Papers by Mohamed Alnakip
A total of 160 samples (20 each of raw cow's milk and seven dairy products; pasteurized
milk, sma... more A total of 160 samples (20 each of raw cow's milk and seven dairy products; pasteurized
milk, small and large scales-manufactured ice cream, infant formulas, full-fat milk powder,
rice pudding and yoghurt) were investigated for the presence of B. cereus. Biochemical
tests followed by PCR were carried out to confirm the suspected B. cereus isolates. Overall
44 samples yielded Bacillus-like growth of which 34 were positive for B. cereus. The highest
occurrence % of B. cereus was detected in raw cow's milk (60 %), and rice pudding (55 %). Non-B.
cereus isolates were identified based on 16S rRNA GS and 7 isolates of B. licheniformis and 3
isolates of B. subtilis were obtained. No psychrotolerant B. cereus strains were detected in all
samples. Evidence evolved from our results confirms the need for authorities and producers
to adopt B. cereus as a reference in microbiological hazard control, particularly for dairy
products.
A total of 50 raw cow’s milk samples were collected from different areas of Elsharkia
province, E... more A total of 50 raw cow’s milk samples were collected from different areas of Elsharkia
province, Egypt for characterizing lactic acid bacteria (LAB) load. Using 16S rRNA gene
sequencing, a total of 41 LAB isolates have been identified corresponding to Enterococcus
sp. (51.22 %) as the most predominant LAB genus, followed in order by Aerococcus (26.82 %),
Lactococcus (7.32 %), Lactobacillus (7.32 %), Leuconostic (4.88 %) and Pediococcus (2.44 %)
genera. All isolates were identified to species level with exception of one strain (Lc. lactis
subsp. cremoris) that has been assigned to subspecies. The phylogenetic dendrogram created
has allowed good discrimination between all isolated LAB species identified with this study.
Results showed a wide diversity among isolated LAB from raw milk in Elsharkia province.
The impact of LAB presence in raw cow’s milk on dairy safety has been discussed.
Mastitis is a common, serious and highly multi-factorial disease affecting dairy industry worldwi... more Mastitis is a common, serious and highly multi-factorial disease affecting dairy industry worldwide causing annual financial losses exceeding thirty five billion dollars. Streptococci remains as an important group responsible for high percentages of both contagious and environmental mastitis. Unfortunately, their routine diagnosis via phenotypic, biochemical and serological methods is a difficult and time-consuming process. Nowadays, 16S rRNA gene sequencing is used in bacterial identification proving high reliability and accuracy. Moreover, MALDI-TOF MS (Matrix-assisted laser desorption ionization-time of flight mass spectrometry) is extensively applied and constitutes a revolution in microbial diagnostics nowadays. Actually, diagnosis of mastitis-causative Streptococci was rarely carried out by the two above mentioned tools. As a consequence, we have employed the two tools in this work in order to identify with a high accuracy six types of mastitis causative streptococci comprisin...
Mastitis complex is considered the utmost threaten to global dairy industry due to 3 perspectives... more Mastitis complex is considered the utmost threaten to global dairy industry due to 3 perspectives; economic, hygienic, and legal. This complex is generally considered to be of infectious nature, and a wide variety of bacteria are being incriminated as the main causative microbial group. Generally, control and treatment of mastitis pathogens especially those cause outbreaks and high economic losses, and better understanding of mastitis nature in some epidemics require efficient diagnosis. Because of the large number of bacterial species capable of causing such complex, and unfortunately the exhibition of great similarity between some species and subspecies based on some biochemical and serological tools, there is a great dependence for their differentiation on genomic base nowadays. In this sense, the present work studies the efficiency of some target genes including; 16S Ribosomal RNA [16S rRNA], 23S rRNA, Elongation factor TU (TUF), and Gyrase subunit B [GyrB] for discrimination be...
