Virulence-associated Genes Research Articles

Virulence Determinants Are Unevenly Distributed Within Streptomyces Species and Strains Causing Potato Common Scab in the Province of Quebec, Canada.

Potato common scab is an important bacterial disease afflicting potatoes around the world. Better knowledge of the local Streptomyces spp. populations causing this disease is key to developing durable control strategies. In this study, we isolated 230 Streptomyces strains from scab-infected potato tubers harvested from commercial potato fields located across the province of Quebec, Canada. The genetic diversity of this collection was first studied using repetitive element-based PCR fingerprinting, and the genomes of 36 representative strains were sequenced using PacBio's sequencing technology. This enabled us to identify the strains to the species level, to study the distribution of previously characterized virulence-associated genes and clusters, and to explore the repertoires of putative plant cell wall-degrading enzymes. In parallel, the virulence of the 36 strains was evaluated using a potato tuber slice assay. The diversity was higher than previously reported, as 11 phytopathogenic species were found across the province. Among them, S. scabiei and S. acidiscabies were the most abundant as well as the most virulent. Strains belonging to these two species harbored numerous virulence determinants, including the thaxtomin biosynthetic gene cluster. By contrast, most weakly virulent strains lacked this cluster but harbored at least one known virulence determinant. The results obtained suggest that a higher number of virulence-associated genes and clusters in the genome of phytopathogenic Streptomyces spp. are associated with greater virulence. This study contributes to increasing the publicly available genomic resources of scab-causing Streptomyces spp. and expands our knowledge on the diversity and virulence of this important bacterial pathogen.

Public health concern of antimicrobial resistance and virulence determinants in E. coli isolates from oysters in Egypt

The emergence of critical-priority E. coli, carrying a wide array of resistance and virulence factors through food sources, poses a significant challenge to public health. This study aimed to investigate the potential role of oysters sold in Egypt as a source for E. coli, identify their resistance and virulence-associated gene profiles, and assess associated zoonotic risks. A total of 33 pooled fresh oyster samples were obtained from various retail fish markets in Egypt and examined bacteriologically for the presence of E. coli. Antimicrobial resistance was performed by the disk-diffusion method, and the multiple antibiotic resistance index (MAR) was calculated. All isolates were screened for extended-spectrum beta-lactamase (ESBL) (blaTEM, blaSHV, blaCTX−M, and blaOXA−1), plasmid-mediated AmpC blaCMY−2, and carbapenemases (blaKPC, blaNDM, blaVIM, and blaOXA−48) genes by Polymerase chain reaction. Moreover, the presence of virulence-encoding genes was investigated. The virulent MDR strains were clustered using R with the pheatmap package. The prevalence of E. coli was 72.7% (24 out of 33), with 66.7% of the isolates classified as multi-drug resistant, and 75% exhibited MAR values exceeding the 0.2 threshold. Different antimicrobial sensitivity phenotypes and genotype profiles were identified in E. coli isolates. The most prevalent gene detected among all isolates was blaTEM (22/24, 91.7%). Notably, all non-ESBL producers were positive for blaCMY2. Carbapenem-resistant and carbapenem-intermediate strains were carbapenemase producers, with the predominance of the blaKPC gene (11/24, 45.8%). Remarkably, twelve out of sixteen virulence genes were identified, with papC (21/24, 87.5%) and sfa (16/24, 66.7%) genes being the most prevalent. Most isolates carry virulence genes primarily associated with extra-intestinal pathogenic E. coli (ExPEC) (87.5%) and enteropathogenic (EPEC) (70.8%) pathotypes. Four E. coli isolates exhibit cluster patterns. This study provides the first insight into the emergence of virulent MDR E. coli among oysters in Egypt. It underscores the potential role of oysters as a source for disseminating these strains within aquatic ecosystems, presenting a possible threat to public health.

