Genetic relatedness and virulence potential of Salmonella Schwarzengrund strains with or without an IncFIB-IncFIC(FII) fusion plasmid isolated from food and clinical sources.

A total of 55 food and clinical S. Schwarzengrund isolates were assayed for plasmid content, among which an IncFIB-IncFIC(FII) fusion plasmid, conferring streptomycin resistance, was detected in 17 isolates. Among the 17 isolates, 9 were food isolates primarily collected from poultry meat, and 8 clinical isolates collected from stool, urine, and gallbladder. SNP-based phylogenetic analyses showed that the isolates carrying the fusion plasmid formed a subclade indicating the plasmid was acquired and is now maintained by the lineage. Phylogenetic analysis of the plasmid suggested it is derived from avian pathogenic plasmids and might confer an adaptive advantage to the S. Schwarzengrund isolates within birds. IncFIB-IncFIC(FII) fusion plasmids from all food and three clinical isolates were self-conjugative and successfully transferred into E. coli J53 by conjugation. Food and clinical isolates had similar virulome profiles and were able to invade human Caco-2 cells. However, the IncFIB-IncFIC(FII) plasmid did not significantly add to their invasion and persistence potential in human Caco-2 cells.

Complete genome sequence of two chromosomes of Vibrio metoecus strain ZF102 isolated from the abdominal cavity of moribund laboratory zebrafish (Danio rerio).

Vibrio metoecus was isolated from the abdominal cavity of moribund laboratory zebrafish. We report complete genomic sequences of V. metoecus strain ZF102 that has two circular chromosomes of 2,872,299 and 1,170,691 bp and two plasmids of 5,265 and 2,361 bp.

Genotypic analyses of IncHI2 plasmids from enteric bacteria.

Incompatibility (Inc) HI2 plasmids are large (typically > 200 kb), transmissible plasmids that encode antimicrobial resistance (AMR), heavy metal resistance (HMR) and disinfectants/biocide resistance (DBR). To better understand the distribution and diversity of resistance-encoding genes among IncHI2 plasmids, computational approaches were used to evaluate resistance and transfer-associated genes among the plasmids. Complete IncHI2 plasmid (N = 667) sequences were extracted from GenBank and analyzed using AMRFinderPlus, IntegronFinder and Plasmid Transfer Factor database. The most common IncHI2-carrying genera included Enterobacter (N = 209), Escherichia (N = 208), and Salmonella (N = 204). Resistance genes distribution was diverse, with plasmids from Escherichia and Salmonella showing general similarity in comparison to Enterobacter and other taxa, which grouped together. Plasmids from Enterobacter and other taxa had a higher prevalence of multiple mercury resistance genes and arsenic resistance gene, arsC, compared to Escherichia and Salmonella. For sulfonamide resistance, sul1 was more common among Enterobacter and other taxa, compared to sul2 and sul3 for Escherichia and Salmonella. Similar gene diversity trends were also observed for tetracyclines, quinolones, ß-lactams, and colistin. Over 99% of plasmids carried at least 25 IncHI2-associated conjugal transfer genes. These findings highlight the diversity and dissemination potential for resistance across different enteric bacteria and value of computational-based approaches for the resistance-gene assessment.

Infection biology of Salmonella enterica.

Salmonella enterica is the leading cause of bacterial foodborne illness in the USA, with an estimated 95% of salmonellosis cases due to the consumption of contaminated food products. Salmonella can cause several different disease syndromes, with the most common being gastroenteritis, followed by bacteremia and typhoid fever. Among the over 2,600 currently identified serotypes/serovars, some are mostly host-restricted and host-adapted, while the majority of serotypes can infect a broader range of host species and are associated with causing both livestock and human disease. Salmonella serotypes and strains within serovars can vary considerably in the severity of disease that may result from infection, with some serovars that are more highly associated with invasive disease in humans, while others predominantly cause mild gastroenteritis. These observed clinical differences may be caused by the genetic make-up and diversity of the serovars. Salmonella virulence systems are very complex containing several virulence-associated genes with different functions that contribute to its pathogenicity. The different clinical syndromes are associated with unique groups of virulence genes, and strains often differ in the array of virulence traits they display. On the chromosome, virulence genes are often clustered in regions known as Salmonella pathogenicity islands (SPIs), which are scattered throughout different Salmonella genomes and encode factors essential for adhesion, invasion, survival, and replication within the host. Plasmids can also carry various genes that contribute to Salmonella pathogenicity. For example, strains from several serovars associated with significant human disease, including Choleraesuis, Dublin, Enteritidis, Newport, and Typhimurium, can carry virulence plasmids with genes contributing to attachment, immune system evasion, and other roles. The goal of this comprehensive review is to provide key information on the Salmonella virulence, including the contributions of genes encoded in SPIs and plasmids during Salmonella pathogenesis.

