Intracellular iron concentration is tightly regulated to maintain cell viability. Iron plays impo... more Intracellular iron concentration is tightly regulated to maintain cell viability. Iron plays important roles in electron transport, nucleic acid synthesis, and oxidative stress. A Mycobacterium avium subsp. paratuberculosis (MAP)-specific genomic island carries a putative metal transport operon that includes MAP3773c, which encodes a Fur-like protein. Although well characterized as a global regulator of iron homeostasis in multiple bacteria, the function of Fur (ferric uptake regulator) in MAP is unknown as this organism also carries IdeR (iron dependent regulator), a native iron regulatory protein specific to mycobacteria. Computational analysis using PRODORIC identified 23 different pathways involved in respiration, metabolism, and virulence that were likely regulated by MAP3773c. Thus, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) was performed to confirm the putative regulon of MAP3773c (Fur-like protein) in MAP. ChIP-Seq revealed enriched bindi...
Mycobacterium tuberculosis variant bovis (MBO) has one of the widest known mammalian host ranges,... more Mycobacterium tuberculosis variant bovis (MBO) has one of the widest known mammalian host ranges, including humans. Despite characterization of this pathogen in the 1800s, and whole genome sequencing of a UK strain (AF2122) nearly two decades ago, the basis of its host specificity and pathogenicity remains poorly understood. Recent experimental calf infection studies show that MBO strain Ravenel (MBO Ravenel) is attenuated in the cattle host. In the present study, experimental infections were performed to define attenuation and whole genome sequencing completed to identify regions of differences (RD) and single nucleotide polymorphisms (SNPs) to explain the observed attenuation. Comparative genomic analysis of MBO Ravenel against three pathogenic strains of MBO (strains AF2122-97, 10-7428 and 95-1315) was performed. Experimental infection studies on 5 calves each, with either MBO Ravenel or 95-1315, revealed no visible lesions in all 5 animals in the Ravenel group despite robust IFN...
The contribution of Mycobacterium bovis to the proportion of tuberculosis cases in humans is unkn... more The contribution of Mycobacterium bovis to the proportion of tuberculosis cases in humans is unknown. A retrospective study was undertaken on archived Mycobacterium tuberculosis complex (MTBC) isolates from a reference laboratory in Uganda to identify the prevalence of human M. bovis infection. A total of 5676 isolates maintained in this repository were queried and 136 isolates were identified as pyrazinamide resistant, a hallmark phenotype of M. bovis. Of these, 1.5% (n = 2) isolates were confirmed as M. bovis by using regions of difference PCR analysis. The overall size of whole genome sequences (WGSs) of these two M. bovis isolates were ~4.272 Mb (M. bovis Bz_31150 isolated from a captive chimpanzee) and 4.17 Mb (M. bovis B2_7505 from a human patient), respectively. Alignment of these genomes against 15 MTBC genome sequences revealed 7248 single nucleotide polumorphisms (SNPs). Theses SNPs were used for phylogenetic analysis that indicated a strong relationship between M. bovis a...
OBJECTIVE To develop a noninvasive biomarker-based detection system specific for Mycobacterium bo... more OBJECTIVE To develop a noninvasive biomarker-based detection system specific for Mycobacterium bovis for monitoring infection in wild animals. SAMPLE Serum samples from 8 experimentally infected yearling white-tailed deer (Odocoileus virginianus) and 3 age-matched control deer and from 393 Minnesota Department of Natural Resources hunter-harvested white-tailed deer in northwest Minnesota. PROCEDURES 8 yearling deer were inoculated with 2 × 108 CFUs of virulent M bovis strain 1315 (day 0), and sera were obtained on days 0, 19, 48, and 60; sera were obtained from 3 uninoculated control deer on those same days. Sera from these deer and 9 M bovis-positive hunter-harvested deer were tested for 3 Mycobacterium-specific biomarkers (MB1895c, MB2515c, and polyketide synthase 5) by use of an indirect ELISA. That same ELISA was used to test sera obtained from 384 exposed noninfected deer in northwest Minnesota from 2007 through 2010, concurrent with an outbreak of tuberculosis involving cattle...
