The use of a CYP51C gene based PCR-RFLP assay for simultaneous detection and identification of Fusarium avenaceum and F. tricinctum in wheat

Contamination of cereals with mycotoxins such as beauvericin (BEA), enniatins (Ens) and moniliformin (MON) is mainly caused by Fusarium avenaceum and F. tricinctum. This is a world-wide problem which requires rapid and sensitive detection methods. To allow for high throughput screening of large numbers of samples, a diagnostic PCR method was developed for the simultaneous detection of F. avenaceum and F. tricinctum. The interspecific divergence found in the Fusarium-specific CYP51C gene was used to design species-specific PCR primers. The specificity of the assay was demonstrated for DNA samples extracted from a wide range of Fusarium species belonging to the Fusarium head blight (FHB) complex, as well as for naturally-infected grain samples. The PCR-amplified products were digested with the restriction enzyme XbaI to enable differentiation between F. avenaceum and F. tricinctum. This PCR- restriction fragment length polymorphism (RFLP) assay proved to be a simple and relatively inexpensive method highly suited for routine detection and identification of F. avenaceum and F. tricinctum in wheat samples.     

Fusarium sibiricum sp. nov, a novel type A trichothecene-producing Fusarium from northern Asia closely related to F. sporotrichioides and F. langsethiae

Production of type A trichothecenes has been reported in the closely related species Fusarium langsethiae and F. sporotrichioides. Here, we characterized a collection of Fusarium isolates from Siberia and the Russian Far East (hereafter Asian isolates) that produce high levels of the type A trichothecene T-2 toxin and are similar in morphology to the type A trichothecene-producing F. langsethiae, and to F. poae which often produces the type B trichothecene nivalenol. The Asian isolates possess unique macroscopic and microscopic characters and have a unique TG repeat in the nuclear ribosomal intergenic spacer (IGS rDNA) region. In Asian isolates, the TRI1-TRI16 locus, which determines type A versus type B trichothecene production in other species, is more similar in organization and sequence to the TRI1-TRI16 locus in F. sporotrichioides and F. langsethiae than to that in F. poae. Phylogenetic analysis of the TRI1 and TRI16 gene coding regions indicates that the genes in the Asian isolates are more closely related to those of F. sporotrichioides than F. langsethiae. Phylogenetic analysis of the beta-tubulin, translation elongation factor, RNA polymerase II and phosphate permease gene sequences resolved the Asian isolates into a well-supported sister lineage to F. sporotrichioides, with F. langsethiae forming a sister lineage to F. sporotrichioides and the Asian isolates. The Asian isolates are conspecific with Norwegian isolate IBT 9959 based on morphological and molecular analyses. In addition, the European F. langsethiae isolates from Finland and Russia were resolved into two distinct subgroups based on analyses of translation elongation factor and IGS rDNA sequences. Nucleotide polymorphisms within the IGS rDNA were used to design PCR primers that successfully differentiated the Asian isolates from F. sporotrichioides and F. langsethiae. Based on these data, we formally propose that the Asian isolates together with Norwegian isolate IBT 9959 comprise a novel phylogenetic species, F. sibiricum, while the two subgroups of F. langsethiae only represent intraspecific groups.     

Utility of the phylotoxigenic relationships among trichothecene-producing Fusarium species for predicting their mycotoxin-producing potential

