VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on

Antimicrobial Resistance and Zoonotic Potential of Nontyphoidal Salmonella From Household Dogs

BACKGROUND

Companion animals, like household dogs, are an overlooked transmission point for zoonotic pathogens such as nontyphoidal Salmonella (NTS). Given the proximity of dogs to humans and the use of critically important antibiotics in companion animal medicine, household dogs represent a risk for the spread of antimicrobial-resistant (AMR) Salmonella.

METHODS AND RESULTS

To this end, we aimed to leverage existing biosurveillance infrastructure to investigate AMR and the zoonotic potential of NTS isolated from dogs and humans. We identified all NTS strains isolated from domestic dogs via the Veterinary Laboratory Investigation and Response Network between May 2017 and March 2023 (N = 87), and spatiotemporally matched strains isolated from humans in the NCBI Pathogen Isolate Browser (N = 77). These 164 strains, collected from 17 states in the United States, formed the basis of our analysis. Strains isolated from dogs comprised diverse serovars, with most being clinically relevant to human health. All strains possessed AMR determinants for drug classes deemed critically or highly important by the World Health Organization. We identified sixteen NTS isolates from humans closely related to ≥1 of six dog-associated strains.

CONCLUSIONS

Collectively, our data emphasize the importance of antimicrobial stewardship and sustained biosurveillance beyond human- and agriculture-associated veterinary medicine, using a One-Health framework that accounts for all transmission points including companion animals.

Molecular Characterization of Whole Genome Sequencing of Salmonella spp. in Shapingba District, Chongqing, China, 2016-2023

In recent years, Salmonella infection is a major global public health concern, particularly in food safety. This study analyzed the genomes of 102 Salmonella strains isolated between 2016 and 2023 from food, foodborne disease patients, and food poisoning incidents, focusing on their molecular characteristics, antibiotic resistance genes (ARGs), and virulence genes. S. enterica serovar Enteritidis (37.3%) and S. enterica serovar Typhimurium (21.6%, including its monophasic variant 1,4,[5],12:i:-) were the main strains among 22 serotypes. Multilocus sequence typing revealed 23 sequence types (STs), with ST11, ST19, and ST34 as the most prevalent. All strains carried at least 24 ARGs. Detection rates for aac(6')-Iy, blaTEM-1, and sul2 ranged from 44.1% to 63.7%, mainly in S. Enteritidis and S. Typhimurium. Rates for qnrS1, sul1, and aadA were 12.8% to 16.7%, while mcr-1 appeared in one ST34 S. Typhimurium strain. All strains contained at least 98 virulence genes. The genes pefABCD, mig-5, and spvBCD were in 48.0% of strains, while rck was found in 36.3%, mainly linked to S. Enteritidis and S. Typhimurium. The tssM gene was found in 37.3% of the strains, exclusively in S. Enteritidis. Core genome single nucleotide polymorphisms (cgSNPs) analysis grouped the strains into nine clusters, with 75.5% belonging to three major groups. Food poisoning event 1 was correlated with cluster 3, while events 2 and 3 were linked to cluster 1. Across events, SNP differences among strains were ≤6. Strains with SNP differences ≤10 were also found in other clusters. This method is promising for tracking sporadic cases and identifying potential foodborne safety incidents. Salmonella strains in the region exhibit substantial genetic diversity, demonstrating the efficacy of cgSNPs analysis for source tracking. Ongoing surveillance is essential given the prevalence of ARGs and virulence genes. This study provides a data foundation for local Salmonella epidemiology.

Polysaccharide lyase PL3.3 possibly potentiating Clostridioides difficile clinical symptoms based on complete genome analysis of RT046/ST35 and RT012/ST54

Clostridioides difficile has rapidly become a major cause of nosocomial infectious diarrhea worldwide due to the misuse of antibiotics. Our previous study confirmed that RT046/ST35 strain is associated with more severe clinical symptoms compared to RT012/ST54 strain. We conducted genome comparison of the RT046/ST35 and RT012/ST54 strains using whole-genome sequencing technology. The RT046/ST35 strain had a genome length of 7,869,254 bp with a GC content of 29.49%. The original length of the RT012/ST54 strain was 7,499,568 bp with a GC content of 29.64%. Additionally, we detected plasmid1 in the RT046/ST54 strain. We found that the RT046/ST35 strain had more genomic islands compared to the RT012/ST54 strain, and we identified polysaccharide lyase (PL) in the region around 2.2 M. Furthermore, we discovered that the increased severity of clinical symptoms in the RT046/ST35 strain compared to the RT012/ST54 strain was unrelated to virulence factors and emphasized the potential crucial role of PL in RT046/ST35. There were almost no differences in eggNOG annotation and KEGG annotation between RT046/ST35 and RT012/ST54. RT046/ST35 had more mRNA processes in GO annotation. In conclusion, our study suggests that the core factor contributing to the more serious clinical symptoms of the RT046/ST35 strain compared to the RT012/ST54 strain is possibly PL.

Quaternary Ammonium Compounds: A New Driver and Hidden Threat for mcr-1 Prevalence in Hospital Wastewater and Human Feces

The emergence of mobile colistin resistance gene mcr-1 has attracted global attention. The prevalence of mcr-1-positive Escherichia coli (MCRPEC) in humans largely decreased following the ban of colistin as an animal growth promoter in China. However, the prevalence of MCRPEC in the hospital environment and the relationship between disinfectants and mcr-1 remain unclear. We found that MCRPEC prevalence was low in the feces of healthy humans attending physical examinations in six hospitals (4.6%, 71/1532) but high in hospital wastewater (50.0%, 27/54). mcr-1 was mainly located on IncI2 (63.0% in wastewater and 62.0% in feces) and IncHI2 plasmids (18.5% in wastewater and 21.1% in feces). High similarity of the mcr-1 context and its carrying plasmids was observed in human and wastewater MCRPEC, with several isolates clustering together. The coexistence of the ESBL gene blaCTX-M with mcr-1 occurred in 19.7% of IncI2 plasmids. Notably, 60.0% of IncHI2 plasmids exhibited co-occurrence of mcr-1 with the disinfectant resistance gene (DRG) qacEΔ1, conferring resistance to quaternary ammonium compounds (QACs). We revealed that QACs, rather than the other two types of disinfectants─ortho-phthalaldehyde (OPA) and povidone-iodine (PVP-I)─select for plasmids carrying both qacEΔ1 and mcr-1 and elevate their conjugative transfer frequency. Monitoring of DRGs in MCRPEC and managing disinfectant use are urgently needed in healthcare settings to mitigate the spread of colistin resistance from hospital environments to inpatients.

Application of a novel phage vB_CjeM_WX1 to control Campylobacter jejuni in foods

Campylobacter jejuni is one of the leading causes of human gastroenteritis. Phage biocontrol is recognized as a natural, environmentally friendly technique that effectively targets pathogens in various foods. In this study, a novel C. jejuni phage named vB_CjeM_WX1 (WX1) was isolated from chicken feces. According to the morphology and genomic analysis, the phage belongs to the Eucampyvirinae genus within the subfamily of Caudoviricetes WX1 exhibited favorable physiological characteristics, as it could maintain its activity even under extreme conditions such as high temperatures (70 °C), acidity (pH = 4), alkalinity (pH = 12), NaCl concentration (1000 mM) and was UV-resistant for 50 min. WX1 could lyse 35 strains of C. jejuni, all of which are highly virulent and multi-drug resistant. Among them, 10 strains of C. jejuni exhibit strong biofilm formation, a critical factor in bacterial persistence and resistance to environmental stressors. The lysis rate of WX1 reached up to 47.3 % in 76 strains of C. jejuni. Phage WX1 inhibited the growth of multi-drug resistant, high virulence and strong biofilm C. jejuni 178-2B in NZCYM broth, as well as greatly reduced biofilm formation on stainless-steel, polyethylene surfaces, and glass. Moreover, phage WX1 decreased the number of C. jejuni in chicken skin to below the detection limit within 48 h. Therefore, phage WX1 can be used in food processing environments and poultry farming, both primary production and during slaughter with a great prospect.

From sequence to significance: A thorough investigation of the distinctive genome features uncovered in C. Werkmanii strain NIB003

Citrobacter werkmanii (C. werkmanii), an opportunistic urinary bacterium that causes diarrhea, is poorly understood. Our research focuses on genetic features that are crucial to disease development, such as pathogenic interactions, antibiotic resistance, virulence genes and genetic variation. Following its morphological, biochemical, and molecular identification, the whole genome of C. werkmanii strain NIB003 was sequenced in Bangladesh for the first time. Despite having around 80% whole genome conservation, the research shows that the Bangladeshi strain forms a separate phylogenetic cluster. This emphasises the genetic variability within C. werkmanii, resulting in particular modifications at the strain level and changes in its ability to cause disease. The results of the genetic diversity analysis indicate that the Bangladeshi sequenced genome is more diverse than the other strains due to the existence of unique features, such as the presence of t-RNA binding domain and N-6 adenine-specific DNA methylases.

Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection

The influx of whole genome sequencing (WGS) data in the public health and clinical diagnostic sectors has created a need for data analysis methods and bioinformatics expertise, which can be a bottleneck for many laboratories. At Sciensano, the Belgian national public health institute, an intuitive and user-friendly bioinformatics tool portal was implemented using Galaxy, an open-source platform for data analysis and workflow creation. The Galaxy @Sciensano instance is available to both internal and external scientists and offers a wide range of tools provided by the community, complemented by over 50 custom tools and pipelines developed in-house. The tool selection is currently focused primarily on the analysis of WGS data generated using Illumina sequencing for microbial pathogen typing, characterization and outbreak detection, but it also addresses specific use cases for other data types. Our Galaxy instance includes several custom-developed 'push-button' pipelines, which are user-friendly and intuitive stand-alone tools that perform complete characterization of bacterial isolates based on WGS data and generate interactive HTML output reports with key findings. These pipelines include quality control, de novo assembly, sequence typing, antimicrobial resistance prediction and several relevant species-specific assays. They are tailored for pathogens with active genomic surveillance programs, and clinical relevance, such as Escherichia coli, Listeria monocytogenes, Salmonella spp. and Mycobacterium tuberculosis. These tools and pipelines utilize internationally recognized databases such as PubMLST, EnteroBase, and the NCBI National Database of Antibiotic Resistant Organisms, which are automatically synchronized on a regular basis to ensure up-to-date results. Many of these pipelines are part of the routine activities of Belgian national reference centers and laboratories, some of which use them under ISO accreditation. This resource is publicly available for noncommercial use at https://galaxy.sciensano.be/ and can help other laboratories establish reliable, traceable and reproducible bioinformatics analyses for pathogens encountered in public health settings.

