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Asish K. Mukhopadhyay - One of the best experts on this subject based on the ideXlab platform.
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Haitian-like Genetic Traits with creeping MIC of Azithromycin in Vibrio cholerae O1 isolates from Puducherry, India
Journal of medical microbiology, 2020Co-Authors: Regina Sumitha Mohanraj, Prosenjit Samanta, Asish K. Mukhopadhyay, Jharna MandalAbstract:Introduction. The emergence of novel strains of Vibrio cholerae O1 El Tor biotype has gained attention due to causing several epidemics around the world. Variant strains have evolved as a result of the acquisition of genes that confer extended virulence and pathogenicity. Aim. This study aimed to determine the presence of the most recently emerging Haitian-like Genetic Traits among the isolates from Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, Southern India. We also wanted to detect the prevalence of the sulfamethoxazole and trimethoprim (SXT) element, which is an integrating conjugative element (ICE) and the antimicrobial resistance genes present in our isolates. Methodology. Identification of Haitian-specific alleles was done by mismatched amplification mutation assay PCR (MAMA-PCR). The presence of SXT elements was carried out by PCR by detecting int, eex, att-prfC and setR genes. Detection of antibiotic resistance determinant, sul(1,2,3); dfr(A1,18,5) for trimethoprim resistance, tet(A,B,C,D,E,Y,G,M), tet34 for tetracycline resistance and erm(A,B,C), mph(A,B), ere(A,B), msr(A,D) for azithromycin resistance were targeted by PCR. The MIC of tetracycline, ciprofloxacin and azithromycin was determined by the E-test method. Results. Of the 95 isolates, 60 % of the isolates were found to carry Haitian-specific alleles of ctxB, tcpA and rtxA gene, 100 % of the isolates were found to carry SXT elements. All the isolates harboured the four conserved genes of the SXT element, except one which had only eex, att-prfC, setR genes. About 99 % harboured sul2 and dfrA1 genes. No tet and macrolide genes were detected. We observed a progressive increase in the MIC of azithromycin ranging from 0.75 µg ml−1 to 2 µg ml−1. Conclusion. None of the isolates were the prototype El Tor biotype. All the isolates were a Haitian variant. The presence of SXT elements across all our isolates and their creeping MIC of azithromycin is a matter of concern. Further testing for other Genetic determinants of resistance will be carried out in our future studies.
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Dissemination of newly emerged polymyxin B sensitive Vibrio cholerae O1 containing Haitian-like Genetic Traits in different parts of India.
Journal of medical microbiology, 2018Co-Authors: Prosenjit Samanta, Goutam Chowdhury, Shanta Dutta, Arindam Naha, Rudra Narayan Saha, Sounak Sarkar, Ranjan K. Nandy, Keinosuke Okamoto, Asish K. MukhopadhyayAbstract:Purpose. Two natural epidemic biotypes of Vibrio cholerae O1, classical and El Tor, exhibit different patterns of sensitivity against the antimicrobial peptide polymyxin B. This difference in sensitivity has been one of the major markers in biotype classification system for several decades. A recent report regarding the emergence of polymyxin B-sensitive El Tor V. cholerae O1 in Kolkata has motivated us to track the spread of the strains containing this important trait, along with Haitian-like Genetic content, in different parts of India. Methodology. We have collected 260 clinical V. cholerae O1 strains from 12 states in India and screened them for polymyxin B susceptibility. Genetic characterization was also performed to study the tcpA, ctxB and rtxA genotypes by allele-specific polymerase chain reaction (PCR) and nucleotide sequencing. Results. Interestingly, 88.85 % of the isolates were found to be sensitive to polymyxin B. All of the states, with the exception of Assam, had polymyxin B-sensitive V. cholerae strains and complete replacement with this strain was found in eight of the states. However, from 2016 onwards, all the strains tested showed sensitivity to polymyxin B. Allele-specific PCR and sequencing confirmed that all strains possessed Haitian-like Genetic Traits. Conclusion. Polymyxin B-sensitive strains have begun to spread throughout India and may lead to the revision of the biotype classification. The dissemination of these new variant strains needs to be carefully monitored in different endemic populations through active holistic surveillance to understand their clinical and epidemiological consequences.