Species of the genus Fusarium are well-known plant pathogens and mycotoxigenic fusaria are associated with health hazards to humans and animals. There is a need to understand the mechanisms of mycotoxin production by Fusarium species and to predict which produce mycotoxins. In this study, the Fusarium phylogenetic tree was first inferred among trichothecene producers and related species. We reconstructed the maximum likelihood (ML) tree based on the combined data from nucleotide sequences of rDNA cluster regions, the β-tubulin gene (β-tub) and the elongation factor 1α gene (EF-1α). Second, based on this tree topology, the ancestral states of the producing potential of type A and B trichothecenes (TriA and TriB), zearalenone (ZEN), moniliformin (MON), beauvericin (BEA) and enniatins (ENN) were reconstructed using the maximum parsimony (MP) method based on the observed production by extant species as reported in the literature. Finally, the species having the potential to produce each of these six mycotoxins was predicted on the basis of the parsimonious analysis. The ML tree indicated that the Fusarium species analysed in this study could be divided into two major clades. Clade I was divided into four distinct subclades: I-a, I-b, I-c and I-d. Furthermore, the parsimony reconstruction suggested that the potential for producing MON and ZEN was gained or lost only once, and that the producing potential for TriA and TriB, BEA and ENN was repeatedly gained and lost during the evolutionary history of the Fusarium species analysed in this study. Interestingly, the results showed the possibility that several species, about which reports were scarce with regard to mycotoxin production, have the potential to produce one or more of the six evaluated in this study. The phylogenetic information therefore helps one to predict the mycotoxin-producing potential by Fusarium species, and these “phylotoxigenic relationships” may be useful for predicting the pathogenicity of fungi.     

Tyramine production among lactic acid bacteria and other species isolated from kimchi

Lactic acid bacteria (LAB) are naturally found in fermented vegetable products. The ability of 230 kimchi bacterial isolates was investigated to produce tyramine by biochemical and genetic methods. The production of tyramine was determined by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). The presence of the gene encoding the corresponding tyrosine decarboxylase was also determined by PCR assay. After the production of tyramine was confirmed by chromatographic and molecular methods, the bacterial isolates producing the amine were identified by 16S rRNA gene sequence and species-specific PCR analyses. Only a small proportion of the bacterial isolates (14/230 isolates) decarboxylated tyrosine in vitro. All of the 14 bacterial isolates that produced tyramine were shown to possess the tdc gene, indicating that a positive correlation existed between the production of tyramine and the presence of the corresponding decarboxylase gene. The 14 isolates included three LAB species and one other species: Lactobacillus brevis (six), Lactobacillus curvatus (four), Leuconostoc mesenteroides (two), and Staphylococcus hominis (two). This study demonstrated that only a small proportion of LAB and other microbiota growing in kimchi had the ability to produce tyramine.     

Molecular characterization and antibiotic resistance profiling of Campylobacter isolated from cattle in Polish slaughterhouses

A total of 812 samples from bovine hides and the corresponding carcasses collected at the slaughterhouse level in the eastern part of Poland were examined for the presence of Campylobacter jejuni and Campylobacter coli. Recovered isolates were confirmed using species-specific PCR, characterized by the presence of 11 putative virulence genes and antimicrobial susceptibility was determined using a microbroth dilution method. Furthermore, the genotypic relatedness of the isolates was determined by PFGE profiling and virulence pattern cluster analysis. The prevalence of Campylobacter was 25.6% and 2.7% in bovine hide and carcass samples, respectively. The presence of virulence markers varied between C. jejuni and C. coli species however, the majority of strains possessed the cadF, flhA, flaA genes, irrespective of the bacterial species and origin. The lower number of the strains was positive for the invasive associated markers – virB11 and wlaN. Antibiotic profiling showed that campylobacters were most frequently resistant to quinolones and fluoroquinolones (nalidixic acid and ciprofloxacin, 38.3% of each, respectively) followed by streptomycin (24.3%) and tetracycline (20.9%). Resistance to erythromycin and gentamicin was demonstrated in 4.3% and 2.6% of strains, respectively. Comparisons of the PFGE and virulence marker profiles of the isolates reflected the high genetic diversity of Campylobacter tested. Moreover, a poor correlation between the PFGE type, pathogenic gene marker and antimicrobial resistance patterns was observed.     

