Search

Your search keyword '"Phelan, Jody E."' showing total 188 results
Start Over Author "Phelan, Jody E." Search Limiters Full Text Publication Year Range Last 50 years
188 results on '"Phelan, Jody E."'

1. Newly Identified Mycobacterium africanum Lineage 10, Central Africa

Author

Guyeux, Christophe, Senelle, Gaetan, Le Meur, Adrien, Supply, Philip, Gaudin, Cyril, Phelan, Jody E., Clark, Taane G., Rigouts, Leen, de Jong, Bouke, Sola, Christophe, and Refregier, Guislaine

Subjects
Central Africa -- Health aspects -- Environmental aspects, Mycobacterium -- Identification and classification -- Genetic aspects -- Natural history, Mycobacteria -- Identification and classification -- Genetic aspects -- Natural history, Tuberculosis -- Causes of -- Risk factors, Health
Abstract

The traditional view of restricted diversity among bacterial agents causing human and animal tuberculosis is being revised thanks to wide use of wholegenome sequencing (WGS). Besides Mycobacterium canettii, representative of [...]

Published
2024
Full Text
View/download PDF

10. Molecular characterisation of second-line drug resistance among drug resistant tuberculosis patients tested in Uganda: a two and a half-year’s review

Author

Mujuni, Dennis, Kasemire, Dianah Linda, Ibanda, Ivan, Kabugo, Joel, Nsawotebba, Andrew, Phelan, Jody E., Majwala, Robert Kaos, Tugumisirize, Didas, Nyombi, Abdunoor, Orena, Beatrice, Turyahabwe, Irene, Byabajungu, Henry, Nadunga, Diana, Musisi, Kenneth, Joloba, Moses Lutakoome, and Ssengooba, Willy

Published
2022
Full Text
View/download PDF

14. Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines.

Author

Wang, Linfeng, Lim, Dodge R., Phelan, Jody E., Reyes, Lorenzo T., Palparan, Alma G., Sanchez, Maria Guileane C., Asuncion, Louella Abigail A., Tujan, Ma. Angelica A., Medado, Inez Andrea P., Daga, Chona Mae A., Llames, Jo-Hannah S., Mitarai, Satoshi, Murase, Yoshiro, Morishige, Yuta, Ang, Concepcion F., Malabad, John Carlo M., Montoya, Jaime C., Hafalla, Julius C., Campino, Susana, and Hibberd, Martin L.

Subjects
WHOLE genome sequencing, RIFAMPIN, MYCOBACTERIUM tuberculosis, NUCLEOTIDE sequencing, SEQUENCE analysis, GENETIC variation
Abstract

The Philippines is a high-incidence country for tuberculosis, with the increasing prevalence of multi- (MDR-TB) and extensively-drug (XDR-TB) resistant Mycobacterium tuberculosis strains posing difficulties to disease control. Understanding the genetic diversity of circulating strains can provide insights into underlying drug resistance mutations and transmission dynamics, thereby assisting the design of diagnostic tools, including those using next generation sequencing (NGS) platforms. By analysing genome sequencing data of 732 isolates from Philippines drug-resistance survey collections spanning from 2011 to 2019, we found that the majority belonged to lineages L1 (531/732; 72.5%) and L4 (European-American; n = 174; 23.8%), with the Manila strain (L1.2.1.2.1) being the most prominent (475/531). Approximately two-thirds of isolates were found to be at least MDR-TB (483/732; 66.0%), and potential XDR-TB genotypic resistance was observed (3/732; 0.4%), highlighting an emerging problem in the country. Genotypic resistance was highly concordant with laboratory drug susceptibility testing. By finding isolates with (near-)identical genomic variation, five major clusters containing a total of 114 isolates were identified: all containing either L1 or L4 isolates with at least MDR-TB resistance and spanning multiple years of collection. Closer inspection of clusters revealed transmission in prisons, some involving isolates with XDR-TB, and mutations linked to third-line drug bedaquiline. We have also identified previously unreported mutations linked to resistance for isoniazid, rifampicin, ethambutol, and fluoroquinolones. Overall, this study provides important insights into the genetic diversity, transmission and circulating drug resistance mutations of M. tuberculosis in the Philippines, thereby informing clinical and surveillance decision-making, which is increasingly using NGS platforms. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

15. Multi-platform whole genome sequencing for tuberculosis clinical and surveillance applications

Author

Thorpe, Joseph, primary, Sawaengdee, Waritta, additional, Ward, Daniel, additional, Campos, Monica, additional, Wichukchinda, Nuanjun, additional, Chaiyasirinroje, Boonchai, additional, Thanraka, Aungkana, additional, Chumpol, Jaluporn, additional, Phelan, Jody E., additional, Campino, Susana, additional, Mahasirimongkol, Surakameth, additional, and Clark, Taane G., additional

