Exploration of Extracellular Vesicle Long Non-Coding RNAs in Serum of Patients with Cervical Cancer.

INTRODUCTION: Cervical cancer (CC) is the fourth most common cancer type and a leading cause of cancer-related deaths in women worldwide. Its underlying molecular mechanisms are unclear. Cancer cell-derived extracellular vesicles (EVs) are involved in cancer development and progression by delivering regulatory factors, including microRNAs and long non-coding RNAs (lncRNAs). METHODS: Here, we identified the EV lncRNA expression profiles associated with different developmental stages of CC using next-generation sequencing. EVs from the serum of patients with stages I-III CC and healthy donors were characterized using EV marker immunoblotting and transmission electron microscopy. RESULTS: The EV concentration increases with progression of the disease. Most particles had a 100-250-nm diameter, and their sizes were similar in all groups. We identified many lncRNAs that were uniquely and differentially expressed (DE) in patients with different stages of CC. The pathway analysis results indicated that the upregulated DE EV lncRNAs abundant in stages I and II were associated with cell proliferation and inflammation and cancer progression pathways, respectively. LINC00941, LINC01910, LINC02454, and DSG2-AS1 were highly expressed, suggesting poor overall survival of CC patients. Interestingly, DSG2-AS1 was associated with the human papillomavirus infection pathway through AKT3, DLG1, and COL6A2 genes. CONCLUSION: This is the first study that reports the levels of EVs and their lncRNA contents change during cancer development, demonstrating the existence of a unique vesicle-mediated cell-to-cell communication network underlying cancer progression.

Investigation of potential rubber-degrading bacteria and genes involved.

COVID-19 pandemic has generated high demand for natural rubber gloves (NR) leading to crucial issues of rubber waste and waste management such as burning, dumping, stockpiling, discarding waste in landfills. Hence, rubber biodegradation by microorganisms is an alternative solution to the problem. The biodegradation method is environmentally friendly but normally extremely slow. Numerous microorganisms can degrade NR as a source of carbon and energy. In this study, Rhodococcus pyridinivorans KU1 was isolated from the consortium CK from previous study. The 40% rubber weight loss was detected after incubated for 2 months. The bacterial colonization and cavities on the surface of rubber were identified using a scanning electron microscope (SEM). The result demonstrated the critical degradation of the rubber surface, indicating that bacteria can degrade rubber and use it as their sole carbon source. The result of whole-genome sequencing (WGS) revealed a gene that is 99.9% identical to lcp which is responsible for poly (cis-1,4-isoprene) degradation. The results from Meta16S rRNA sequencing showed that the microbial communities were slightly shifted during the 2-month degradation, depending on the presence of monomers or oligomers appeared during the degradation process. The majority of species were soil bacteria such as phylum Proteobacteria, Actinobacteria, and Firmicutes. Members of Pseudoxanthomonas seemed to be the dominant degraders throughout the degradation.

Short-term use of Lacticaseibacillus rhamnosus SD11 and the oral microbiome: Low caries RCT study.

OBJECTIVES: The objective of the study was to investigate the effect of short-term lozenges containing Lacticaseibacillus rhamnosus SD11 on cariogenic pathogens and on oral microbiota. MATERIALS AND METHODS: This double-blind, randomized, controlled trial included 121 subjects and was randomly divided into the control and probiotic group. All subjects were blindly administered to receive the control- or probiotic L. rhamnosus SD11 lozenges every day for 4 weeks and then followed up for another 4 weeks. RESULTS: After probiotic consumption, the probiotic group had significantly lower levels of Streptococcus mutans and significantly higher levels of total lactobacilli at 4 and 8 weeks compared with the baseline. The 16S rRNA sequencing revealed an increase in bacterial diversity and beneficial bacteria in the Firmicutes phylum, Bacilli class, and a reduction in the mutans streptococci group in the probiotic group. The opposite results were found in the control group. This study did not find any caries increment, nor did the subjects have any side effects after product consumption. CONCLUSION: With the limitation of a short-time study in low caries children, it showed that L. rhamnosus SD11 could increase beneficial bacteria in the Firmicutes phylum and Bacilli class that might support good oral health in children.

Association between Mycobacterium tuberculosis genotype and diabetes mellitus/hypertension: a molecular study.