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Genetic Traits of Vibrio cholerae O1 Haitian isolates that are absent in contemporary strains from Kolkata, India.
PloS one, 2014Co-Authors: Priyanka Ghosh, Thandavarayan Ramamurthy, Arindam Naha, Gururaja P. Pazhani, Asish K. MukhopadhyayAbstract:The world's worst cholera epidemic in Haiti (2010) coerced to trace the origin and dissemination of the causative agent Vibrio cholerae O1 for proper management of cholera. Sequence analysis of the Haitian strain showed several variations in the genes encoding cholera toxin B subunit (ctxB); toxin-co-regulated pilus (tcpA), repeat in toxins (rtxA), quinolone resistance-determining region (QRDR) of gyrase A (gyrA), rstB of RS element along with the change in the number of repeat sequences at the promoter region of ctxAB. Our earlier studies showed that variant tcpA (tcpA CIRS) and ctxB (ctxB7) first appeared in Kolkata during 2003 and 2006, respectively. The present study revealed that a variant rtxA was first isolated in Kolkata during 2004 and probably formed the Genetic background for the emergence of the ctxB7 allele as we were unable to detect a single strain with the combination of El Tor rtxA and ctxB7. The variant gyrA was first time detected in Kolkata during 1994. The Kolkata strains contained four heptad repeats (TTTTGAT) in their CT promoter regions whereas Haitian strains carried 5 heptad repeats. Haitian strains had 3 nucleotide deletions at the rstB gene, which is a unique feature of the classical biotype strains. But the Kolkata strains did not have such deletion mutations in the rstB. Our study demonstrated the existence of some Haitian Genetic Traits in Kolkata isolates along with the dissimilarities in genomic content with respect to rstB and ctxAB promoter region. Finally, we conclude that Haitian variant strain may be evolved due to sequential event in the Indian subcontinent strain with some cryptic modification in the genome.
Papa Ndour - One of the best experts on this subject based on the ideXlab platform.
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Pearl Millet Genetic Traits Shape Rhizobacterial Diversity and Modulate Rhizosphere Aggregation.
Frontiers in plant science, 2017Co-Authors: Papa Ndour, Mariama Gueye, Mohamed Barakat, Philippe Ortet, Marie Bertrand-huleux, Anne-laure Pablo, Damien Dezette, Lydie Chapuis-lardy, Komi Assigbetsé, Ndjido Ardo KaneAbstract:Root exudation contributes to soil carbon allocation and also to microbial C and energy supply, which subsequently impacts soil aggregation around roots. Biologically-driven soil structuration is an important driver of soil fertility. Plant Genetic determinants of exudation and more generally of factors promoting rhizosphere soil aggregation are largely unknown. Here, we characterized rhizosphere aggregation in a panel of 86 pearl millet inbred lines using a ratio of root-adhering soil dry mass per root tissue dry mass (RAS/RT). This ratio showed significant variations between lines, with a roughly two fold amplitude between lowest and highest average values. For 9 lines with contrasting aggregation properties, we then compared the bacterial diversity and composition in root-adhering soil. Bacterial α-diversity metrics decreased with the “RAS/RT ratio”. Regarding taxonomic composition, the Rhizobiales were stimulated in lines showing high aggregation level whereas Bacillales were more abundant in lines with low ratio. 184 strains of cultivable exopolysaccharides-producing bacteria have been isolated from the rhizosphere of some lines, including members from Rhizobiales and Bacillales. However, at this stage, we could not find a correlation between abundance of EPS-producing species orthologs in bacterial communities and the ratio RAS/RT. These results illustrated the impact of cereals Genetic trait variation on soil physical properties and microbial diversity. This opens the possibility of considering plant breeding to help management of soil carbon content and physical characteristics through carbon rhizodeposition in soil.