VFDB 2025: an integrated resource for exploring anti-virulence compounds

With the escalating crisis of bacterial multidrug resistance, anti-virulence therapeutic strategies have emerged as a highly promising alternative to conventional antibiotic treatments. Anti-virulence compounds are specifically designed to target virulence factors (VFs), disarming pathogens without affecting bacterial growth and thus reduce the selective pressure for resistance development. However, due to the complexity of bacterial pathogenesis, no anti-virulence small molecules have been approved for clinical use thus far, despite the documentation of hundreds of potential candidates. To provide valuable reference resources for drug design, repurposing, and target selection, the virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) has systematically collected public data on anti-virulence compounds through extensive literature mining, and further integrated this information with its existing knowledge of bacterial VFs. To date, the VFDB has curated a comprehensive dataset of 902 anti-virulence compounds across 17 superclasses reported by 262 studies worldwide. By cross-linking the current knowledge of bacterial VFs with information on relevant compounds (e.g. classification, chemical structure, molecular targets and mechanisms of action), the VFDB aims to bridge the gap between chemists and microbiologists, providing crucial insights for the development of innovative and effective antibacterial therapies to combat bacterial infections and address antibiotic resistance.

An unignorable human health risk posed by antibiotic resistome and microbiome in urban rivers: Insights from Beijing, China

Urban rivers are the main water bodies humans frequently come into contact with, so the risks posed are closely monitored. Antibiotic resistance genes (ARGs) residues in reclaimed water pose serious risks to human health. There are urgent needs to improve the understanding of distribution of and risks posed by ARGs in urban rivers. In this study, shotgun metagenomic approach was used to characterize ARGs, mobile genetic elements (MGEs), and virulence factors (VFs) in water and sediment from Xinfeng River in Beijing and to identify microbes, potential antibiotic resistant bacteria, and human pathogens (HPs). MGE, microbial community, VF, and ARG co-occurrences were used to assess the environmental risks posed by ARGs. The results indicated that quinolone was the most abundant ARG type and that tufA and fusA were the two dominant ARG subtypes. Wetland effluent increased ARG abundance in the river, and the effect was detected even 50 m downstream. ARG abundances and distribution in the river had difference in different seasons. The dominant bacteria in the river were Proteobacteria, Bacteroidetes, and Actinobacteria, and 59 HPs were detected. In total, 69 MGEs and 19 VFs were found. Co-occurrence networks indicated that potential antibiotic resistant bacteria, MGEs, VFs, and ARGs in the river significantly correlated, indicating the potential risks posed by ARGs. The results improve our understanding of ARG distribution and environmental risks in urban river water. More attention should be paid to controlling environmental risks posed by ARGs in urban river and reclaimed water.

Epidemiology of antimicrobial resistance in commensal Escherichia coli from healthy dairy cattle on a Mediterranean pasture-based system of Australia: A cross-sectional study

This study aimed to determine the prevalence of antimicrobial resistance (AMR) in commensal Escherichia coli from healthy lactating cows and calves in the Mediterranean pasture-based feeding dairy system of Western Australia (WA). Fecal samples were collected from healthy adult lactating cows and healthy calves from dairy farms in WA. Presumptive commensal E. coli was isolated from these samples and confirmed using matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry. Broth microdilution was used to assess the prevalence and the phenotypic AMR profiles of the E. coli isolates to 8 antimicrobial agents of dairy industry and human importance. The minimum inhibitory concentration for each isolate was interpreted using the epidemiologic cutoff (ECOFF) and Clinical and Laboratory Standards Institute breakpoints. Genomic characterization provided multilocus sequence types and AMR genes for a selection of isolates categorized as nonwild type (NWT) by ECOFF values for the combination of ampicillin, trimethoprim-sulfamethoxazole, and tetracycline. From a total of 1,117 fecal samples (633 adult, 484 calf) collected across 26 randomly selected farms, 891 commensal E. coli isolates were recovered (541 adult, 350 calf). Commensal E. coli classified as NWT was highest for ampicillin for both adult (68.8%; 95% CI [64.7, 72.7]) and calf feces (67.1%; 95% CI [62.0, 72.0]). A large proportion of tetracycline NWT and trimethoprim-sulfamethoxazole NWT organisms were also identified from calf feces, being 44.0% (95% CI [38.7, 49.4]) and 24.6% (95% CI [20.2, 29.4]), respectively. Clinical resistance prevalence was low, being higher for calves than for adult feces for ampicillin (adult: 7.8%, 95% CI [5.7, 10.3]; calf: 30.0%, 95% CI [25.2, 35.1]), tetracycline (adult: 6.3%, 95% CI [4.4, 8.7]; calf: 40.3%, 95% CI [35.1, 45.6]), and trimethoprim-sulfamethoxazole (adult: 2.6%, 95% CI [1.4, 4.3]; calf: 22.0%, 95% CI [17.7, 26.7]). Commensal E. coli originating from calf feces was significantly higher in NWT prevalence compared with adult feces for ciprofloxacin, gentamicin, tetracycline, and trimethoprim-sulfamethoxazole. The overall number of antimicrobials an isolate was classified as NWT toward varied among farms and was significantly higher for isolates originating from calf rather than adult feces. The strain type and sampling source of the commensal E. coli investigated were both associated with the commonality of the resultant resistance genome. Clinical resistance and NWT classification were highest for ampicillin, tetracycline, and trimethoprim-sulfamethoxazole, all antimicrobials commonly used in the treatment of dairy cattle in Australia. Although highly variable across farms, commensal E. coli isolated from healthy dairy calf feces had significantly higher NWT and multidrug resistance (MDR) prevalence compared with feces from healthy adult lactating dairy cows. The resistant genome identified in MDR isolates, although not always consistent with the phenotype, included QnrS1 and genes encoding AmpC β-lactamase and aminoglycoside phosphotransferase.

Massilia shenzhen sp. nov., isolated from blood of one premature infant, causing sepsis

This study explores a premature infant with respiratory failure and pneumonia, suggestive of neonatal sepsis. Despite initially negative clinical specimens, blood testing revealed a pathogen. MALDI-TOF-MS and physiological tests initially failed to identify it accurately. Subsequent analysis of the 16S rRNA gene, housekeeping genes, and whole genome sequencing placed it in the genus Massilia. Average Nucleotide Identities (ANIs) indicated 88.47 % similarity with the type strain of Massilia norwichensis. Detailed characterization showed it as Gram-negative, aerobic, flagellated, measuring 0.45-0.55 × 1.75-2.40 μm. Major fatty acids included C16:0, C16:1ω7c, C18:1ω7c, and cyclo-C17:0. Minimum inhibitory concentrations to ceftazidime, penicillin, and meropenem were <0.032 μg/mL, ≤0.75 μg/mL, and <0.002 μg/mL respectively. Phylogenetic analysis, fatty acid composition, and physiological parameters confirmed it as Massilia shenzhen sp. nov., with strain GZ0329T. Given limited research on Massilia drug resistance, ceftazidime and imipenem show promise in treating Massilia infections.

Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications

A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including Escherichia coli, Klebsiella/Raoultella spp., Salmonella spp. and Vibrio spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.

Molecular Epidemiology and Antimicrobial Resistance of Klebsiella pneumoniae Strains Isolated From Dairy Cows in Xinjiang, China

BACKGROUND

Klebsiella pneumoniae is an opportunistic pathogen that causes severe infections in humans and animals. Nonetheless, little is known about the molecular epidemiology of mastitis-associated K. pneumoniae in dairy cows.

OBJECTIVES

This cross-sectional study investigated the epidemiology and antimicrobial resistance (AMR) of K. pneumoniae in 700 milk samples collected from cows with and without mastitis in seven dairy farms in Xinjiang, China.

METHODS

K. pneumoniae was identified by PCR amplification of the khe gene and the automated VITEK 2 Compact System. Resistance against 18 antimicrobial agents was analysed by broth microdilution. Forty-four new strains were sequenced by whole-genome sequencing (WGS). WGS data were searched for the presence of AMR and virulence genes. Genotypic characterization was performed by multilocus sequence typing and the analysis of wzi allele types and K and O antigens.

RESULTS

K. pneumoniae isolates were found in 131 samples (18.7%). The prevalence of K. pneumoniae in cows with clinical and subclinical mastitis was higher than that in healthy cows (27.1%, 23.2% and 7.3%, respectively). WGS identified 27 wzi allele types, 16 K antigen serotypes, 6 O antigen serotypes and 25 sequence types. Phylogenetic analysis showed high genomic diversity in K. pneumoniae. The rate of resistance to tetracycline and cefazolin was 39.7% and 31.3%, and the multidrug resistance rate was 26.7%. Thirty-nine AMR genes conferring resistance to nine antibiotic classes and 57 virulence genes were identified in new isolates. AMR and virulence genes were more prevalent in known human isolates than in new isolates.

CONCLUSIONS

These results improve our understanding of the epidemiology and resistance status of mastitis-associated K. pneumoniae strains. The emergence and spread of multidrug-resistant K. pneumoniae strains threaten food safety and public health.

Nasopharyngeal carriage of Staphylococcus aureus in a rural population, Sierra Leone

BACKGROUND

Nasopharyngeal colonization with Staphylococcus aureus is a risk factor for subsequent infection. Isolates from colonization can therefore provide important information on virulence factors and antimicrobial resistance when data from clinical isolates are lacking. The aim of this study was to assess colonization rates, resistance patterns and selected virulence factors of S. aureus from rural Sierra Leone.