Longitudinal study of avian pathogenic Escherichia coli (APEC) serogroups associated with disease in Georgia poultry using molecular serology and virulence gene analysis

ABSTRACT Avian pathogenic Escherichia coli (APEC) is a significant cause of morbidity, mortality, and production loss to the poultry industry worldwide. Here, we characterized 569 E. coli isolates from avian-diagnosed colibacillosis cases from the state of Georgia, USA. In total, 339 isolates were assigned into 32 serogroups with the majority classifying as O78, O2, O25, O8, O1, O86, O18, and O15. Serogroup O25 was found to link with broilers, while broiler breeders were more often associated with serogroup O1 and pet/ hobby birds with serogroup O8. In addition, some serogroups (O1) were more prevalent in the summer and fall. Analysis for virulence-associated genes (VAGs) found 23.20% of isolates did not harbour any genes linked with the APEC pathotype, while ColV plasmid-associated genes (iroN, ompT, hlyF, iss, and aerJ) were frequently detected among most isolates (with 80–96% prevalence) and some of these genes were linked with serogroup. Phylogenetic analysis, classified isolates into phylogenetic groups B2 (34%), F (19%), A (15%), and G (9%). The phylogenetic group B2 isolates also harboured the highest number of VAGs. This study highlights that the current APEC-causing disease in birds in the State of Georgia has identified several emerging serogroups possessing several VAGs that could potentially lead to challenges in colibacillosis control. RESEARCH HIGHLIGHTS Several emerging APEC serogroups were observed in Georgia poultry populations. An association between APEC serogroups and bird type was observed. The prevalence of different APEC serogroups was influenced by season. A multiplex PCR assay targeting common serogroups of APEC in Georgia poultry was developed.

Resistance patterns, virulence determinants, and biofilm genes of multidrug-resistant Pseudomonas aeruginosa isolated from fish and fish handlers

Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic bacterium that is widely distributed in aquatic environments and causes major economic losses in fish and public health hazards.This study aimed to identify the occurrence of P. aeruginosa in samples collected from fish and fish handlers, and to investigate the antimicrobial susceptibility, virulence determinants, and biofilm genes of P. aeruginosa isolates. A total of 276 samples were cross-sectionally collected from Nile tilapia (53), Golden grey mullet (52), Mediterranean horse mackerel (50), Striped red mullet (71), and fish handlers (50) at five different retail fish markets in Damietta Governorate, Egypt. Pseudomonas species (spp.) were biochemically identified in 57.9% of the total examined samples. Peudomonas aeruginosa were the most prevalent species isolated from the fish and human samples via PCR technique. Peudomonas aeruginosa isolates exhibited full resistance (100%) to tobramycin (TOB), gentamicin (CN), and colistin (CL), with a high level of susceptibility (88.5%) to imipenem (IPM) using the disk diffusion method. Most P. aeruginosa isolates (84.6%) exhibited drug resistance, with 61.5% were multidrug resistance (MDR) and 23.1% were extensive drug resistance (XDR). Most isolates had at least four virulence-associated genes (lasB, toxA, exoU, and oprL) and three biofilm genes (psIA, peIA, and lasR) by using uniplex PCR. The lasI, and rhlR Quorum Sensing (QS) genes were identified in 84.6% and 61.5% in the examined P. aeruginosa isolates, respectively. The highest mortality rate in Nile tilapia experimentally infected with P. aeruginosa isolate encoding most of virulent genes. Multivariate analyses revealed high heterogeneity among the examined isolates. This study revealed the emergence of virulent and drug resistant P. aeruginosa isolates in fish, poses high risks to consumers and food. Thus, strict hygienic measures should be considered when catching, handling, and storing fish, in addition to the routine application of antimicrobial susceptibility testing.

Isolation, characterization, and application of a novel Pseudomonas fluorescens phage vB_PF_Y1-MI in contaminated milk.

