Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency in testing differential abundance.

The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Surprisingly, many microbiome studies have performed both experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, suggesting that an integrative analysis of both datasets could enhance the testing power for these signatures.

Methicillin-Resistant Staphylococcus aureus Bacteremia Relapses Show Diverse Genomic Profiles but Convergence in Bacteremia-Associated Genes.

Background: Recurrence of methicillin-resistant Staphylococcus aureus (MRSA) bacteremia is a high risk complication for patients. Distinguishing persistent lineages from new infections is not standardized across clinical studies.

Methods: We investigated factors contributing to recurrence of MRSA bacteremia among subjects in Philadelphia, Pennsylvania.

A fluorescence-based protocol to monitor bacterial antagonism.

Bacteria are often found in polymicrobial communities where competition for limited space and resources drives antagonistic interactions. Therefore, bacteria have evolved various antibacterial weapons to outcompete their neighbors. These antagonistic interactions can have profound effects on the structure, dynamics, and composition of bacterial communities.

Genomic investigation of MRSA bacteremia relapse reveals diverse genomic profiles but convergence in bacteremia-associated genes.

Background: Recurrence of methicillin-resistant (MRSA) bacteremia is a high risk complication for patients. Distinguishing persistent lineages from new infections is not standardized across clinical studies.

Methods: We investigated factors contributing to recurrence of MRSA bacteremia among subjects in Philadelphia, Pennsylvania.

Comparative genomic analysis of emerging non-typeable (NTHi) causing emerging septic arthritis in Atlanta.

Background: is a Gram-negative bacterium that can exist as a commensal organism or cause a range of diseases, from ear infections to invasive conditions like meningitis. While encapsulated strains have historically been linked to severe diseases, non-typeable (NTHi) strains, lacking an intact capsule locus, have emerged as the leading cause of invasive infections, particularly following the widespread use of the serotype b (Hib) vaccine.

Methods: In response to a significant increase in invasive NTHi infections among persons living with HIV in metropolitan Atlanta during 2017-2018, we conducted a comparative genomic analysis of two predominant NTHi clones, C1 and C2, identified during this period.

Whole-genome automated assembly pipeline for strains from reference, and clinical samples using the integrated CtGAP pipeline.

Whole genome sequencing (WGS) is pivotal for the molecular characterization of ()-the leading bacterial cause of sexually transmitted infections and infectious blindness worldwide. WGS can inform epidemiologic, public health and outbreak investigations of these human-restricted pathogens. However, challenges persist in generating high-quality genomes for downstream analyses given its obligate intracellular nature and difficulty with propagation.

Intraspecific Diversity of Populations Isolated from Cystic Fibrosis Respiratory Infections.

Chronic bacterial infections are often polymicrobial, comprising multiple bacterial species or variants of the same species. Because chronic infections may last for decades, they have the potential to generate high levels of intraspecific variation through within-host diversification over time, and the potential for superinfections to occur through the introduction of multiple pathogen populations to the ongoing infection. Traditional methods for identifying infective agents generally involve isolating one single colony from a given sample, usually after selecting for a specific pathogen or antibiotic resistance profile.

Defense Heterogeneity in Host Populations Gives Rise to Pathogen Diversity.

AbstractHost organisms can harbor microbial symbionts that defend them from pathogen infection in addition to the resistance encoded by the host genome. Here, we investigated how variation in defenses, generated from host genetic background and symbiont presence, affects the emergence of pathogen genetic diversity across evolutionary time. We passaged the opportunistic pathogen through populations of the nematode varying in genetic-based defenses and prevalence of a protective symbiont.

Host and antibiotic jointly select for greater virulence in .

Widespread antibiotic usage has resulted in the rapid evolution of drug-resistant bacterial pathogens and poses significant threats to public health. Resolving how pathogens respond to antibiotics under different contexts is critical for understanding disease emergence and evolution going forward. The impact of antibiotics has been demonstrated most directly through pathogen passaging experiments.

Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar.

Background: Tracking the spread of antibiotic resistant bacteria is critical to reduce global morbidity and mortality associated with human and animal infections. There is a need to understand the role that wild animals in maintenance and transfer of antibiotic resistance genes (ARGs).

Methods: This study used metagenomics to identify and compare the abundance of bacterial species and ARGs detected in the gut microbiomes from sympatric humans and wild mouse lemurs in a forest-dominated, roadless region of Madagascar near Ranomafana National Park.

Chlamydia suis undergoes interclade recombination promoting Tet-island exchange.

