International Journal of Environmental Research and Public Health
Metal mesh devices (MMDs) are novel materials that enable the precise separation of particles by ... more Metal mesh devices (MMDs) are novel materials that enable the precise separation of particles by size. Structurally, MMDs consist of a periodic arrangement of square apertures of characteristic shapes and sizes on a thin nickel membrane. The present study describes the separation of aerosol particles using palm-top-size collection devices equipped with three types of MMDs differing in pore size. Aerosols were collected at a farm located in the suburbs of Nairobi, Kenya; aerosol particles were isolated, and pathogenic bacteria were identified in this microflora by next-generation sequencing analysis. The composition of the microflora in aerosol particles was found to depend on particle size. Gene fragments were obtained from the collected aerosols by PCR using primers specific for the genus Mycobacterium. This analysis showed that Mycobacterium obuense, a non-tuberculous species of mycobacteria that causes lung diseases, was present in these aerosols. These findings showed that appli...
The American Journal of Tropical Medicine and Hygiene, 2019
Providencia alcalifaciens is a member of the family Enterobacteriaceae that has been commonly imp... more Providencia alcalifaciens is a member of the family Enterobacteriaceae that has been commonly implicated as a causative agent of diarrheal infection in humans and animals. Recent outbreaks of P. alcalifaciens in both developing and developed countries have raised public health concerns. Several studies have suggested that P. alcalifaciens can cause diarrhea by invading the intestinal mucosa, although its pathogenicity has not been well established. Often routine laboratory investigations that seek etiological agents of diarrhea do not actively pursue P. alcalifaciens detection. Therefore, routine laboratory diagnosis should be given more attention for better understanding the epidemiology and pathogenicity of P. alcalifaciens.
The American Journal of Tropical Medicine and Hygiene, 2019
Bacillus pumilus has rarely been reported as a cause of human infections. We report a case of a B... more Bacillus pumilus has rarely been reported as a cause of human infections. We report a case of a B. pumilus causing food poisoning in an adult male. A 51-year-old Japanese man complained of severe abdominal cramps, fever with chills, diarrhea, dizziness, and loss of appetite after eating reheated rice with stewed minced meat purchased from a Kenyan restaurant. Bacillus pumilus was isolated from blood culture and was identified using a biochemical test and 16S rRNA gene sequencing analysis. The patient was treated with probiotics and ciprofloxacin and recovered after 3 days. To our knowledge, this is the first report describing the potential role of B. pumilus as a foodborne pathogen in Kenya and highlights the importance of good hygiene and food preparation practices.
The American Journal of Tropical Medicine and Hygiene, 2016
In an outbreak of gastroenteritis in December 2009, in Mandera, Kenya, Escherichia coli O-nontypa... more In an outbreak of gastroenteritis in December 2009, in Mandera, Kenya, Escherichia coli O-nontypable (ONT) strain was isolated from stool specimens of patients (18/24, 75%). The E. coli ONT organisms could not be assigned to any of the recognized diarrheagenic groups of E. coli. However, they possessed the enteroaggregative E. coli heat-stable enterotoxin-1 gene. The cell-free culture filtrates of the E. coli ONT strain isolated from the outbreak cases induced considerable amount of fluid accumulation in suckling mouse intestine, indicating production of an enterotoxic factor(s). These results identify E. coli that did not have any diarrheagenic characteristics except astA as the etiological agent of the diarrheal outbreak in Mandera. It is however considered necessary to characterize the fluid accumulation factor(s) to determine whether any novel toxins were responsible for the fluid accumulation. Moreover, it is important to study dissemination of strains producing the enterotoxic factor(s) to assess their public health significance distribution in the environment.