Complete genome sequences of 17 Salmonella enterica serovar Schwarzengrund isolates carrying an IncFIB-IncFIC (FII) fusion plasmid.

Seventeen Salmonella enterica serovar Schwarzengrund isolates from chicken (n = 9) and clinical samples including stool (n = 6), urine (n = 1), and gallbladder (n = 1) were sequenced and found to carry an IncFIB-IncFIC (FII) fusion plasmid of approximately 145 Kb. This information provides reference genomic data for comparative studies of S. Schwarzengrund pathogenicity and plasmid genetics.

Versatile allelic replacement and self-excising integrative vectors for plasmid genome mutation and complementation.

IMPORTANCE: In spite of the dissemination of multidrug-resistant plasmids among Gram-negative pathogens, including those carrying virulence genes, vector tools for studying plasmid-born genes are lacking. The allelic replacement vectors can be used to generate plasmid or chromosomal mutations including markless point mutations. This is the first report describing a self-excising integrative vector that can be used as a stable single-copy complementing tool to study medically important pathogens including in vivo studies without the need for antibiotic selection. Overall, our newly developed vectors can be applied for the assessment of the function of plasmid-encoded genes by specifically creating mutations, moving large operons between plasmids and to/from the chromosome, and complementing phenotypes associated with gene mutation. Furthermore, the vectors express chromophores for the detection of target gene modification or colony isolation, avoiding time-consuming screening procedures.

Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria.

Introduction: Type IV secretion systems (T4SSs) are integral parts of the conjugation process in enteric bacteria. These secretion systems are encoded within the transfer (tra) regions of plasmids, including those that harbor antimicrobial resistance (AMR) genes. The conjugal transfer of resistance plasmids can lead to the dissemination of AMR among bacterial populations. Methods: To facilitate the analyses of the conjugation-associated genes, transfer related genes associated with key groups of AMR plasmids were identified, extracted from GenBank and used to generate a plasmid transfer gene dataset that is part of the Virulence and Plasmid Transfer Factor Database at FDA, serving as the foundation for computational tools for the comparison of the conjugal transfer genes. To assess the genetic feature of the transfer gene database, genes/proteins of the same name (e.g., traI/TraI) or predicted function (VirD4 ATPase homologs) were compared across the different plasmid types to assess sequence diversity. Two analyses tools, the Plasmid Transfer Factor Profile Assessment and Plasmid Transfer Factor Comparison tools, were developed to evaluate the transfer genes located on plasmids and to facilitate the comparison of plasmids from multiple sequence files. To assess the database and associated tools, plasmid, and whole genome sequencing (WGS) data were extracted from GenBank and previous WGS experiments in our lab and assessed using the analysis tools. Results: Overall, the plasmid transfer database and associated tools proved to be very useful for evaluating the different plasmid types, their association with T4SSs, and increased our understanding how conjugative plasmids contribute to the dissemination of AMR genes.

Recalls of tattoo and permanent makeup inks in the United States and a follow-up microbiological survey of inks with a previous recall history.

In this study, we collected voluntary recall records of tattoo and permanent makeup ink from the U.S. Food and Drug Administration (US FDA) Enforcement Report Database. The recall records contain information, such as recall date, manufacturer, ink color, reason for recall, and the microorganisms detected from the ink samples. Between 2003 and 2021, a total of 15 voluntary tattoo ink recalls occurred in the U.S. market, involving over 200 tattoo inks marketed by 13 manufacturers and one distributor. Fourteen recalls were due to microbial contamination, and one recall was due to allergic reaction. As follow-up, a microbiological survey of 28 tattoo inks of new batches from seven manufacturers having products that were previously recalled was conducted. Aerobic plate count (APC) and enrichment culture methods based on the FDA's Bacteriological Analytical Manual (BAM) were used to detect microbial contamination. The results revealed that six out of 28 tattoo inks were contaminated with bacteria and were produced by two manufacturers. The level of microbial contamination was less than 250 CFU/g in three of the tattoo inks and between 1 × 103 and 1 × 105 CFU/g in the other three inks. Eleven bacterial isolates were identified, including spore-forming Bacillus-related species and potentially pathogenic species. Overall, this study shows that some tattoo ink products produced by manufacturers with a recall history continue to be contaminated with microorganisms. This highlights the need for ongoing monitoring and quality control of such products.

CPGminer: An Interactive Dashboard to Explore the Genomic Features and Taxonomy of Complete Prokaryotic Genomes.