METHODS

Residents of randomly selected houses in Masanga, Sierra Leone were included in a cross-sectional study (8-11/2023). Participants were tested for nasopharyngeal S. aureus colonization using selective culture media. Risk factors for colonization were documented in a standardized questionnaire. Isolates were genotyped and tested for antimicrobial susceptibility and selected virulence factors (e.g. Panton-Valentine leukocidin, capsular types).

RESULTS

Of 300 participants (62.7 % females, median age: 16 years), 168 (56 %) were colonized with S. aureus-related complex; six participants carried two different S. aureus genotypes, resulting in a total number of 174 isolates. Resistance to penicillin was predominant (97.1 %, 169/174), followed by tetracycline (66.1 %, 115/174), co-trimoxazole (56.9 %, 99/174) and oxacillin (24.1 %, 42/174, all mecA-positive, mostly associated with ST8/PVL-negative). PVL gene was detected in 21.3 % of isolates (37/174) mainly associated with ST15 and ST152. Except for past use of antimicrobials (p = 0.019), no specific risk factors such as comorbidities including hemoglobin variants were associated with S. aureus nasopharyngeal colonization.

CONCLUSION

The prevalence of methicillin-resistant and PVL-positive methicillin-susceptible S. aureus (MRSA/MSSA) is high in a rural community of asymptomatic carriers in Sierra Leone. Measures to contain the spread of MRSA, also in the community, are needed.

Tiled Amplicon Sequencing Enables Culture-free Whole-Genome Sequencing of Pathogenic Bacteria From Clinical Specimens

Pathogen sequencing is an important tool for disease surveillance and demonstrated its high value during the COVID-19 pandemic. Viral sequencing during the pandemic allowed us to track disease spread, quickly identify new variants, and guide the development of vaccines. Tiled amplicon sequencing, in which a panel of primers is used for multiplex amplification of fragments across an entire genome, was the cornerstone of SARS-CoV-2 sequencing. The speed, reliability, and cost-effectiveness of this method led to its implementation in academic and public health laboratories across the world and adaptation to a broad range of viral pathogens. However, similar methods are not available for larger bacterial genomes, for which whole-genome sequencing typically requires in vitro culture. This increases costs, error rates and turnaround times. The need to culture poses particular problems for medically important bacteria such as Mycobacterium tuberculosis, which are slow to grow and challenging to culture. As a proof of concept, we developed two novel whole-genome amplicon panels for M. tuberculosis and Streptococcus pneumoniae. Applying our amplicon panels to clinical samples, we show the ability to classify pathogen subgroups and to reliably identify markers of drug resistance without culturing. Development of this work in clinical settings has the potential to dramatically reduce the time of diagnosis of drug resistance for multiple drugs in parallel, enabling earlier intervention for high priority pathogens.

Virome assembly reveals draft genomes of native Pseudomonas phages isolated from a paediatric bronchoalveolar lavage sample

We present lung virome data recovered through shotgun metagenomics in bronchoalveolar lavage fluid from an infant with cystic fibrosis, who tested positive for Stenotrophomonas maltophilia infection. Using a bioinformatic pipeline for virus characterization in shotgun metagenomic data, we identified five viral contigs representing Pseudomonas phages classified as Caudoviricetes.

Whole Genome Sequencing of a Non-O1/O139-Group Vibrio cholerae Isolated from a Patient with a Bloodstream Infection

Background

Diarrhea caused by non-O1/O139-group V. cholerae (NOVC) tends to be mild and can be readily overlooked. In this report, a NOVC strain designated XXM was isolated from the blood of a 68-year-old male undergoing surgical treatment for a bile duct malignancy in October 2023.

Methods

XXM was identified through a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Virulence genes were detected using a V. cholerae ctxA/ctxB virulence gene dual real-time fluorescent PCR kit. AST-GN13 and AST-GN334 cards were used to test the resistance against 16 antibiotics with a Vitek2 compact system. The genomic and phylogenetic characteristics of XXM were established through whole genome sequencing (WGS).

Results

Serum agglutination tests revealed the isolate to be a non-O1/non-O139 strain. The strain was sensitive to all 16 tested antibiotics and did not carry the ctxA/ctxB gene. MLST analyses identified the XXM strain as ST1538. WGS analyses identified 8 classes of virulence genes with different functions. A total of 3.541 bacterial genes, including 3.482 from V. cholerae, were annoted using the Non-Redundant Protein Sequence (NR) database. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses annotated 32 genes including 17 key proteins involved in the V. cholerae biofilm pathway. Comparative analyses using the Pathogen Host Interactions Database (PHI) identified the YbeY gene. Evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) was used to annotate 3280 genes in 21 categories. Phylogenetic analyses revealed that strain XXM was closely related to V. cholerae strain Man9.

Conclusion

The XXM carries multiple virulence genes, and this genomic analysis of the XXM in comparison with other NOVC strains provides important information for an improved understanding of the pathogenicity of NOVC in clinical samples.

Antibiotic susceptibility testing and molecular characterization based on whole-genome sequencing of Streptococcus pneumoniae isolates from pediatric infections at the National Regional Medical Center of Southwest China during the COVID-19 pandemic

Background

Streptococcus pneumoniae is a transmitted respiratory pathogen that causes high morbidity and mortality in children, especially those under 5 years of age. During the implementation of population control measures for COVID-19 in mainland China, the Streptococcus pneumoniae detection rate in pediatric patients decreased. However, with the second wave of the COVID-19 pandemic (2022), the incidence of pneumococcal disease (PD) and even invasive pneumococcal disease (IPD) began to rise again.

Methods

This study was conducted from August 2022 to September 2023 at a national regional medical center based mainly in West China Second University Hospital, Sichuan University. The demographic and clinical characteristics of S. pneumoniae-infected pediatric patients were analyzed. All S. pneumoniae isolates were subjected to standardized clinical sample inoculation, culture, subculture, and identification procedures. Next-generation sequencing and analysis were used to determine serotypes and sequence types (STs) and evaluate antibiotic resistance- and virulence-related genes. Antimicrobial susceptibility was determined in AST dishes via the broth microdilution method.

Results

The prevalent serotypes in the IPD patients were 14, 6A, and 23F, and the prevalent serotypes in the NIPD patients were 19F and 6A. A significant difference in the proportion of patients with serotype 14 was noted between the two groups. A total of 23 STs were identified and classified into 13 different GPSC lineages, including 4 novel STs (ST18449, ST18451, ST18464 and ST18466) and 1 novel allele (ddl1209). According to the interpretation breakpoints for non-meningitis infections, the resistance/nonsusceptibility rates of invasive isolates were as follows: penicillin (0.0%/8.3%), amoxicillin (0.0%/0.0%), cefotaxime (8.3%/16.6%), ceftriaxone (8.3%/8.3%), and cefepime (0.0%/8.3%). The resistance/nonsusceptibility rates of invasive isolates according to the meningitis breakpoints were as follows: penicillin (100.0%), cefotaxime (16.7%/33.4%), ceftriaxone (8.3%/50.0%), and cefepime (8.3%/66.7%). All the isolates were susceptible to rifampicin, levofloxacin, moxifloxacin, linezolid and vancomycin. In addition, the characteristics of the antibiotic resistance-related genes and virulence genes of serotype 19F were significantly different from those of the other serotypes.

Conclusion

These data provide valuable information for understanding pediatric pneumococcal disease during the second outbreak of COVID-19 in Southwest China and will contribute to the prevention and treatment of S. pneumoniae infection.

Characterization of novel sequence type 12531 and O8:H7 serotype carbapenem-resistant Escherichia coli with strong swimming and intestinal epithelial cell barrier migration abilities

Carbapenem-resistant Enterobacteriaceae have become widely prevalent globally because of antibiotic misuse and the spread of drug-resistant plasmids, where carbapenem-resistant Escherichia coli (CREC) is one of the most common and prevalent pathogens. Furthermore, E. coli has been identified as a member of normal gut flora and does not cause disease under normal circumstances. However, certain strains of E. coli, due to the expression of virulence genes, can cause severe intestinal and extra-intestinal infections. Therefore, clinically, drug resistance and pathogenic E. coli strains are significantly challenging to treat. In this study, a novel CREC strain DC8855 was isolated from the ascites of a patient with intestinal perforation, identified as a novel sequence type 12531 (ST12531) and an unreported serotype O8:H7. It was revealed that the resistance of ST12531 CREC was predominantly conferred by an IncFII(K) plasmid carrying blaNDM-4. Furthermore, phylogenetic analysis indicated that this is the first discovery of such plasmids in China and the first identification in E. coli. Moreover, regarding virulence, the swimming assays, qRT-PCR, and in vitro intestinal barrier model indicated that DC8855 had significantly higher motility, flagella gene expression, and intestinal epithelial cell barrier migration ability than the other sequence types CREC strains (ST167 and ST410). In conclusion, this study identified novel CREC which was multidrug resistant as well as enteropathogenic and therefore requires continuous monitoring.

Genomic Investigation and Comparative Analysis of European High-Risk Clone of Acinetobacter baumannii ST2

Multidrug-resistant Acinetobacter baumannii is a major concern in healthcare institutions worldwide. Several reports described the dissemination of A. baumannii high-risk clones that are responsible for a high number of difficult-to-treat infections. In our study, 19 multidrug-resistant A. baumannii strains from Budapest, Hungary, were investigated based on whole-genome sequencing (WGS). The obtained results were analysed together with data from 433 strains of A. baumannii from the Pathogenwatch database. WGS analysis of 19 A. baumannii strains detected that 12 belonged to ST2 and seven belonged to ST636. Among ST2 strains, 11 out of 12 carried either blaOXA-23 or blaOXA-58 genes; however, all strains of ST636 uniformly carried blaOXA-72 gene. All strains of ST2 and ST636 carried blaOXA-66 and blaADC-25 genes. Based on core genome multilocus sequence typing (cgMLST), 10 strains of ST2 belonged to cgMLST906, one strain to cgMLST458, and one strain to cgMLST1320; by contrast, all strains of ST636 belonged to cgMLST1178. Certain virulence determinants were present in all strains of both ST2 and ST636, namely, Ata, Bap, BfmRS, T2SS and PNAG. Interestingly, OmpA was present in all strains of ST2, but it was absent in all strains of ST636. Comparative analysis of 19 strains of this study and the collection of 433 isolates from Pathogenwatch database, proved a diverse clonal distribution of high-risk A. baumannii clones in Europe. The major clone in Europe is ST2, which is present all over the continent. However, ST636 has been mainly reported in Eastern Europe. Interestingly, cgMLSTs of ST2 correspond to the production of different beta-lactamases, namely, OXA-82 in cgMLST116, OXA-72 in cgMLST506, and cgMLST556, PER-1 in cgMLST456 and cgMLST1041. Our study demonstrates that the ST2 high-risk clone of A. baumannii is the most widespread in Europe; however, based on cgMLST analysis, a detailed detection of beta-lactamase production can be determined.