The food industry has incurred substantial losses from contamination by Pseudomonas fluorescens, emphasizing the critical importance of implementing effective control strategies. Phages are potential sterilizers due to their specific killing abilities and the difficulty bacteria face in developing resistance. However, a significant barrier to their development is the lack of diversity among phage types. In this study, we characterized a novel lytic P. fluorescens phage, named vB_PF_Y1-MI. Phage vB_PF_Y1-MI displayed a latent period of nearly 10min and a high burst size of 1493 PFU/cell. This phage showed good activity over a wide range of temperature (up to 70°C) and pH (3-12). The genome of phage vB_PF_Y1-MI spans 93,233bp with a GC content of 45%. It encompasses 174 open-reading frames and 19 tRNA genes, while no lysogeny or virulence-associated genes were detected. Phylogenetic analysis positions it as a novel unassigned evolutionary lineage within the Caudoviricetes class among related dsDNA phages. Our study provides foundational insights into vB_PF_Y1-MI and emphasizes its potential as an effective biological control agent against P. fluorescens. This research offers crucial theoretical groundwork and technical support for subsequent efforts in preventing and controlling P. fluorescens contamination.

Characterization of neurologic disease-associated Streptococcus suis strains within the United States swine herd and use of diagnostic tools.

Streptococcus suis negatively impacts swine health, posing diagnostic and preventative challenges. S. suis can induce disease and also quietly reside on mucosal surfaces. The limited use of diagnostic tools to identify disease-associated strains and rule out differential diagnoses, alongside the complex ecology of S. suis, poses significant challenges in comprehending this important pathogen and defining pathotypes. This study evaluated 2,379 S. suis central nervous system (CNS) isolates from diagnostic submissions between 2015 and 2019. Isolates originating from submissions with histologic evidence of CNS infection (n = 1,032) were further characterized by standard and advanced diagnostic techniques. We identified 29 S. suis serotypes and 4 reclassified serotypes as putative causes of CNS disease. Among these, serotypes 1 and 7 emerged as the predominant putative causes of CNS infection (32% of submissions). Furthermore, 51 sequence types (STs), of which 15 were novel, were detected with ST1 predominating. Through whole-genome sequencing of 145 isolates, we observed that five commonly used virulence-associated genes (VAGs; epf, mrp, sly, ofs, and srtF) were not present in most disease-associated isolates, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) yielded false-positive results in 7% of isolates. These data indicate that (i) clinical signs and site of isolation alone are insufficient for defining a pathotype, (ii) S. suis serotypes and STs associated with CNS infection are more diverse than previously reported, (iii) MALDI-TOF MS may need to be supplemented with additional diagnostic tools for precise S. suis identification, and (iv) VAGs remain an unreliable means for identifying isolates associated with CNS disease.IMPORTANCEStreptococcus suis is an important and complex systemic bacterial pathogen of swine. Characterization of S. suis strains originating from pigs with histologic confirmation of neurologic disease is limited. Review of swine diagnostic submissions revealed that fewer than half of cases from which S. suis was isolated from the brain had histologic evidence of neurologic disease. This finding demonstrates that clinical signs and site of isolation alone are not sufficient for identifying a neurologic disease-associated strain. Characterization of strains originating from cases with evidence of disease using classic and advanced diagnostic techniques revealed that neurologic disease-associated strains are diverse and commonly lack genes previously associated with virulence.

Genome characterization of Shewanella algae in Hainan Province, China.

