Pascal Lapierre

Wadsworth Center, NYS Department of Health · Division of Translational Medicine

The unprecedented precision and resolution of whole genome sequencing (WGS) can provide definitive identification of infectious agents for epidemiological outbreak tracking. WGS approaches, however, are frequently impeded by low pathogen DNA recovery from available primary specimens or unculturable samples. A cost-effective hybrid capture assay for...

Lyme disease is the most common vector-borne disease in North America and Europe. The clinical manifestations of Lyme disease vary based on the genospecies of the infecting Borrelia burgdorferi spirochete, but the microbial genetic elements underlying these associations are not known. Here, we report the whole genome sequence (WGS) and analysis of...

Whole-genome sequencing (WGS) can predict drug resistance and antimicrobial susceptibility in Mycobacterium tuberculosis complex (MTBC) and has shown promise in partially replacing culture-based phenotypic drug susceptibility testing (pDST). We performed a two-year side by side study comparing the prediction of drug resistance and antimicrobial sus...

Mycobacterium tuberculosis complex (MTBC) infections are treated with combinations of antibiotics; however, these regimens are not as efficacious against multidrug and extensively drug resistant MTBC. Phenotypic (growth-based) drug susceptibility testing on slow growing bacteria like MTBC requires many weeks to months to complete, whereas sequencin...

Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of, genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia coli transcription factor PhoB, a response regulator that controls transcription of genes involve...

Lyme disease is the most common vector-borne disease in North America and Europe. The clinical manifestations of Lyme disease vary based on the genospecies of the infecting Borrelia burgdorferi spirochete, but the microbial genetic elements underlying these associations are not known. Here, we report the whole genome sequence (WGS) and analysis of...

Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia coli transcription factor PhoB, a response regulator that controls transcription of genes involved...

Nontuberculous mycobacteria (NTM) are environmental bacteria commonly found in soil and water in almost every part of the world. While usually non-pathogenic, they can cause acute respiratory and cutaneous infections under certain circumstances or in patients with underlying medical conditions. Contrary to members of the Mycobacterium tuberculosis...

We report the unusual genotypic characterization of a bacterium isolated from a clinical sample of a patient who grew up in Bangladesh and lives in the United States. Using whole-genome sequencing, we identified the bacterium as a member of the Mycobacterium tuberculosis complex (MTBC). Phylogenetic placement of this strain suggests a new MTBC geno...

In 2017, the New York State Department of Health investigated a large Klebsiella pneumoniae outbreak in a healthcare facility. A retrospective analysis was conducted to compare the use of multiple molecular typing methods for characterizing the outbreak. Forty-four isolates were characterized using the rapid real-time PCR OpGen Acuitas® AMR Gene Pa...

Since 1978, the New York State Department of Health’s public health laboratory, Wadsworth Center (WC), in collaboration with epidemiology and environmental partners, has been committed to providing comprehensive public health testing for Legionella in New York. Statewide, clinical case counts have been increasing over time, with the highest numbers...

Background Transmission of pathogens by vector mosquitoes is intrinsically linked with mosquito’s reproductive strategy because anautogenous mosquitoes require vertebrate blood to develop a batch of eggs. Each cycle of egg maturation is tightly linked with the intake of a fresh blood meal for most species. Mosquitoes that acquire pathogens during t...

Rapid and reliable detection of rifampin (RIF) resistance is critical for the diagnosis and treatment of drug-resistant and multi-drug resistant (MDR) tuberculosis. Discordant RIF phenotype/genotype susceptibility results remain a challenge due to the presence of rpoB mutations which do not confer high levels of RIF resistance as have been exhibite...

The E484K mutation in the spike protein of SARS CoV-2 contributes to immune escape from monoclonal antibodies as well as neutralizing antibodies in COVID-19 convalescent plasma. It appears in two variants of concern – B.1.351 and P.1 - but has evolved multiple times in different SARS-CoV-2 lineages, suggesting an adaptive advantage. Here we report...

Legionnaires’ disease, a severe lung infection caused by the bacterium Legionella pneumophila , occurs as single cases or in outbreaks that are actively tracked by public health departments. To determine the point source of an outbreak, clinical isolates need to be compared to environmental samples to find matching isolates. One confounding factor...