Published
2024
Full Text
View/download PDF

17. Genomic analysis of Salmonella enterica from Metropolitan Manila abattoirs and markets reveals insights into circulating virulence and antimicrobial resistance genotypes

Author

Mora, Jonah Feliza B., primary, Meclat, Vanessa Yvonne B., additional, Calayag, Alyzza Marie B., additional, Campino, Susana, additional, Hafalla, Julius C. R., additional, Hibberd, Martin L., additional, Phelan, Jody E., additional, Clark, Taane G., additional, and Rivera, Windell L., additional

Published
2024
Full Text
View/download PDF

18. Clusters of Drug-Resistant Mycobacterium tuberculosis Detected by Whole-Genome Sequence Analysis of Nationwide Sample, Thailand, 2014-2017

Author

Nonghanphithak, Ditthawat, Chaiprasert, Angkana, Smithtikarn, Saijai, Kamolwat, Phalin, Pungrassami, Petchawan, Chongsuvivatwong, Virasakdi, Mahasirimongkol, Surakameth, Reechaipichitkul, Wipa, Leepiyasakulchai, Chaniya, Phelan, Jody E., Blair, David, Clark, Taane G., and Faksri, Kiatichai

Subjects
Nucleotide sequencing -- Usage, Drug resistance in microorganisms -- Distribution, DNA sequencing -- Usage, Tuberculosis -- Risk factors -- Distribution, Cluster analysis -- Methods, Mycobacterium tuberculosis -- Genetic aspects -- Distribution, Company distribution practices, Health
Abstract

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a major global public health issue. Southeast Asia contributes notably (44%) to global TB cases. Thailand is in the top 30 countries for [...]

Published
2021
Full Text
View/download PDF

28. The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China

Author

Jiang, Qi, primary, Liu, Hai-Can, additional, Liu, Qing-Yun, additional, Phelan, Jody E., additional, Tao, Feng-Xi, additional, Zhao, Xiu-Qin, additional, Wang, Jian, additional, Glynn, Judith R., additional, Takiff, Howard E., additional, Clark, Taane G., additional, Wan, Kang-Lin, additional, and Gao, Qian, additional

Published
2023
Full Text
View/download PDF

32. Functional genetic variation in pe/ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host.

Author

Josefina Gómez-González, Paula, Grabowska, Anna D., Tientcheu, Leopold D., Tsolaki, Anthony G., Hibberd, Martin L., Campino, Susana, Phelan, Jody E., and Clark, Taane G.

Subjects
MYCOBACTERIUM tuberculosis, GENETIC variation, GENE rearrangement, GENE families, SOCIAL interaction, PERSONAL protective equipment
Abstract

Introduction: Around 10% of the coding potential of Mycobacterium tuberculosisis constituted by two poorly understood gene families, the pe and ppe loci, thought to be involved in host-pathogen interactions. Their repetitive nature and high GC content have hindered sequence analysis, leading to exclusion from whole-genome studies. Understanding the genetic diversity of pe/ppe families is essential to facilitate their potential translation into tools for tuberculosis prevention and treatment. Methods: To investigate the genetic diversity of the 169 pe/ppe genes, we performed a sequence analysis across 73 long-read assemblies representing seven different lineages of M. tuberculosis and M. bovis BCG. Individual pe/ppe gene alignments were extracted and diversity and conservation across the different lineages studied. Results: The pe/ppe genes were classified into three groups based on the level of protein sequence conservation relative to H37Rv, finding that >50% were conserved, with indels in pe_pgrs and ppe_mptr sub-families being major drivers of structural variation. Gene rearrangements, such as duplications and gene fusions, were observed between pe and pe_pgrs genes. Inter-lineage diversity revealed lineage-specific SNPs and indels. Discussion: The high level of pe/ppe genes conservation, together with the lineage-specific findings, suggest their phylogenetic informativeness. However, structural variants and gene rearrangements differing from the reference were also identified, with potential implications for pathogenicity. Overall, improving our knowledge of these complex gene families may have insights into pathogenicity and inform the development of much-needed tools for tuberculosis control. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

34. Second-line drug resistance markers as proxy indicators of time to sputum culture conversion among second-line drug resistant tuberculosis patients tested in Uganda: A cross-sectional study

Author

Mujuni, Dennis, primary, Ssengooba, Willy, additional, Ibanda, Ivan, additional, Kabugo, Joel Solomon, additional, Kasemire, Dianah Linda, additional, Nampewo, Elizabeth, additional, Nsawotebba, Andrew, additional, Phelan, Jody E, additional, Tugumisirize, Didas, additional, Orena, Beatrice, additional, Byabajungu, Henry, additional, Ntenkaire, Nathan, additional, Nadunga, Diana, additional, Tumwine, Julius, additional, Musisi, Kenneth, additional, Joloba, Moses, additional, Kim, Seungmo, additional, Kokas, Ikwap, additional, Mukani, William Olaho, additional, Kungu, Joseph, additional, and Afayoa, Mathias, additional