Shewanella algae is an emerging marine zoonotic pathogen. In this study, we first reported the Shewanella algae infections in patients and animals in Hainan Province, China. Currently, there is still relatively little known about the whole-genome characteristics of Shewanella algae in most tropical regions, including in southern China. Here, we sequenced the 62 Shewanella algae strains isolated from Hainan Province and combined with the whole genomes sequences of 144 Shewanella algae genomes from public databases to analyze genomic features. Phylogenetic analysis revealed that Shewanella algae is widely distributed in the marine environments of both temperate and tropical countries, exhibiting close phylogenetic relationships with genomes isolated from patients, animals, and plants. Thereby confirming that exposure to marine environments is a risk factor for Shewanella algae infections. Average nucleotide identity analysis indicated that the clonally identical genomes could be isolated from patients with different sample types at different times. Pan-genome analysis identified a total of 21,909 genes, including 1,563 core genes, 8,292 strain-specific genes, and 12,054 accessory genes. Multiple putative virulence-associated genes were identified, encompassing 14 categories and 16 subcategories, with 171 distinct virulence factors. Three different plasmid replicon types were detected in 33 genomes. Eleven classes of antibiotic resistance genes and 352 integrons were identified. Antimicrobial susceptibility testing revealed a high resistance rate to imipenem and colistin among the strains studied, with 5 strains exhibiting multidrug resistance. However, they were all sensitive to amikacin, minocycline, and tigecycline. Our findings clarify the genomic characteristics and population structure of Shewanella algae in Hainan Province. The results offer insights into the genetic basis of pathogenicity in Shewanella algae and enhance our understanding of its global phylogeography.

Whole-genome comparative analysis of the genetic, virulence and antimicrobial resistance diversity of Campylobacter spp. from Spain

Whole-Genome Sequencing has the potential to be an effective method for surveillance and control of foodborne diseases. This study aims to determine the genetic relatedness and prevalence of virulence-associated genes and antimicrobial resistance determinants in 135 Campylobacter jejuni, seven Campylobacter coli and three Campylobacter lari isolates from the poultry supply chain and hospital in Spain. The isolates showed a wide genetic diversity between and within species with Clonal Complex 21 the most frequent lineage found. Among species, C. jejuni showed the highest prevalence of virulence genes (287/333) in which a high occurring variability was observed in the capsule biosynthesis and transport, O-linked flagellar glycosylation and lipooligosaccharide biosynthesis loci, with a great impact of phase-variation that led to 72 different virulence gene patterns among all isolates. High prevalence (> 90 %) of blaOXA-type β-lactamase genes and mutations in DNA gyrase gene associated with fluoroquinolones resistance were observed, and at a frequency similar to the tet(O) gene in C. jejuni (93 %) and C. coli (86 %), both of which also harboured resistance determinants to aminoglycosides with a higher occurrence rate in C. coli (43 %), that was the only species in which mutations in the 23S ribosomal subunit conferring resistance to erythromycin were identified (43 %). The present study constitutes the largest genomic survey of Campylobacter isolates in Spain providing insight into the prevalence and diversity of the pathogen along the poultry supply chain in the country.

Emergence of extensively drug-resistant hypervirulent Acinetobacter baumannii isolated from patients with bacteremia: bacterial phenotype and virulence analysis

ObjectivesIndividuals infected with extensively drug-resistant (XDR) Acinetobacter baumannii are difficult to cure and have a high mortality rate. In this study, we compared the genomic and phenotypic differences between XDR and non-multidrug-resistant (MDR) A. baumannii and further characterized hypervirulent XDR A. baumannii. MethodsA total of 1,403 Acinetobacter isolates were collected from patients with bacteremia between 1997 and 2015. Antimicrobial susceptibility test was performed to categorize isolates into non-MDR, MDR, and XDR groups. The presence of selected virulence-associated genes was determined by PCR. Bacterial phenotypes, including iron acquisition, biofilm formation, capsule production, and virulence to larvae and mice, were determined. ResultsMultilocus sequence types revealed the high prevalence of ST2 (81.6%) and ST129 (18.4%) among 49 XDR isolates and sequence types of 18 non-MDR isolates were more diverse. Virulence-associated phenotypic assays showed that XDR isolates had higher iron acquisition ability and capsule production and higher virulence to Galleria mellonella larvae. However, their biofilm formation ability was lower compared to that of non-MDR isolates. XDR isolates contained more virulence genes, tonB, hemO, abaI, and ptk, while non-MDR isolates contained more pld and ompA. Twenty-one XDR isolates caused <20% larvae survival rate after 7 days post-infection were defined as hypervirulent XDR isolates. Among them, isolates 1677 (ST129) and 929-1 (ST2) also caused the death of all infected mice within two days. ConclusionSome subpopulations of highly drug-resistant ST2 also exhibit high virulence. Therefore, it is of utmost importance to continue monitoring the spread of hypervirulent XDR A. baumannii isolates.