Background: The obligate intracellular bacterial family Chlamydiaceae comprises a number of different species that cause disease in various vertebrate hosts including humans. Chlamydia suis, primarily found in the gastrointestinal tract of pigs, is the only species of the Chlamydiaceae family to have naturally gained tetracycline resistance (TetR), through a genomic island (Tet-island), integrated into the middle of chromosomal invasin-like gene inv. Previous studies have hypothesised that the uptake of the Tet-island from a host outside the Chlamydiaceae family was a unique event, followed by spread among C.

Corrigendum: Patterns of within-host spread of between vagina, endocervix and rectum revealed by comparative genomic analysis.

[This corrects the article DOI: 10.3389/fmicb.2023.

Average nucleotide identity-based strain grouping allows identification of strain-specific genes in the pangenome.

Unlabelled: causes both hospital- and community-acquired infections in humans worldwide. Due to the high incidence of infection, is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public Illumina whole-genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains.

Genomic insights into the evolution of secondary metabolism of and its allies, specialized fungal symbionts of fungus-farming ants.

The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment.

Strain Differences in Bloodstream and Skin Infection: Methicillin-Resistant Isolated in 2018-2021 in a Single Health System.

is a common cause of skin and soft-tissue infections (SSTIs) and has become the most common cause of bloodstream infections (BSIs) in recent years, but whether the strains causing these two clinical syndromes overlap has not been studied adequately. USA300/500 (clonal complex [CC] 8-sequence type [ST] 8) and USA100 (CC5-ST5) have dominated among methicillin-resistant (MRSA) strains in the United States since the early 2000s. We compared the genomes of unselected MRSA isolates from 131 SSTIs with those from 145 BSIs at a single US center in overlapping periods in 2018-2021.

A laboratory-based predictive pathway for the development of high-level resistance to corallopyronin A, an inhibitor of bacterial RNA polymerase.

Unlabelled: The continued emergence of strains that express resistance to multiple antibiotics, including the last drug for empiric monotherapy (ceftriaxone), necessitates the development of new treatment options to cure gonorrheal infections. Toward this goal, we recently reported that corallopyronin A (CorA), which targets the switch region of the β' subunit (RpoC) of bacterial DNA-dependent RNA polymerase (RNAP), has potent anti-gonococcal activity against a panel of multidrug-resistant clinical strains. Moreover, in that study, CorA could eliminate gonococcal infection of primary human epithelial cells and gonococci in a biofilm state.

Factors associated with foreign body infection in methicillin-resistant bacteremia.

Background: We aimed to compare patient characteristics, MRSA sequence types, and biofilm production of MRSA strains that did and did not cause a foreign body infection in patients with MRSA bloodstream infections (BSI).

Methods: All adult patients with MRSA BSI hospitalized in two hospitals were identified by clinical microbiology laboratory surveillance. Only patients who had at least one implanted foreign body during the episode of BSI were included.

Incomplete immunity in a natural animal-microbiota interaction selects for higher pathogen virulence.

Incomplete immunity in recovered hosts is predicted to favor more virulent pathogens upon re-infection in the population. The microbiota colonizing animals can generate a similarly long-lasting, partial immune response, allowing for infection but dampened disease severity. We tracked the evolutionary trajectories of a widespread pathogen (Pseudomonas aeruginosa), experimentally passaged through populations of nematodes immune-primed by a natural microbiota member (P.

Experimentally evolved shows increased survival in the presence of by acquiring mutations in the amino acid transporter, GltT.

When cultured together under standard laboratory conditions has been shown to be an effective inhibitor of . However, and are commonly observed in coinfections of individuals with cystic fibrosis (CF) and in chronic wounds. Previous work from our group revealed that isolates from CF infections are able to persist in the presence of strain PAO1 with a range of tolerances with some isolates being eliminated entirely and others maintaining large populations.

Average Nucleotide Identity based strain grouping allows identification of strain-specific genes in the pangenome.

causes both hospital and community acquired infections in humans worldwide. Due to the high incidence of infection is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public Illumina whole genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains.

The role of hypermutation and collateral sensitivity in antimicrobial resistance diversity of populations in cystic fibrosis lung infection.

is an opportunistic pathogen which causes chronic, drug-resistant lung infections in cystic fibrosis (CF) patients. In this study, we explore the role of genomic diversification and evolutionary trade-offs in antimicrobial resistance (AMR) diversity within populations sourced from CF lung infections. We analyzed 300 clinical isolates from four CF patients (75 per patient) and found that genomic diversity is not a consistent indicator of phenotypic AMR diversity.

Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without infection in Fiji.

() is the most common sexually transmitted bacterium globally. Endocervical and vaginal microbiome interactions are rarely examined within the context of or among vulnerable populations. We evaluated 258 vaginal and 92 paired endocervical samples from Fijian women using metagenomic shotgun sequencing.