Phylogenetic characterization and ochratoxin A--fumonisin profile of black Aspergillus isolated from grapes in Argentina

Aspergillus section Nigri populations isolated from seven growing regions from Argentina were characterized by sequencing in order to identify species responsible for production of ochratoxin A (OTA) and fumonisins (FB_s). Sequences of genes encoding calmodulin, β-tubulin, the second largest subunit of RNA polymerase II and translation elongation factor 1 alpha were analysed. The phylogenetic analysis showed the presence of six lineages: A. carbonarius, A. tubingensis, A. niger, A. japonicus, A. homomorphus and A. foetidus grouped in four major clusters. The molecular tools used allowed the identification for the first time of A. homomorphus from vineyards. OTA production confirmed the importance of A. carbonarius as the main ochratoxigenic species isolated and, to a variable degree, of A. niger and A. tubingensis, which were by far the most commonly occurring species on grapes in Argentina. The only strains able to produce OTA and fumonisins (B₂-B₄) belong to the A. niger cluster.     

Development of a method for the identification of scombroid and common substitute species in seafood products by FINS

In the present work, a method for the authentication of scombroid products was developed, by means of FINS (Forensically Informative Nucleotide Sequencing) technique (Polymerase Chain Reaction (PCR) followed by phylogenetic analysis). The methodology developed allows the identification of most important scombroid species using the mitochondrial cytochrome b as molecular marker. Due to the different commercial value of the species belonging to this family, substitutions between species in seafood products can take place.     

Preliminary virulence genotyping and phylogeny of Escherichia coli from the gut of pigs at slaughtering stage in Brazil

In the current study we screened Escherichia coli from intestine of pigs slaughtered in Mato Grosso, Brazil, for virulence-markers related to human disease. Furthermore, we employed for the first time a phylogenetic assay to explore the association between phylogeny and virulence genotype in E. coli from finished swine. A low prevalence (7.8%) of E. coli harbouring virulence genes was observed. Among the positive isolates, 3.3% could be classified as atypical EPEC, 2.2% as STEC and 2.2% as CDT harbouring E. coli. Virulence genes were not found to co-occur in a strain. Phylogenetic determination of isolates revealed a low prevalence of E. coli lineages related to disease. Therefore, preliminary sampling of 74 pigs indicated that slaughter swine may not be major reservoirs of E. coli capable of causing human disease. In light of the significant association between phylogeny and virulence genotype, we also underscored the phylogenetic grouping of strains as a valuable tool for E. coli surveillance programmes in slaughterhouses.     

Molecular biodiversity of mycotoxigenic fungi that threaten food safety

Fungal biodiversity is one of the most important contributors to the occurrence and severity of mycotoxin contamination of crop plants. Phenotypic and metabolic plasticity has enabled mycotoxigenic fungi to colonize a broad range of agriculturally important crops and to adapt to a range of environmental conditions. New mycotoxin-commodity combinations provide evidence for the ability of fungi to adapt to changing conditions and the emergence of genotypes that confer enhanced aggressiveness toward plants and/or altered mycotoxin production profiles. Perhaps the most important contributor to qualitative differences in mycotoxin production among fungi is variation in mycotoxin biosynthetic genes. Molecular genetic and biochemical analyses of toxigenic fungi have elucidated specific differences in biosynthetic genes that are responsible for intra- and inter-specific differences in mycotoxin production. For Aspergillus and Fusarium, the mycotoxigenic genera of greatest concern, variation in biosynthetic genes responsible for production of individual families of mycotoxins appears to be the result of evolutionary adaptation. Examples of such variation have been reported for: a) aflatoxin biosynthetic genes in Aspergillus flavus and Aspergillus parasiticus; b) trichothecene biosynthetic genes within and among Fusarium species; and c) fumonisin biosynthetic genes in Aspergillus and Fusarium species. Understanding the variation in these biosynthetic genes and the basis for variation in mycotoxin production is important for accurate assessment of the risks that fungi pose to food safety and for prevention of mycotoxin contamination of crops in the field and in storage.     

