribution, groups I and IV are cosmopolitan, group II is more prevalent in Europe, and group V is found in North America and Nova Scotia. Various molecular approaches can be used to genotype C. burnetii [43]. Among these approaches is multispacer sequencing (MST), a technique that targets the non-coding intergenic regions of the genome through PCR amplification followed by sequencing. The MST typing method for C. burnetii was developed by Glazunova et al. and optimised by Hornstra et al. [44,45]. The main advantage of MST typing lies in its inter-laboratory reliability, which is inherent to the sequencing approach. However, compared with other methods, this technique is more expensive and time-consuming to perform, while also requiring DNA extracts of high quality and concentration. Compared with MST typing, the MLVA (Multiple-Locus Variable-number Tandem Repeat) method is faster because it does not require sequencing of PCR amplicons. The ability to perform multiplex tests using multiple fluorochromes reduces the amount of DNA required. One drawback, however, is the variability in fragment size estimates among different capillary electrophoresis instruments, which may hinder direct comparisons of results across different laboratories [46].

4. Scientific Research and Selection Criteria

A literature search following the PRISMA guidelines was conducted to identify and evaluate relevant scientific articles published on the genetic diversity and phylogenetic structure of C. burnetii infection in Africa from 2006 to 2026. Searches were conducted in two scientific databases (Harzing’s Publish or Perish and ResearchRabbit) using the search engines Cochrane, PubMed, Web of Science, Scopus, and Semantic Scholar, as well as Medline and CrossRef. The terms used in the search bar were “Q fever,” “Coxiellosis,” “Coxiella burnetii,” “genetic diversity,” “phylogenetic structure,” “C. burnetii strain,” and “Africa.” The target population included cattle, sheep, goats, ticks, rodents, and humans. This literature review focused specifically on research conducted on the genetic diversity and phylogenetic structure of C. burnetii strains. For greater precision, the review was limited to studies conducted in Africa. Following this review, relevant articles were selected and analysed to extract information regarding the genetic diversity and phylogenetic structuring of C. burnetii strains. For bibliographic reference management, the Zotero software was used; duplicate references were identified based on the authors, article title, year of publication, issue number, volume, and publisher. The selection criteria were based on publications in English from January 2006 to January 2026 focusing on domestic ruminants, ticks, rodents, and humans in Africa. Second, molecular data, genetic diversity, and phylogenetic structure were analysed, and an assessment of validity was conducted.

5. Distribution of C. burnetii Infection in Africa

Q fever, caused by C. burnetii, has a documented distribution in Africa, but this picture remains incomplete due to underdiagnosis in several regions of Africa. Available data show a high concentration of studies in North Africa, accounting for 40–50% of C. burnetii infection studies. Regarding infection prevalence, rates in East Africa range from 25% to 35%; in West Africa, the figures are approximately 15% to 25%; and finally, in Southern Africa, the rate is 10% [14,41]. This uneven distribution reflects diagnostic and research capabilities rather than the actual prevalence of the infection on the African continent. Several studies indicate that C. burnetii is likely endemic in African livestock systems, particularly in pastoral settings where contact between animals, humans, and the environment facilitates transmission, and most cases remain undetected and unreported. As shown in Table 1, the literature search conducted using various search engines yielded 96 articles and 3 theses related to the genetic diversity of C. burnetii strains. Eighty-six articles were excluded based on the inclusion criteria. Thirteen articles met the inclusion criteria and were therefore selected for this systematic review. The data from the 13 articles meeting the inclusion criteria were synthesised. Indeed, Table 1 presents the geographic distribution in Africa, diagnostic and molecular typing methods, the genetic diversity of C. burnetii, and the variability of the species in question. Of the 13 articles, 2 were from West Africa using MST genotyping, 5 from North Africa using MST and MLVA genotyping, 3 from East Africa using MST, MLVA, and VNTR genotyping, and 3 from Southern Africa using icd gene typing and MLVA. Table 1, aslo summarises research conducted on the genetic diversity of C. burnetii strains in Africa from 2014 to 2026, involving various hosts, namely ticks, cattle, goats, sheep, rodents, dogs, and humans, using different molecular diagnostic methods (PCR, qPCR, MST, MLVA, and icd gene typing). These studies reveal significant genetic heterogeneity, with the identification of several new genotypes depending on the region. Inter-species transmission (animals–ticks–humans) appears to be common, indicating a high zoonotic potential. However, certain lineages show similarities across geographic regions or with human strains, suggesting continent-wide spread and underscoring the need for improved genetic surveillance. In West Africa, significant genetic variability has been observed, with several new genotypes identified in Guinea as well as in Senegal. In North Africa, the dominant genotype in circulation is MST20, which has been observed in multiple hosts, indicating multi-host transmission and the emergence of new genetic profiles. The data show that in East Africa, genetic diversity is high, with new African genotypes suggesting that vectors play a role in maintaining the pathogen. As for Southern Africa, there is genetic variability among the different hosts and a similarity to strains from Europe and the Middle East.

