The current study was conducted to determine the phylogroups and antibiotic susceptibilities of Escherichia coli isolates recovered from fecal samples of Anatolian Ground Squirrels (Spermophilus xanthoprymnus) and to examine the relationship between them. Eighty-two E. coli isolates obtained from 150 fecal samples were investigated. The quadruplex polymerase chain reaction (PCR), phylogroup C-, and E-specific mPCR were subjected to phylogenetic typing of the isolates. The susceptibilities to fifteen antibiotics of the isolates were detected by the disk diffusion method. In the result of phylogenetic typing, phylogroup B2 was most predominant (58.6%), followed by B1 (25.6%), E (8.5%), C (4.9%), and D (2.4%). The phylogroup A, F, and Escherichia clades were not detected. The antibiotic susceptibility test revealed that 59.8% (49/82) and 19.5% (16/82) of E. coli isolates were resistant to at least one antibiotic and multidrug-resistant (MDR), respectively. Twenty-six (31.7%), 19 (23.2%), 11 (13.4%), and 10 (12.2%) of the isolates were found to be resistant to gentamicin, tetracycline, amoxicillin-clavulanic acid, and cefoxitin. Of the 49 E. coli isolates that were found to be resistant to any antibiotic analyzed, 30, 13, 4, and 2 were located in phylogroup B2, B1, E, and D, respectively. MDR isolates were mostly located in both phylogroup B1 (31.3%) and B2 (31.3%). In conclusion, data from the current study suggest that the isolates may potentially have pathogenic properties, since the majority (69.5%) of E. coli isolates from fecal samples of Spermophilus xanthoprymnus were located in the pathogenic phylogroup and resistance to various antibiotics was detected.

UNASSIGNED: Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae including Escherichia coli (E. coli), are recognized as a global public health threat due to their multidrug-resistant (MDR) phenotypes and their rapid dissemination in aquatic environments. Nevertheless, studies investigating the prevalence and antimicrobial resistance (AMR) profile of ESBL-producing E. coli in Lebanese surface water are limited.
UNASSIGNED: This study aimed to assess the physicochemical properties and microbial contamination load and to determine the distribution of AMR patterns of ESBL-producing E. coli in surface water samples from different sites in the North Governorate of Lebanon.
UNASSIGNED: Water samples were collected from 25 major sites in North Lebanon. These samples were analyzed for the presence of total coliforms, E. coli, and fecal enterococci. Phenotypic and genetic characterizations were then performed for E. coli isolates to determine their resistance patterns and phylogenetic groups.
UNASSIGNED: Fifty-six samples out of 100 samples were positive for ESBL-producing E. coli, mostly harboring blaCTX-M (40/56, 71%) including blaCTX-M-15 (33/40, 82%), blaTEM gene (36/56, 64%), blaSHV (20/56, 36%), and blaOXA (16/56, 29%) including blaOXA-48 gene (11/16, 69%). Most ESBL-producing E. coli isolates belonged to the extra-intestinal pathogenic phylogroup B2 (40/56, 71.4%) while 10/56 (17.9%) belonged to the commensal phylogroup A.
UNASSIGNED: Our results highlight the need to implement effective water monitoring strategies to control transmission of ESBL-producing E. coli in surface water and thus reduce the burden on human and animal health.

Escherichia coli (E. coli) causes various infections in humans and animals. The biofilm-forming ability of E. coli has increased antimicrobial resistance and capacity to cause recurrent and chronic infections. This study determined the biofilm-forming ability of E. coli isolated from extraintestinal infections of humans, chickens, and dogs in relation to the phylogroup, type of infection, and antibiotic resistance. Isolates from chickens showed significantly higher biofilm-forming ability compared to those causing urinary tract infections in humans (p = 0.0001). Further, isolates belonging to phylogroup B1 displayed a higher likelihood to form biofilms. Resistance to ciprofloxacin and trimethoprim-sulfamethoxazole was positively correlated with biofilm-forming ability. Harbouring plasmid-mediated quinolone resistance gene, qnrS was also positively correlated with biofilm formation. This study provides insight into factors such as phylogroup and the type of infections that could enhance biofilm formation, as well as genotypic and phenotypic antibiotic resistance that could correlate with the ability to form biofilms.

Clostridium perfringens causes gas gangrene and food poisoning in humans, and monitoring this bacterium is important for public health. Although whole-genome sequencing is useful to comprehensively understand the virulence, resistome, and global genetic relatedness of bacteria, limited genomic data from environmental sources and developing countries hamper our understanding of the richness of the intrinsic genomic diversity of this pathogen. Here, we successfully accumulated the genetic data on C. perfringens strains isolated from hospital effluent and provided the first evidence that predicted pathogenic C. perfringens may be disseminated in the clinical environment in Ghana. Our findings suggest the importance of risk assessment in the environment as well as the clinical setting to mitigate the potential outbreak of C. perfringens food poisoning in Ghana.