Background: The epidemiology of enteric pathogens has not been well studied in Kenya because of w... more Background: The epidemiology of enteric pathogens has not been well studied in Kenya because of wide disparities in health status across the country. Therefore, the present study describes the prevalence of enteropathogenic bacteria, their seasonal variation, and antibiotic resistance profiles among hospitalized diarrheic children in a suburban region of central Kenya. Methods: Fecal samples were collected between July 2009 and December 2013 from a total of 1410 children younger than 5 years, hospitalized with acute diarrhea in Kiambu County Hospital, Kenya. Conventional culture, biochemical, and molecular methods were conducted to identify causative bacterial pathogens and their virulence factors. Antimicrobial susceptibility tests were performed using E-test strips and VITEK-2 advanced expert system (AES) to evaluate the drug-resistance pattern of the isolates. Results: Of the 1410 isolates, bacterial infections were identified in 474 cases. Diarrheagenic Escherichia coli (DEC) was the most frequently isolated pathogen (86.5%). Other pathogens such as Aeromonas (5.5%), Shigella (4%), Salmonella (3.4%), Providencia (3.2%), Vibrio spp. (1.1%), Yersinia enterocolitica (1.1%), and Plesiomonas shigelloides (0.2%) were also identified. Mixed bacterial infection was observed among 11.1% of the cases. The highest infection rate was found during the dry season (59.3%, p = 0.04). Most of the DEC was found to be multidrug resistant to trimethoprim/ sulfamethoxazole 97.6%, amoxicillin 97.6%, erythromycin 96.9%, ampicillin 96.6%, and streptomycin 89%. Conclusions: This study suggests that DEC is the leading diarrhea-causing bacterial pathogen circulating in central Kenya, and seasonality has a significant effect on its transmission. Proper antibiotic prescription and susceptibility testing is important to guide appropriate antimicrobial therapy.
In this study, a sensitive fluorescence sensor was developed for the detection of small, fluoresc... more In this study, a sensitive fluorescence sensor was developed for the detection of small, fluorescence-labeled particles dispersed in a solution. The prototype system comprises of a laser confocal optical system and a mechanical sample stage to detect photon bursting of fluorescence-labeled small particles in sample volumes less than 5 μL within 3 minutes. To examine the feasibility of the prototype system as a diagnostic tool, assemblages of rotavirus and fluorescence-labeled antibody were analyzed. The detection sensitivity for rotavirus was 1 × 10 4 pfu/mL. Rotavirus in stool samples from patients with acute gastroenteritis was also detected. The advantages and disadvantages of this immunosensor with respect to ELISA and RT-PCR, the current gold standards for virus detection, are discussed.
The American Journal of Tropical Medicine and Hygiene, 2015
Providencia alcalifaciens is an emerging bacterial pathogen known to cause acute gastroenteritis ... more Providencia alcalifaciens is an emerging bacterial pathogen known to cause acute gastroenteritis in children and travelers. In July 2013, P. alcalifaciens was isolated from four children appearing for diarrhea at Kiambu District Hospital (KDH) in Kenya. This study describes the outbreak investigation, which aimed to identify the source and mechanisms of infection. We identified seven primary and four secondary cases. Among primary cases were four mothers who had children and experienced mild diarrhea after eating mashed potatoes. The mothers reported feeding children after visiting the toilet and washing their hands without soap. P. alcalifaciens was detected from all secondary cases, and the isolates were found to be clonal by random amplified polymorphic DNA (RAPD) fingerprinting. Our study suggests that the outbreak was caused by P. alcalifaciens, although no fluid accumulation was observed in rabbit ileal loops. The vehicle of the outbreak was believed to be the mashed potato dish, but the source of P. alcalifaciens could not be confirmed. We found that lack of hygiene, inadequate food storage, and improper hand washing before food preparation was the likely cause of the current outbreak. This is the first report of a foodborne infection caused by P. alcalifaciens in Kenya.
A bioassay-guided fractionation of methanol extract of Aristolochia bracteolata whole plant was c... more A bioassay-guided fractionation of methanol extract of Aristolochia bracteolata whole plant was carried out in order to evaluate its antimicrobial activity and to identify the active compounds in this extract. Antibacterial and antifungal activities of methanol extract against gram-positive, gram-negative, and fungal strains were investigated by the agar disk diffusion method. Among the strains tested, Moraxella catarrhalis and sea urchin-derived Bacillus sp. showed the highest sensitivity towards the methanol extract and hence they are used as test organisms for the bioassay-guided fractionation. From this extract, aristolochic acid 1 (AA-1) has been isolated and has showed the greatest antibacterial activity against both standard strain and clinical isolates of Moraxella catarrhalis with equal minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of 25 and 50 μg/mL. Modification of the AA-1 to AA-1 methyl ester completely abolished the antibact...