Molecular characteristics of drug-susceptible Mycobacterium tuberculosis clinical isolates based on treatment duration.

In this study, we performed comparative genomic and transcriptomic analysis of clinical isolates of Mycobacterium tuberculosis collected from patients with drug-susceptible tuberculosis (DS-TB). The clinical isolates were categorized based on treatment duration: standard 6 months or >6 months. Study participants were recruited from a 2016 to 2018 tuberculosis cohort, and clinical M. tuberculosis isolates were collected from the sputum of patients with tuberculosis. We analyzed the genome and transcriptome of the isolated M. tuberculosis. Genomic analysis revealed a specific non-synonymous single-nucleotide polymorphism in pe_pgrs9 and ppe34, exclusive to the group treated for >6 months. Transcriptomic analysis revealed increased expression of various virulence-associated protein family genes and decreased expression of ribosomal protein genes and ppe38 genes in the group treated for >6 months. The identified genetic variation and gene expression patterns may influence treatment outcomes by modulating host immune responses, increasing virulence, and potentially contributing to persister cell formation in M. tuberculosis. This study provides insights into the genetic and transcriptomic factors associated with prolonged DS-TB treatment. However, our study identified molecular characteristics using a small sample size, and further detailed studies are warranted.

Molecular Identification and Bioinformatics Analysis of Anaplasma marginale Moonlighting Proteins as Possible Antigenic Targets.

Diseases of veterinary importance, such as bovine Anaplasmosis, cause significant economic losses. Due to this, the study of various proteins of the causal agent Anaplasma marginale has focused on surface proteins. However, a vaccine for this disease is not yet available. To this end, in this work, moonlighting proteins (MLPs) are presented as an alternative approach for the design of immunogens against A. marginale. The proteins of the strain MEX-15-099-01 were analyzed, and its MLPs were identified. Subsequently, four virulence-associated MLP genes were selected and identified using PCR. The proteins were analyzed using a structural homology approach and the collection of B-cell epitopes was predicted for each MLP. Finally, a pair of AmEno peptides were synthesized and the antigenic potential was tested using an iELISA. Our bioinformatics analysis revealed the potential of AmEno, AmGroEl, AmEF-Tu, and AmDnaK proteins as promising candidates for designing immunogens. The PCR allowed the gene sequence identification in the genome of the strain MEX-15-099-01. Notably, AmEno-derived synthetic peptides showed antigenicity in an ELISA. Our study has shed light on the potential use of MLPs for immunogen design, demonstrating the antigenic potential of AmEno.

Molecular characterization of Streptococcus suis isolates recovered from diseased pigs in Europe

Streptococcus suis is a major swine pathogen and zoonotic agent, causing important economic losses to the porcine industry. Here, we used genomics approaches to characterize 251 S. suis isolates recovered from diseased pigs across Belgium, France, Germany, Hungary, the Netherlands, Spain, and the United Kingdom. We identified 13 serotypes, being serotypes 9 and 2 the most prevalent, and 34 sequence types (STs), including 16 novel STs, although ST16 and ST1 dominated the strain population. Phylogenetic analysis revealed complex genetic relationships, notable geographic clustering, and potential differential capacity for capsular switching among serotype 9 isolates. We found antimicrobial resistance (AMR) genes in 85.3% of the isolates, with high frequencies of genes conferring resistance to tetracyclines and macrolides. Specifically, 49.4% of the isolates harbored the tetO gene, and 64.9% possessed the ermB gene. Additionally, we observed a diverse array of virulence-associated genes (VAGs), including the classical VAGs mrp, epf, and sly, with variable presence across different genotypes. The high genetic diversity among European S. suis isolates highlights the importance of targeted antimicrobial use and flexible vaccine strategies. Rapid strain characterization is crucial for optimizing swine health management, enabling tailored interventions like the development of autovaccines to mitigate S. suis infections.