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Pearl Millet Genetic Traits Shape Rhizobacterial Diversity and Modulate Rhizosphere Aggregation
Frontiers in Plant Science, 2017Co-Authors: Papa Ndour, Mariama Gueye, Mohamed Barakat, Philippe Ortet, Marie Bertrand-huleux, Anne-laure Pablo, Damien Dezette, Lydie Chapuis-lardy, Komi Assigbetsé, Ndjido KaneAbstract:Root exudation contributes to soil carbon allocation and also to microbial C and energy supply, which subsequently impacts soil aggregation around roots. Biologically-driven soil structural formation is an important driver of soil fertility. Plant Genetic determinants of exudation and more generally of factors promoting rhizosphere soil aggregation are largely unknown. Here, we characterized rhizosphere aggregation in a panel of 86 pearl millet inbred lines using a ratio of root-adhering soil dry mass per root tissue dry mass (RAS/RT). This ratio showed significant variations between lines, with a roughly 2-fold amplitude between lowest and highest average values. For 9 lines with contrasting aggregation properties, we then compared the bacterial diversity and composition in root-adhering soil. Bacterial α-diversity metrics increased with the " RAS/RT ratio. " Regarding taxonomic composition, the Rhizobiales were stimulated in lines showing high aggregation level whereas Bacillales were more abundant in lines with low ratio. 184 strains of cultivable exopolysaccharides-producing bacteria have been isolated from the rhizosphere of some lines, including members from Rhizobiales and Bacillales. However, at this stage, we could not find a correlation between abundance of EPS-producing species in bacterial communities and the ratio RAS/RT. These results illustrated the impact of cereals Genetic trait variation on soil physical properties and microbial diversity. This opens the possibility of considering plant breeding to help management of soil carbon content and physical characteristics through carbon rhizodeposition in soil.
Ndjido Kane - One of the best experts on this subject based on the ideXlab platform.
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Pearl Millet Genetic Traits Shape Rhizobacterial Diversity and Modulate Rhizosphere Aggregation
Frontiers in Plant Science, 2017Co-Authors: Papa Ndour, Mariama Gueye, Mohamed Barakat, Philippe Ortet, Marie Bertrand-huleux, Anne-laure Pablo, Damien Dezette, Lydie Chapuis-lardy, Komi Assigbetsé, Ndjido KaneAbstract:Root exudation contributes to soil carbon allocation and also to microbial C and energy supply, which subsequently impacts soil aggregation around roots. Biologically-driven soil structural formation is an important driver of soil fertility. Plant Genetic determinants of exudation and more generally of factors promoting rhizosphere soil aggregation are largely unknown. Here, we characterized rhizosphere aggregation in a panel of 86 pearl millet inbred lines using a ratio of root-adhering soil dry mass per root tissue dry mass (RAS/RT). This ratio showed significant variations between lines, with a roughly 2-fold amplitude between lowest and highest average values. For 9 lines with contrasting aggregation properties, we then compared the bacterial diversity and composition in root-adhering soil. Bacterial α-diversity metrics increased with the " RAS/RT ratio. " Regarding taxonomic composition, the Rhizobiales were stimulated in lines showing high aggregation level whereas Bacillales were more abundant in lines with low ratio. 184 strains of cultivable exopolysaccharides-producing bacteria have been isolated from the rhizosphere of some lines, including members from Rhizobiales and Bacillales. However, at this stage, we could not find a correlation between abundance of EPS-producing species in bacterial communities and the ratio RAS/RT. These results illustrated the impact of cereals Genetic trait variation on soil physical properties and microbial diversity. This opens the possibility of considering plant breeding to help management of soil carbon content and physical characteristics through carbon rhizodeposition in soil.
Ndjido Ardo Kane - One of the best experts on this subject based on the ideXlab platform.
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Pearl Millet Genetic Traits Shape Rhizobacterial Diversity and Modulate Rhizosphere Aggregation.