Next-generation sequencing technologies are being rapidly adopted as a tool of choice for diagnostic and outbreak investigation in public health laboratories. However, costs of operation and the need for specialized staff remain major hurdles for laboratories with limited resources for implementing these technologies. This project aimed to assess t...

Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the United States and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different spe...

During 2016-2017, three rabid terrestrial animals were discovered in the raccoon rabies virus-free zone of Long Island, New York, USA. Whole-genome sequencing and phylogenetic analyses revealed the likely origins of the viruses, enabling the rabies outbreak response (often costly and time-consuming) to be done less expensively and more efficiently.

Whole-genome sequencing (WGS) of pathogens from pure culture provides unparalleled accuracy and comprehensive results at a cost that is advantageous compared to traditional diagnostic methods. Sequencing pathogens directly from a primary clinical specimen would help circumvent the need for culture and in the process, substantially shorten the time...

In Escherichia coli, one Sigma factor recognizes the majority of promoters, and six “alternative” Sigma factors recognize specific subsets of promoters. The alternative Sigma factor FliA (σ²⁸) recognizes promoters upstream of many flagellar genes. We previously showed that most E. coli FliA binding sites are located inside genes. However, it was un...

Nus factors are broadly conserved across bacterial species, and are often essential for viability. A complex of five Nus factors (NusB, NusE, NusA, NusG and SuhB) is considered to be a dedicated regulator of ribosomal RNA folding, and has been shown to prevent Rho-dependent transcription termination. Here, we identify an additional cellular functio...

During the summer of 2015, New York, New York, USA, had one of the largest and deadliest outbreaks of Legionnaires’ disease in the history of the United States. A total of 138 cases and 16 deaths were linked to a single cooling tower in the South Bronx. Analysis of environmental samples and clinical isolates showed that sporadic cases of legionello...

The incidence of Legionnaires’ disease in the United States has been increasing since 2000. Outbreaks and clusters are associated with decorative, recreational, domestic, and industrial water systems, with the largest outbreaks being caused by cooling towers. Since 2006, 6 community-associated Legionnaires’ disease outbreaks have occurred in New Yo...

Epidemic curves for 6 Legionnaires’ disease outbreaks, by illness onset date, New York City, New York, USA, 2006–2015.

We report a case of lymphadenitis caused by Mycobacterium orygis in an immunocompetent person in Stony Brook, New York, USA. Initial real-time PCR assay failed to provide a final subspecies identification within the M. tuberculosis complex, but whole-genome sequencing characterized the isolate as M. orygis. © 2017, Centers for Disease Control and P...

Recent work has revealed that large numbers of promoters in bacteria are located inside genes. In contrast, almost all studies of transcription have focused on promoters upstream of genes. Bacterial promoters are recognized by Sigma factors that associate with initiating RNA polymerase. In Escherichia coli , one Sigma factor recognizes the majority...

Nus factors are broadly conserved across bacterial species, and are often essential for viability. A complex of five Nus factors (NusB, NusE, NusA, NusG and SuhB) is considered to be a dedicated regulator of ribosomal RNA folding, and has been shown to prevent Rho-dependent transcription termination. We have established the first cellular function...

Whole-genome sequencing (WGS) is a newer alternative for tuberculosis (TB) diagnostics, capable of providing rapid drug resistance profiles while performing species identification and capturing the data necessary for genotyping. Our laboratory developed and validated a comprehensive and sensitive WGS assay to characterize Mycobacterium tuberculosis...

Objectives: Infections caused by Legionella are the leading cause of waterborne disease outbreaks in the United States. We investigated a large outbreak of Legionnaires' disease in New York City in summer 2015 to characterize patients, risk factors for mortality, and environmental exposures. Methods: We defined cases as patients with pneumonia a...

Conseting mycobacteria Mycobacteria encompass several slow-growing pathogens, including organisms that cause leprosy and tuberculosis. Mycobacteria use a component of their ESX (or Type VII) secretion system for a distinctive form of genetic exchange called distributive conjugal DNA transfer. Gray et al. investigated a quicker-growing model species...

We report here the complete genome sequences of three Legionella pneumophila isolates that are associated with a Legionnaires’ disease outbreak in New York in 2012. Two clinical isolates (D7630 and D7632) and one environmental isolate (D7631) were recovered from this outbreak. A single isolate-specific virulence gene was found in D7632. These isola...