BACKGROUND: A paucity of studies focused on the genetic association that tuberculosis (TB) patients with non-communicable diseases (NCDs) are more likely to be infected with Mycobacterium tuberculosis (MTB) with more potent virulence on anti-TB drug resistance than those without NCDs. The study aimed to document the predominant genotype, determine the association between MTB genotypes and NCD status and drug resistance. METHODS: We conducted a molecular study in 105 TB patients based on a cross-sectional study focused on the comorbid relationship between chronic conditions and TB among 1773 subjects from September 1, 2019 to August 30, 2020 in Guizhou, China. The participants were investigated through face-to-face interviews, followed by NCDs screening. The DNA of MTB isolates was extracted prior to genotyping using 24 loci MIRU-VNTR. The subsequent evaluations were performed by phylogenetic trees, combined with tests of statistical power, Chi-square or Fisher and multivariate logistic regression analysis. RESULTS: The Beijing family of Lineage 2 (East Asia) was the predominant genotype accounting for 43.8% (46/105), followed by Lineage 4 (Euro-America) strains, including Uganda I (34.3%, 36/105), and the NEW-1 (9.5%, 10/105). The proportion of Beijing strain in patients with and without NCDS was 28.6% (8/28) and 49.4% (38/77), respectively, with a statistical power test value of 24.3%. No significant association was detected between MTB genotype and NCD status. A low clustering rate (2.9%) was identified, consisting of two clusters. The rates of global, mono-, poly- and multi-drug resistance were 16.2% (17/105), 14.3% (15/105), 1.0% (1/105) and 4.8% (5/105), respectively. The drug-resistant rates of rifampicin, isoniazid, and streptomycin, were 6.7% (7/105), 11.4% (12/105) and 5.7% (6/105), respectively. Isoniazid resistance was significantly associated with the Beijing genotype of Lineage 2 (19.6% versus 5.1%). CONCLUSIONS: The Lineage 2 East Asia/Beijing genotype is the dominant genotype of the local MTB with endogenous infection preponderating. Not enough evidence is detected to support the association between the MTB genotype and diabetes/hypertension. Isoniazid resistance is associated with the Lineage 2 East Asia/Beijing strain.

Fecal microbiome alterations in pediatric patients with short bowel syndrome receiving a rotating cycle of gastrointestinal prophylactic antibiotics.

BACKGROUND: Pediatric patients with short bowel syndrome (SBS) are at risk of developing small intestinal bacterial overgrowth (SIBO). Prevention of SIBO using cyclic enteric antibiotics has been implemented to control the balance in microbial ecosystems, although its effectiveness has not been well studied. PURPOSE: This study aimed to explore the change in the gut microbial composition in SBS patients during cyclic antibiotic phases and antibiotic-free period, and to compare the microbiota composition between healthy controls and SBS patients. METHOD: SBS patients taking oral metronidazole alternating with trimethoprim-sulfamethoxazole (TMP-SMT) and antibiotic-free conditions as a '10-day cyclic protocol' were involved in fecal microbiome study using Illumina 16S sequencing. RESULTS: When healthy control possessed the majority of Bacteroidetes spp. (54%) and Firmicutes spp. (33%), the microbial composition in SBS patients especially Firmicutes spp. and Proteobacteria spp. was prominently changed in each phase of treatment. In antibiotic-free period, SBS patients displayed 49% Firmicutes and 36% Proteobacteria. However, higher Proteobacteria than Firmicutes were detected at the commencement of metronidazole (58% versus 33%). Similarly, 56% Proteobacteria and 27% Firmicutes were found during TMP-SMT. Escherichia coli increased prominently during the antibiotic periods. CONCLUSION: Prophylactic antibiotics change the gut microbiota composition in an unfavorable direction, especially when repeatedly used for a long period. This practice should be reconsidered. LEVEL OF EVIDENCE: III.

Water depth outweighs reef condition in shaping non-geniculate coralline algae-associated microbial communities in coral reefs: A case study from Thailand.