Viral symptoms, such as yellowing, leaf deformation, mottling, vein clearing, and reduced yield, were observed in cucurbits in Iran. This study aimed to detect the main suspected causal agent, cucurbit aphid-borne yellows virus (CABYV), in Iran and analyze the genetic diversity among isolates. Two hundred samples were collected from different growing areas between 2019 and 2022. PCR amplification was performed on the P3 and P4 genes. The sequences of 18 Iranian isolates were obtained and deposited in GenBank. Recombination, phylogenetic, and population genetics studies were then carried out for the complete genome and all ORFs sequences, together with other isolates in GenBank. The nucleotide identities of the overlapped ORF3/4 sequences of Iranian isolates were 94.8 to 99.5% among themselves, and with other tested isolates ranging from 94.3 to 99.3%. Phylogenetic trees based on the complete genome and the overlapped ORF3/4 showed two major clades, namely Asian and Mediterranean, and the new isolates from Iran were positioned in both clades. The obtained results also suggest that all the genes and two clades of CABYV populations were under negative selection pressure. Furthermore, rare gene flow between these two clades (FST > 0.33) confirmed the high genetic separation among them.

Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap\'s coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.

Longitudinal studies of extraintestinal pathogenic Escherichia coli (ExPEC) and epidemic clones of E. coli in association with New Delhi metallo-β-lactamase (blaNDM) in septicaemic neonates are rare. This study captured the diversity of 80 E. coli isolates collected from septicaemic neonates in terms of antibiotic susceptibility, resistome, phylogroups, sequence types (ST), virulome, plasmids, and integron types over a decade (2009 to 2019). Most of the isolates were multidrug-resistant and, 44% of them were carbapenem-resistant, primarily due to blaNDM. NDM-1 was the sole NDM-variant present in conjugative IncFIA/FIB/FII replicons until 2013, and it was subsequently replaced by other variants, such as NDM-5/-7 found in IncX3/FII. A core genome analysis for blaNDM+ve isolates showed the heterogeneity of the isolates. Fifty percent of the infections were caused by isolates of phylogroups B2 (34%), D (11.25%), and F (4%), whereas the other half were caused by phylogroups A (25%), B1 (11.25%), and C (14%). The isolates were further distributed in approximately 20 clonal complexes (STC), including five epidemic clones (ST131, ST167, ST410, ST648, and ST405). ST167 and ST131 (subclade H30Rx) were dominant, with most of the ST167 being blaNDM+ve and blaCTX-M-15+ve. In contrast, the majority of ST131 isolates were blaNDM-ve but blaCTX-M-15+ve, and they possessed more virulence determinants than did ST167. A single nucleotide polymorphism (SNP)-based comparative genome analysis of epidemic clones ST167 and ST131 in a global context revealed that the study isolates were present in close proximity but were distant from global isolates. The presence of antibiotic-resistant epidemic clones causing sepsis calls for a modification of the recommended antibiotics with which to treat neonatal sepsis. IMPORTANCE Multidrug-resistant and virulent ExPEC causing sepsis in neonates is a challenge to neonatal health. The presence of enzymes, such as carbapenemases (blaNDM) that hydrolyze most β-lactam antibiotic compounds, result in difficulties when treating neonates. The characterization of ExPECs collected over 10 years showed that 44% of ExPECs were carbapenem-resistant, possessing transmissible blaNDM genes. The isolates belonged to different phylogroups that are considered to be either commensals or virulent. The isolates were distributed in around 20 clonal complexes (STC), including two predominant epidemic clones (ST131 and ST167). ST167 possessed few virulence determinants but was blaNDM+ve. In contrast, ST131 harbored several virulence determinants but was blaNDM-ve. A comparison of the genomes of these epidemic clones in a global context revealed that the study isolates were present in close proximity but were distant from global isolates. The presence of epidemic clones in a vulnerable population with contrasting characteristics and the presence of resistance genes call for strict vigilance.