Genetic, virulence, and antimicrobial resistance characteristics associated with distinct morphotypes in ST11 carbapenem-resistant Klebsiella pneumoniae

ST11 is the most common lineage among carbapenem-resistant Klebsiella pneumoniae (CRKP) infections in Asia. Diverse morphotypes resulting from genetic mutations are associated with significant differences in microbial characteristics among K. pneumoniae isolates. Here, we investigated the genetic determinants and critical characteristics associated with distinct morphotypes of ST11 CRKP. An ST11-KL47 CRKP isolate carrying a pLVPK-like virulence plasmid was isolated from a patient with a bloodstream infection; the isolate had the "mcsw" morphotype. Two distinct morphotypes ("ntrd" and "msdw") were derived from this strain during in vitro passage. Whole genome sequencing was used to identify mutations that cause the distinct morphotypes of ST11 CRKP. Transmission electron microscopy, antimicrobial susceptibility tests, growth assays, biofilm formation, virulence assays, membrane permeability assays, and RNA-seq analysis were used to investigate the specific characteristics associated with different morphotypes of ST11 CRKP. Compared with the parental mcsw morphotype, the ntrd morphotype resulted from mutation of genes involved in capsular polysaccharide biosynthesis (wza, wzc, and wbaP), a result validated by gene knockout experiments. This morphotype showed capsule deficiency and lower virulence potential, but higher biofilm production. By contrast, the msdw morphotype displayed competition deficiency and increased susceptibility to chlorhexidine and polymyxin B. Further analyses indicated that these characteristics were caused by interruption of the sigma factor gene rpoN by insertion mutations and deletion of the rpoN gene, which attenuated membrane integrity presumably by downregulating the phage shock protein operon. These data expand current understanding of genetic, virulence, and antimicrobial resistance characteristics associated with distinct morphotypes in ST11 CRKP.

New Campylobacter Lineages in New Zealand Freshwater: Pathogenesis and Public Health Implications

This study investigated the diversity of thermophilic Campylobacter species isolated from three New Zealand freshwater catchments affected by pastoral and urban activities. Utilising matrix-assisted laser desorption ionisation-time of flight and whole genome sequence analysis, the study identified Campylobacter jejuni (n = 46, 46.0%), C. coli (n = 39, 39%), C. lari (n = 4, 4.0%), and two novel Campylobacter species lineages (n = 11, 11%). Core genome sequence analysis provided evidence of prolonged persistence or continuous faecal shedding of closely related strains. The C. jejuni isolates displayed distinct sequence types (STs) associated with human, ruminant, and environmental sources, whereas the C. coli STs included waterborne ST3302 and ST7774. Recombination events affecting loci implicated in human pathogenesis and environmental persistence were observed, particularly in the cdtABC operon (encoding the cytolethal distending toxin) of non-human C. jejuni STs. A low diversity of antimicrobial resistance genes (aadE-Cc in C. coli), with genotype/phenotype concordance for tetracycline resistance (tetO) in three ST177 isolates, was noted. The data suggest the existence of two types of naturalised waterborne Campylobacter: environmentally persistent strains originating from waterbirds and new environmental species not linked to human campylobacteriosis. Identifying and understanding naturalised Campylobacter species is crucial for accurate waterborne public health risk assessments and the effective allocation of resources for water quality management.

Genomic epidemiology of Clostridioides difficile sequence type 35 reveals intraspecies and interspecies clonal transmission

Clostridioides difficile sequence type (ST) 35 has been found in humans and animals worldwide. However, its genomic epidemiology and clonal transmission have not been explored in detail. In this study, 176 C. difficile ST35 isolates from six countries were sequenced. Genomic diversity, clonal transmission and epidemiological data were analyzed. Sporulation and virulence capacities were measured. Four ribotypes (RT) were identified including RT046 (97.2%), RT656 (1.1%), RT427 (0.6%), and RT AI-78 (1.1%). Phylogenetic analysis of 176 ST35 genomes, along with 50 publicly available genomes, revealed two distinctive lineages without time-, region-, or source-dependent distribution. However, the distribution of antimicrobial resistance genes differed significantly between the two lineages. Nosocomial and communal transmission occurred in humans with the isolates differed by ≤ two core-genome single-nucleotide polymorphism (cgSNPs) and clonal circulation was found in pigs with the isolates differed by ≤ four cgSNPs. Notably, interspecies clonal transmission was identified among three patients with community acquired C. difficile infection and pigs with epidemiological links, differed by ≤ nine cgSNPs. Toxin B (TcdB) concentrations were significantly higher in human isolates compared to pig isolates, and ST35 isolates exhibited stronger sporulation capacities than other STs. Our study provided new genomic insights and epidemiological evidence of C. difficile ST35 intraspecies and interspecies clonal transmission, which can also be facilitated by its strong sporulation capacity.

A prospective cohort study to investigate the transmission and burden of Staphylococcus aureus in Sri Lanka

Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of infection in both community and healthcare settings, and the household may be a central component linking these two environments. Strategies to prevent S. aureus transmission and thereby reduce the risk of infection must be informed by a detailed understanding of local epidemiology. These data are typically lacking in many low- and middle-income countries. Therefore, we aimed to investigate the circulation of infecting S. aureus strains in Sri Lanka, with a focus on the community and healthcare interface. A prospective longitudinal cohort study was performed between July and December 2021. Index patients with S. aureus infection and up to four of their household contacts were enrolled in the study. Colonization was assessed by sampling participants' nose and axilla at two time points over 3 months of follow-up. Whole-genome sequencing (WGS) was used to characterize isolates and assess strain similarity to identify transmission episodes and environmental clusters. A total of 153 participants were recruited, including 42 S. aureus-positive index patients and 111 household contacts. The baseline prevalence of S. aureus colonization amongst household contacts was 11.7% (13/111), of which 30.8% (4/13) were methicillin-resistant. A total of 88 S. aureus isolates underwent WGS and three multilocus sequence types predominated: ST672, ST5 and ST6. Each type had unique virulence characteristics but was identified in both community and healthcare environments. Colonization of household members with the index's infecting strain was not detected. S. aureus is a major cause of morbidity and mortality in low-resource settings such as Sri Lanka, yet little is known about risk factors and transmission networks. In this descriptive study, we have identified a small number of strains that appear to be well established and capable of causing both severe infection and asymptomatic colonization. Transmission of S. aureus did not appear to be occurring frequently in the household, and, therefore, preventative strategies that target high-risk groups may be more successful than universal community-based measures.

Staphylococcus aureus colonizing the skin microbiota of adults with severe atopic dermatitis exhibits genomic diversity and convergence in biofilm traits

Atopic dermatitis (AD) is a chronic inflammatory skin disorder exacerbated by Staphylococcus aureus colonization. The specific factors that drive S. aureus overgrowth and persistence in AD remain poorly understood. This study analyzed skin barrier functions and microbiome diversity in lesional (LE) and non-lesional (NL) forearm sites of individuals with severe AD compared to healthy control subjects (HS). Notable differences were found in transepidermal water loss, stratum corneum hydration, and microbiome composition. Cutibacterium was more prevalent in HS, while S. aureus and S. lugdunensis were predominantly found in AD LE skin. The results highlighted that microbial balance depends on inter-species competition. Specifically, network analysis at the genus level demonstrated that overall bacterial correlations were higher in HS, indicating a more stable microbial community. Notably, network analysis at the species level revealed that S. aureus engaged in competitive interactions in NL and LE but not in HS. Whole-genome sequencing (WGS) showed considerable genetic diversity among S. aureus strains from AD. Despite this variability, the isolates exhibited convergence in key phenotypic traits such as adhesion and biofilm formation, which are crucial for microbial persistence. These common phenotypes suggest an adaptive evolution, driven by competition in the AD skin microenvironment, of S. aureus and underscoring the interplay between genetic diversity and phenotypic convergence in microbial adaptation.

KPC variants conferring resistance to ceftazidime-avibactam in Pseudomonas aeruginosa strains

BACKGROUND

This study aimed to characterize three KPC variants (KPC-33, KPC-100, and KPC-201) obtained from a clinical isolate of Pseudomonas aeruginosa (#700), along with two induced strains C109 and C108.

METHODS

Genomic DNAs of #700 (ST235), C109 (ST463), and C108 (ST1076) were sequenced using Illumina and Oxford Nanopore technologies. The transferability and stability of the plasmid was assessed through conjugation experiments and plasmid stability experiments, respectively. Minimum inhibitory concentrations of bacterial strains were determined using broth microdilution methods. In vitro induction was performed using ceftazidime-avibactam (CZA) at concentrations of 6/4 µg/ml. Linear genomic alignments were visualized using Easyfig, and protein structure modeling of the novel KPC variant (KPC-201) was conducted using PyMol.

RESULTS

The plasmids carrying the KPC variants in the three CZA-resistant strains (C109, C108, and #700) had sizes of 39,251 bp (KPC-100), 394,978 bp (KPC-201), and 48,994 bp (KPC-33). All three plasmids belonged to the IncP-like incompatibility (Inc) groups, and the plasmid exhibited relatively high plasmid stability, KPC-33 and KPC-201-harboring plasmids were successfully transferred to the recipient strain P. aeruginosa PAO1rifR. The genetic environments of the three blaKPC genes differed from each other. The mobile elements of the three blaKPC genes were as follows, TnAS1-IS26-ΔISKpn27-blaKPC-33-ISKpn6-IS26, IS6-ΔISKpn27-blaKPC-100-ISKpn6-IS26-Tn3-IS26, and IS6100-ISKpn27-blaKPC-201-ISKpn6-TnAS1. Notably, the length of ΔISKpn27 upstream of the blaKPC-33 and blaKPC-100 genes were remarkably short, measuring 114 bp and 56 bp, respectively, deviating significantly from typical lengths associated with ISKpn27 elements. Moreover, the novel KPC variant, KPC-201, featured a deletion of amino acids LDR at positions 161-163 in KPC-3, resulting in a looser pocket structure contributing to its avibactam resistance.