Unlabelled: A total of 30 Legionella pneumophila serogroup 1 isolates representing 10 separate legionellosis laboratory investigations ("outbreaks") that occurred in New York State between 2004 and 2012 were selected for evaluation of whole-genome sequencing (WGS) approaches for molecular subtyping of this organism. Clinical and environmental isol...

Here, we report the release of a draft genome assembly of a Gram-positive cocci Branchiibius sp. NY16-3462-2 with a high-GC content, sequenced from a mixed clinical sample containing Mycobacterium tuberculosis . This genome is the first publicly available sequence from a representative of the genus Branchiibius .

RNA-seq technologies have provided significant insight into the transcription networks of mycobacteria. However, such studies provide no definitive information on the translational landscape. Here, we use a combination of high-throughput transcriptome and proteome-profiling approaches to more rigorously understand protein expression in two mycobact...

Author Summary Bacterial RNA polymerases must associate with a σ factor to bind to promoter DNA sequences upstream of genes and initiate transcription. There are two families of σ factor: σ70 and σ54. Members of the σ54 family are distinct from members of the σ70 family in their ability to bind promoter DNA sequences, in association with RNA polyme...

Salmonella enterica serovar Enteritidis is a significant cause of gastrointestinal illness in the United States, however, current molecular subtyping methods lack resolution for this highly clonal serovar. Advances in next-generation sequencing technologies have made it possible to examine whole-genome sequencing (WGS) as a potential molecular subt...

Eight independent isolates of a Gram reaction negative, non-motile rod, were recovered from clinical specimens of New York State patients between the years 2005-2013. Four of these isolates were characterized in a polyphasic study that involved phenotypic, phylogenetic, and genotypic methodologies. Based on 16S rRNA gene sequence identity and phylo...

There are trillions of microbes found throughout the human body and they exceed the number of eukaryotic cells by ten-fold. Metagenomic studies have revealed that the majority of these microbes are found within the gut, playing an important role in the host’s digestion and nutrition. The complexity of the animal digestive tract, unculturable microb...

The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used an...

Inteins are self-splicing parasitic genetic elements found in all domains of life. These genetic elements are found in highly conserved positions in conserved proteins. One protein family that has been invaded by inteins is the vacuolar and archaeal catalytic ATPase subunits (vma-1). There are two intein insertion sites in this protein, "a" and "b"...

Marinobacter lipolyticus strain SM19, isolated from saline soil in Spain, is a moderately halophilic bacterium belonging to the class Gammaproteobacteria. Here, we report the draft genome sequence of this strain, which consists of a 4.0-Mb chromosome and which is able to produce the halophilic enzyme lipase LipBL.

Publication of the genome sequence of Thermotoga maritima highlighted its extensive sharing of genes with archaea. Subsequent analyses have shown that the amount of gene exchange is less than first estimated and the addition of new genome sequences to databases is likely to make future enumerations of archaeal gene exchanges more difficult. We pres...

Supermatrix and supertree analyses are frequently used to more accurately recover vertical evolutionary history but debate still exists over which method provides greater reliability. Traditional methods that resolve relationships among organisms from single genes are often unreliable because of the frequent lack of strong phylogenetic signal and t...

Centromeres are essential cis-elements on chromosomes that are crucial for the stable transmission of genetic information during mitotic and meiotic cell divisions. Different species employ a variety of centromere configurations, from small genetically defined centromeres in budding yeast to holocentric centromeres that occupy entire chromosomes in...

Speciation of sexually reproducing organisms requires reproductive barriers. Prokaryotes reproduce asexually but often exchange DNA by lateral gene transfer mechanisms and recombination [1], yet distinct lineages are still observed. Thus, barriers to gene flow such as geographic isolation, genetic incompatibility or a physiological inability to tra...

The frequent exchange of genetic material among prokaryotes means that extracting a majority or plurality phylogenetic signal from many gene families, and the identification of gene families that are in significant conflict with the plurality signal is a frequent task in comparative genomics, and especially in phylogenomic analyses. Decomposition o...

Phylogenetic reconstruction using DNA and protein sequences has allowed the reconstruction of evolutionary histories encompassing all life. We present and discuss a means to incorporate much of this rich narrative into a single model that acknowledges the discrete evolutionary units that constitute the organism. Briefly, this Rooted Net of Life gen...