G12 rotaviruses are globally emerging rotavirus strains causing severe childhood diarrhea. Howeve... more G12 rotaviruses are globally emerging rotavirus strains causing severe childhood diarrhea. However, the whole genomes of only a few G12 strains have been fully sequenced and analyzed, of which only one G12P[4] and one G12P[6] are from Africa. In this study, we sequenced and characterized the complete genomes of three G12 strains (RVA/Human-tc/KEN/KDH633/2010/G12P[6], RVA/Human-tc/KEN/KDH651/2010/G12P[8], and RVA/Human-tc/KEN/KDH684/2010/G12P[6]) identified in three stool specimens from children with acute diarrhea in Kenya, Africa. On whole genomic analysis, all three Kenyan G12 strains were found to have a Wa-like genetic backbone: G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strains KDH633 and KDH684) and G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strain KDH651). Phylogenetic analysis showed that most genes of the three strains examined in this study were genetically related to globally circulating human G1, G9, and G12 strains. Of note is that the NSP4 genes of strains KDH633 and KDH684 appeared to be of porcine origin, suggesting the occurrence of reassortment between human and porcine strains. Furthermore, strains KDH633 and KDH684 were very closely related to each other in all the 11 gene segments, indicating derivation of the two strains from a common origin. On the other hand, strain KDH651 consistently formed distinct clusters of 10 of the 11 gene segments (VP1-2, VP4, VP6-7, and NSP1-5), indicating a distinct origin of strain KDH651 from that of strains KDH633 and KDH684. To our knowledge, this is the first report on whole genome-based characterization of G12 strains that have emerged in Kenya. Our observations will provide important insights into the evolutionary dynamics of emerging G12 rotaviruses in Africa.
The availability of the dnaJ1 gene for identifying Mycobacterium species was examined by analyzin... more The availability of the dnaJ1 gene for identifying Mycobacterium species was examined by analyzing the complete dnaJ1 sequences (approximately 1200 bp) of 56 species (54 of them were type strains) and comparing sequence homologies with those of the 16S rRNA gene and other housekeeping genes (rpoB, hsp65). Among the 56 Mycobacterium species, the mean sequence similarity of the dnaJ1 gene (80.4%) was significantly less than that of the 16S rRNA, rpoB and hsp65 genes (96.6%, 91.3% and 91.1%, respectively), indicating a high discriminatory power of the dnaJ1 gene. Seventy-one clinical isolates were correctly clustered to the corresponding type strains, showing isolates belonging to the same species. In order to propose a method for strain identification, we identified an area with a high degree of polymorphism, bordered by conserved sequences, that can be used as universal primers for PCR amplification and sequencing. The sequence of this fragment (approximately 350 bp) allows accurate species identification and may be used as a new tool for the identification of Mycobacterium species.
International Journal of Systematic and Evolutionary Microbiology, 2007
The interrelationships of 27 Aeromonas strains were investigated using dnaJ sequences and DNA–DNA... more The interrelationships of 27 Aeromonas strains were investigated using dnaJ sequences and DNA–DNA hybridization. dnaJ sequence similarities showed a stronger relationship with DNA–DNA relatedness values than did 16S rRNA gene sequence similarities. Additionally, dnaJ sequence analysis, with interspecies divergence over 5.2 % in most cases, gave better resolution than 16S rRNA gene sequences for the differentiation of strains at the species level. Relationships among Aeromonas species were therefore elucidated on the basis of dnaJ sequences and DNA–DNA reassociation. Strains of Aeromonas encheleia and Aeromonas sp. HG11 were unquestionably grouped in the same genetic species, since they shared 98.7 % dnaJ sequence similarity and 82–85 % genomic relatedness. The phylogenetically close relationships obtained from dnaJ sequence analysis (1.7–3.3 % genetic distance) were corroborated by high DNA–DNA relatedness (73–97 %) to support the previous suggestion that Aeromonas culicicola and Ae...
International Journal of Systematic and Evolutionary Microbiology, 2007
In the last few years, many attempts have been made to use conserved gene sequences for identific... more In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies ofStaphylococcusspecies. In an effort to identify a more reliable approach, adnaJgene sequence-based database was created. In this study, an approximately 883 bp portion of thednaJgene sequence from 45 staphylococcal type strains was compared with 16S rRNA and other conserved gene (hsp60,sodAandrpoB) sequences available in public databases. Nucleotide sequence comparisons revealed that the staphylococcaldnaJgene showed higher discrimination (mean similarity 77.6 %) than the 16S rRNA (mean similarity 97.4 %),rpoB(mean similarity 86 %),hsp60(mean similarity 82 %) andsodA(mean similarity 81.5 %) genes. Analysis of thednaJgene sequence from 20Staphylococcusisolates representing two clinically important species showed <1 % sequence divergence. Phylogenetic data obtained from thednaJgene sequence were in general agreement with those of 16S rRNA gene sequen...