CONCLUSIONS

KPC-201, identified as a novel KPC variant, exhibits resistance to CZA. The presence of multiple mobile elements surrounding the blaKPC-variant genes on stable plasmids is concerning. Urgent preventive measures are crucial to curb its dissemination in clinical settings.

Whole genome sequence data of ZEN-degrading strain Levilactobacillus brevis PYN10_6_2 isolated from Tenebrio molitor larval feces

Levilactobacillus brevis PYN10_6_2, a lactic acid bacterial strain previously isolated from Tenebrio molitor larval feces, possesses the ability to convert zearalenone (ZEN) to α-/β-Zearalenol (α-/β-ZEL). However, the genes involved in the ZEN reduction reaction and the biosafety of this strain remain unknown. In this study, we sequenced, assembled, and annotated the whole genome of L. brevis PYN10_6_2. Genomic sequencing was conducted using short-read sequencing on the Illumina HiSeq X Ten platform and long-read sequencing on the PacBio RS II Single Molecule Real-Time (SMRT) platform. The assembled genome consisted of one circular chromosome, four circular plasmids, with a total size of 2,745,725 bp and a G + C content of 45.52 %. Annotation identified 2,660 coding sequences, 5 rRNAs, 66 tRNAs, and a single CRISPR locus. Average nucleotide identity (ANI) between L. brevis PYN10_6_2 and L. brevis DSM 20054T yielded a value of 98.94 %. Further in-depth analysis revealed 182 antibiotic resistance genes, 237 putative virulence genes, 2 prophages, and 10 genomic islands. Additionally, functional annotation through COG and KEGG databases revealed the presence of three genes encoding 3α- and 3β-hydroxysteroid dehydrogenase (3α-/3β-HSD) within the bacterial chromosome. This comprehensive genomic characterization provides valuable insights into the genetic basis of L. brevis PYN10_6_2's ZEN-reducing ability and its biosafety profile.

Whole genome sequencing reveals circulation of potentially virulent Listeria innocua strains with novel genomic features in cattle farm environments in Dhaka, Bangladesh

Through the last decade, Listeria spp. has been detected in food and environmental samples in Bangladesh. However, the genomic information of this bacterium that prevails in the country remains scarce. This study analyzed the complete genome sequences of two Listeria spp. isolates obtained from cow dung and their drinking water collected from a cattle farm in Dhaka, Bangladesh. Both the isolates were identified as Listeria innocua, which shared almost identical genomic features. The genome sequences demonstrated the presence of 13 virulence genes associated with invasion (iap/cwhA, gtcA, and lpeA), surface protein anchoring (lspA), adherence (fbpA, and lap), intracellular survival (lplA1, and prsA2), peptidoglycan modification (oatA, and pdgA), and heat stress (clpC, clpE, and clpP). Additionally, the gene fosX, conferring resistance to fosfomycin, and two copper resistance-associated genes, copC and csoR, were identified in both. The genome sequences also revealed two plasmid replicons, rep25 and rep32, along with three insertion sequences [ISLmo3 (CP022021), ISLmo7 (CP006611), ISS1N (M37395)]. Notably, a composite transposon [CN_8789_ISS1N (M37395)], was detected in both L. innocua isolates, representing the first documented occurrence of this particular composite transposon in any reported Listeria species. Furthermore, the genomes contained four prophage regions [Listeria phage LP-030-2 (NC_021539), Listeria phage vB_LmoS_188 (NC_028871), Listeria phage A118 (NC_003216) and Escherichia phage RCS47 (NC_042128)]. Two CRISPR arrays were also identified, one belonging to the family type II-A. Multilocus Sequence Typing (MLST) analysis classified the L. innocua isolates of the same sequence type, ST-637. Single nucleotide polymorphism (SNP) analysis uncovered the presence of 231-340 SNPs between the L. innocua isolates and their closely related global lineage. In contrast, only 42 SNPs were identified between the two isolates, suggesting a potential transmission of L. innocua between cow dung and cattle farm water. The presence of L. innocua isolates harboring virulence genes associated with ruminant infection in the cattle farm environment of Bangladesh raises significant concerns about the potential presence of other human and animal pathogens. This poses a serious threat to the cattle farming industry. Additionally, the genomic analysis of the L. innocua isolates enhances our understanding of the evolutionary dynamics of Listeria species.

Desiccation tolerance and reduced antibiotic resistance: Key drivers in ST239-III to ST22-IV MRSA clonal replacement at a Malaysian teaching hospital

Molecular surveillance of methicillin-resistant Staphylococcus aureus (MRSA) isolated from Hospital Canselor Tuanku Muhriz (HCTM), a Malaysian teaching hospital revealed clonal replacement events of SCCmec type III-SCCmercury to SCCmec type IV strains before the year 2017; however, the reasons behind this phenomenon are still unclear. This study aimed to identify factors associated with the clonal replacement using genomic sequencing and phenotypic investigations (antibiogram profiling, growth rate and desiccation tolerance determination, survival in vancomycin sub-minimum inhibitory concentration (MIC) determination) of representative HCTM MRSA strains isolated in four-year intervals from 2005 - 2017 (n = 16). HCTM Antimicrobial Stewardship (AMS) and Infection Prevention and Control (IPC) policies were also reviewed. Phylogenetic analyses revealed the presence of 3 major MRSA lineages: ST239-III, ST22-IV and ST6-IV; MRSAs with the same STs shared similar core and accessory genomes. Majority of the ST239-III strains isolated in earlier years of the surveillance (2005, 2009 and 2013) were resistant to many antibiotics and harboured multiple AMR and virulence genes compared to ST22-IV and ST6-IV strains (isolated in 2013 and 2017). Interestingly, ST22-IV and ST6-IV MRSAs grew significantly faster and were more resistant to desiccation than ST239-III (p < 0.05), even though the later clone survived better post-vancomycin exposure. Intriguingly, ST22-IV was outcompeted by ST239-III in broth co-cultures; though it survived better when desiccated together with ST239-III. Higher desiccation tolerance and fewer carriage of AMR genes by ST22-IV, together with reduction of antibiotic selection pressure in HCTM (due to AMS and IPC policies) during 2005 - 2017 may have provided the clone a competitive edge in replacing the previously dominant ST239-III in HCTM. This study highlights the importance of MRSA surveillance for a clearer picture of circulating clones and clonal changes. To our knowledge, this is the first genomic epidemiology study of MRSA in Malaysia, which will serve as baseline genomic data for future surveillance.

Comprehensive lung microbial gene and genome catalogs assist the mechanism survey of Mesomycoplasma hyopneumoniae strains causing pig lung lesions

Understanding the community structure of the lower respiratory tract microbiome is crucial for elucidating its roles in respiratory tract diseases. However, there are few studies about this topic due to the difficulty in obtaining microbial samples from both healthy and disease individuals. Here, using 744 high-depth metagenomic sequencing data of lower respiratory tract microbial samples from 675 well-phenotyped pigs, we constructed a lung microbial gene catalog containing the largest scale of 10,031,593 nonredundant genes to date, 44.8% of which are novel. We obtained 356 metagenome-assembled genomes (MAGs) which were further clustered into 256 species-level genome bins with 41.8% being first reported in the current databases. Based on these data sets and through integrated analysis of the isolation of the related bacterial strains, in vitro infection, and RNA sequencing, we identified and confirmed that Mesomycoplasma hyopneumoniae (M. hyopneumoniae) MAG_47 and its adhesion-related virulence factors (VFs) were associated with lung lesions in pigs. Differential expression levels of adhesion- and immunomodulation-related VFs likely determined the heterogenicity of adhesion and pathogenicity among M. hyopneumoniae strains. M. hyopneumoniae adhesion activated several pathways, including nuclear factor kappa-light-chain-enhancer of activated B, mitogen-activated protein kinase, cell apoptosis, T helper 1 and T helper 2 cell differentiation, tumor necrosis factor signaling, interleukin-6/janus kinase 2/signal transducer and activator of transcription signaling, and response to reactive oxygen species, leading to cilium loss, epithelial cell‒cell barrier disruption, and lung tissue lesions. Finally, we observed the similar phylogenetic compositions of the lung microbiome between humans with Mycoplasma pneumoniae and pigs infected with M. hyopneumoniae. The results provided important insights into pig lower respiratory tract microbiome and its relationship with lung health.

Integrating Diagnostic Approaches in Infant Bacterial Meningitis Caused by a Non-K1 Escherichia coli: A Case Report

BACKGROUND

Infant meningitis, particularly caused by Escherichia coli, remains a life-threatening condition, especially in premature and low-weight infants. Infections of the central nervous system can be fatal, necessitating prompt diagnosis and appropriate treatment. Acute infections caused by various pathogens, including E. coli, often present with similar clinical symptoms. The rapid identification of pathogens and their antimicrobial resistance mechanisms is critical for timely and effective treatment. We report the case of an 8-month-old patient who presented with fever, diarrhea, and convulsive seizures and was subsequently diagnosed with meningitis. Despite initial empirical treatment with ceftriaxone, the patient's condition worsened.

METHODS

At Bambino Gesù Children's Hospital, molecular diagnostic tools, including the FilmArray Meningitis/Encephalitis and Blood Culture Identification panels, were employed.

RESULTS

Although the Meningitis panel did not detect any pathogens due to the lack of the specific bacterial target, the off-label use of the Blood Culture Identification panel identified a non-K1 Escherichia coli strain carrying the CTX-M resistance gene, an extended-spectrum beta-lactamase (ESBL). Despite the rapid diagnostic approach and adjustment of antibiotic therapy, the patient succumbed to the infection due to the strain's high virulence and multidrug resistance. Whole-genome sequencing further characterized the strain, revealing that it belonged to the ST131 group, a highly resistant and virulent strain associated with sepsis.