Published
2023
Full Text
View/download PDF

35. Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines

Author

Phelan, Jody E., Lim, Dodge R., Mitarai, Satoshi, de Sessions, Paola Florez, Tujan, Ma. Angelica A., Reyes, Lorenzo T., Medado, Inez Andrea P., Palparan, Alma G., Naim, Ahmad Nazri Mohamed, Jie, Song, Segubre-Mercado, Edelwisa, Simoes, Beatriz, Campino, Susana, Hafalla, Julius C., Murase, Yoshiro, Morishige, Yuta, Hibberd, Martin L., Kato, Seiya, Ama, Ma. Cecilia G., and Clark, Taane G.

Published
2019
Full Text
View/download PDF

38. Genomic and functional portrait of multidrug-resistant, hydrogen sulfide (H2S)-producing variants of Escherichia coli.

Author

Mazumder, Razib, Hussain, Arif, Rahman, Mohammad Mustafizur, Phelan, Jody E., Campino, Susana, Abdullah, Ahmed, Clark, Taane G., and Mondal, Dinesh

Subjects
ESCHERICHIA coli, HYDROGEN sulfide, GENOMICS, NUCLEOTIDE sequencing, DRUG resistance in bacteria, DRUG resistance in microorganisms
Abstract

Atypical Escherichia coli forms exhibit unusual characteristics compared to typical strains. The H2S-producing variants of some atypical E. coli strains cause a wide range of illnesses in humans and animals. However, there are sparse reports on such strains worldwide. We performed whole-genome sequencing (WGS) and detailed characterization of four H2S-producing E. coli variants from poultry and human clinical sources in Dhaka, Bangladesh. All four isolates were confirmed as E. coli using biochemical tests and genomic analysis, and were multidrug-resistant (MDR). WGS analysis including an additional Chinese strain, revealed diverse STs among the five H2S-producing E. coli genomes, with clonal complex ST10 being detected in 2 out of 5 genomes. The predominant phylogroup detected was group A (n = 4/5). The blaTEM1B (n = 5/5) was the most predominant extended-spectrum beta-lactamase (ESBL) gene, followed by different alleles of blaCTX-M (blaCTX-M -55,-65,-123; n = 3/5). Multiple plasmid replicons were detected, with IncX being the most common. One E. coli strain was classified as enteropathogenic E. coli. The genomes of all five isolates harbored five primary and four secondary function genes related to H2S production. These findings suggest the potential of these isolates to cause disease and spread antibiotic resistance. Therefore, such atypical E. coli forms should be included in differential diagnosis to understand the pathogenicity, antimicrobial resistance and evolution of H2S-producing E. coli. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

40. A next generation targeted amplicon sequencing method to screen for insecticide resistance mutations in Aedes aegypti populations reveals a rdl mutation in mosquitoes from Cabo Verde

Author

Collins, Emma L., primary, Phelan, Jody E., additional, Hubner, Magdalena, additional, Spadar, Anton, additional, Campos, Monica, additional, Ward, Daniel, additional, Acford-Palmer, Holly, additional, Gomes, Ana Rita, additional, Silva, Keily, additional, Ferrero Gomez, Lara, additional, Clark, Taane G., additional, and Campino, Susana, additional

Published
2022
Full Text
View/download PDF

42. Molecular characterization of drug-resistant Mycobacterium tuberculosis among Filipino patients derived from the national tuberculosis prevalence survey Philippines 2016

Author

Montoya, Jaime C, Malabad, John Carlo M, Ang, Concepcion F, Reyes, Lorenzo T, Basilio, Ramon P, Lim, Dodge R, Amarillo, Maria Lourdes E, Ama, Ma Cecilia G, Phelan, Jody E, Hibberd, Martin L, and Clark, Taane G

Abstract

Tuberculosis, caused by Mycobacterium tuberculosis, remains a high burden disease and leading cause of mortality in the Philippines. Understanding the genetic diversity of M. tuberculosis strains in the population, including those that are multi-drug resistant (MDR), will aid in formulating strategies for effective TB control and prevention. By whole genome sequencing of M. tuberculosis isolates (n = 100) from patients of the Philippine 2016 National Tuberculosis Prevalence Survey, we sought to provide a baseline assessment of the genotypic and phylogenetic characteristics of the isolates. The majority (96/100) of the isolates were EAI2-Manila strain-type (lineage 1), with one Lineage 2 (Beijing), one Lineage 3 (CAS1), and two Lineage 4 (LAM9) strains. The EAI2-Manila clade was not significantly associated with patient's phenotypic and in silico drug resistance profile. Five (5/6) MDR-TB isolates predicted by in silico profiling were concordant with phenotypic drug resistance profile. Twenty-one mutations were identified in nine drug resistance-related genes, all of which have been reported in previous studies. Overall, the results from this study contribute to the growing data on the molecular characteristics of Philippine M. tuberculosis isolates, which can help in developing tools for rapid diagnosis of TB in the country, and thereby reducing the high burden of disease.