Red calcified non-geniculate coralline algae (NGCA) provide habitat structures, stabilize reef structures, and foster coral larval settlement and metamorphosis. Moreover, the microbes associated with NGCA are dependent on the NGCA host species and are affected by environmental factors; however, little is known about the influence of reef conditions and depth gradients on the associated microbial communities and NGCA. In this study, we collected NGCA under different reef conditions and depth gradients and characterized the microbial communities using the V3-V4 hypervariable regions of the 16S rRNA gene. Metagenomic analysis revealed 2 domains, 51 phyla, 123 classes, and 210 genera. The NGCA-associated bacterial communities were dominated by Proteobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, and Acidobacteriota. Gammaproteobacteria and Alphaproteobacteria were the most abundant bacterial classes. Differences in microbial diversity and richness were not apparent between reef conditions and depth gradients. However, there was a significant difference in bacterial evenness among the depth gradients. The bacterial abundance associated with NGCA was greater in deep zones than in shallow zones. The shallow zone exhibited a greater relative abundance of all gene functions than the deep zone, indicating differences in the distribution of gene functions. This study showed that the microbial communities associated with red calcified NGCA are diverse, and that the depth gradient affects their abundance and evenness, highlighting the need for further research to understand the functional roles of these microbial communities in coral reef conservation.

Unlocking the genetic potential of Lacticaseibacillus rhamnosus strains: Medical applications of a promising probiotic for human and animal health.

Lacticaseibacillus rhamnosus is a group of probiotic strains that have gained popularity for their potential health benefits such as promoting digestive health, boosting the immune system, improving lactose digestion, preventing and treating antibiotic-associated diarrhea, reducing the severity and duration of certain infections, and preventing the formation of dental plaque. In particular, L. rhamnosus strains SD4 and SD11 have promising human and animal health applications due to their ability to inhibit the growth of harmful pathogens. This study presents an in silico genomic analysis of L. rhamnosus strains SD4 and SD11. We analyzed draft genomes and conducted comparative genome analyses against several other probiotic strains, aiming to gain insights into the genomes of the two strains and to compare them to related strains isolated from other sources. We also aimed to clarify the functional mechanisms and adaptation of these strains to specific environments. Comprehensive insights into the genomes of L. rhamnosus SD4 and SD11 could enhance our understanding of their capacity to colonize, adapt, and exhibit probiotic properties after administration. This study holds significance in advancing our understanding of the potential health benefits associated with these strains and in elucidating the underlying mechanisms responsible for their effectiveness in humans and animals.

Differential Abundances of Bdellovibrio and Rheinheimera in the Oral Microbiota of Neonates With and Without Clinical Sepsis.

BACKGROUND: Neonatal sepsis is associated with high rates of morbidity and mortality, long hospital stays and high cost of care, thereby inflicting a burden on health care systems. Oral care with breast milk has been shown to modify the intestinal tract microbiota and immune system. Herein, we attempted to identify probiotics that may be beneficial to prevent or treat neonatal sepsis. METHODS: This was a secondary analysis comparing the microbiota during oropharyngeal care in very-low-birth-weight infants with and without clinical sepsis. Oral samples were collected before oral feeding was initiated. The primary outcome was oral microbiota composition including diversity, relative abundance and linear discriminant analysis effect size. RESULTS: Sixty-three neonates, including 39 and 24 with and without clinical sepsis, respectively, were enrolled. The medians gestational age and birth weight were 29 (27-30) weeks and 1010 (808-1263) g. Neonates with clinical sepsis had lower gestational age, birth weight (both P < 0.001) and lower rate of oral care with breast milk ( P = 0.03), but higher doses and days of antibiotic exposure (both P < 0.001) compared to neonates without clinical sepsis. No differences in alpha and beta diversities were found between groups and Streptococcus agalactiae was the most common bacteria in both groups. Linear discriminant analysis effect size analysis revealed that neonates without clinical sepsis had significantly higher abundances of order Bdellovibrionales, family Bdellovibrionaceae, genus Bdellovibrio and genus Rheinheimera . CONCLUSIONS: Neonates without clinical sepsis had a significantly greater abundance of the Bdellovibrio and Rheinheimera genera.

Lyophilized cell-free supernatants of Limosilactobacillus fermentum T0701 exhibited antibacterial activity against Helicobacter pylori.