Molecular characterization and fumonisin production by Fusarium verticillioides isolated from corn grains of different geographic origins in Brazil

Gibberella moniliformis is most commonly associated with maize worldwide and produces high levels of fumonisins, some of the most agriculturally important mycotoxins. Studies demonstrate that molecular methods can be helpful for a rapid identification of Fusarium species and their levels of toxin production. The purpose of this research was to apply molecular methods (AFLP, TEF-1α partial gene sequencing and PCR based on MAT alleles) for the identification of Fusarium species isolated from Brazilian corn and to verify if real time RT-PCR technique based on FUM1 and FUM19 genes is appropriated to estimate fumonisins B₁ and B₂ production levels. Among the isolated strains, 96 were identified as Fusarium verticillioides, and four as other Fusarium species. Concordant phylogenies were obtained by AFLP and TEF-1α sequencing, permitting the classification of the different species into distinct clades. Concerning MAT alleles, 70% of the F. verticillioides isolates carried the MAT-1 and 30% MAT-2. A significant correlation was observed between the expression of the genes and toxin production r = 0.95 and r = 0.79 (correlation of FUM1 with FB₁ and FB₂, respectively, P < 0.0001); r = 0.93 and r = 0.78 (correlation of FUM19 with FB₁ and FB₂, respectively, P < 0.0001). Molecular methods used in this study were found to be useful for the rapid identification of Fusarium species. The high and significant correlation between FUM1 and FUM19 expression and fumonisins production suggests that real time RT-PCR is suitable for studies considering the influence of abiotic and biotic factors on expression of these genes. This is the first report concerning the expression of fumonisin biosynthetic genes in Fusarium strains isolated from Brazilian agricultural commodity.     

A peach (Prunus persica)-specific gene, Lhcb2, used as an endogenous reference gene for qualitative and real-time quantitative PCR to detect fruit products

Among the methods used to detect food adulteration, the amplification of endogenous reference genes is particularly important. Endogenous reference genes for many different species, such as cotton, papaya, maize and others, have been reported, yet an endogenous reference gene for the peach is still lacking. In this paper, the chlorophyll a/b-binding protein (Lhcb2) gene was identified as a species-specific gene for the peach. Lhcb2 was assayed in 4 species of peaches and 8 non-peach species by both qualitative and quantitative PCR. No amplification was observed in other species. The detection limit of quantitative PCR was as low as 5 pg of DNA, equal to 9 copies, and Southern blot analysis confirmed that the Lhcb2 gene was present in a single copy in the peach genome. All of these experiments indicated that the Lhcb2 gene is a useful endogenous reference gene for the detection of peach material via both qualitative and quantitative PCR assays, even in the processed food samples such as juices containing peach.     

Characterization of nonochratoxigenic strains of Aspergillus carbonarius from grapes

Aspergillus carbonarius is the main responsible source of ochratoxin A (OTA) in food commodities such as wine, grapes or dried vine fruits from main viticultural regions worldwide. Besides, OTA production is a very consistent property of this species and for this reason atoxigenic isolates of A. carbonarius are very rarely found in natural environments. In the present study, for the first time, three nonochratoxigenic wild strains of A. carbonarius have been discovered, unambiguously identified, characterized in deep and compared to ochratoxigenic strains of the same species. In addition, polyketide synthase (pks) genes suggested to be involved in OTA biosynthesis were also screened in these strains. The identification of the strains was confirmed by ITS-5.8S rRNA, β-tubulin and calmodulin gene sequencing. The three atoxigenic strains did not produce OTA in a conducive culture medium at any of the temperatures and times of incubation tested. Five ketosynthase domains from pks genes previously described in A. carbonarius were detected both in ochratoxigenic and in nonochratoxigenic strains. Atoxigenic strains of A. carbonarius could be useful as biotechnological agents to be used in food industry and as biological agents for control of OTA production in vineyards and other crops.     