Diagnostic Microbiology and Infectious Disease, 2007
Phylogenetic relations within the family Enterobacteriaceae were analyzed using partial dnaJ sequ... more Phylogenetic relations within the family Enterobacteriaceae were analyzed using partial dnaJ sequences of 165 strains belonging to 93 species from 27 enterobacterial genera. The dnaJ phylogeny was in relative agreement with that constructed by 16S rDNA sequences, but more monophyletic groups were obtained from the dnaJ tree than from the 16S rDNA tree. The degree of divergence of the dnaJ gene was approximately 6 times greater than that of 16S rDNA. Also, the dnaJ gene showed the most discriminatory power in comparison with tuf and atpD genes, facilitating clear differentiation of any 2 enterobacterial species by dnaJ sequence analysis. The application of dnaJ sequences to the identification was confirmed by assigning 72 clinical isolates to the correct enterobacterial species. Our data indicate that analysis of the dnaJ gene sequences can be used as a powerful marker for phylogenetic study and identification at the species level of the family Enterobacteriaceae.
The anti-allergic mechanism of heat-killed Lactobacillus acidophilus strain L-92 has not been ful... more The anti-allergic mechanism of heat-killed Lactobacillus acidophilus strain L-92 has not been fully investigated. Recent studies have reported that CD4 CD25 Foxp3 (forkhead box P3) T regulatory (Treg) cells play important roles in controlling allergic diseases. Hence, we examined the effect of orally administered L-92 on CD4 CD25 Foxp3 cell populations. BALB/c mice were supplemented daily with L-92 by gavage for 5 weeks. 2,4-Dinitrofluorobenzene (DNFB) was used to induce allergic contact dermatitis (ACD) in mice. Fluorescent-activated cell sorter (FACS) analysis was used to determine CD4 CD25 Foxp3 T cell populations in spleen and cervical lymph nodes (CLN). Interleukin-10 (IL-10), transforming growth factor-β (TGF-β), and Foxp3 mRNA expressions in mouse ear skin were investigated by real-time reverse transcription-polymerase chain reaction (RT-PCR). The percentage of CD4 CD25 Foxp3 T cell populations were significantly increased in both spleen and CLN of L-92-fed group than vehicle and control. In addition, L-92 produced higher levels of Foxp3, IL-10 and TGF-β compared to control mice. These results suggest that L-92 can up-regulate the number of Treg cells to suppress the progression of DNFB-induced contact dermatitis in mice.
Japanese journal of infectious diseases, Jan 28, 2017
This study aimed to investigate the incidence of rotavirus and enteric bacterial infections among... more This study aimed to investigate the incidence of rotavirus and enteric bacterial infections among children up to five years old with diarrhea living in suburban and rural areas in Kenya. It was a cross-sectional descriptive study, and a total of 1060 diarrheal fecal specimens were obtained from 722 children at the Kiambu County Hospital (KCH) located in a suburban area and 338 children from the Mbita District Hospital (MDH) located in a rural part of western Kenya, between August 2011 and December 2013. Of the 1060 isolates, group A rotavirus (RVA) was detected in 29.6% (214/722) and 11.3% (38/338) fecal specimens from KCH and MDH respectively. Diarrheagenic Escherichia coli (DEC) was found to be the most frequently isolated bacterial pathogens in both study areas (32.8% at KCH and 44.1% at MDH). Two different mixed infection patterns (virus/bacteria and bacteria/bacteria) were observed among patients. A significantly higher infection rate of rotavirus (17.6%, p = 0.001) and DEC (10...
The utility of the dnaJ gene for identifying Vibrio species was investigated by analyzing dnaJ se... more The utility of the dnaJ gene for identifying Vibrio species was investigated by analyzing dnaJ sequences of 57 type strains and 22 clinical strains and comparing sequence homologies with those of the 16S rDNA gene and other housekeeping genes (recA, rpoA, hsp60). Among the 57 Vibrio species, the mean sequence similarity of the dnaJ gene (77.9%) was significantly less than that of the 16S rDNA gene (97.2%), indicating a high discriminatory power of the dnaJ gene. Most Vibrio species were, therefore, differentiated well by dnaJ sequence analysis. Compared to other housekeeping genes, the dnaJ gene showed better resolution than recA or rpoA for differentiating Vibrio coralliilyticus from Vibrio neptunius and Vibrio harveyi from Vibrio rotiferianus. Among the clinical strains, all 22 human pathogenic strains, including an atypical strain, were correctly identified by the dnaJ sequence. Our findings suggest that analysis of the dnaJ gene sequence can be used as a new tool for the identification of Vibrio species.