Antibiotic therapy is the standard of care for urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC). However, previous antibiotic therapy may impart a selective pressure that influences the population structure and pathogenic potential of infecting UPEC strains. Here, we conducted a 3-year study using whole-genome-sequencing analysis and retrospective medical record review to characterize how antibiotic exposure influenced the phenotypic antibiotic resistance, acquired resistome, virulome, and population structure of 88 UTI-causing E. coli strains from dogs. A majority of UTI-associated E. coli strains were from phylogroup B2 and clustered within sequence type 372. Previous antibiotic exposure was associated with a population shift toward UPEC from phylogroups other than the typical urovirulent phylogroup B2. The specific virulence profiles within the accessory virulome that were associated with antibiotic use were elicited by the effect of antibiotics on UPEC phylogenetic structure. Among phylogroup B2, antibiotic exposure increased the quantity of genes within the resistome and the odds of developing reduced susceptibility to at least one antibiotic. Non-B2 UPEC strains harbored a more diverse and greater resistome that conferred reduced susceptibility to multiple antibiotic classes following antibiotic exposure. Collectively, these data suggest that previous antibiotic exposure establishes an environment that provides a selective edge to non-B2 UPEC strains through their diverse and abundant antibiotic resistance genes, despite their lack of urovirulence genes. Our findings highlight the necessity for judicious use of antibiotics as we uncover another mechanism by which antibiotic exposure and resistance can influence the dynamics of bacterial infectious disease. IMPORTANCE Urinary tract infections (UTIs) are one of the most common infections of dogs and humans. While antibiotic therapy is the standard of care for UTIs and other infections, antibiotic exposure may influence the pathogenic profile of subsequent infections. We used whole-genome sequencing and retrospective medical record review to characterize the effect of systemic antibiotic therapy on the resistance, virulence, and population structure of 88 UTI-causing UPEC strains isolated from dogs. Our results indicate that antibiotic exposure alters the population structure of infecting UPEC strains, providing a selective edge for non-B2 phylogroups that harbor diverse and abundant resistance gene catalogues but fewer urovirulence genes. These findings highlight how antibiotic resistance can influence pathogen infection dynamics and have clinical implications for the judicious use of antibiotics for bacterial infections.

UNASSIGNED: Staphylococcus aureus (S. aureus) is a highly pathogenic and adaptable Gram-positive bacterium that exhibits persistence in various environments. The toxin-antitoxin (TA) system plays a crucial role in the defense mechanism of bacterial pathogens, allowing them to survive in stressful conditions. While TA systems in clinical pathogens have been extensively studied, there is limited knowledge regarding the diversity and evolutionary complexities of TA systems in S. aureus.
UNASSIGNED: We conducted a comprehensive in silico survey using 621 publicly available S. aureus isolates. We employed bioinformatic search and prediction tools, including SLING, TADB2.0, and TASmania, to identify TA systems within the genomes of S. aureus.
UNASSIGNED: Our analysis revealed a median of seven TA systems per genome, with three type II TA groups (HD, HD_3, and YoeB) being present in over 80% of the strains. Additionally, we observed that TA genes were predominantly encoded in the chromosomal DNA, with some TA systems also found within the Staphylococcal Cassette Chromosomal mec (SCCmec) genomic islands.
UNASSIGNED: This study provides a comprehensive overview of the diversity and prevalence of TA systems in S. aureus. The findings enhance our understanding of these putative TA genes and their potential implications in S. aureus ecology and disease management. Moreover, this knowledge could guide the development of novel antimicrobial strategies.

Shiga toxin-producing Escherichia coli (STEC) are globally significant foodborne pathogens. Dairy calves are a known reservoir of both O157 and non-O157 STEC. The objective of this study was to comprehensively evaluate the genomic attributes, diversity, virulence factors, and antimicrobial resistance gene (ARG) profiles of the STEC from preweaned and postweaned dairy calves in commercial dairy herds.
In total, 31 non-O157 STEC were identified as part of a larger study focused on the pangenome of >1000 E. coli isolates from the faeces of preweaned and postweaned dairy calves on commercial dairy farms. These 31 genomes were sequenced on an Illumina NextSeq500 platform.
Based on the phylogenetic analyses, the STEC isolates were determined to be polyphyletic, with at least three phylogroups: A (32%), B1 (58%), and G (3%). These phylogroups represented at least 16 sequence types and 11 serogroups, including two of the \'big six\' serogroups, O103 and O111. Several Shiga toxin gene subtypes were identified in the genomes, including stx1a, stx2a, stx2c, stx2d, and stx2g. Using the ResFinder database, the majority of the isolates (>50%) were determined to be multidrug-resistant strains because they harboured genes conferring resistance to three or more classes of antimicrobials, including some of human health significance (e.g., β-lactams, macrolides, and fosfomycin). Additionally, non-O157 STEC strain persistence and transmission within a farm was observed.
Dairy calves are a reservoir of phylogenomically diverse multidrug-resistant non-O157 STEC. Information from this study may inform assessments of public health risk and guide preharvest prevention strategies focusing on STEC reservoirs.