Prokaryotes, the earliest forms of life on Earth, play crucial roles in global biogeochemical processes in virtually all ecosystems. The ever-increasing amount of prokaryotic genome sequencing data provides a wealth of information to examine fundamental and applied questions through systematic genome comparison. Genomic features, such as genome size and GC content, and taxonomy-centric genomic features of complete prokaryotic genomes (CPGs) are crucial for various fields of microbial research and education, yet they are often overlooked. Additionally, creating systematically curated datasets that align with research concerns is an essential yet challenging task for wet-lab researchers. In this study, we introduce CPGminer, a user-friendly tool that allows researchers to quickly and easily examine the genomic features and taxonomy of CPGs and curate genome datasets. We also provide several examples to demonstrate its practical utility in addressing descriptive questions.

Genome sequence of Gordonia alkaliphila strain WW102, isolated from influent wastewater at a research center with multiple-species research animal facilities.

Gordonia alkaliphila is a little known mesophilic Gram-positive rod-shaped bacterium. We report the 3.85-Mbp genome sequence of G. alkaliphila strain WW102, isolated from wastewater at a research center with multiple-species laboratory animal facilities. The genome predicted FadD32 gene clusters that are involved in the biosynthesis of mycolic acids as found in Mycobacterium tuberculosis.

Complete genome sequence of Shigella flexneri strain P099 from the gum of an adult rhesus monkey, Macaca mulatta, with gingivitis.

Shigella flexneri was associated with gingivitis, a periodontal disease, in the rhesus monkey. We report the circularized 4.8-Mbp complete genome of Shigella flexneri strain P099 isolated from the gum of an adult rhesus monkey, Macaca mulatta, with clinical symptoms of gingivitis.

Complete Genome Sequence of Invasive MLST-Untypeable Serotype 3 xpt-Deficient Streptococcus pneumoniae Strain B1900, Isolated from the Brain of an Infant Rhesus Monkey (Macaca mulatta) That Died of Meningitis.

Serotype 3 Streptococcus pneumoniae is associated with major invasive pneumococcal diseases in humans. We report the circularized 2.0-Mbp complete genome sequence of invasive serotype 3 S. pneumoniae strain B1900, untypeable by multilocus sequence typing (MLST). This strain was isolated from the brain of an infant rhesus monkey (Macaca mulatta) that suddenly died of meningitis with no clinical symptoms.

Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants.

Microbial contamination is the inadvertent presence of microbes or their byproducts in materials or environments [...].

Complete Genome Sequence of Terrisporobacter glycolicus Strain WW3900, Isolated from Influent Wastewater at a Research Center with Multiple-Species Research Animal Facilities.

Terrisporobacter glycolicus is an emerging obligate anaerobic pathogen. We report the 3.9-Mbp genome sequence of T. glycolicus strain WW3900, which was isolated from wastewater at a research center with laboratory animal facilities. The genome sequence predicted a biosynthetic gene cluster encoding an S-adenosylmethionine enzyme and other synthetic genes associated with potential antimicrobial producers.

Complete Genome Sequence of Metabacillus litoralis Strain NCTR108, Isolated from Commercial Tattoo Ink.

Metabacillus litoralis is part of the newly proposed genus Metabacillus. The bacterium was first isolated from a Yellow Sea tidal flat in 2005. As of May 2022, there are five genomic assemblies deposited in GenBank. We report the 5.2-Mbp genome sequence of M. litoralis strain NCTR108, from commercial tattoo ink.

Microbial Genetics and Clonal Dissemination of Salmonella enterica Serotype Javiana Isolated from Human Populations in Arkansas, USA

Salmonella is estimated to cause over a million infections and ~400 deaths annually in the U.S. Salmonella enterica serotype Javiana strains (n = 409) that predominantly originated from the State of Arkansas over a six-year period (2003 to 2008) were studied. This period coincided with a rapid rise in the incidence of S. Javiana infections in the U.S. Children under the age of 10 displayed the highest prevalence of S. Javiana infections, regardless of sex or year of detection. Antimicrobial susceptibility to 15 different antimicrobials was assessed and 92% (n = 375) were resistant to at least one of the antimicrobials. Approximately 89% of the isolates were resistant to sulfisoxazole alone and 3% (n = 11) were resistant to different antimicrobials, including gentamicin, ciprofloxacin or ceftiofur. The pulsed-field gel electrophoresis (PFGE) analyses assessed the genotypic diversity and distribution of S. Javiana strains using XbaI restriction. Nine major clusters were identified and isolates from each group were digested with the restriction enzyme AvrII. Isolates with identical profiles of XbaI and AvrII were found to be disseminated in human populations. These distinct "types" of S. Javiana were persistent in human populations for multiple years. A subset of isolates (n = 19) with unique resistance phenotypes underwent plasmid and incompatibility (Inc) type analyses and the isolates resistant to more than one antimicrobial harbored multiple plasmids (<3 to 165 kb). Furthermore, these strains possessed 14 virulence genes, including pagC, cdtB, and iroN. The whole genome sequences (WGS) of 18 isolates that mostly originated from Arkansas from 2003 to 2011 were compared with isolates collected from different areas in the U.S. in 1999, indicating the perseverance of S. Javiana in disseminating antimicrobial resistance and virulence genes.