International Journal of Environmental Research and Public Health
Metal mesh devices (MMDs) are novel materials that enable the precise separation of particles by ... more Metal mesh devices (MMDs) are novel materials that enable the precise separation of particles by size. Structurally, MMDs consist of a periodic arrangement of square apertures of characteristic shapes and sizes on a thin nickel membrane. The present study describes the separation of aerosol particles using palm-top-size collection devices equipped with three types of MMDs differing in pore size. Aerosols were collected at a farm located in the suburbs of Nairobi, Kenya; aerosol particles were isolated, and pathogenic bacteria were identified in this microflora by next-generation sequencing analysis. The composition of the microflora in aerosol particles was found to depend on particle size. Gene fragments were obtained from the collected aerosols by PCR using primers specific for the genus Mycobacterium. This analysis showed that Mycobacterium obuense, a non-tuberculous species of mycobacteria that causes lung diseases, was present in these aerosols. These findings showed that appli...
The American Journal of Tropical Medicine and Hygiene, 2019
Providencia alcalifaciens is a member of the family Enterobacteriaceae that has been commonly imp... more Providencia alcalifaciens is a member of the family Enterobacteriaceae that has been commonly implicated as a causative agent of diarrheal infection in humans and animals. Recent outbreaks of P. alcalifaciens in both developing and developed countries have raised public health concerns. Several studies have suggested that P. alcalifaciens can cause diarrhea by invading the intestinal mucosa, although its pathogenicity has not been well established. Often routine laboratory investigations that seek etiological agents of diarrhea do not actively pursue P. alcalifaciens detection. Therefore, routine laboratory diagnosis should be given more attention for better understanding the epidemiology and pathogenicity of P. alcalifaciens.
The American Journal of Tropical Medicine and Hygiene, 2019
Bacillus pumilus has rarely been reported as a cause of human infections. We report a case of a B... more Bacillus pumilus has rarely been reported as a cause of human infections. We report a case of a B. pumilus causing food poisoning in an adult male. A 51-year-old Japanese man complained of severe abdominal cramps, fever with chills, diarrhea, dizziness, and loss of appetite after eating reheated rice with stewed minced meat purchased from a Kenyan restaurant. Bacillus pumilus was isolated from blood culture and was identified using a biochemical test and 16S rRNA gene sequencing analysis. The patient was treated with probiotics and ciprofloxacin and recovered after 3 days. To our knowledge, this is the first report describing the potential role of B. pumilus as a foodborne pathogen in Kenya and highlights the importance of good hygiene and food preparation practices.
The American Journal of Tropical Medicine and Hygiene, 2016
In an outbreak of gastroenteritis in December 2009, in Mandera, Kenya, Escherichia coli O-nontypa... more In an outbreak of gastroenteritis in December 2009, in Mandera, Kenya, Escherichia coli O-nontypable (ONT) strain was isolated from stool specimens of patients (18/24, 75%). The E. coli ONT organisms could not be assigned to any of the recognized diarrheagenic groups of E. coli. However, they possessed the enteroaggregative E. coli heat-stable enterotoxin-1 gene. The cell-free culture filtrates of the E. coli ONT strain isolated from the outbreak cases induced considerable amount of fluid accumulation in suckling mouse intestine, indicating production of an enterotoxic factor(s). These results identify E. coli that did not have any diarrheagenic characteristics except astA as the etiological agent of the diarrheal outbreak in Mandera. It is however considered necessary to characterize the fluid accumulation factor(s) to determine whether any novel toxins were responsible for the fluid accumulation. Moreover, it is important to study dissemination of strains producing the enterotoxic factor(s) to assess their public health significance distribution in the environment.