Mastitis is a common, serious and easily disseminated infection in dairy herds and constitutes a ... more Mastitis is a common, serious and easily disseminated infection in dairy herds and constitutes a major cause for economic losses worldwide. Among incriminated pathogens, streptococci are considered as common relevant agents. Unfortunately, the routine diagnosis of streptococcal infections via phenotypic and serological methods is a difficult and time-consuming process. 16S rRNA gene sequencing is well established extensively used as a universal gold standard method for the microbial identification and phylogenetic classification of prokaryotic species, genera, and families. In this sense, a comparative identification of 24 isolates of mastitic origin previously recognized as Streptococcus sp. via automated biochemical VITEK-2 system, has been done against the gold standard, 16S rRNA gene sequencing. The identification of the most relevant Streptococcus spp. involved in bovine mastitis has not shown high accuracy and reliability by VITEK-2 system as obtained by 16S rRNA gene sequenci...
Journal of Veterinary Medicine, 2014
The health of dairy animals, particularly the milk-producing mammary glands, is essential to the ... more The health of dairy animals, particularly the milk-producing mammary glands, is essential to the dairy industry because of the crucial hygienic and economic aspects of ensuring production of high quality milk. Due to its high prevalence, mastitis is considered the most important threat to dairy industry, due to its impacts on animal health and milk production and thus on economic benefits. The MG is protected by several defence mechanisms that prevent microbial penetration and surveillance. However, several factors can attenuate the host immune response (IR), and the possession of various virulence and resistance factors by different mastitis-causing microorganisms greatly limits immune defences and promotes establishment of intramammary infections (IMIs). A comprehensive understanding of MG immunity in both healthy and inflammatory conditions will be an important key to understand the nature of IMIs caused by specific pathogens and greatly contributes to the development of effective control methods and appropriate detection techniques. Consequently, this review aims to provide a detailed overview of antimicrobial defences in the MG under healthy and inflammatory conditions. In this sense, we will focus on pathogen-dependent variations in IRs mounted by the host during IMI and discuss the potential ramifications of these variations.
Mastitis is a common, serious and easily disseminated infection in dairy herds in which streptoco... more Mastitis is a common, serious and easily disseminated infection in dairy herds in which streptococci are incriminated as relevant causative agents. Unfortunately, the routine diagnosis of streptococcal infections via phenotypic, biochemical and serological methods is a difficult and time-consuming process. Currently, MALDI-TOF MS (matrix-assisted laser desorption ionisation-time of flight mass spectrometry) is extensively applied and represents a revolution in microbial diagnostics. To the best of our knowledge, this work represents the first application of MALDI-TOF MS for the identification of streptococci involved in both contagious and environmental bovine mastitis. Our results were compared to a phylogenetic analysis based on the 16S rRNA gene sequencing. For this purpose, a total of 14 different streptococci strains isolated from milk of bovine mastitis cases, plus five reference strains were considered in this study. All Streptococcus spp. exhibited spectral variability at the genus and species level. The peaks with m/z values of and 5955 were determined as genus-specific peaks for all studied strains. The discrimination of the most relevant Streptococcus spp. involved in bovine mastitis was facilitated by both 16S rRNA gene sequencing and MALDI-TOF MS fingerprinting. Remarkably, MALDI-TOF MS fingerprinting was found to be at least as robust as 16S rRNA gene sequencing. Moreover, MALDI-TOF MS allowed a much cheaper, faster analysis, exhibiting high confidence and reliability for the identification and the intra-specific characterization of mastitis-causing streptococci, thus proving to be a powerful diagnostic tool that can be used independently for identification purposes.
Bacillus genus includes foodborne pathogenic and spoilage-associated species, such as Bacillus ce... more Bacillus genus includes foodborne pathogenic and spoilage-associated species, such as Bacillus cereus,
Bacillus licheniformis, Bacillus subtilis and Bacillus pumilus. Bacillus is also a heterogeneous genus that
includes closely related species that are difficult to discriminate among, especially when well-conserved
genes such as 16S rRNA and 23S rRNA are considered. The main goal of the present work was to study the
usefulness of three housekeeping genes, the TU elongation factor (tuf), the DNA gyrase b subunit (gyrB)
and the RNA polymerase b subunit (rpoB) genes, for use in differentiating among the most important
foodborne Bacillus spp. sequences from 20 foodborne isolated Bacillus strains, and sequences belonging
to different Bacillus spp. retrieved from the GenBank were analysed. In general terms, gyrB, rpoB and tuf
gene regions for the strains considered in this study exhibited interspecific similarities of 57.8%, 67.23%
and 77.66% respectively. Novel tufGPF and tufGPR universal primers targeted to the tuf gene were
designed and proved to be useful for the amplification of all Bacillus spp considered. In conclusion, the tuf
gene can be considered to be a good target for the differential characterisation of foodborne Bacillus
species, especially for differentiating B. subtilis and B. cereus from other closely related species.