Swine play a key role in the ecology and transmission of influenza A viruses (IAVs) between speci... more Swine play a key role in the ecology and transmission of influenza A viruses (IAVs) between species. However, the epidemiology and diversity of swine IAVs is not completely understood. In this cohort study, we sampled on a weekly basis 132 3-week old pigs for 15 weeks. We found two overlapping epidemic events of infection in which most pigs (98.4%) tested PCR positive for IAVs. The prevalence rate of infection ranged between 0 and 86% per week and the incidence density ranged between 0 and 71 cases per 100 pigs-week. Three distinct influenza viral groups (VGs) replicating as a “swarm” of viruses were identified (swine H1-gamma, H1-beta, and H3-cluster-IV IAVs) and co-circulated at different proportions over time suggesting differential allele fitness. Furthermore, using deep genome sequencing 13 distinct viral genome constellations were differentiated. Moreover, 78% of the pigs had recurrent infections with IAVs closely related to each other or IAVs clearly distinct. Our results dem...
Annals of the New York Academy of Sciences, May 1, 2017
Humans face a grand quality-of-life challenge as growing demands for resources for an ever-expand... more Humans face a grand quality-of-life challenge as growing demands for resources for an ever-expanding population threaten the existence of wildlife populations, degrade land, and pollute air and water. Public investment and policy decisions that will shape future interactions of humans, animals, and the environment need scientific input to help find common ground for durable and sustainable success. The Second International Conference on One Medicine One Science brought together a broad range of scientists, trainees, regulatory authorities, and health experts from 34 countries to inform and discuss the human impacts of air quality; the complexities of water quality, access, and conflicts; the opportunities and uncertainties in precision medicine; and the role of science communication in health policy formulation. Workshops focused on the roles and development of physician-scientists and multidisciplinary teams in complex problem solving, Big Data tools for analysis and visualization,...
Influenza A viruses (IAVs) are endemic in swine and represent a public health risk. However, ther... more Influenza A viruses (IAVs) are endemic in swine and represent a public health risk. However, there is limited information on the genetic diversity of swine IAVs within farrow-to-wean farms, which is where most pigs are born. In this longitudinal study, we sampled 5 farrow-to-wean farms during a year and collected 4,190 individual nasal swabs from three distinct pig subpopulations. 207 (4.9%) samples tested PCR positive for IAV, and 124 IAVs were isolated. We sequenced the complete genome of 123 IAV isolates, and found 31 H1N1, 26 H1N2, 63 H3N2 and 3 mixed IAVs. Based on the IAV hemagglutinin seven different influenza A viral groups (VGs) were identified. Most of the remaining IAV gene segments allowed us to differentiate the same VGs although an additional viral group was identified for gene segment 3 (PA). Moreover, the co-detection of more than one IAV VG was documented at different levels (farm, subpopulation, and individual pigs) highlighting the environment for potential IAV re...
Cell communication and signaling : CCS, Dec 1, 2016
Mycobacterium avium subsp. paratuberculosis (MAP) is an intracellular pathogen and is the causati... more Mycobacterium avium subsp. paratuberculosis (MAP) is an intracellular pathogen and is the causative agent of…
The swine-human interface created at agricultural fairs, along with the generation of and mainten... more The swine-human interface created at agricultural fairs, along with the generation of and maintenance of influenza A virus diversity in exhibition swine, presents an ongoing threat to public health. Nucleotide sequences of influenza A virus isolates collected from exhibition swine in Ohio ( n = 262) and Indiana ( n = 103) during 2009 to 2013 were used to investigate viral evolution and movement within this niche sector of the swine industry. Phylogenetic and Bayesian analyses were employed to identify introductions of influenza A virus to exhibition swine and study viral population dynamics. In 2013 alone, we identified 10 independent introductions of influenza A virus into Ohio and/or Indiana exhibition swine. Frequently, viruses from the same introduction were identified at multiple fairs within the region, providing evidence of rapid and widespread viral movement within the exhibition swine populations of the two states. While pigs moving from fair to fair to fair is possible in ...
Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease... more Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease in cattle and sheep, has unique iron requirements in that it is mycobactin-dependent for cultivation in vitro. The iron-dependent regulator (IdeR) is a well-characterized global regulator responsible for maintaining iron homeostasis in Mycobacterium tuberculosis (MTB). We identified an orthologous segment in the MAP genome, MAP2827, with >93 % amino acid identity to MTB IdeR. Electrophoretic mobility shift assays and DNase protection assays confirmed that MAP2827 binds the 19 bp consensus motif (iron box) on the MAP genome. Sequencing of MAP2827 from multiple isolates revealed a non-synonymous change (R91G) exclusive to sheep strains. Reporter gene assays and quantitative real-time RT-PCR assays in two diverse MAP strains and in an ideR deletion mutant of M. smegmatis (mc(2)155) suggested that both sheep MAP IdeR (sIdeR) and cattle MAP IdeR (cIdeR) repress mbtB transcription at high ...
Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc, 2015
Despite active research into methicillin-resistant Staphylococcus aureus (MRSA) in pigs since 200... more Despite active research into methicillin-resistant Staphylococcus aureus (MRSA) in pigs since 2004, the ecology of the susceptible ancestral organism has been neglected. A longitudinal study of pigs in 2 intensive production systems was conducted to investigate the effects of age and anatomical site on detection of S. aureus. Sampling was replicated in 2 cohorts per farm, with swabs collected from the nares, tonsils, skin (axilla), and rectum in lactating sows, suckling, weaned, and market-age pigs, plus the vagina of sows. No MRSA were isolated, but S. aureus was detected in a least 1 site in 175 (91.1%) out of 192 pigs. Pig-level prevalence did not differ among the age groups, but the proportion of positive samples (all sites) was higher in market-age pigs (75.2%) and nursery-age pigs (63.2%) than in sows (40.7%) and suckling piglets (38%). Prevalence did not differ among nasal (67.9%), skin (62.3%), and tonsil (61.7%) swabs, but was lower in rectal (42%) and vaginal swabs (39.6%)...
Genetic heterogeneity of Mycoplasma hyopneumoniae in pigs has been reported, however there has be... more Genetic heterogeneity of Mycoplasma hyopneumoniae in pigs has been reported, however there has been limited reproducibility on the molecular methods employed so far. The aim of this study was to modify and standardize a high-resolution multiple locus variable number tandem repeat analysis (MLVA), to investigate the genetic variability of M. hyopneumoniae circulating in the United States of America (USA), Brazil, Mexico and Spain. The MLVA was standardized on the basis of the number of tandem repeats in two Mycoplasma adhesins, P97 and P146, which are proteins involved in the adherence of the pathogen to cilia. A total of 355 samples obtained from the four countries were analyzed. The Simpson's diversity index for the assay was D=0.976 when samples from all countries were combined. A large number of MLVA types (n=139) were identified, suggesting that multiple M. hyopneumoniae variants are circulating in swine. The locus P97 had 17 different types with 2-18 repeats. The P146 locus...
Intracellular iron concentration is tightly regulated to maintain cell viability. Iron plays impo... more Intracellular iron concentration is tightly regulated to maintain cell viability. Iron plays important roles in electron transport, nucleic acid synthesis, and oxidative stress. A Mycobacterium avium subsp. paratuberculosis (MAP)-specific genomic island carries a putative metal transport operon that includes MAP3773c, which encodes a Fur-like protein. Although well characterized as a global regulator of iron homeostasis in multiple bacteria, the function of Fur (ferric uptake regulator) in MAP is unknown as this organism also carries IdeR (iron dependent regulator), a native iron regulatory protein specific to mycobacteria. Computational analysis using PRODORIC identified 23 different pathways involved in respiration, metabolism, and virulence that were likely regulated by MAP3773c. Thus, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) was performed to confirm the putative regulon of MAP3773c (Fur-like protein) in MAP. ChIP-Seq revealed enriched bindi...
Mycobacterium tuberculosis variant bovis (MBO) has one of the widest known mammalian host ranges,... more Mycobacterium tuberculosis variant bovis (MBO) has one of the widest known mammalian host ranges, including humans. Despite characterization of this pathogen in the 1800s, and whole genome sequencing of a UK strain (AF2122) nearly two decades ago, the basis of its host specificity and pathogenicity remains poorly understood. Recent experimental calf infection studies show that MBO strain Ravenel (MBO Ravenel) is attenuated in the cattle host. In the present study, experimental infections were performed to define attenuation and whole genome sequencing completed to identify regions of differences (RD) and single nucleotide polymorphisms (SNPs) to explain the observed attenuation. Comparative genomic analysis of MBO Ravenel against three pathogenic strains of MBO (strains AF2122-97, 10-7428 and 95-1315) was performed. Experimental infection studies on 5 calves each, with either MBO Ravenel or 95-1315, revealed no visible lesions in all 5 animals in the Ravenel group despite robust IFN...