Helicobacter pylori is a prominent gastrointestinal pathogen associated with various gastrointestinal illnesses. It presents substantial health risks due to its antibiotic resistance. Therefore, it is crucial to identify alternative treatments for H. pylori infections. Limosilactobacillus spp exhibit probiotic properties with beneficial effects in humans; however, the mechanisms by which it counteracts H. pylori infection are unknown. This study aimed to evaluate the potential of Limosilactobacillus fermentum T0701 lyophilized cell-free supernatants (LCFS) against H. pylori. The LCFS has varying antimicrobial activities, with inhibition zones of up to 10.67 mm. The minimum inhibitory concentration and minimum bacterial concentration of LCFS are 6.25-25.00 mg/mL and 6.25 mg/mL to > 50.00 mg/mL, respectively, indicating its capability to inhibit H. pylori. There is morphological damage observed in H. pylori treated with LCFS. Additionally, H. pylori adhesion to AGS cells (human gastric adenocarcinoma epithelial cells) reduces by 74.23%, highlighting the LCFS role in preventing bacterial colonization. Moreover, LCFS exhibits no cytotoxicity or morphological changes in AGS cells, and with no detected virulence or antimicrobial resistance genes, further supporting its safety profile. L. fermentum T0701 LCFS shows promise as a safe and effective non-toxic agent against H. pylori, with the potential to prevent gastric colonization.

Probiotic Insights from the Genomic Exploration of Lacticaseibacillus paracasei Strains Isolated from Fermented Palm Sap.

This study focused on L. paracasei strains isolated from fermented palm sap in southern Thailand that exhibit potential probiotic characteristics, including antibiotic susceptibility, resistance to gastrointestinal stresses, and antimicrobial activity against various pathogens. However, a thorough investigation of the whole genome sequences of L. paracasei isolates is required to ensure their safety and probiotic properties for human applications. This study aimed to sequence the genome of L. paracasei isolated from fermented palm sap, to assess its safety profile, and to conduct a comprehensive comparative genomic analysis with other Lacticaseibacillus species. The genome sizes of the seven L. paracasei strains ranged from 3,070,747 bp to 3,131,129 bp, with a GC content between 46.11% and 46.17% supporting their classification as nomadic lactobacilli. In addition, the minimal presence of cloud genes and a significant number of core genes suggest a high degree of relatedness among the strains. Meanwhile, phylogenetic analysis of core genes revealed that the strains possessed distinct genes and were grouped into two distinct clades. Genomic analysis revealed key genes associated with probiotic functions, such as those involved in gastrointestinal, oxidative stress resistance, vitamin synthesis, and biofilm disruption. This study is consistent with previous studies that used whole-genome sequencing and bioinformatics to assess the safety and potential benefits of probiotics in various food fermentation processes. Our findings provide valuable insights into the potential use of seven L. paracasei strains isolated from fermented palm sap as probiotic and postbiotic candidates in functional foods and pharmaceuticals.

Association of biofilm formation, antimicrobial resistance, clinical characteristics, and clinical outcomes among Acinetobacter baumannii isolates from patients with ventilator-associated pneumonia.

INTRODUCTION: Biofilm formation is an important virulence factor of Acinetobacter baumannii. Here, we examined the biofilm formation of archived A. baumannii causing ventilator-associated pneumonia (VAP). METHODS: Eighteen and twenty isolates of A. baumannii causing bacteremic pneumonia and non-bacteremic pneumonia were included, respectively. Antimicrobial susceptibility testing was performed by broth microdilution method, while biofilm formation was evaluated by microtiter dish biofilm formation assay. RESULTS: All 38 isolates were still susceptible to colistin and tigecycline, whereas almost all isolates were non-susceptible (intermediate to resistant) to several antimicrobial agents, especially ceftriaxone and cefotaxime. Approximately, 44% of bacteremic isolates and 50% of non-bacteremic isolates were classified as carbapenem-resistant A. baumannii (CRAB). Biofilm formation was detected in 42% of the studied isolates. Bacteremia among the patients infected with biofilm-producing isolates was significantly higher than in those infected with non-biofilm-producing isolates. The antimicrobial susceptibilities of A. baumannii with biofilm formation were lower than those without biofilm formation, but the differences did not have statistical significance. The patients infected with non-biofilm-producing isolates had good clinical and non-clinical outcomes than those infected with biofilm-producing isolates. The survival rate of patients diagnosed with VAP due to biofilm-producing A. baumannii was lower than in those patients diagnosed with VAP due to non-biofilm-producing isolates. CONCLUSION: Biofilm formation of A. baumannii causing VAP was associated with antimicrobial resistance and bacteremia as well as unfavorable clinical outcomes.