Minimum parsimony counts supporting each of the possible trees (A) and rings (B). The lowest count is used to determine if the data supports a tree or a ring [3]. In the original analyses by Lake [2], the best ring had a minimum parsimony count of 581 versus 625 for the best supported tree (first column). Best supported trees or rings for each test...

List of all possible trees and rings for five taxa sampling. Each possible tree and ring is listed with the compatible presence-absence pattern of gene families (Pfam) given in Figure 1. For example, the tree and ring corresponding to ABCDR are shown at the left of each table. A corresponds to Actinobacteria, B to Bacilli, C to Clostridia, D for do...

In 2009, James Lake introduced a new hypothesis in which reticulate phylogeny reconstruction is used to elucidate the origin of gram-negative bacteria (Nature 460: 967-971). The presented data supported the gram-negative bacteria originating from an ancient endosymbiosis between the Actinobacteria and Clostridia. His conclusion was based on a prese...

In 2009, James Lake introduced a new hypothesis in which reticulate phylogeny reconstruction is used to elucidate the origin of Gram-negative bacteria. The presented data supported the Gram-negative bacteria originating from an ancient endosymbiosis between the Actinobacteria and Clostridia. His conclusion was based on a presence-absence analysis o...

A new initiative provides comparative genomicists with a more complete picture of genome diversity. Here we discuss the improved sampling strategy.

Genome analysis of three Frankia sp. strains has revealed a high number of transposable elements in two of the strains. Twelve out of the 20 major families of bacterial Insertion Sequence (IS) elements are represented in the 148 annotated transposases of Frankia strain HFPCcI3 (CcI3) comprising 3% of its total coding sequences (CDS). EAN1pec (EAN)...

Ions near the high-end border of a mass defect distribution plot for native peptide fragment ions have potential as signature markers that are based on mass-to-charge ratio determination. The specificity of these marker ions, including phosphoryl ions, can be improved by removing interfering isobaric ions from the border region on the distribution...

Since publication of the first Thermotogales genome, Thermotoga maritima strain MSB8, single- and multi-gene analyses have disagreed on the phylogenetic position of this order of Bacteria. Here we present the genome sequences of 4 additional members of the Thermotogales (Tt. petrophila, Tt. lettingae, Thermosipho melanesiensis, and Fervidobacterium...

The 'pan-genome' denotes the set of all genes present in the genomes of a group of organisms. Here, we extend the pan-genome concept to higher taxonomic units. Using 573 sequenced genomes, we estimate the size of the bacterial pan-genome based on the frequency of occurrences of genes among sampled genomes. Using gene- and genome-centered approaches...

The mal genes that encode maltose transporters have undergone extensive lateral transfer among ancestors of the archaea Thermococcus litoralis and Pyrococcus furiosus. Bacterial hyperthermophiles of the order Thermotogales live among these archaea and so may have shared in these transfers. The genome sequence of Thermotoga maritima bears evidence o...

Transmembrane helices of Tt. maritima MalF1 bacterial homologs as predicted by TMpred. Plots derived from TMpred [27] are shown. Solid and dashed lines depict inside to outside and outside to inside orientations of the helices predicted by TMpred, respectively.

Frankia are nitrogen-fixing actinomycetes that form root nodules with dicotyledonous plants in eight families of distantly related angiosperms. The paucity of genetic information stemming from the absence of standard genetic tools has been a major obstacle in our understanding of actinorhizal symbiosis. Although we are trying to resolve this situat...

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N(2)-fixing root nodules on diverse and globa...

With the advent of whole genome sequencing, it became apparent that horizontal transfer gene (HGT) is not limited to a few specific sets of genes nor does it only occur between a few select species. It is now believed that such gene transfers have played a predominant role for evolution of life, especially for prokaryotic species. Over the course o...

The presence of an A/V-type ATPase in different Thermus species and in the deeper branching species Meiothermus ruber and Deinococcus radiodurans suggests that the presence of the archaeal-type ATPase is a primitive character of the Deinococci that was acquired through horizontal gene transfer (HGT). However, the presence of a bacterial type F-ATPa...

Tracing organismal histories on the timescale of the tree of life remains one of the challenging tasks in evolutionary biology. The hotly debated questions include the evolutionary relationship between the three domains of life (e.g., which of the three domains are sister domains, are the domains para-, poly-, or monophyletic) and the location of t...