Frontiers in plant science, 2017Co-Authors: Papa Ndour, Mariama Gueye, Mohamed Barakat, Philippe Ortet, Marie Bertrand-huleux, Anne-laure Pablo, Damien Dezette, Lydie Chapuis-lardy, Komi Assigbetsé, Ndjido Ardo KaneAbstract:Root exudation contributes to soil carbon allocation and also to microbial C and energy supply, which subsequently impacts soil aggregation around roots. Biologically-driven soil structuration is an important driver of soil fertility. Plant Genetic determinants of exudation and more generally of factors promoting rhizosphere soil aggregation are largely unknown. Here, we characterized rhizosphere aggregation in a panel of 86 pearl millet inbred lines using a ratio of root-adhering soil dry mass per root tissue dry mass (RAS/RT). This ratio showed significant variations between lines, with a roughly two fold amplitude between lowest and highest average values. For 9 lines with contrasting aggregation properties, we then compared the bacterial diversity and composition in root-adhering soil. Bacterial α-diversity metrics decreased with the “RAS/RT ratio”. Regarding taxonomic composition, the Rhizobiales were stimulated in lines showing high aggregation level whereas Bacillales were more abundant in lines with low ratio. 184 strains of cultivable exopolysaccharides-producing bacteria have been isolated from the rhizosphere of some lines, including members from Rhizobiales and Bacillales. However, at this stage, we could not find a correlation between abundance of EPS-producing species orthologs in bacterial communities and the ratio RAS/RT. These results illustrated the impact of cereals Genetic trait variation on soil physical properties and microbial diversity. This opens the possibility of considering plant breeding to help management of soil carbon content and physical characteristics through carbon rhizodeposition in soil.
Prosenjit Samanta - One of the best experts on this subject based on the ideXlab platform.
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Haitian-like Genetic Traits with creeping MIC of Azithromycin in Vibrio cholerae O1 isolates from Puducherry, India
Journal of medical microbiology, 2020Co-Authors: Regina Sumitha Mohanraj, Prosenjit Samanta, Asish K. Mukhopadhyay, Jharna MandalAbstract:Introduction. The emergence of novel strains of Vibrio cholerae O1 El Tor biotype has gained attention due to causing several epidemics around the world. Variant strains have evolved as a result of the acquisition of genes that confer extended virulence and pathogenicity. Aim. This study aimed to determine the presence of the most recently emerging Haitian-like Genetic Traits among the isolates from Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, Southern India. We also wanted to detect the prevalence of the sulfamethoxazole and trimethoprim (SXT) element, which is an integrating conjugative element (ICE) and the antimicrobial resistance genes present in our isolates. Methodology. Identification of Haitian-specific alleles was done by mismatched amplification mutation assay PCR (MAMA-PCR). The presence of SXT elements was carried out by PCR by detecting int, eex, att-prfC and setR genes. Detection of antibiotic resistance determinant, sul(1,2,3); dfr(A1,18,5) for trimethoprim resistance, tet(A,B,C,D,E,Y,G,M), tet34 for tetracycline resistance and erm(A,B,C), mph(A,B), ere(A,B), msr(A,D) for azithromycin resistance were targeted by PCR. The MIC of tetracycline, ciprofloxacin and azithromycin was determined by the E-test method. Results. Of the 95 isolates, 60 % of the isolates were found to carry Haitian-specific alleles of ctxB, tcpA and rtxA gene, 100 % of the isolates were found to carry SXT elements. All the isolates harboured the four conserved genes of the SXT element, except one which had only eex, att-prfC, setR genes. About 99 % harboured sul2 and dfrA1 genes. No tet and macrolide genes were detected. We observed a progressive increase in the MIC of azithromycin ranging from 0.75 µg ml−1 to 2 µg ml−1. Conclusion. None of the isolates were the prototype El Tor biotype. All the isolates were a Haitian variant. The presence of SXT elements across all our isolates and their creeping MIC of azithromycin is a matter of concern. Further testing for other Genetic determinants of resistance will be carried out in our future studies.