Enterococcus is a controversial genus due to its great variability; this genus includes pathogeni... more Enterococcus is a controversial genus due to its great variability; this genus includes pathogenic strains, spoilage strains, and apparently safe strains including some probiotic strains. Previous studies focused on the characterization of strains of Enterococcus spp. involved in nosocomial infections. However, little research has been conducted on Enterococcus strains in foodstuffs. In the present work, 36 strains of different species of Enterococcus have been characterized by means of MALDI-TOF MS, resulting in highly specific mass spectral fingerprints. Characteristic peak masses common to certain bacterial
species of Enterococcus have been identified. Thus, a peak at m/z 4426 ± 1 was assigned as a genus-specific biomarker. In addition, phyloproteomic relationships based on the mass spectral data were compared to the results of a phylogenetic analysis based on the 16S rRNA gene sequence. A better grouping at the species level was observed in
the phyloproteomic tree, especially for the Enterococcus faecium group. Presumably, the assortment of some strains or ecotypes could be related to their ecological niche specialization. The approach described in this study leads the way toward the rapid and specific identification of different strains and species of Enterococcus in food based on molecular
proteinmarkers, aiming at the early detection of pathogenic strains and strains implicated in food poisoning or food spoilage.
Food safety is one of the highest public health priorities at the national,
community and interna... more Food safety is one of the highest public health priorities at the national,
community and international levels. The globalization of the food supply
and the increased complexity of the food chain have recently defi ned the
closely related areas of “food quality” and “food safety” as important
priorities in the food sector. Food scandals that have occurred over the last
20 years, an increase in international food trading and the identifi cation of
emerging risks have led to an increasing demand for safer products that
do not present health hazards for the consumer. One of the major aims of
“food safety” is to avoid health risks that are caused by the consumption
of food products, including microbiological hazards, pesticide residues, misuse of food additives and the presence of chemical or biological toxin
contaminants, all of which render the food adulterated and unfi t for human
consumption. In contrast, “food quality” encompasses all attributes that
infl uence the value of a food product. Such attributes can be negative (i.e.,
spoilage, contamination with fi lth, discoloration and off-odors) or positive
(i.e., origin, color, fl avor, texture and the processing method of the food)
(FAO 2003).
To ensure the safety of the global food supply and minimize socioeconomic
losses due to food safety threats, the early identifi cation of
vulnerabilities in the food chain and the implementation of effective
prevention systems are essential. The World Health Organization (WHO)
has launched an initiative to estimate the burden of foodborne illness
on a global scale (Stein et al. 2007). This initiative involves experts of the
Foodborne Epidemiology Reference Group (FERG), which assembles and assesses global evidence regarding foodborne disease epidemiology
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Papers by Mohamed Alnakip
milk, small and large scales-manufactured ice cream, infant formulas, full-fat milk powder,
rice pudding and yoghurt) were investigated for the presence of B. cereus. Biochemical
tests followed by PCR were carried out to confirm the suspected B. cereus isolates. Overall
44 samples yielded Bacillus-like growth of which 34 were positive for B. cereus. The highest
occurrence % of B. cereus was detected in raw cow's milk (60 %), and rice pudding (55 %). Non-B.
cereus isolates were identified based on 16S rRNA GS and 7 isolates of B. licheniformis and 3
isolates of B. subtilis were obtained. No psychrotolerant B. cereus strains were detected in all
samples. Evidence evolved from our results confirms the need for authorities and producers
to adopt B. cereus as a reference in microbiological hazard control, particularly for dairy
products.
province, Egypt for characterizing lactic acid bacteria (LAB) load. Using 16S rRNA gene
sequencing, a total of 41 LAB isolates have been identified corresponding to Enterococcus
sp. (51.22 %) as the most predominant LAB genus, followed in order by Aerococcus (26.82 %),
Lactococcus (7.32 %), Lactobacillus (7.32 %), Leuconostic (4.88 %) and Pediococcus (2.44 %)
genera. All isolates were identified to species level with exception of one strain (Lc. lactis
subsp. cremoris) that has been assigned to subspecies. The phylogenetic dendrogram created
has allowed good discrimination between all isolated LAB species identified with this study.