Application of species-specific PCR for the identification of dried bonito product (Katsuobushi)

The species-specific PCR (polymerase chain reaction) method was developed to identify the species of dried bonito product (Katsuobushi) produced from Euthynnus pelamis, E. affinis, Auxis rochei, A. thazard, and Sarda orientalis. The 1141 bp complete mitochondrial cytochrome b genes of five bonito species and other five related Scombridae species were established, and then five pairs of species-specific primer were designed to amplify short length fragments among bonito species. The developed species-specific PCR method was successfully applied to authenticate species of commercial dried bonito products. Hence, this method really provided a useful and academic technique to identify the sources of bonito product.     

Short communication: Genetic characterization of antimicrobial resistance in Acinetobacter isolates recovered from bulk tank milk

A total of 176 Acinetobacter isolates, including 57 Acinetobacter baumannii originally obtained from 2,287 bulk tank milk (BTM) samples in Korea was investigated for the genetic basis of antimicrobial resistance using molecular methods. In addition, the occurrence and cassette content of integrons were examined and the genetic diversity of A. baumannii strains identified was evaluated. Aminoglycoside-modifying enzyme genes were detected in 15 (88.2%) of the 17 aminoglycoside-resistant Acinetobacter isolates tested. The most common aminoglycoside-modifying enzyme gene identified was adenylyltransferase gene aadB (n = 9), followed by phosphotransferase genes aphA6 (n = 7) and aphA1 (n = 5). Of the 31 isolates resistant to tetracycline, tet(39) was detected in 20 of them. The genetic basis of resistance to sulfonamide was identified in 15 (53.6%) of 28 trimethoprim-sulfamethoxazole-resistant isolates and 9 (32.1%) of them carried both sul1 and sul2 genes. A bla_ADC-7-like gene was detected in 1 β-lactam-resistant A. baumannii. Furthermore, class 1 integron was identified in 11 Acinetobacter isolates. Two gene cassettes dfrA15, conferring resistance to trimethoprim, and aadA2, conferring resistance to aminoglycosides, were identified in 8 Acinetobacter isolates. None of the isolates was positive for class 2 or class 3 integrons. Pulsed-field gel electrophoresis revealed that most of the A. baumannii strains from BTM samples were genetically diverse, indicating that the occurrence of A. baumannii strains in BTM was not the result of dissemination of a single clone. Elucidation of resistance mechanisms associated with the resistance phenotype and a better understanding of resistance genes may help in the development of strategies to control infections, such as mastitis, and to prevent further dissemination of antibiotic resistance genes. To the best of our knowledge, this is the first report of molecular characterization of antimicrobial-resistant Acinetobacter spp. from milk.     

The gyrase B gene as a molecular marker to resolve interspecific relationships within the Acetobacter pasteurianus group and a novel target for species-specific PCR

Members of the Acetobacter pasteurianus are popular acetic acid bacteria (AAB) for the production of vinegar. Neither phenotypic nor the most frequently applied genotypic marker (16S ribosomal DNA) provides sufficient resolution for accurate identification of the AAB strains. In this study, the gyrB gene was used for species discrimination by direct DNA sequencing and as marker in a species-specific PCR assay. All examined A. pasteurianus strains were clearly distinguished from the closely related species by comparative sequence analysis of the gyrB gene. The average sequence similarity for the gyrB gene (82.2 %) among type strains was significantly lower than that of the 16S rRNA sequence (98.2 %). Therefore, the gyrB gene can be proposed as an additional molecular marker for A. pasteurianus and related taxa that provides higher resolution than 16S rRNA. In addition, the species-specific primers were also developed based on the gyrB and 16S rRNA gene sequences, which were then employed for PCR using the template DNA of Acetobacter strains. The PCR primer pairs were shown to be specific for A. pasteurianus, A. peroxydans and papayae. Our data indicate that the phylogenetic relationships in the A. pasteurianus group are easily resolved by direct sequencing of the gyrB gene and combined with species-specific PCR assays.     