6. Assessment of zoonotic potential

Analysis of the pathogenicity of African isolates highlights a major zoonotic risk. Clinical studies in humans combined with molecular typing have demonstrated the direct involvement of the ST19 genotype, endemic in West Africa, in the emergence of rural outbreaks characterised by severe acute pneumonia and persistent fevers [61]. Furthermore, African strains possess the genetic traits required for high human virulence, such as the com1 and adaA genes and the QpDG or QpH1 plasmids involved in cellular penetration and immune evasion. The clinical impact of these characteristics is most evident in North Africa [45]. Clinical studies such as Mediannikov et al. report that infections with ST19 frequently cause severe acute pneumonia and prolonged fever, in contrast to the often-milder presentation of other genotypes. The differential virulence of C. burnetii genotypes is increasingly recognised, with Group I strains (of which ST19 is a representative) considered more virulent in animal and human models [61].

7. Prevention and Treatment of C. burnetii Infection

In animals, vaccination has proven to be the most effective preventive approach for reducing seroprevalence and controlling transmission. Inactivated or live-attenuated vaccines significantly reduce the incidence of abortions and the bacterial load excreted in parturition products. Vaccinating pregnant females before conception is essential and must be combined with biosecurity measures, including the isolation of pregnant females, the disinfection of farrowing areas, and the safe disposal of birthing waste [62]. The administration of tetracycline has proven effective in reducing the incidence of abortions. However, this treatment neither eliminates the infection within the herd nor suppresses excretion of C. burnetii [62]. In cases of serial abortions, preventive treatment with metaphylactics and oxytetracycline is essential for pregnant females that have not yet aborted. This treatment must be repeated after 1–2 weeks until calving [63]. This treatment in affected cattle can only be effective if carried out diligently. Pregnant cows that could not be vaccinated must receive repeated doses of oxytetracycline (and progesterone if necessary). In humans, prevention relies on avoiding exposure to C. burnetii (on farms, in laboratories) by wearing personal protective equipment, decontaminating surfaces with bleach or 70% alcohol, and isolating pregnant women from contact with potentially infected animals. Vaccination with Coxevac is recommended for at-risk personnel (veterinarians, farmers, laboratory staff) [64]. However, doxycycline is the best treatment; it is administered at a dose of 200 mg per day in two divided doses for 2 to 3 weeks [26]. In case of relapse, treatment should be extended. Rifampicin should be used if tetracyclines are contraindicated [64]. The combination of doxycycline and a quinolone for 48 months is recommended. This treatment appears to be more effective, but recurrences have been observed after several years [64]. This recurrence is due to the fact that the antibiotics used have no bactericidal effect against C. burnetiid [65]. When a lysosomotropic alkalising agent such as hydroxychloroquine is used, the bactericidal properties of doxycycline are restored [64]. The combination of doxycycline and quinolones during pregnancy appears to be effective in preventing the risks of miscarriage and neonatal mortality. However, it does not reduce the risk of the mother developing a chronic form of the disease [26].