CONCLUSIONS

This case highlights the importance of integrating advanced molecular diagnostics, such as whole-genome sequencing, with traditional methods to improve pathogen detection, especially in cases of emerging resistant strains that are not covered by standard diagnostic panels. It also emphasizes the need for the continuous adaptation of diagnostic tools to include non-K1 E. coli strains for more comprehensive and timely meningitis diagnosis.

Molecular evidence that GBS early neonatal sepsis results from ascending infection: comparative hybrid genomics analyses show that microorganisms in the vaginal ecosystem, amniotic fluid, chorioamniotic membranes, and neonatal blood are the same

OBJECTIVES

Streptococcus agalactiae, or Group B Streptococcus (GBS), is a leading cause of neonatal sepsis. Materno-fetal transmission of the microorganisms present in the lower genital tract/perineum is considered to be the most frequent mode for acquisition of infection. It has also been proposed that, in a subset of cases, GBS causes acute chorioamnionitis, intraamniotic infection, and fetal/neonatal sepsis. However, the evidence to support this ascending pathway is derived from microbiologic studies that rely on cultivation methods, which do not have the resolution to determine if the microorganisms causing neonatal sepsis are the same as those found in the amniotic fluid and the vaginal ecosystem.

METHODS

We used whole genome sequencing of the microorganisms isolated from the vagina, amniotic fluid, chorioamniotic membranes, and neonatal blood (four isolates) in a case of early neonatal sepsis. Using hybrid genome assembly, we characterized the genomic features including virulence factors and antimicrobial resistance in four isolates from the same mother, placenta, and newborn.

RESULTS

Whole genome sequencing revealed that the microorganisms in the four clinical isolates corresponded to S. agalactiae sequence type 1, clonal complexes 1, and serotype Ib. Comparative genomic analysis illustrated similar DNA sequences of the four genomes.

CONCLUSIONS

This study presents the first evidence of the genomic similarity of microorganisms in the vaginal ecosystem, the space between the chorioamniotic membranes of the placenta, amniotic fluid, and neonatal blood.

Whole-Genome Sequence and Characterization of Ralstonia solanacearum MLY102 Isolated from Infected Tobacco Stalks

BACKGROUND/OBJECTIVES

Bacterial wilt disease is a soil-borne disease caused by Ralstonia solanacearum that causes huge losses to crop economies worldwide.

METHODS

In this work, strain MLY102 was isolated and further identified as R. solanacearum from a diseased tobacco stalk. The genomic properties of MLY102 were explored by performing biochemical characterization, genome sequencing, compositional analysis, functional annotation and comparative genomic analysis.

RESULTS

MLY102 had a pinkish-red color in the center of the colony surrounded by a milky-white liquid with fluidity on TTC medium. The biochemical results revealed that MLY102 can utilize carbon sources, including D-glucose (dGLU), cane sugar (SAC) and D-trehalose dihydrate (dTRE). Genome sequencing through the DNBSEQ and PacBio platforms revealed a genome size of 5.72 Mb with a G+C content of 67.59%. The genome consists of a circular chromosome and a circular giant plasmid with 5283 protein-coding genes. A comparison of the genomes revealed that MLY102 is closely related to GMI1000 and CMR15 but has 498 special genes and 13 homologous genes in the species-specific gene family, indicating a high degree of genomic uniqueness.

CONCLUSIONS

The unique characteristics and genomic data of MLY102 can provide important reference values for the prevention and control of bacterial wilt disease.

Isolation, characterization, and whole genome sequencing analysis of Aeromonas veronii from Channa argus in China

Aeromonas veronii has emerged as a significant pathogen that impacts both fish and mammals. Recently, an infectious disease characterized by multiple ulcers on the body surface with a high mortality rate occurred in Channa argus cultured in Jiangsu Province, China. A Gram-negative bacterial strain (Aer12) was isolated from the body surface of the diseased fish and identified as A. veronii by the physiological, biochemical, and 16 S rRNA gene analysis. Intra-peritoneal injection of Aer12 into the healthy C. argus resulted in the development of multiple ulcers on the body surface, and the histopathological results showed that muscle tissue rupture was the most severe symptom. Aer12 showed both protease and lipase activities with no β-hemolytic activity. Furthermore, Aer12 contained seven virulence genes (aer, act, alt, fla, ascV, aexT, and ela) and one antibiotic resistance gene (qnrS) identified by the PCR assay. The results of whole genome sequencing revealed that Aer12 had a circular chromosome that measured 4,719,428 bp. It comprised 4301 predicted protein-coding sequences (CDS) in addition to 31 rRNA, 124 tRNA, and 49 sRNA genes. Furthermore, a total of 676 virulence genes and 216 antibiotic resistance genes have been predicted. Aer12 was susceptible to 21 antibiotics, including ampicillin and erythromycin. The results of Chinese herbs susceptibility assay showed that Aer12 was highly susceptible to Sanguisorba officinalis, Galla chinensis, and Schisandra chinensis. The results of this study will serve as a reference for future research on the pathogenic mechanism of A. veronii and the prevention and control of bacterial diseases in C. argus farming.

Draft genome sequence of Listeria aquatica strain SG_BD1, isolated from a cow dung sample in Bangladesh

Here, we present the genome of Listeria aquatica strain SG_BD1, isolated from cow dung in Dhaka, Bangladesh, and assembled after Oxford Nanopore sequencing. The genome is 2,690,148 bp with 2,855 predicted coding DNA sequences, G + C content of 39.6%, and displays a putative virulence gene clpP and 9 CRISPRs.

Complete genome sequences of sucrose non-fermenting non-O1/non-O139 Vibrio cholerae isolated from human soft tissue infection

This paper describes the hybrid genome assembly of sucrose non-fermenting non-O1/non-O139 Vibrio cholerae isolated from human soft tissue infection. The hybrid assembled genome comprises two circular chromosomes with lengths of 3,001,999 bp and 1,264,051 bp, respectively, with a G + C content of 47.38%.

Genomic diversity of Salmonella Typhimurium and its monophasic variant in pig and pork production in France

Salmonella Typhimurium and its monophasic variant (Salmonella 4,[5],12:i:-) are among the most prevalent serovars worldwide. Even though these serovars have been the focus of many studies, their spread has not yet been investigated in French pig herds and slaughterhouses at a regional scale. Here, we characterized the genomic diversity of 188 Salmonella strains belonging to sequence type (ST) 19 and 34. These strains were isolated from pigs in metropolitan France between 2014 and 2019. Samples were collected from 10 regions, three of which together represent 75% of French pig production in 2020. To contextualize the French Salmonella genomes at a worldwide level, 193 ST 34 genomes from three continents and 14 countries were also included. This study revealed little diversity in ST 34 strains circulating in France, suggesting that one or two clones are spreading within pig herds and slaughterhouses. In silico virulence and antimicrobial resistance genes were investigated to understand the prevalence of these strains among farmed pigs and in the slaughterhouse environment. A comparison with ST 34 isolates from other countries highlighted the genomic specificity of the ST 34 monophasic variants in France, with some exceptions concerning isolates from bordering countries. This work provides new insights into the dynamics of S. Typhimurium and its monophasic variant sampled in French pig herds and slaughterhouses.

IMPORTANCE

Salmonellosis is a leading cause of bacterial infection in humans and animals around the world. This study provides a snapshot of the genomic diversity of one of the most prevalent Salmonella serovars (Salmonella Typhimurium and Salmonella 4,[5],12:i:-) circulating on French pig farms between 2013 and 2021. We investigated the link between geographical and genomic diversity. The analyses revealed little diversity of the strains, suggesting that one or two clones are spreading within French pig herds. We also in silico screened genetic elements that could explain the prevalence of these strains among farmed pigs and in the slaughterhouse environment. Finally, the comparison with isolates from other countries highlighted the genomic specificity of these two French sequence type 34 clones. This work provides new insights into the dynamics of S. Typhimurium and S. 4,[5],12:i:- sampled from pig herds and slaughterhouses in France, thus laying the foundations for future analyses.

Phylogenomics of novel clones of Aeromonas veronii recovered from a freshwater lake reveals unique biosynthetic gene clusters

Aquatic ecosystems serve as crucial reservoirs for pathogens and antimicrobial resistance genes, thus presenting a significant global health risk. Here, we investigated the phylogenomics of Aeromonas veronii from Lake Wilcox in Ontario. Among the 11 bacterial isolates, nine were identified as A. veronii. Notably, 67% of A. veronii isolates were potential human pathogens. Considerable genetic diversity was noted among the A. veronii isolates, suggesting the lake as a reservoir for multiple human pathogenic strains. Comparison of the A. veronii sequenced with global A. veronii genomes highlighted significant genetic diversity and suggests widespread dissemination of strains. All the isolates carried chromosomal genes encoding resistance to β-lactams. Although virulence gene content differed between human and non-human pathogenic strains, type III secretion systems was associated with human pathogenic isolates. The assessment of AMR genes in global isolates showed that β-lactam and tetracycline resistance genes were predominant. Although the machine learning-based pangenome-wide association approach performed did not yield any source-based genes, some genes were enriched in a few isolates from different sources. The mrkABCDF operon that mediates biofilm formation and genes encoding resistance to colistin, chloramphenicol, trimethoprim, and tetracycline were enriched in animal products, whereas macrolide resistance genes and Inc plasmid-types were linked to the aquatic environment. Novel biosynthetic gene clusters were identified, suggesting that A. veronii with varying pathogenic potential could produce unique secondary metabolites. There is a need for continuous tracking of pathogens in aquatic ecosystems to contribute to our understanding of their evolutionary dynamics and the ecological roles of their genetic elements.

IMPORTANCE

Lakes and other aquatic ecosystems can harbor harmful bacteria that can make people sick and resist antibiotics, posing a significant global health risk. In this study, we investigated Aeromonas veronii, a Gram-negative bacteria found in Lake Wilcox in Ontario. We used various techniques, including whole-genome sequencing (WGS), to analyze the bacteria and found that many of the isolates had the potential to cause human disease. We also discovered significant genetic diversity among the isolates, indicating that the lake may be a reservoir for multiple human pathogenic strains. All isolates carried genes that confer resistance to antibiotics, and some virulence genes were associated with human pathogenic isolates. This study highlights the importance of monitoring aquatic ecosystems for harmful bacteria to better understand their evolution, potential for human pathogenicity, and the ecological roles of their genetic elements. This knowledge can inform strategies for preventing the spread of antibiotic-resistant bacteria and protecting public health.