Results showed a wide diversity among isolated LAB from raw milk in Elsharkia province.
The impact of LAB presence in raw cow’s milk on dairy safety has been discussed.
Bacillus licheniformis, Bacillus subtilis and Bacillus pumilus. Bacillus is also a heterogeneous genus that
includes closely related species that are difficult to discriminate among, especially when well-conserved
genes such as 16S rRNA and 23S rRNA are considered. The main goal of the present work was to study the
usefulness of three housekeeping genes, the TU elongation factor (tuf), the DNA gyrase b subunit (gyrB)
and the RNA polymerase b subunit (rpoB) genes, for use in differentiating among the most important
foodborne Bacillus spp. sequences from 20 foodborne isolated Bacillus strains, and sequences belonging
to different Bacillus spp. retrieved from the GenBank were analysed. In general terms, gyrB, rpoB and tuf
gene regions for the strains considered in this study exhibited interspecific similarities of 57.8%, 67.23%
and 77.66% respectively. Novel tufGPF and tufGPR universal primers targeted to the tuf gene were
designed and proved to be useful for the amplification of all Bacillus spp considered. In conclusion, the tuf
gene can be considered to be a good target for the differential characterisation of foodborne Bacillus
species, especially for differentiating B. subtilis and B. cereus from other closely related species.
species of Enterococcus have been identified. Thus, a peak at m/z 4426 ± 1 was assigned as a genus-specific biomarker. In addition, phyloproteomic relationships based on the mass spectral data were compared to the results of a phylogenetic analysis based on the 16S rRNA gene sequence. A better grouping at the species level was observed in
the phyloproteomic tree, especially for the Enterococcus faecium group. Presumably, the assortment of some strains or ecotypes could be related to their ecological niche specialization. The approach described in this study leads the way toward the rapid and specific identification of different strains and species of Enterococcus in food based on molecular
proteinmarkers, aiming at the early detection of pathogenic strains and strains implicated in food poisoning or food spoilage.
community and international levels. The globalization of the food supply
and the increased complexity of the food chain have recently defi ned the
closely related areas of “food quality” and “food safety” as important
priorities in the food sector. Food scandals that have occurred over the last
20 years, an increase in international food trading and the identifi cation of
emerging risks have led to an increasing demand for safer products that
do not present health hazards for the consumer. One of the major aims of
“food safety” is to avoid health risks that are caused by the consumption
of food products, including microbiological hazards, pesticide residues, misuse of food additives and the presence of chemical or biological toxin
contaminants, all of which render the food adulterated and unfi t for human
consumption. In contrast, “food quality” encompasses all attributes that
infl uence the value of a food product. Such attributes can be negative (i.e.,
spoilage, contamination with fi lth, discoloration and off-odors) or positive
(i.e., origin, color, fl avor, texture and the processing method of the food)
(FAO 2003).
To ensure the safety of the global food supply and minimize socioeconomic
losses due to food safety threats, the early identifi cation of
vulnerabilities in the food chain and the implementation of effective
prevention systems are essential. The World Health Organization (WHO)
has launched an initiative to estimate the burden of foodborne illness
on a global scale (Stein et al. 2007). This initiative involves experts of the
Foodborne Epidemiology Reference Group (FERG), which assembles and assesses global evidence regarding foodborne disease epidemiology
milk, small and large scales-manufactured ice cream, infant formulas, full-fat milk powder,
rice pudding and yoghurt) were investigated for the presence of B. cereus. Biochemical
tests followed by PCR were carried out to confirm the suspected B. cereus isolates. Overall
44 samples yielded Bacillus-like growth of which 34 were positive for B. cereus. The highest
occurrence % of B. cereus was detected in raw cow's milk (60 %), and rice pudding (55 %). Non-B.