8. Discussion

This systematic review is the first synthesis mapping the molecular variability and phylogenetic structure of C. burnetii strains across Africa. The analysis reveals a unique pattern of African genotypes, distinct from European and North American patterns. [66]. The near-total absence of genotypes other than ST19 in West Africa suggests a long history of coevolution between this bacterial lineage, local ruminant breeds, and extensive or transhumant livestock systems. This genetic structure has implications for epidemiological approaches and molecular methods. Most commercial PCR kits and primers used were designed based on European reference strains. The intergenic variations observed in African strains may result in false negatives or unreliable genotyping results, leading to an underestimation of the actual prevalence [4]. Access to molecular approaches and genome sequencing has led to remarkable advances in bacterial typing. These methods enable researchers to establish direct links and study evolutionary relationships between different strains using bioinformatics. Whole-genome sequencing is the gold standard for direct comparison between strains. Furthermore, differentiation of C. burnetii strains based on sequencing of the 16S rDNA, com1, mucZ, and isocitrate dehydrogenase genes does not provide sufficient information due to the high similarity (more than 99% homology) among the different strains during sequence analysis [67]. Thus, these methods do not allow for the differentiation of the various strains of C. burnetii. This research is based on incomplete or partially sequenced genetic fragments, which limits the resolution of phylogenetic approaches [61]. A wide variety of methods have been developed for genotyping C. burnetii, notably whole-genome sequencing (WGS), which is the most innovative method for future research on C. burnetii. This method yields genetic data that can be used to analyze entire genomes as well as phylogenetic relationships, thereby providing insights into the mechanisms of evolution and virulence. According to recent research, WGS is considered the gold standard for molecular characterization and epidemiological surveillance [3,62,63].

Advances in understanding the genetic variability and epidemiology of C. burnetii infection could have significant public health implications. A better understanding of the distribution of C. burnetii is needed to improve the differential diagnosis of febrile syndromes in humans [70]. In Africa, Q fever is underdiagnosed due to the similarity of its clinical manifestations with other febrile zoonotic diseases. Furthermore, laboratory facilities capable of performing these tests are often insufficient in Africa. Consequently, the importance of Q fever, spotted fever rickettsioses (SFGR), and typhus rickettsioses (TGR) as causes of acute febrile syndromes in sub-Saharan Africa remains poorly understood [71]. The studies conducted could be based on the development of a regional strategy incorporating the One Health approach, which relies on cooperation between the human and animal health sectors. This collaboration would be important for the surveillance of C. burnetii infection. Strengthening collaboration among the various sectors could help improve the prevention of zoonotic disease risks and optimize the management of Q fever outbreaks in West Africa [14,65]. However, Guinea appears to be a priority area for epidemiological investigation, as the country has several factors that promote the circulation and zoonotic transmission of this bacterium, including extensive livestock farming, high cross-border movement of livestock, and close contact between humans and animals.

The interpretation of the data remains limited due to the heterogeneity of the diagnostic and typing methods used, as well as the limited geographic coverage. The disparity in PCR diagnostic methods targeting the IS1111 repetitive element, the varying MLVA panels, and the non-uniform MST protocols may introduce significant biases when comparing results across different regions. The limited representativeness of the data, with research concentrated in certain, better-documented areas, restricts the generalizability of the results to the entire African continent [14,38].

9. Conclusion

This systematic review provides an initial mapping of the genetic diversity of Coxiella burnetii in Africa and reveals marked heterogeneity among circulating genotypes, with several strains distinct from the genotypes typically observed in Europe. Analysis of phylogenetic data confirms significant interspecies transmission and a high zoonotic potential, particularly evident among small ruminants in West and North Africa. The recurrent presence of virulence genes (adaA, com1) and associated plasmids (QpDG, QpH1) in African isolates underscores the urgency of developing integrated genomic surveillance in line with the One Health approach. Coordinated efforts are needed to establish African C. burnetii genomics networks, standardize genotyping protocols, and adopt whole-genome sequencing (WGS) as the gold standard, particularly in regions with high prevalence of zoonotic infection.