Streptococcus suis Strains with Novel and Previously Undescribed Capsular Loci Circulate in Europe

Streptococcus suis (S. suis) causes serious diseases in pigs, and certain serotypes also pose a risk to humans. The expression of capsular polysaccharides (CPS) is considered an important virulence property of the pathogen. Recently, some serotypes have been reclassified as other organisms, while novel S. suis serotypes are being described. Although the CPS can be typed by serological methods using antisera, the presence of unique sequences for each capsular polysaccharide synthesis locus (cps locus) enables convenient PCR-based serotyping. In this study, we characterized 33 non-serotypeable S. suis strains obtained from diseased pigs in the Czech Republic by sequencing and analyzing the cps locus. Phylogenetic analysis of cpn60 confirmed that all isolates belong to the S. suis species. Four isolates had cps loci similar to the previously described reference S. suis serotypes. Eleven isolates were classified as recently described novel cps loci (NCLs). Nine isolates had substitutions, insertions and/or deletions in their cps loci and showed only partial similarity to the already described NCLs. Another eight isolates had previously undescribed cps locus structures and were proposed as novel NCLs. One isolate had lost the genes encoding capsule biosynthesis. Only four sequence types (ST) had two isolates each; the rest had unique STs. Two isolates harbored the classical virulence associated genes (VAGs) mrp and sly. Another isolate had only the mrp gene, while a different isolate harbored only the sly gene. This study provides insight into untypeable isolates in the Czech Republic, highlighting the genetic diversity and potential for novel serotype identification.

Diarrheagenic Escherichia coli in Stool Specimens Collected from Patients Attending Primary Healthcare Facilities in Ethiopia: Whole-Genome Sequencing-Based Molecular Characterization.

The diarrheagenic Escherichia coli (DEC) is the major cause of diarrheal diseases in Africa, including Ethiopia. However, the genetic diversity of E. coli pathotypes found in Ethiopia has not been studied well. This study aimed to characterize potential DEC belonging to enteropathogenic (EPEC), Shiga toxin-producing (STEC), enteroaggregative (EAEC), enterotoxigenic (ETEC), and enteroinvasive (EIEC) E. coli pathotypes from stool specimens of patients attending primary healthcare units (n = 260) in Addis Ababa and Hossana using whole-genome sequencing. Real-time PCR assays were used to identify DEC isolates belonging to EPEC, STEC, EAEC, ETEC, and EIEC pathotypes, which were then subjected to whole-genome sequencing on the Illumina platform. Twenty-four whole-genome nucleotide sequences of DEC strains with good enough quality were analyzed for virulence-associated genes (VAGs), antibiotic resistance genes (ARGs), phylogenetic groups, serogroups, and sequence types. The majority (62.5%) of DEC isolates belonged to the phylogenetic group B1. The identified DEC isolates belonged to 21 different serogroups and 17 different sequence types. All tested DEC isolates carried multiple VAGs and ARGs. The findings highlight the high diversity in the population structure of the studied DEC isolates, which is important for designing targeted interventions to reduce the diarrheal burden in Ethiopia.

Regulatory insight for a Zn2Cys6 transcription factor controlling effector-mediated virulence in a fungal pathogen of wheat.