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Dissemination of newly emerged polymyxin B sensitive Vibrio cholerae O1 containing Haitian-like Genetic Traits in different parts of India.
Journal of medical microbiology, 2018Co-Authors: Prosenjit Samanta, Goutam Chowdhury, Shanta Dutta, Arindam Naha, Rudra Narayan Saha, Sounak Sarkar, Ranjan K. Nandy, Keinosuke Okamoto, Asish K. MukhopadhyayAbstract:Purpose. Two natural epidemic biotypes of Vibrio cholerae O1, classical and El Tor, exhibit different patterns of sensitivity against the antimicrobial peptide polymyxin B. This difference in sensitivity has been one of the major markers in biotype classification system for several decades. A recent report regarding the emergence of polymyxin B-sensitive El Tor V. cholerae O1 in Kolkata has motivated us to track the spread of the strains containing this important trait, along with Haitian-like Genetic content, in different parts of India. Methodology. We have collected 260 clinical V. cholerae O1 strains from 12 states in India and screened them for polymyxin B susceptibility. Genetic characterization was also performed to study the tcpA, ctxB and rtxA genotypes by allele-specific polymerase chain reaction (PCR) and nucleotide sequencing. Results. Interestingly, 88.85 % of the isolates were found to be sensitive to polymyxin B. All of the states, with the exception of Assam, had polymyxin B-sensitive V. cholerae strains and complete replacement with this strain was found in eight of the states. However, from 2016 onwards, all the strains tested showed sensitivity to polymyxin B. Allele-specific PCR and sequencing confirmed that all strains possessed Haitian-like Genetic Traits. Conclusion. Polymyxin B-sensitive strains have begun to spread throughout India and may lead to the revision of the biotype classification. The dissemination of these new variant strains needs to be carefully monitored in different endemic populations through active holistic surveillance to understand their clinical and epidemiological consequences.
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Characterization of Vibrio cholerae O1 strains that trace the origin of Haitian-like Genetic Traits.
Infection genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2017Co-Authors: Priyanka Ghosh, Dhirendra Kumar, Goutam Chowdhury, Puneeta Singh, Prosenjit Samanta, Shanta Dutta, Thandavarayan Ramamurthy, Neera Sharma, Preety Sinha, Yogendra PrasadAbstract:Vibrio cholerae O1 is the etiological agent of the severe diarrheal disease cholera. The bacterium has recently been causing outbreaks in Haiti with catastrophic effects. Numerous mutations have been reported in V. cholerae O1 strains associated with the Haitian outbreak. These mutations encompass among other the genes encoding virulence factors such as the pilin subunit of the toxin-co-regulated pilus (tcpA), cholera toxin B subunit (ctxB), repeat in toxins (rtxA), and other genes such as the quinolone resistance-determining region (QRDR) of gyrase A (gyrA), rstB of RS element along with the alteration in the number of repeat sequences at the promoter region of ctxAB. Given the numerous Genetic changes in those Haitian isolates, we decided to investigate the possible origins of those variations in the Indian subcontinent. Thus, we determined the Genetic Traits among V. cholerae O1 strains in Delhi, India. A total of 175 strains isolated from cholera patients during 2004 to 2012 were analysed in the present study. Our results showed that all the tested strains carried Haitian type tcpA (tcpACIRS) and variant gyrA indicating their first appearance before 2004 in Delhi. The Haitian variant rtxA and ctxB7 were first detected in Delhi during 2004 and 2006, respectively. Interestingly, not a single strain with the combination of El Tor rtxA and ctxB7 was detected in this study. The Delhi strains carried four heptad repeats (TTTTGAT) in the CT promoter region whereas Haitian strains carried 5 such repeats. Delhi strains did not have any deletion mutations in the rstB like Haitian strains. Overall, our study demonstrates the sequential accumulation of Haitian-like Genetic Traits among V. cholerae O1 strains in Delhi at different time points prior to the Haitian cholera outbreak.