Background: The epidemiology of enteric pathogens has not been well studied in Kenya because of w... more Background: The epidemiology of enteric pathogens has not been well studied in Kenya because of wide disparities in health status across the country. Therefore, the present study describes the prevalence of enteropathogenic bacteria, their seasonal variation, and antibiotic resistance profiles among hospitalized diarrheic children in a suburban region of central Kenya. Methods: Fecal samples were collected between July 2009 and December 2013 from a total of 1410 children younger than 5 years, hospitalized with acute diarrhea in Kiambu County Hospital, Kenya. Conventional culture, biochemical, and molecular methods were conducted to identify causative bacterial pathogens and their virulence factors. Antimicrobial susceptibility tests were performed using E-test strips and VITEK-2 advanced expert system (AES) to evaluate the drug-resistance pattern of the isolates. Results: Of the 1410 isolates, bacterial infections were identified in 474 cases. Diarrheagenic Escherichia coli (DEC) was the most frequently isolated pathogen (86.5%). Other pathogens such as Aeromonas (5.5%), Shigella (4%), Salmonella (3.4%), Providencia (3.2%), Vibrio spp. (1.1%), Yersinia enterocolitica (1.1%), and Plesiomonas shigelloides (0.2%) were also identified. Mixed bacterial infection was observed among 11.1% of the cases. The highest infection rate was found during the dry season (59.3%, p = 0.04). Most of the DEC was found to be multidrug resistant to trimethoprim/ sulfamethoxazole 97.6%, amoxicillin 97.6%, erythromycin 96.9%, ampicillin 96.6%, and streptomycin 89%. Conclusions: This study suggests that DEC is the leading diarrhea-causing bacterial pathogen circulating in central Kenya, and seasonality has a significant effect on its transmission. Proper antibiotic prescription and susceptibility testing is important to guide appropriate antimicrobial therapy.
In this study, a sensitive fluorescence sensor was developed for the detection of small, fluoresc... more In this study, a sensitive fluorescence sensor was developed for the detection of small, fluorescence-labeled particles dispersed in a solution. The prototype system comprises of a laser confocal optical system and a mechanical sample stage to detect photon bursting of fluorescence-labeled small particles in sample volumes less than 5 μL within 3 minutes. To examine the feasibility of the prototype system as a diagnostic tool, assemblages of rotavirus and fluorescence-labeled antibody were analyzed. The detection sensitivity for rotavirus was 1 × 10 4 pfu/mL. Rotavirus in stool samples from patients with acute gastroenteritis was also detected. The advantages and disadvantages of this immunosensor with respect to ELISA and RT-PCR, the current gold standards for virus detection, are discussed.
The American Journal of Tropical Medicine and Hygiene, 2015
Providencia alcalifaciens is an emerging bacterial pathogen known to cause acute gastroenteritis ... more Providencia alcalifaciens is an emerging bacterial pathogen known to cause acute gastroenteritis in children and travelers. In July 2013, P. alcalifaciens was isolated from four children appearing for diarrhea at Kiambu District Hospital (KDH) in Kenya. This study describes the outbreak investigation, which aimed to identify the source and mechanisms of infection. We identified seven primary and four secondary cases. Among primary cases were four mothers who had children and experienced mild diarrhea after eating mashed potatoes. The mothers reported feeding children after visiting the toilet and washing their hands without soap. P. alcalifaciens was detected from all secondary cases, and the isolates were found to be clonal by random amplified polymorphic DNA (RAPD) fingerprinting. Our study suggests that the outbreak was caused by P. alcalifaciens, although no fluid accumulation was observed in rabbit ileal loops. The vehicle of the outbreak was believed to be the mashed potato dish, but the source of P. alcalifaciens could not be confirmed. We found that lack of hygiene, inadequate food storage, and improper hand washing before food preparation was the likely cause of the current outbreak. This is the first report of a foodborne infection caused by P. alcalifaciens in Kenya.
A bioassay-guided fractionation of methanol extract of Aristolochia bracteolata whole plant was c... more A bioassay-guided fractionation of methanol extract of Aristolochia bracteolata whole plant was carried out in order to evaluate its antimicrobial activity and to identify the active compounds in this extract. Antibacterial and antifungal activities of methanol extract against gram-positive, gram-negative, and fungal strains were investigated by the agar disk diffusion method. Among the strains tested, Moraxella catarrhalis and sea urchin-derived Bacillus sp. showed the highest sensitivity towards the methanol extract and hence they are used as test organisms for the bioassay-guided fractionation. From this extract, aristolochic acid 1 (AA-1) has been isolated and has showed the greatest antibacterial activity against both standard strain and clinical isolates of Moraxella catarrhalis with equal minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of 25 and 50 μg/mL. Modification of the AA-1 to AA-1 methyl ester completely abolished the antibact...