Discrimination of dairy industry isolates of the Lactobacillus casei group

Lactobacilli are a major part of the microflora of the gut and of many fermented dairy products, and are found in a variety of environments. Lactobacillus casei, Lactobacillus paracasei, Lactobacillus rhamnosus, and Lactobacillus zeae form a closely related taxonomic group within the facultatively heterofermentative lactobacilli. The classification and nomenclature of these bacteria are controversial. In this study, relationships between these species were investigated using type strains and dairy industry isolates examined with DNA-based techniques and conventional carbohydrate use tests. Carbohydrate use patterns gave poor discrimination of some species, but DNA PCR using specific primers targeted to sequences of the 16S rRNA gene discriminated 4 types consistent with the currently recognized species. Pulsed-field agarose gel electrophoresis of chromosomal NotI restriction fragments identified 18 different band patterns from 21 independent Lactobacillus isolates and confirmed the identity of L. casei strains from 2 culture collections (CSCC 5203 and ASCC 290), both representing the type strain of L. casei. Some isolates were reclassified as L. rhamnosus, suggesting that the prevalence of L. rhamnosus as a natural component of the microflora of dairy foods and dairy environments has previously been underestimated. These methods can provide a practical basis for discrimination of the species and identification of individual industrial strains.     

Phylogenetic analyses and toxigenic profiles of Fusarium equiseti and Fusarium acuminatum isolated from cereals from Southern Europe

Fusarium equiseti and Fusarium acuminatum are toxigenic species that contaminate cereal crops from diverse climatic regions. They are common in Spanish cereals. The information available on their phylogenetics and toxigenic profiles is, however, insufficient to assist risk evaluation. In this work, phylogenetic analyses were performed using partial sequences of the translation elongation factor gene (EF-1α) of F. equiseti and F. acuminatum strains isolated from barley and wheat from Spain and other countries. The Northern and Southern European F. equiseti strains largely separated into two phylogenetically distinct clusters. This suggests the existence of two distinct populations within this species, explaining its presence in these regions of markedly different climate. Production of type A and B trichothecenes by the Spanish strains, examined in wheat cultures using a multitoxin analytical method, indicated that F. equiseti could produce deoxynivalenol and nivalenol and other trichothecenes, at concentrations that might represent a significant risk of toxin contamination for Southern European cereals. F. acuminatum showed low intraspecific genetic variability and 58% of the strains could produce deoxynivalenol at low level. Neither species was found to produce T-2 or HT-2 toxins. The present results provide important phylogenetic and toxigenic information essential for the accurate prediction of toxigenic risk.     

Biogenic amines formation in Streptococcus thermophilus isolated from home-made natural yogurt

Twelve different biogenic amines formation in 58 isolates of Streptococcus thermophilus from home-made natural yogurt were investigated in histidine (HDB) and lysine decarboxylase broth (LDB). All S. thermophilus isolates had an ability to produce twelve different biogenic amines in HDB and LDB. Most of the S. thermophilus isolates formed low amounts of histamine (1–50 mg/L) from histidine. Apart from one isolate, S. thermophilus produced tyramine at low (47 isolates) and medium (10 isolates) levels. The amount of each specific biogenic amine produced by S. thermophilus was generally lower than 100 mg L⁻¹. Also, the presence of hdcA gene was investigated using PCR technique and relation between gene and histamine production was conducted in S. thermophilus isolates. This study showed that most of the S. thermophilus isolates have the ability to form biogenic amines, especially histamine, and tyramine, which is an important consideration when selecting strains as starter cultures.     