The regulation of virulence in plant-pathogenic fungi has emerged as a key area of importance underlying host infections. Recent work has highlighted individual transcription factors (TFs) that serve important roles. A prominent example is PnPf2, a member of the Zn2Cys6 family of fungal TFs, which controls the expression of effectors and other virulence-associated genes in Parastagonospora nodorum during infection of wheat. PnPf2 orthologues are similarly important for other major fungal pathogens during infection of their respective host plants, and have also been shown to control polysaccharide metabolism in model saprophytes. In each case, the direct genomic targets and associated regulatory mechanisms were unknown. Significant insight was made here by investigating PnPf2 through chromatin-immunoprecipitation (ChIP) and mutagenesis approaches in P. nodorum. Two distinct binding motifs were characterised as positive regulatory elements and direct PnPf2 targets identified. These encompass known effectors and other components associated with the P. nodorum pathogenic lifestyle, such as carbohydrate-active enzymes and nutrient assimilators. The results support a direct involvement of PnPf2 in coordinating virulence on wheat. Other prominent PnPf2 targets included TF-encoding genes. While novel functions were observed for the TFs PnPro1, PnAda1, PnEbr1 and the carbon-catabolite repressor PnCreA, our investigation upheld PnPf2 as the predominant transcriptional regulator characterised in terms of direct and specific coordination of virulence on wheat, and provides important mechanistic insights that may be conserved for homologous TFs in other fungi.

Unravelling the main genomic features of Mycoplasma equirhinis

BackgroundMycoplasma spp. are wall-less bacteria with small genomes (usually 0.5–1.5 Mb). Many Mycoplasma (M.) species are known to colonize the respiratory tract of both humans and livestock animals, where they act as primary pathogens or opportunists. M. equirhinis was described for the first time in 1975 in horses but has been poorly studied since, despite regular reports of around 14% prevalence in equine respiratory disorders. We recently showed that M. equirhinis is not a primary pathogen but could play a role in co-infections of the respiratory tract. This study was a set up to propose the first genomic characterization to better our understanding of the M. equirhinis species.ResultsFour circularized genomes, two of which were generated here, were compared in terms of synteny, gene content, and specific features associated with virulence or genome plasticity. An additional 20 scaffold-level genomes were used to analyse intra-species diversity through a pangenome phylogenetic approach. The M. equirhinis species showed consistent genomic homogeneity, pointing to potential clonality of isolates despite their varied geographical origins (UK, Japan and various places in France). Three different classes of mobile genetic elements have been detected: insertion sequences related to the IS1634 family, a putative prophage related to M. arthritidis and integrative conjugative elements related to M. arginini. The core genome harbours the typical putative virulence-associated genes of mycoplasmas mainly involved in cytoadherence and immune escape.ConclusionM. equirhinis is a highly syntenic, homogeneous species with a limited repertoire of mobile genetic elements and putative virulence genes.

Detection and characterization of multidrug resistant Escherichia coli carrying virulence gene isolated from broilers in Bangladesh.

The emergence and dissemination of multidrug resistant (MDR) bacteria pose a severe threat to public health by limiting clinical treatment and prophylactic options. This study investigates the prevalence of Escherichia coli in broilers, their phenotypic antimicrobial resistance (AMR) profiles and the presence of virulence-associated genes (VAGs) and antimicrobial resistance genes (ARGs) using polymerase chain reaction (PCR). A total of 216 pooled cloacal samples were collected from 1080 broilers across six districts of Bangladesh. Each pooled sample comprised randomly selected cloacal swabs from five birds per farm. E. coli isolates were identified using standard bacteriological approach, followed by biochemical assays and PCR. Antimicrobial susceptibility was assessed using the Kirby-Bauer disc diffusion method, and the presence of ARGs and VAGs was determined via PCR. Five selected isolates were partially sequenced for five VAGs using Sanger sequencing. A total of 177 E. coli isolates (81.94%, 95% confidence interval: 76.24%-86.53%) were identified. The isolates showed the highest resistance to ampicillin (93.79%), followed by tetracycline (91.53%), erythromycin (89.27%) and ciprofloxacin (87%). Conversely, ceftriaxone (80.79%) showed highest susceptibility, followed by gentamicin (37.29%) and neomycin (31.07%). All isolates were MDR, with a multiple antibiotic resistance indexes were <0.3. A significant percentage (16.38%) of E. coli isolates were MDR to five antimicrobial classes and harboured blaTEM, sul1, ere (A), tetA, tetB and tetC genes. The highest prevalent ARGs were blaTEM (88.14%) followed by ere (A) (83.62%) and sul 1 (72.32%). The prevalence of VAGs was astA (56.50%), iucD (31.07%), iss (21.47%), irp2 (15.82%) and cva/cvi (3.39%), respectively. This study highlights the presence of ARGs contributing to the development of MDR in E. coli carrying VAGs in broilers. Effective monitoring and surveillance of antimicrobial usage in poultry production systems are urgently required to prevent emergence and dissemination of AMR.