The contribution of Mycobacterium bovis to the proportion of tuberculosis cases in humans is unkn... more The contribution of Mycobacterium bovis to the proportion of tuberculosis cases in humans is unknown. A retrospective study was undertaken on archived Mycobacterium tuberculosis complex (MTBC) isolates from a reference laboratory in Uganda to identify the prevalence of human M. bovis infection. A total of 5676 isolates maintained in this repository were queried and 136 isolates were identified as pyrazinamide resistant, a hallmark phenotype of M. bovis. Of these, 1.5% (n = 2) isolates were confirmed as M. bovis by using regions of difference PCR analysis. The overall size of whole genome sequences (WGSs) of these two M. bovis isolates were ~4.272 Mb (M. bovis Bz_31150 isolated from a captive chimpanzee) and 4.17 Mb (M. bovis B2_7505 from a human patient), respectively. Alignment of these genomes against 15 MTBC genome sequences revealed 7248 single nucleotide polumorphisms (SNPs). Theses SNPs were used for phylogenetic analysis that indicated a strong relationship between M. bovis a...
OBJECTIVE To develop a noninvasive biomarker-based detection system specific for Mycobacterium bo... more OBJECTIVE To develop a noninvasive biomarker-based detection system specific for Mycobacterium bovis for monitoring infection in wild animals. SAMPLE Serum samples from 8 experimentally infected yearling white-tailed deer (Odocoileus virginianus) and 3 age-matched control deer and from 393 Minnesota Department of Natural Resources hunter-harvested white-tailed deer in northwest Minnesota. PROCEDURES 8 yearling deer were inoculated with 2 × 108 CFUs of virulent M bovis strain 1315 (day 0), and sera were obtained on days 0, 19, 48, and 60; sera were obtained from 3 uninoculated control deer on those same days. Sera from these deer and 9 M bovis-positive hunter-harvested deer were tested for 3 Mycobacterium-specific biomarkers (MB1895c, MB2515c, and polyketide synthase 5) by use of an indirect ELISA. That same ELISA was used to test sera obtained from 384 exposed noninfected deer in northwest Minnesota from 2007 through 2010, concurrent with an outbreak of tuberculosis involving cattle...
Swine play a key role in the ecology and transmission of influenza A viruses (IAVs) between speci... more Swine play a key role in the ecology and transmission of influenza A viruses (IAVs) between species. However, the epidemiology and diversity of swine IAVs is not completely understood. In this cohort study, we sampled on a weekly basis 132 3-week old pigs for 15 weeks. We found two overlapping epidemic events of infection in which most pigs (98.4%) tested PCR positive for IAVs. The prevalence rate of infection ranged between 0 and 86% per week and the incidence density ranged between 0 and 71 cases per 100 pigs-week. Three distinct influenza viral groups (VGs) replicating as a “swarm” of viruses were identified (swine H1-gamma, H1-beta, and H3-cluster-IV IAVs) and co-circulated at different proportions over time suggesting differential allele fitness. Furthermore, using deep genome sequencing 13 distinct viral genome constellations were differentiated. Moreover, 78% of the pigs had recurrent infections with IAVs closely related to each other or IAVs clearly distinct. Our results dem...
Annals of the New York Academy of Sciences, May 1, 2017
Humans face a grand quality-of-life challenge as growing demands for resources for an ever-expand... more Humans face a grand quality-of-life challenge as growing demands for resources for an ever-expanding population threaten the existence of wildlife populations, degrade land, and pollute air and water. Public investment and policy decisions that will shape future interactions of humans, animals, and the environment need scientific input to help find common ground for durable and sustainable success. The Second International Conference on One Medicine One Science brought together a broad range of scientists, trainees, regulatory authorities, and health experts from 34 countries to inform and discuss the human impacts of air quality; the complexities of water quality, access, and conflicts; the opportunities and uncertainties in precision medicine; and the role of science communication in health policy formulation. Workshops focused on the roles and development of physician-scientists and multidisciplinary teams in complex problem solving, Big Data tools for analysis and visualization,...
Influenza A viruses (IAVs) are endemic in swine and represent a public health risk. However, ther... more Influenza A viruses (IAVs) are endemic in swine and represent a public health risk. However, there is limited information on the genetic diversity of swine IAVs within farrow-to-wean farms, which is where most pigs are born. In this longitudinal study, we sampled 5 farrow-to-wean farms during a year and collected 4,190 individual nasal swabs from three distinct pig subpopulations. 207 (4.9%) samples tested PCR positive for IAV, and 124 IAVs were isolated. We sequenced the complete genome of 123 IAV isolates, and found 31 H1N1, 26 H1N2, 63 H3N2 and 3 mixed IAVs. Based on the IAV hemagglutinin seven different influenza A viral groups (VGs) were identified. Most of the remaining IAV gene segments allowed us to differentiate the same VGs although an additional viral group was identified for gene segment 3 (PA). Moreover, the co-detection of more than one IAV VG was documented at different levels (farm, subpopulation, and individual pigs) highlighting the environment for potential IAV re...