Genomic Characterization of Multidrug-Resistant Enterobacteriaceae Clinical Isolates from Southern Thailand Hospitals: Unraveling Antimicrobial Resistance and Virulence Mechanisms.

The emergence and spread of antimicrobial resistance (AMR) among Enterobacteriaceae pose significant threats to global public health. In this study, we conducted a short-term surveillance effort in Southern Thailand hospitals to characterize the genomic diversity, AMR profiles, and virulence factors of Enterobacteriaceae strains. We identified 241 carbapenem-resistant Enterobacteriaceae, of which 12 were selected for whole-genome sequencing (WGS) and genome analysis. The strains included Proteus mirabilis, Serratia nevei, Klebsiella variicola, Klebsiella aerogenes, Klebsiella indica, Klebsiella grimontii, Phytobacter ursingii, Phytobacter palmae, Kosakonia spp., and Citrobacter freundii. The strains exhibited high levels of multidrug resistance, including resistance to carbapenem antibiotics. Whole-genome sequencing revealed a diverse array of antimicrobial resistance genes (ARGs), with strains carrying genes for ß-lactamase, efflux pumps, and resistance to other antibiotic classes. Additionally, stress response, metal tolerance, and virulence-associated genes were identified, highlighting the adaptability and pathogenic potential of these strains. A plasmid analysis identified several plasmid replicons, including IncA/C2, IncFIB(K), and Col440I, as well as several plasmids identical to those found globally, indicating the potential for the horizontal gene transfer of ARGs. Importantly, this study also identified a novel species of Kosakonia spp. PSU27, adding to the understanding of the genetic diversity and resistance mechanisms of Enterobacteriaceae in Southern Thailand. The results reported in this study highlight the critical importance of implementing effective antimicrobial management programs and developing innovative treatment approaches to urgently tackle AMR.

Virulent properties and genomic diversity of Vibrio vulnificus isolated from environment, human, diseased fish.

The incidence of Vibrio vulnificus infections, with high mortality rates in humans and aquatic animals, has escalated, highlighting a significant public health challenge. Currently, reliable markers to identify strains with high virulence potential are lacking, and the understanding of evolutionary drivers behind the emergence of pathogenic strains is limited. In this study, we analyzed the distribution of virulent genotypes and phenotypes to discern the infectious potential of V. vulnificus strains isolated from three distinct sources. Most isolates, traditionally classified as biotype 1, possessed the virulence-correlated gene-C type. Environmental isolates predominantly exhibited YJ-like alleles, while clinical and diseased fish isolates were significantly associated with the nanA gene and pathogenicity region XII. Hemolytic activity was primarily observed in the culture supernatants of clinical and diseased fish isolates. Genetic relationships, as determined by multiple-locus variable-number tandem repeat analysis, suggested that strains originating from the same source tended to cluster together. However, multilocus sequence typing revealed considerable genetic diversity across clusters and sources. A phylogenetic analysis using single nucleotide polymorphisms of diseased fish strains alongside publicly available genomes demonstrated a high degree of evolutionary relatedness within and across different isolation sources. Notably, our findings reveal no direct correlation between phylogenetic patterns, isolation sources, and virulence capabilities. This underscores the necessity for proactive risk management strategies to address pathogenic V. vulnificus strains emerging from environmental reservoirs.IMPORTANCEAs the global incidence of Vibrio vulnificus infections rises, impacting human health and marine aquacultures, understanding the pathogenicity of environmental strains remains critical yet underexplored. This study addresses this gap by evaluating the virulence potential and genetic relatedness of V. vulnificus strains, focusing on environmental origins. We conduct an extensive genotypic analysis and phenotypic assessment, including virulence testing in a wax moth model. Our findings aim to uncover genetic and evolutionary factors that drive pathogenic strain emergence in the environment. This research advances our ability to identify reliable virulence markers and understand the distribution of pathogenic strains, offering significant insights for public health and environmental risk management.

Discovery of Novel Potential Prognostic Markers and Targeted Therapy to Overcome Chemotherapy Resistance in an Advanced-Stage Wilms Tumor.