Structural analysis of VirD4 a type IV ATPase encoded by transmissible plasmids of Salmonella enterica isolated from poultry products.

Bacterial species have evolved with a wide variety of cellular devices, and they employ these devices for communication and transfer of genetic materials and toxins. They are classified into secretory system types I to VI based on their structure, composition, and functional activity. Specifically, the bacterial type IV secretory system (T4SS) is a more versatile system than the other secretory systems because it is involved in the transfer of genetic materials, proteins, and toxins to the host cells or other bacterial species. The T4SS machinery is made up of several proteins with distinct functions and forms a complex which spans the inner and outer membranes. This secretory machinery contains three ATPases that are the driving force for the functionality of this apparatus. At the initial stage of the secretion process, the selection of substrate molecules and processing occurs at the cytoplasmic region (also known as relaxosome), and then transfer mechanisms occur through the secretion complex. In this process, the VirD4 ATPase is the first molecule that initiates substrate selection, which is subsequently delivered to the secretory machinery. In the protein data bank (PDB), no structural information is available for the VirD4 ATPase to understand the functional property. In this manuscript, we have modeled VirD4 structure in the Gram-negative bacterium Salmonella enterica and described the predicted functional importance. The sequence alignment shows that VirD4 of S. enterica contains several insertion regions as compared with the template structure (pdb:1E9R) used for homology modeling. In this study, we hypothesized that the insertion regions could play a role in the flexible movement of the hexameric unit during the relaxosome processing or transfer of the substrate.

Complete Genome Sequence of Campylobacter coli Strain P4581, a Hybrid Carrying Campylobacter jejuni Genomic Content, Isolated from Rhesus Monkey, Macaca mulatta.

Campylobacter coli is a leading bacterial cause of human gastroenteritis. We reported the circularized 1.8-Mbp complete genome of MLST type 1055 C. coli strain P4581 isolated from a rhesus monkey, Macaca mulatta, hybridizing Illumina short- and Nanopore long-reads.

Antimicrobial Resistance and Increased Virulence of Salmonella.

This special issue of Microorganisms highlights the importance of antimicrobial resistance (AMR) and increased virulence of Salmonella with multiple research papers [...].

Genomic Diversity, Antimicrobial Resistance, and Virulence Gene Profiles of Salmonella Serovar Kentucky Isolated from Humans, Food, and Animal Ceca Content Sources in the United States.

Salmonella serovar Kentucky is frequently isolated from chickens and dairy cattle, but recovery from humans is comparatively low based on the U.S. National Antimicrobial Resistance Monitoring System (NARMS) reports. We aimed to better describe the genetic diversity, antimicrobial resistance, and virulence determinants of Salmonella Kentucky isolates from humans, food animal ceca, retail meat and poultry products, imported foods and food products, and other samples. We analyzed the genomes of 774 Salmonella Kentucky isolates and found that 63% (54/86) of human isolates were sequence type (ST)198, 33% (29/86) were ST152, and 3.5% (3/86) were ST314. Ninety-one percent (570/629) of cecal isolates and retail meat and poultry isolates were ST152 or ST152-like (one allele difference), and 9.2% (58/629) were ST198. Isolates from imported food were mostly ST198 (60%, 22/37) and ST314 (29.7%, 11/37). ST198 isolates clustered into two main lineages. Clade ST198.2 comprised almost entirely isolates from humans and imported foods, all containing triple mutations in the quinolone resistance-determining region (QRDR) that confer resistance to fluoroquinolones. Clade ST198.1 contained isolates from humans, ceca, retail meat and poultry products, and imported foods that largely lacked QRDR mutations. ST152 isolates from cattle had a lineage (Clade 2) distinct from ST152 isolates from chicken (Clade 4), and half of ST152 human isolates clustered within two other clades (Clades 1 and 3), largely distinct from Clades 2 and 4. Although clinical illness associated with Salmonella Kentucky is low, ST198 appears to account for most human infections in the Unites States but is uncommon among ceca of domestic food animals and retail meat and poultry products. These findings, combined with human exposure data, suggest that fluoroquinolone-resistant ST198 infections may be linked to the consumption of food products that are imported or consumed while traveling. We also found unique differences in the composition of virulence genes and antimicrobial resistance genes among the clades, which may provide clues to the host specificity and pathogenicity of Salmonella Kentucky lineages.