Evaluation of genetic markers for identifying isolates of the species of the genus Fusarium

BACKGROUND: Members of the genus Fusarium are well known as one of the most important plant pathogens causing food spoilage and loss worldwide. Moreover, they are associated with human and animal diseases through contaminated foods because they produce mycotoxins. To control fungal hazards of plants, animals and humans, there is a need for a rapid, easy and accurate identification system of Fusarium isolates with molecular methods. RESULTS: To specify genes appropriate for identifying isolates of various Fusarium species, we sequenced the 18S rRNA gene (rDNA), internal transcribed spacer region 1, 5.8S rDNA, 28S rDNA, β‐tubulin gene (β‐tub), and aminoadipate reductase gene (lys2), and subsequently calculated the nucleotide sequence homology with pair‐wise comparison of all tested strains and inferred the ratio of the nucleotide substitution rates of each gene. Inter‐species nucleotide sequence homology of β‐tub and lys2 ranged from 83.5 to 99.4% and 56.5 to 99.0%, respectively. The result indicated that sequence homologies of these genes against reference sequences in a database have a high possibility of identifying unknown Fusarium isolates when it is more than 99.0%, because these genes had no inter‐species pair‐wise combinations that had 100% homologies. Other markers often showed 100% homology in inter‐species pair‐wise combinations. The nucleotide substitution rate of lys2 was the highest among the six genes. CONCLUSION: The lys2 is the most appropriate genetic marker with high resolution for identifying isolates of the genus Fusarium among the six genes we examined in this study. Copyright © 2011 Society of Chemical Industry     

Prevalence and comparison of Streptococcus infantarius subsp. infantarius and Streptococcus gallolyticus subsp. macedonicus in raw and fermented dairy products from East and West Africa

Streptococcus infantarius subsp. infantarius (Sii) and Streptococcus gallolyticus subsp. macedonicus are members of the Streptococcus bovis/Streptococcus equinus complex (SBSEC) associated with human infections. SBSEC-related endocarditis was furthermore associated with rural residency in Southern Europe. SBSEC members are increasingly isolated as predominant species from fermented dairy products in Europe, Asia and Africa. African variants of Sii displayed dairy adaptations to lactose metabolism paralleling those of Streptococcus thermophilus including genome decay. In this study, the aim was to assess the prevalence of Sii and possibly other SBSEC members in dairy products of East and West Africa in order to identify their habitat, estimate their importance in dairy fermentation processes and determine geographic areas affected by this potential health risk. Presumptive SBSEC members were isolated on semi-selective M17 and SM agar media. Subsequent genotypic identification of isolates was based on rep-PCR fingerprinting and SBSEC-specific16S rRNA gene PCR assay. Detailed identification was achieved through application of novel primers enhancing the binding stringency in partial groES/groEL gene amplification and subsequent DNA sequencing. The presence of S. thermophilus-like lacS and lacZ genes in the SBSEC isolates was determined to elucidate the prevalence of this dairy adaptation. Isolates (n = 754) were obtained from 72 raw and 95 fermented milk samples from Côte d'Ivoire and Kenya on semi-selective agar media. Colonies of Sii were not detected from raw milk despite high microbial titers of approximately 10⁶ CFU/mL on M17 agar medium. However, after spontaneous milk fermentation Sii was genotypically identified in 94.1% of Kenyan samples and 60.8% of Kenyan isolates. Sii prevalence in Côte d'Ivoire displayed seasonal variations in samples from 32.3% (June) to 40.0% (Dec/Jan) and isolates from 20.5% (June) to 27.7% (Dec/Jan) present at titers of 10⁶–10⁸ CFU/mL. lacS and lacZ genes were detected in all Kenyan and 25.8% (June) to 65.4% (Dec/Jan) of Ivorian Sii isolates. Regional differences in prevalence of Sii and dairy adaptations were observed, but no clear effect of dairy animal, fermentation procedure and climate was revealed. Conclusively, the high prevalence of Sii in Kenya, Côte d'Ivoire in addition to Somalia, Sudan and Mali strongly indicates a pivotal role of Sii in traditional African dairy fermentations potentially paralleling that of typical western dairy species S. thermophilus. Putative health risks associated with the consumption of high amounts of live Sii and potential different degrees of evolutionary adaptation or ecological colonization require further epidemiologic and genomic investigations, particularly in Africa.