Genome-wide comparative analysis of clinical and environmental strains of the opportunistic pathogen Paracoccus yeei (Alphaproteobacteria)

Introduction

Paracoccus yeei is the first species in the genus Paracoccus to be implicated in opportunistic infections in humans. As a result, P. yeei strains provide a valuable model for exploring how bacteria shift from a saprophytic to a pathogenic lifestyle, as well as for investigating the role of horizontally transferred DNA in this transition. In order to gain deeper insights into the unique characteristics of this bacterium and the molecular mechanisms underlying its opportunistic behavior, a comparative physiological and genomic analysis of P. yeei strains was performed.

Results

Complete genomic sequences of 7 P. yeei isolates (both clinical and environmental) were obtained and analyzed. All genomes have a multipartite structure comprising numerous extrachromosomal replicons (59 different ECRs in total), including large chromids of the DnaA-like and RepB families. Within the mobile part of the P. yeei genomes (ECRs and transposable elements, TEs), a novel non-autonomous MITE-type element was identified. Detailed genus-wide comparative genomic analysis permitted the identification of P. yeei-specific genes, including several putative virulence determinants. One of these, the URE gene cluster, determines the ureolytic activity of P. yeei strains-a unique feature among Paracoccus spp. This activity is induced by the inclusion of urea in the growth medium and is dependent on the presence of an intact nikR regulatory gene, which presumably regulates expression of nickel (urease cofactor) transporter genes.

Discussion

This in-depth comparative analysis provides a detailed insight into the structure, composition and properties of P. yeei genomes. Several predicted virulence determinants (including URE gene clusters) were identified within ECRs, indicating an important role for the flexible genome in determining the opportunistic properties of this bacterium.

Molecular characterization of Staphylococcus aureus from nasal samples of healthy pet cats

The objective of this study was to characterize Staphylococcus aureus isolates recovered from the nasal samples of healthy pet cats in Algiers province. A total of 138 nasal swabs were collected. Antimicrobial susceptibility was conducted using the disk-diffusion method and the VITEK-2 susceptibility system. Whole genome sequencing was performed to identify multiple-locus sequence typing, antimicrobial and virulence genes. Staphylococcus aureus isolates were detected in 23 cats. Among these, 11 were methicillin-resistant S. aureus (MRSA) (one isolate/sample). Three sequence types (ST6, ST5, and ST1) were identified in MRSA, with the predominance of ST6 (n = 7). Seven distinct STs [ST398, ST97, ST15, ST7, ST291, ST5043, and a new ST, (ST9219)] were detected in methicillin-sensitive S. aureus. All MRSA isolates harbored the mecA gene and SCCmec-type-IVa. MRSA exhibited resistance to tetracycline [n = 3/tet(L) and tet(M); n = 1/tet(K)], kanamycin-tobramycin [n = 3/ant(4')-Ia), amikacin-kanamycin (n = 1/aph(3')-IIIa], and erythromycin-clindamycin [n = 1/erm(C)]. Seven S. aureus isolates were multidrug resistant. All the isolates were negative for lukS/lukF-PV and tst-1 genes, while 20 isolates were IEC-positive. This study revealed a diversity of genetic lineages in S. aureus strains isolated from nasal samples of pet cats, including multidrug-resistant and toxigenic strains. The presence of IEC-positive S. aureus suggests possible human-animal transmission.

Investigating the adherence factors of Escherichia coli at the bovine recto-anal junction

Shiga toxin-producing Escherichia coli (STEC) are major foodborne pathogens that result in thousands of hospitalizations each year in the United States. Cattle, the natural reservoir, harbor STEC asymptomatically at the recto-anal junction (RAJ). The molecular mechanisms that allow STEC and non-STEC E. coli to adhere to the RAJ are not fully understood, in part because most adherence studies utilize human cell culture models. To identify a set of bovine-specific E. coli adherence factors, we used the primary RAJ squamous epithelial (RSE) cell-adherence assay to coculture RSE cells from healthy Holstein cattle with diverse E. coli strains from bovine and nonbovine sources. We hypothesized that a comparative genomic analysis of the strains would reveal factors associated with RSE adherence. After performing adherence assays with historical strains from the E. coli Reference Center (n = 62) and strains newly isolated from the RAJ (n = 15), we used the bioinformatic tool Roary to create a pangenome of this collection. We classified strains as either low or high adherence and using the Scoary program compiled a list of accessory genes correlated with the "high adherence" strains. While none of the correlations were statistically significant, several gene clusters were associated with the high-adherence phenotype, including two that encode uncharacterized proteins. We also demonstrated that non-STEC E. coli strains from the RAJ are more adherent than other isolates and can outcompete STEC in coculture with RSEs. Further analysis of adherence-associated gene clusters may lead to an improved understanding of the molecular mechanisms of RSE adherence and may help develop probiotics targeting STEC in cattle.

IMPORTANCE

E. coli strains that produce Shiga toxin cause foodborne illness in humans but colonize cattle asymptomatically. The molecular mechanisms that E. coli uses to adhere to cattle cells are largely unknown. Various strategies are used to control E. coli in livestock and limit the risk of outbreaks. These include vaccinating animals against common E. coli strains and supplementing their feed with probiotics to reduce the carriage of pathogens. No strategy is completely effective, and probiotics often fail to colonize the animals. We sought to clarify the genes required for E. coli adherence in cattle by quantifying the attachment to bovine cells in a diverse set of bacteria. We also isolated nonpathogenic E. coli from healthy cows and showed that a representative isolate could outcompete pathogenic strains in cocultures. We propose that the focused study of these strains and their adherence factors will better inform the design of probiotics and vaccines for livestock.

Isolation and characterization of Bifidobacterium spp. from breast milk with different human milk oligosaccharides utilization and anti-inflammatory capacity

Breast milk is the best source of nutrition for infants. Human milk oligosaccharides (HMOs) and the corresponding HMOs-consuming Bifidobacterium positively influence infant health. This study aims to isolate and characterize Bifidobacterium from breast milk of healthy Chinese mothers, identifying the most efficacious strains for inclusion in simulated maternal milk formulas. Nine Bifidobacterium strains (two of B. breve and seven of B. infantis) were isolated, exhibiting a broad spectrum of probiotic potential. This included tolerance to simulated infant gastrointestinal conditions, notable adhesion, antibacterial, antioxidant activities, and HMOs utilization ability. Lacto-N-Tetraose (LNT) is preferred in early growth among Bifidobacterium isolates. B. breve showed a preference for LNT, whereas B. infantis showed a preference for fucosylated HMOs, and displayed reduced utilization of sialylated HMOs. They also exhibited robust safety profiles, including no hemolytic activity, an appropriate D/L lactate-producing ratio, and non-toxicity in an acute oral toxicity assay on mice. It is noteworthy that B. breve N-90, O-147, B. infantis O-161 and R-1 exhibited anti-inflammatory effects in LPS-induced RAW 264.7 cells. Specifically, a notable reduction in TNF-α levels was observed in pre-treatment, while a decrease in IL-1β and IL-6 levels in co-treatment. B. breve N-90 and B. infantis R-1 were identified finally as promising probiotic candidates. Their whole-genome sequencing analysis confirmed presence of functional genes associated with gastrointestinal colonization, antioxidation, and glycoside hydrolase activity on HMOs. The annotation for antibiotic resistance and virulence genes concurred with phenotypes, further validating the safety. Breast milk is a good source for Bifidobacteria isolation, while Bifidobacteria utilize HMOs in a strain-dependent manner. The two selected strains, B. breve N-90 and B. infantis R-1, are potential candidates for inclusion in simulated maternal milk formulas and deserved further in vivo investigation for their health-promoting effects.

Construction of core genome multi-locus sequence typing schemes for population structure analyses of Nocardia species

Nocardia, a member of the Actinobacteria phylum, populates diverse habitats globally, with certain species being the cause of various clinical infections in humans. There is paucity of data regarding the population structure of this genus and of established genomic-based phylogenetic methods. We examined the whole genome sequences of 193 isolates spanning five major pathogenic Nocardia species sourced from public databases, encompassing diverse geographic regions. Using the chewBBACA pipeline, a species-specific core genome multilocus sequence typing (cgMLST) schema was created for N. cyriacigeorgica, N. farcinica, N. brasiliensis, N. wallacei, and N. abscessus. Additional genomic features that were examined included virulence factor (VF) profile, total length and open-reading frame count, the core genome length and core gene count, and GC content. Our findings indicated that: (i) N. brasiliensis diverges significantly from the other four species, underscoring its distinct evolutionary trajectory; (ii) the population structures of all species were polyclonal, with phylogenetic clustering occurring in the minority of isolates; (iii) clonal complexes were largely restricted to specific geographical locations, rather than demonstrating a global distribution, and (iv) initial evidence suggests no direct common-source transmission amongst the studied strains. Our study establishes a comprehensive genome-based phylogenetic methodology for population structure of Nocardia species.

Hazard Characterization of Antibiotic-resistant Aeromonas spp. Isolated from Mussel and Oyster Shellstock Available for Retail Purchase in Canada

Surveillance and monitoring of foods for the presence of antimicrobial-resistant (AMR) bacteria are required to assess the risks these bacteria pose to human health. Frequently consumed raw or lightly cooked, live bivalve shellfish such as mussels and oysters can be a source of exposure to AMR bacteria. This study sought to determine the prevalence of third-generation cephalosporin (3GC) and carbapenem-resistant bacteria in live mussel and oyster shellstock available for retail purchase through the course of one calendar year. Just over half of the 180 samples (52%) tested positive for the presence of 3GC-resistant bacteria belonging to thirty distinct bacterial species. Speciation of the isolates was carried out using the Bruker MALDI Biotyper. Serratia spp., Aeromonas spp., and Rahnella spp. were the most frequently isolated groups of bacteria. Antibiotic resistance testing confirmed reduced susceptibility for 3GCs and/or carbapenems in 15 of the 29 Aeromonas isolates. Based on AMR patterns, and species identity, a subset of ten Aeromonas strains was chosen for further characterization by whole genome sequence analysis. Genomic analysis revealed the presence of multiple antibiotic resistance and virulence genes. A number of mobile genetic elements were also identified indicating the potential for horizontal gene transfer. Differences in gene detection by the bioinformatic tools and databases used (ResFinder. CARD RGI, PlasmidFinder, and MobSuite) are discussed. This study highlights the strengths and limitations of using genomics tools to perform hazard characterization of diverse foodborne bacterial species.