Exploring the Potential Probiotic Properties of Bifidobacterium breve DSM 32583-A Novel Strain Isolated from Human Milk.

Human milk is the best nutrition for infants, providing optimal support for the developing immune system and gut microbiota. Hence, it has been used as source for probiotic strain isolation, including members of the genus Bifidobacterium, in an effort to provide beneficial effects to infants who cannot be exclusively breastfed. However, not all supplemented bifidobacteria can effectively colonise the infant gut, nor confer health benefits to the individual infant host; therefore, new isolates are needed to develop a range of dietary products for this specific age group. Here, we investigated the beneficial potential of Bifidobacterium breve DSM 32583 isolated from human milk. We show that in vitro B. breve DSM 32583 exhibited several characteristics considered fundamental for beneficial bacteria, including survival in conditions simulating those present in the digestive tract, adherence to human epithelial cell lines, and inhibition of growth of potentially pathogenic microorganisms. Its antibiotic resistance patterns were comparable to those of known beneficial bifidobacterial strains, and its genome did not contain plasmids nor virulence-associated genes. These results suggest that B. breve DSM 32583 is a potential probiotic candidate.

Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.

The study examined gut microbiome composition across diverse geographical locations in Kazakhstan, spanning urban centers and rural settlements. This allows for thoroughly investigating how urbanization gradients and geographic factors shape the gut microbiome. The study's examination of the gut resistome and prevalence of virulence-associated genes provide essential insights into the public health implications of urbanization-driven microbiome alterations. Collecting comprehensive demographic, dietary, and stool sample data enables the researchers to better understand the relationships between urbanization, nutritional patterns, and gut microbiome composition. The findings have important implications for understanding how urbanization-driven microbiome changes may impact human health and well-being, paving the way for tailored interventions to restore a balanced gut microbial ecology.

Strain of Xanthomonas oryzae pv. oryzae Loses Virulence through Dysregulation of Cardiolipin Synthase.

Small non-coding RNAs (sRNAs) are pivotal post-transcriptional regulatory factors influencing biological activity. Studies on the rice bacterial blight pathogen Xanthomonas oryzae pathovar oryzae strain PXO99A, previously identified a virulence-associated sRNA, trans3287. A mutant strain lacking this sRNA, named SK01, resulted in markedly diminished virulence towards rice. This study aims to further elucidate the underlying bacterial virulent function of trans3287. The expression of trans3287 was quantified in virulence-inducing and standard nutritional conditions to clarify its production mechanism. The detection of virulence-associated genes revealed that trans3287 regulated the synthesis processes of extracellular polysaccharides, lipopolysaccharides, and the type III secretion system. Moreover, bioinformatics prediction and quantitative PCR indicated a potential direct target of trans3287, PXO_03470, encoding cardiolipin synthase. A dual-plasmid system fusing with GFP tag and protein immunoblotting confirmed that sRNA trans3287 negatively regulated PXO_03470. Bacterial biofilms demonstrated trans3287 regulated the disruption of biofilm integrity through cardiolipin synthase. This study provides preliminary insights into the mechanistic underpinnings of the role of sRNA trans3287 in mediating bacterial virulence through cardiolipin synthase.