Wilms tumor (WT), the most prevalent type of renal cancer in children, exhibits overall survival rates exceeding 90%. However, chemotherapy resistance, which occurs in approximately 10% of WT cases, is a major challenge for the treatment of WT, particularly for advanced-stage patients. In this study, we aimed to discover potential mutation markers and drug targets associated with chemotherapy resistance in advanced-stage WT. We performed exome sequencing to detect somatic mutations and molecular targets in 43 WT samples, comprising 26 advanced-stage WTs, of which 7 cases were chemotherapy-resistant. Our analysis revealed four genes (ALPK2, C16orf96, PRKDC, and SVIL) that correlated with chemotherapy resistance and reduced disease-free survival in advanced-stage WT. Additionally, we identified driver mutations in 55 genes within the chemotherapy-resistant group, including 14 druggable cancer driver genes. Based on the mutation profiles of the resistant WT samples, we propose potential therapeutic strategies involving platinum-based agents, PARP inhibitors, and antibiotic/antineoplastic agents. Our findings provide insights into the genetic landscape of WT and offer potential avenues for targeted treatment, particularly for patients with chemotherapy resistance.

Genotypic and phenotypic mechanisms underlying antimicrobial resistance and synergistic efficacy of rifampicin-based combinations against carbapenem-resistant Acinetobacter baumannii.

Purpose: Carbapenem-resistant Acinetobacter baumannii (CRAB) is an urgent concern to public health. This study focuses on exploring the resistance mechanisms and the in vitro results of using rifampicin in combination with conventional antibiotics for the management of CRAB. Methods: The synergistic and bactericidal effects of rifampicin with conventional antibiotics were evaluated using chequerboard assay and time-kill assay, while the phenotypic and genotypic characteristics of resistant determinants were performed by efflux pump detection and whole genome sequencing on 29 isolates from ICU patients with underlying health diseases. Results: The isolates showed multidrug resistance, with over 60% showing addictive responses to rifampicin-based combinations at FICI ranging from 0.6 to 0.8. The time-kill assay revealed 99 % killing for rifampicin and minocycline combination in one isolate at 1/4 MIC rifampicin plus 1/4 MIC minocycline, while a bacteriostatic effect was observed at 1/2 MIC rifampici plus 1/2 MIC for a second isolate. Combination with tigecycline resulted in a 99% killing in two out of three isolates with a 2.5-3 log reduction in CFU at 1/4 MIC rifampicin plus 1/4 MIC tigecycline. Rifampicin plus colistin exhibited bactericidal activity against three out of four isolates. The combinations of rifampicin with ciprofloxacin, chloramphenicol, and trimethoprim-sulfamethoxazole were ineffective against the isolates. In addition, a 4-fold reduction in rifampicin MIC was observed in 2 out of 14 isolates in the presence of an efflux pump inhibitor. The pan-genome study demonstrated a progressive evolution with an accessory genome estimated to cover 58% of the matrix. Seven of the ten sequenced isolates belong to sequence type 2 (ST2), while one isolate each was assigned to ST164, ST16, and ST25. Furthermore, 11 plasmids, 34 antimicrobial resistance (AMR) genes, and 65 virulence-associated genes were predicted from the whole genome data. The blaOXA-23blaADC-25, blaOXA-66, blaPER-7, aph(6)-Id, armA, and arr-3 were prevalent among the isolates. Sequence alignment of the bacteria genome to the reference strain revealed a deleterious mutation in the rpoB gene of 4 isolates. Conclusion: The study suggests that rifampicin in combination with either minocycline, tigecycline, or colistin might be a treatment option for CRAB clinical isolates. In addition, genotypic analysis of the bacteria isolates may inform the clinician of the suitable drug regimen for the management of specific bacteria variants.

Genomic Characterization of Mobile Genetic Elements Associated with Multidrug-Resistant Acinetobacter Non-baumannii Species from Southern Thailand.