Published
2022

45. Whole genome sequencing reveals large deletions and other loss of function mutations in Mycobacterium tuberculosis drug resistance genes

Author

Gomes, Laura C, Campino, Susana, Marinho, Cláudio RF, Clark, Taane G, and Phelan, Jody E

Abstract

Drug resistance in Mycobacterium tuberculosis, the causative agent of tuberculosis disease, arises from genetic mutations in genes coding for drug-targets or drug-converting enzymes. SNPs linked to drug resistance have been extensively studied and form the basis of molecular diagnostics and sequencing-based resistance profiling. However, alternative forms of functional variation such as large deletions and other loss of function (LOF) mutations have received much less attention, but if incorporated into diagnostics they are likely to improve their predictive performance. Our work aimed to characterize the contribution of LOF mutations found in 42 established drug resistance genes linked to 19 anti-tuberculous drugs across 32689 sequenced clinical isolates. The analysed LOF mutations included large deletions (n=586), frameshifts (n=4764) and premature stop codons (n=826). We found LOF mutations in genes strongly linked to pyrazinamide (pncA), isoniazid (katG), capreomycin (tlyA), streptomycin (e.g. gid) and ethionamide (ethA, mshA) (P

Published
2021

47. Additional file 1 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus

Author

Spadar, Anton, Phelan, Jody E., Benavente, Ernest Diez, Campos, Monica, Gomez, Lara Ferrero, Mohareb, Fady, Clark, Taane G., and Campino, Susana

Abstract

Additional file 1: Table S1. Descriptive statistics of excluded and retained sequences. Table S2. Identified endogenous viral elements (EVEs) previously reported with poor or no mapping to AaegL5. Aag2 and AaegL5 contain the same set of EVEs, apart from those noted above. Figure S1. Viral sequences matching to a region on chromosome 2 of Aedes aegypti AaegL5. Figure S2. Effects of changing Basic Local Alignment Search Tool N (BLASTN) word size on matched sequences between Ae. aegypti AaegL5 chromosome 2 (461,306,089���461,312,509) and Xishuangbanna aedes flavivirus (XAFV) genome. Figure S3. Percentage identity and alignment length of all EVEs (from Table 2) as calculated by BLASTN. Figure S4. The ratio of forward genomic strand to total aligning P-element-induced wimpy testis-interacting (piRNA) [25���29 nucleotides (nt)] reads in AaegL5 chromosome 2. Figure S5. Characteristic appearance of AaegL5 regions with flavivirus EVEs. Fourth track of each panel shows EVEs. Figure S6. Clustering of EVEs share of the EVE with at least fivefold read coverage. Figure S7. Geographic clustering of EVEs identified in the reference genome of Aedes albopictus. Figure S8. Alignment length and identity between EVEs in Ae. aegypti AaegL5 and Ae. albopictus AalbF2. Figure S9. Synteny plots of viral integration events.

Published
2021
Full Text
View/download PDF

49. Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto-Beijing genotype

Author

Srilohasin, Prapaporn, primary, Prammananan, Therdsak, additional, Faksri, Kiatichai, additional, Phelan, Jody E., additional, Suriyaphol, Prapat, additional, Kamolwat, Phalin, additional, Smithtikarn, Saijai, additional, Disratthakit, Areeya, additional, Regmi, Sanjib Mani, additional, Leechawengwongs, Manoon, additional, Twee-Hee Ong, Rick, additional, Teo, Yik Ying, additional, Tongsima, Sissades, additional, Clark, Taane G., additional, and Chaiprasert, Angkana, additional

Published
2020
Full Text
View/download PDF

50. Genomic evidence supporting the clonal expansion of extensively drugresistant tuberculosis bacteria belonging to a rare proto-Beijing genotype.

Author

Srilohasin, Prapaporn, Prammananan, Therdsak, Faksri, Kiatichai, Phelan, Jody E., Suriyaphol, Prapat, Kamolwat, Phalin, Smithtikarn, Saijai, Disratthakit, Areeya, Regmi, Sanjib Mani, Leechawengwongs, Manoon, Rick Twee-Hee Ong, Yik Ying Teo, Tongsima, Sissades, Clark, Taane G., and Chaiprasert, Angkana

Published
2020
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results