G12 rotaviruses are globally emerging rotavirus strains causing severe childhood diarrhea. Howeve... more G12 rotaviruses are globally emerging rotavirus strains causing severe childhood diarrhea. However, the whole genomes of only a few G12 strains have been fully sequenced and analyzed, of which only one G12P[4] and one G12P[6] are from Africa. In this study, we sequenced and characterized the complete genomes of three G12 strains (RVA/Human-tc/KEN/KDH633/2010/G12P[6], RVA/Human-tc/KEN/KDH651/2010/G12P[8], and RVA/Human-tc/KEN/KDH684/2010/G12P[6]) identified in three stool specimens from children with acute diarrhea in Kenya, Africa. On whole genomic analysis, all three Kenyan G12 strains were found to have a Wa-like genetic backbone: G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strains KDH633 and KDH684) and G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strain KDH651). Phylogenetic analysis showed that most genes of the three strains examined in this study were genetically related to globally circulating human G1, G9, and G12 strains. Of note is that the NSP4 genes of strains KDH633 and KDH684 appeared to be of porcine origin, suggesting the occurrence of reassortment between human and porcine strains. Furthermore, strains KDH633 and KDH684 were very closely related to each other in all the 11 gene segments, indicating derivation of the two strains from a common origin. On the other hand, strain KDH651 consistently formed distinct clusters of 10 of the 11 gene segments (VP1-2, VP4, VP6-7, and NSP1-5), indicating a distinct origin of strain KDH651 from that of strains KDH633 and KDH684. To our knowledge, this is the first report on whole genome-based characterization of G12 strains that have emerged in Kenya. Our observations will provide important insights into the evolutionary dynamics of emerging G12 rotaviruses in Africa.
The availability of the dnaJ1 gene for identifying Mycobacterium species was examined by analyzin... more The availability of the dnaJ1 gene for identifying Mycobacterium species was examined by analyzing the complete dnaJ1 sequences (approximately 1200 bp) of 56 species (54 of them were type strains) and comparing sequence homologies with those of the 16S rRNA gene and other housekeeping genes (rpoB, hsp65). Among the 56 Mycobacterium species, the mean sequence similarity of the dnaJ1 gene (80.4%) was significantly less than that of the 16S rRNA, rpoB and hsp65 genes (96.6%, 91.3% and 91.1%, respectively), indicating a high discriminatory power of the dnaJ1 gene. Seventy-one clinical isolates were correctly clustered to the corresponding type strains, showing isolates belonging to the same species. In order to propose a method for strain identification, we identified an area with a high degree of polymorphism, bordered by conserved sequences, that can be used as universal primers for PCR amplification and sequencing. The sequence of this fragment (approximately 350 bp) allows accurate species identification and may be used as a new tool for the identification of Mycobacterium species.
International Journal of Systematic and Evolutionary Microbiology, 2007
The interrelationships of 27 Aeromonas strains were investigated using dnaJ sequences and DNA–DNA... more The interrelationships of 27 Aeromonas strains were investigated using dnaJ sequences and DNA–DNA hybridization. dnaJ sequence similarities showed a stronger relationship with DNA–DNA relatedness values than did 16S rRNA gene sequence similarities. Additionally, dnaJ sequence analysis, with interspecies divergence over 5.2 % in most cases, gave better resolution than 16S rRNA gene sequences for the differentiation of strains at the species level. Relationships among Aeromonas species were therefore elucidated on the basis of dnaJ sequences and DNA–DNA reassociation. Strains of Aeromonas encheleia and Aeromonas sp. HG11 were unquestionably grouped in the same genetic species, since they shared 98.7 % dnaJ sequence similarity and 82–85 % genomic relatedness. The phylogenetically close relationships obtained from dnaJ sequence analysis (1.7–3.3 % genetic distance) were corroborated by high DNA–DNA relatedness (73–97 %) to support the previous suggestion that Aeromonas culicicola and Ae...
International Journal of Systematic and Evolutionary Microbiology, 2007
In the last few years, many attempts have been made to use conserved gene sequences for identific... more In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies ofStaphylococcusspecies. In an effort to identify a more reliable approach, adnaJgene sequence-based database was created. In this study, an approximately 883 bp portion of thednaJgene sequence from 45 staphylococcal type strains was compared with 16S rRNA and other conserved gene (hsp60,sodAandrpoB) sequences available in public databases. Nucleotide sequence comparisons revealed that the staphylococcaldnaJgene showed higher discrimination (mean similarity 77.6 %) than the 16S rRNA (mean similarity 97.4 %),rpoB(mean similarity 86 %),hsp60(mean similarity 82 %) andsodA(mean similarity 81.5 %) genes. Analysis of thednaJgene sequence from 20Staphylococcusisolates representing two clinically important species showed <1 % sequence divergence. Phylogenetic data obtained from thednaJgene sequence were in general agreement with those of 16S rRNA gene sequen...