Cell communication and signaling : CCS, Dec 1, 2016
Mycobacterium avium subsp. paratuberculosis (MAP) is an intracellular pathogen and is the causati... more Mycobacterium avium subsp. paratuberculosis (MAP) is an intracellular pathogen and is the causative agent of…
The swine-human interface created at agricultural fairs, along with the generation of and mainten... more The swine-human interface created at agricultural fairs, along with the generation of and maintenance of influenza A virus diversity in exhibition swine, presents an ongoing threat to public health. Nucleotide sequences of influenza A virus isolates collected from exhibition swine in Ohio ( n = 262) and Indiana ( n = 103) during 2009 to 2013 were used to investigate viral evolution and movement within this niche sector of the swine industry. Phylogenetic and Bayesian analyses were employed to identify introductions of influenza A virus to exhibition swine and study viral population dynamics. In 2013 alone, we identified 10 independent introductions of influenza A virus into Ohio and/or Indiana exhibition swine. Frequently, viruses from the same introduction were identified at multiple fairs within the region, providing evidence of rapid and widespread viral movement within the exhibition swine populations of the two states. While pigs moving from fair to fair to fair is possible in ...
Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease... more Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease in cattle and sheep, has unique iron requirements in that it is mycobactin-dependent for cultivation in vitro. The iron-dependent regulator (IdeR) is a well-characterized global regulator responsible for maintaining iron homeostasis in Mycobacterium tuberculosis (MTB). We identified an orthologous segment in the MAP genome, MAP2827, with >93 % amino acid identity to MTB IdeR. Electrophoretic mobility shift assays and DNase protection assays confirmed that MAP2827 binds the 19 bp consensus motif (iron box) on the MAP genome. Sequencing of MAP2827 from multiple isolates revealed a non-synonymous change (R91G) exclusive to sheep strains. Reporter gene assays and quantitative real-time RT-PCR assays in two diverse MAP strains and in an ideR deletion mutant of M. smegmatis (mc(2)155) suggested that both sheep MAP IdeR (sIdeR) and cattle MAP IdeR (cIdeR) repress mbtB transcription at high ...
Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc, 2015
Despite active research into methicillin-resistant Staphylococcus aureus (MRSA) in pigs since 200... more Despite active research into methicillin-resistant Staphylococcus aureus (MRSA) in pigs since 2004, the ecology of the susceptible ancestral organism has been neglected. A longitudinal study of pigs in 2 intensive production systems was conducted to investigate the effects of age and anatomical site on detection of S. aureus. Sampling was replicated in 2 cohorts per farm, with swabs collected from the nares, tonsils, skin (axilla), and rectum in lactating sows, suckling, weaned, and market-age pigs, plus the vagina of sows. No MRSA were isolated, but S. aureus was detected in a least 1 site in 175 (91.1%) out of 192 pigs. Pig-level prevalence did not differ among the age groups, but the proportion of positive samples (all sites) was higher in market-age pigs (75.2%) and nursery-age pigs (63.2%) than in sows (40.7%) and suckling piglets (38%). Prevalence did not differ among nasal (67.9%), skin (62.3%), and tonsil (61.7%) swabs, but was lower in rectal (42%) and vaginal swabs (39.6%)...
Genetic heterogeneity of Mycoplasma hyopneumoniae in pigs has been reported, however there has be... more Genetic heterogeneity of Mycoplasma hyopneumoniae in pigs has been reported, however there has been limited reproducibility on the molecular methods employed so far. The aim of this study was to modify and standardize a high-resolution multiple locus variable number tandem repeat analysis (MLVA), to investigate the genetic variability of M. hyopneumoniae circulating in the United States of America (USA), Brazil, Mexico and Spain. The MLVA was standardized on the basis of the number of tandem repeats in two Mycoplasma adhesins, P97 and P146, which are proteins involved in the adherence of the pathogen to cilia. A total of 355 samples obtained from the four countries were analyzed. The Simpson's diversity index for the assay was D=0.976 when samples from all countries were combined. A large number of MLVA types (n=139) were identified, suggesting that multiple M. hyopneumoniae variants are circulating in swine. The locus P97 had 17 different types with 2-18 repeats. The P146 locus...
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Papers by Srinand Sreevatsan