Cross-Kingdom Pathogenesis of Pantoea alfalfae CQ10: Insights from Transcriptome and Proteome Analyses

In grassland agroecosystems, some plant pathogenic bacteria can cause disease in animals. These strains are known as plant and animal cross-kingdom pathogenic bacteria. In this study, we established an alfalfa root infection model and a mouse model via the gavage administration of the Pantoea alfalfae CQ10 (CQ10) bacterial suspension. It was confirmed that the CQ10 strain caused bacterial leaf blight of alfalfa. Mice inoculated with 0.4 mL of 109 cfu/mL bacterial suspension developed clinical symptoms 48 h later, such as diminished vitality, tendencies to huddle, and lack of appetite, including severe lesions in stomach, liver, kidney, and spleen tissues. CQ10 strains were isolated from mouse feces at different time points of inoculation. Thus, CQ10 is a plant and animal cross-kingdom pathogenic bacterium. Transcriptome and proteome analyses showed that biofilm and iron uptake are important virulence factors of the pathogen CQ10, among which Bap and Lpp regulating biofilm are the key cross-kingdom virulence genes of CQ10. From an evolutionary perspective, insights gained from this dual animal-plant pathogen system may help to elucidate the molecular basis underlying the host specificity of bacterial pathogens. The result provides a theoretical basis for the risk assessment, prevention, and control strategies of new pathogenic bacteria entering a new region.

Biofilm-mediated antibiotic tolerance in Staphylococcus aureus from spinal cord stimulation device-related infections

Staphylococcus aureus is a predominant cause of infections in individuals with spinal cord stimulation (SCS) devices. Biofilm formation complicates these infections, commonly requiring both surgical and antibiotic treatments. This study explored the biofilm matrix composition and antimicrobial susceptibility of planktonic and biofilm-growing S. aureus isolates from individuals with SCS-related infections. Whole-genome sequencing (WGS) examined genotypes, virulome, resistome, and the pan-genome structure. The study also analyzed biofilm matrix composition, early surface adhesion, hemolytic activity, and antibiotic-susceptibility testing. WGS revealed genetic diversity among isolates. One isolate, though oxacillin susceptible, contained the mecA gene. The median number of virulence factor genes per isolate was 58. All isolates harbored the biofilm-related icaA/D genes. When assessing phenotypic characteristics, all strains demonstrated the ability to form biofilms in vitro. The antimicrobial susceptibility profile indicated that oxacillin, rifampin, and teicoplanin showed the highest efficacy against S. aureus biofilm. Conversely, high biofilm tolerance was observed for vancomycin, trimethoprim/sulfamethoxazole, and levofloxacin. These findings suggest that S. aureus isolates are highly virulent and produce robust biofilms. In cases of suspected biofilm infections caused by S. aureus, vancomycin should not be the primary choice due to its low activity against biofilm. Instead, oxacillin, rifampin, and teicoplanin appear to be more effective options to manage SCS infections.IMPORTANCESCS devices are increasingly used to manage chronic pain, but infections associated with these devices, particularly those caused by Staphylococcus aureus, present significant clinical challenges. These infections are often complicated by biofilm formation, which protects bacteria from immune responses and antibiotic treatments, making them difficult to eradicate. Understanding the genetic diversity, virulence, and biofilm characteristics of S. aureus isolates from SCS infections is critical to improving treatment strategies. Our study highlights the need to reconsider commonly used antibiotics like vancomycin, which shows reduced activity against biofilm-growing cells. Identifying more effective alternatives, such as oxacillin, rifampin, and teicoplanin, provides valuable insight for clinicians when managing biofilm-related S. aureus infections in patients with SCS implants. This research contributes to the growing evidence that biofilm formation is crucial in treating device-related infections, emphasizing the importance of tailoring antimicrobial strategies to the biofilm phenotype.

Genomic evidence of Escherichia coli gut population diversity translocation in leukemia patients

Escherichia coli, a commensal species of the human gut, is an opportunistic pathogen that can reach extra-intestinal compartments, including the bloodstream and the bladder, among others. In non-immunosuppressed patients, purifying or neutral evolution of E. coli populations has been reported in the gut. Conversely, it has been suggested that when migrating to extra-intestinal compartments, E. coli genomes undergo diversifying selection as supported by strong evidence for adaptation. The level of genomic polymorphism and the size of the populations translocating from gut to extra-intestinal compartments is largely unknown. To gain insights into the pathophysiology of these translocations, we investigated the level of polymorphism and the evolutionary forces acting on the genomes of 77 E. coli isolated from various compartments in three immunosuppressed patients. Each patient had a unique strain, which was a mutator in one case. In all instances, we observed that translocation encompasses much of the genomic diversity present in the gut. The same signature of selection, whether purifying or diversifying, and as anticipated, neutral for mutator isolates, was observed in both the gut and bloodstream. Additionally, we found a limited number of non-specific mutations among compartments for non-mutator isolates. In all cases, urine isolates were dominated by neutral selection. These findings indicate that substantial proportions of populations are undergoing translocation and that they present a complex compartment-specific pattern of selection at the patient level.IMPORTANCEIt has been suggested that intra and extra-intestinal compartments differentially constrain the evolution of E. coli strains. Whether host particular conditions, such as immunosuppression, could affect the strain evolutionary trajectories remains understudied. We found that, in immunosuppressed patients, large fractions of E. coli gut populations are translocating with variable modifications of the signature of selection for commensal and pathogenic isolates according to the compartment and/or the patient. Such multiple site sampling should be performed in large cohorts of patients to gain a better understanding of E. coli extra-intestinal diseases.

Segatella clades adopt distinct roles within a single individual's gut

Segatella is a prevalent genus within individuals' gut microbiomes worldwide, especially in non-Western populations. Although metagenomic assembly and genome isolation have shed light on its genetic diversity, the lack of available isolates from this genus has resulted in a limited understanding of how members' genetic diversity translates into phenotypic diversity. Within the confines of a single gut microbiome, we have isolated 63 strains from diverse lineages of Segatella. We performed comparative analyses that exposed differences in cellular morphologies, preferences in polysaccharide utilization, yield of short-chain fatty acids, and antibiotic resistance across isolates. We further show that exposure to Segatella isolates either evokes strong or muted transcriptional responses in human intestinal epithelial cells. Our study exposes large phenotypic differences within related Segatella isolates, extending this to host-microbe interactions.

Phenotypic and Molecular Characterization of Staphylococcus aureus in Dairy Farms from Henan Province and the Inner Mongolia Autonomous Region, China

Staphylococcus aureus, a prevalent pathogen associated with infectious and foodborne diseases, is also a significant cause of intramammary infections in dairy farms. This study aimed to determine the phenotypic and molecular characterization of S. aureus in two different stock sizes of dairy farms in Henan province (HN) and the Inner Mongolia autonomous region (IM), China, through biofilm formation, antimicrobial resistance, virulence, and molecular type of S. aureus isolates. In HN, 74 S. aureus isolates (60.7%) were recovered from 122 bulk tank milk samples, while in IM, 24 S. aureus isolates (17.4%) were detected from 161 samples soured from various origins. Notably, 25.7% (19/74) of isolates in HN and 20.8% (5/24) in IM exhibited multidrug-resistant (MDR) phenotypes. Molecular typing revealed distinct patterns: ST97 (n = 32) and spa type t189 (n = 20) predominated in HN, whereas ST50 (n = 13) and spa type t518 (n = 11) were prevalent in IM. Additionally, three isolates harbored both tsst-1 and lukF-PV genes, and two MRSA strains displayed a MDR phenotype in raw milk samples from HN. Biofilm formation was observed in 91.8% strains. Phylogenetic analysis identified two subpopulations (lineages 1 and 2). Among them, cluster 6 in lineage 2 comprised S. aureus strains from three sources within a farm, suggesting potential cross contamination during different stages in IM. Remarkably, among 19 MDR isolates in HN, ST398 MSSA strains exhibited a higher multidrug resistance compared to non-ST398 MSSA strains. This study underscores the high prevalence and diverse characteristics of S. aureus in raw milk, necessitating enhanced surveillance and control measures to mitigate associated risk.

Genomic Analysis of Aeromonas salmonicida ssp. salmonicida Isolates Collected During Multiple Clinical Outbreaks Supports Association with a Single Epidemiological Unit

Outbreaks of furunculosis cause significant losses in salmonid aquaculture worldwide. With a recent rise in antimicrobial resistance, regulatory measures to minimize the use of antibiotics in animal husbandry, including aquaculture, have increased scrutiny and availability of veterinary medical products to control this disease in production facilities. In such a regulatory environment, the utility of autogenous vaccines to assist with disease prevention and control as a veterinary-guided prophylactic measure is of high interest to the producers and veterinary services alike. However, evolving concepts of epidemiological units and epidemiological links need to be considered during approval and acceptance procedures for the application of autogenous vaccines in multiple aquaculture facilities. Here, we present the results of solid-state nanopore sequencing (Oxford Nanopore Technologies, ONT) performed on 54 isolates of Aeromonas salmonicida ssp. salmonicida sampled during clinical outbreaks of furunculosis in different aquaculture facilities from Bavaria, Germany, from 2017 to 2020. All of the performed analyses (phylogeny, single nucleotide polymorphism and 3D protein modeling for major immunogenic proteins) support a high probability that all studied isolates belong to the same epidemiological unit. Simultaneously, we describe a cost/effective method of whole genome analysis with the usage of ONT as a viable strategy to study outbreaks of other pathogens in the field of aquatic veterinary medicine for the purpose of developing the best autogenous vaccine candidates applicable to multiple aquaculture establishments.