Diagnostic Microbiology and Infectious Disease, 2007
Phylogenetic relations within the family Enterobacteriaceae were analyzed using partial dnaJ sequ... more Phylogenetic relations within the family Enterobacteriaceae were analyzed using partial dnaJ sequences of 165 strains belonging to 93 species from 27 enterobacterial genera. The dnaJ phylogeny was in relative agreement with that constructed by 16S rDNA sequences, but more monophyletic groups were obtained from the dnaJ tree than from the 16S rDNA tree. The degree of divergence of the dnaJ gene was approximately 6 times greater than that of 16S rDNA. Also, the dnaJ gene showed the most discriminatory power in comparison with tuf and atpD genes, facilitating clear differentiation of any 2 enterobacterial species by dnaJ sequence analysis. The application of dnaJ sequences to the identification was confirmed by assigning 72 clinical isolates to the correct enterobacterial species. Our data indicate that analysis of the dnaJ gene sequences can be used as a powerful marker for phylogenetic study and identification at the species level of the family Enterobacteriaceae.
The anti-allergic mechanism of heat-killed Lactobacillus acidophilus strain L-92 has not been ful... more The anti-allergic mechanism of heat-killed Lactobacillus acidophilus strain L-92 has not been fully investigated. Recent studies have reported that CD4 CD25 Foxp3 (forkhead box P3) T regulatory (Treg) cells play important roles in controlling allergic diseases. Hence, we examined the effect of orally administered L-92 on CD4 CD25 Foxp3 cell populations. BALB/c mice were supplemented daily with L-92 by gavage for 5 weeks. 2,4-Dinitrofluorobenzene (DNFB) was used to induce allergic contact dermatitis (ACD) in mice. Fluorescent-activated cell sorter (FACS) analysis was used to determine CD4 CD25 Foxp3 T cell populations in spleen and cervical lymph nodes (CLN). Interleukin-10 (IL-10), transforming growth factor-β (TGF-β), and Foxp3 mRNA expressions in mouse ear skin were investigated by real-time reverse transcription-polymerase chain reaction (RT-PCR). The percentage of CD4 CD25 Foxp3 T cell populations were significantly increased in both spleen and CLN of L-92-fed group than vehicle and control. In addition, L-92 produced higher levels of Foxp3, IL-10 and TGF-β compared to control mice. These results suggest that L-92 can up-regulate the number of Treg cells to suppress the progression of DNFB-induced contact dermatitis in mice.
Japanese journal of infectious diseases, Jan 28, 2017
This study aimed to investigate the incidence of rotavirus and enteric bacterial infections among... more This study aimed to investigate the incidence of rotavirus and enteric bacterial infections among children up to five years old with diarrhea living in suburban and rural areas in Kenya. It was a cross-sectional descriptive study, and a total of 1060 diarrheal fecal specimens were obtained from 722 children at the Kiambu County Hospital (KCH) located in a suburban area and 338 children from the Mbita District Hospital (MDH) located in a rural part of western Kenya, between August 2011 and December 2013. Of the 1060 isolates, group A rotavirus (RVA) was detected in 29.6% (214/722) and 11.3% (38/338) fecal specimens from KCH and MDH respectively. Diarrheagenic Escherichia coli (DEC) was found to be the most frequently isolated bacterial pathogens in both study areas (32.8% at KCH and 44.1% at MDH). Two different mixed infection patterns (virus/bacteria and bacteria/bacteria) were observed among patients. A significantly higher infection rate of rotavirus (17.6%, p = 0.001) and DEC (10...
The utility of the dnaJ gene for identifying Vibrio species was investigated by analyzing dnaJ se... more The utility of the dnaJ gene for identifying Vibrio species was investigated by analyzing dnaJ sequences of 57 type strains and 22 clinical strains and comparing sequence homologies with those of the 16S rDNA gene and other housekeeping genes (recA, rpoA, hsp60). Among the 57 Vibrio species, the mean sequence similarity of the dnaJ gene (77.9%) was significantly less than that of the 16S rDNA gene (97.2%), indicating a high discriminatory power of the dnaJ gene. Most Vibrio species were, therefore, differentiated well by dnaJ sequence analysis. Compared to other housekeeping genes, the dnaJ gene showed better resolution than recA or rpoA for differentiating Vibrio coralliilyticus from Vibrio neptunius and Vibrio harveyi from Vibrio rotiferianus. Among the clinical strains, all 22 human pathogenic strains, including an atypical strain, were correctly identified by the dnaJ sequence. Our findings suggest that analysis of the dnaJ gene sequence can be used as a new tool for the identification of Vibrio species.
Uploads
Papers by Mohammad Shah