cereus isolates were identified based on 16S rRNA GS and 7 isolates of B. licheniformis and 3
isolates of B. subtilis were obtained. No psychrotolerant B. cereus strains were detected in all
samples. Evidence evolved from our results confirms the need for authorities and producers
to adopt B. cereus as a reference in microbiological hazard control, particularly for dairy
products.
province, Egypt for characterizing lactic acid bacteria (LAB) load. Using 16S rRNA gene
sequencing, a total of 41 LAB isolates have been identified corresponding to Enterococcus
sp. (51.22 %) as the most predominant LAB genus, followed in order by Aerococcus (26.82 %),
Lactococcus (7.32 %), Lactobacillus (7.32 %), Leuconostic (4.88 %) and Pediococcus (2.44 %)
genera. All isolates were identified to species level with exception of one strain (Lc. lactis
subsp. cremoris) that has been assigned to subspecies. The phylogenetic dendrogram created
has allowed good discrimination between all isolated LAB species identified with this study.
Results showed a wide diversity among isolated LAB from raw milk in Elsharkia province.
The impact of LAB presence in raw cow’s milk on dairy safety has been discussed.
Bacillus licheniformis, Bacillus subtilis and Bacillus pumilus. Bacillus is also a heterogeneous genus that
includes closely related species that are difficult to discriminate among, especially when well-conserved
genes such as 16S rRNA and 23S rRNA are considered. The main goal of the present work was to study the
usefulness of three housekeeping genes, the TU elongation factor (tuf), the DNA gyrase b subunit (gyrB)
and the RNA polymerase b subunit (rpoB) genes, for use in differentiating among the most important
foodborne Bacillus spp. sequences from 20 foodborne isolated Bacillus strains, and sequences belonging
to different Bacillus spp. retrieved from the GenBank were analysed. In general terms, gyrB, rpoB and tuf
gene regions for the strains considered in this study exhibited interspecific similarities of 57.8%, 67.23%
and 77.66% respectively. Novel tufGPF and tufGPR universal primers targeted to the tuf gene were
designed and proved to be useful for the amplification of all Bacillus spp considered. In conclusion, the tuf
gene can be considered to be a good target for the differential characterisation of foodborne Bacillus
species, especially for differentiating B. subtilis and B. cereus from other closely related species.
species of Enterococcus have been identified. Thus, a peak at m/z 4426 ± 1 was assigned as a genus-specific biomarker. In addition, phyloproteomic relationships based on the mass spectral data were compared to the results of a phylogenetic analysis based on the 16S rRNA gene sequence. A better grouping at the species level was observed in
the phyloproteomic tree, especially for the Enterococcus faecium group. Presumably, the assortment of some strains or ecotypes could be related to their ecological niche specialization. The approach described in this study leads the way toward the rapid and specific identification of different strains and species of Enterococcus in food based on molecular
proteinmarkers, aiming at the early detection of pathogenic strains and strains implicated in food poisoning or food spoilage.
community and international levels. The globalization of the food supply
and the increased complexity of the food chain have recently defi ned the
closely related areas of “food quality” and “food safety” as important
priorities in the food sector. Food scandals that have occurred over the last
20 years, an increase in international food trading and the identifi cation of
emerging risks have led to an increasing demand for safer products that
do not present health hazards for the consumer. One of the major aims of
“food safety” is to avoid health risks that are caused by the consumption
of food products, including microbiological hazards, pesticide residues, misuse of food additives and the presence of chemical or biological toxin
contaminants, all of which render the food adulterated and unfi t for human
consumption. In contrast, “food quality” encompasses all attributes that
infl uence the value of a food product. Such attributes can be negative (i.e.,
spoilage, contamination with fi lth, discoloration and off-odors) or positive
(i.e., origin, color, fl avor, texture and the processing method of the food)
(FAO 2003).
To ensure the safety of the global food supply and minimize socioeconomic
losses due to food safety threats, the early identifi cation of
vulnerabilities in the food chain and the implementation of effective
prevention systems are essential. The World Health Organization (WHO)
has launched an initiative to estimate the burden of foodborne illness
on a global scale (Stein et al. 2007). This initiative involves experts of the
Foodborne Epidemiology Reference Group (FERG), which assembles and assesses global evidence regarding foodborne disease epidemiology