This study investigated the genetic diversity, antimicrobial resistance profiles, and virulence characteristics of Acinetobacter non-baumannii isolates obtained from four hospitals in southern Thailand. Clinical data, genome information, and average nucleotide identity (ANI) were analyzed for eight isolates, revealing diverse genetic profiles and novel sequence types (STs). Minimum spanning tree analysis indicated potential clonal spread of certain STs across different geographic regions. Antimicrobial resistance genes (ARGs) were detected in all isolates, with a high prevalence of genes conferring resistance to carbapenems, highlighting the challenge of antimicrobial resistance in Acinetobacter spp. infections. Mobile genetic elements (MGEs) carrying ARGs were also identified, emphasizing the role of horizontal gene transfer in spreading resistance. Evaluation of virulence-associated genes revealed a diverse range of virulence factors, including those related to biofilm formation and antibiotic resistance. However, no direct correlation was found between virulence-associated genes in Acinetobacter spp. and specific clinical outcomes, such as infection severity or patient mortality. This complexity suggests that factors beyond gene presence may influence disease progression and outcomes. This study emphasizes the importance of continued surveillance and molecular epidemiological studies to combat the spread of multidrug-resistant (MDR) Acinetobacter non-baumannii strains. The findings provide valuable insights into the epidemiology and genetic characteristics of this bacteria in southern Thailand, with implications for infection control and antimicrobial management efforts.

Long Duration of Oral Care Using Mother's Own Milk Influences Oral Microbiota and Clinical Outcomes in Very-low-birthweight Infants: Randomized Controlled Trial.

BACKGROUND: Several studies have focused on the clinical outcomes of oral care using colostrum for a limited time (2-5 days) in very-low-birthweight (VLBW) infants. However, the effect of long-term mother's own milk (MOM) on the clinical outcomes and oral microbiota of VLBW infants remains unknown. METHODS: In this randomized controlled trial, VLBW neonates were randomly assigned to oral care by MOM or sterile water (SW) groups until they started oral feeding. The primary outcome was oral microbiota composition including alpha and beta diversity, relative abundance, and linear discriminant analysis effect size (LEfSe). The secondary outcomes were various morbidities and mortality. RESULTS: The baseline characteristics of the two groups did not differ (63 neonates, MOM group, n = 30, oral care 22 days; SW group, n = 33, oral care 27 days). There was no significant difference in alpha and beta diversities between the groups before and after the intervention. The MOM group had a significantly lower rate of clinical sepsis than the SW group (47% vs. 76%, risk ratio = 0.62, 95% CI: 0.40-0.97). The relative abundance of Bifidobacterium bifidum and Faecalibacterium were maintained after MOM care, especially in neonates without clinical sepsis, but decreased after SW care. LEfSe showed that neonates in the MOM and SW groups with clinical sepsis had the highest abundance of Pseudomonas and Gammaproteobacteria, respectively, compared with neonates without sepsis. CONCLUSIONS: A longer duration of oral care using MOM in VLBW infants sustains healthy bacteria and decreases the risk of clinical sepsis.

Population-based prevalence study of common congenital malformations of the alimentary tract and abdominal wall in Thailand: a study using data from the National Health Security Office.

Background: The study aimed to estimate the prevalence of major congenital anomalies of the alimentary system and the abdominal wall in Thailand using a nationwide hospital discharge database from the National Health Security Office (2017-2020). Methods: The study extracted data from records with International Classification of Diseases-10 (ICD-10) codes related to esophageal malformation (ESO), congenital duodenal obstruction (CDO), jejunoileal atresia (INTES), Hirschsprung's disease (HSCR), anorectal malformation (ARM), abdominal wall defects (omphalocele (OMP) and gastroschisis (GAS)), and diaphragmatic hernia from the database with patient age selection set to less than 1 year. Results: A total of 2539 matched ICD-10 records were found in 2376 individuals over the 4-year study period. Concerning foregut anomalies, the prevalence of ESO was 0.88/10 000 births, while that of CDO was 0.54/10 000 births. The prevalence figures of INTES, HSCR, and ARM were 0.44, 4.69, and 2.57 cases per 10 000 births, respectively. For abdominal wall defects, the prevalences of OMP and GAS were 0.25 and 0.61 cases/10 000 births, respectively. The mortality in our cases was 7.1%, and survival analysis found that associated cardiac defects had a statistically significant influence on survival in most anomalies studied. In HSCR, both Down syndrome (DS) (hazard ratio (HR)=7.57, 95% confidence interval (CI)=4.12 to 13.91, p<0.001) and cardiac defects (HR=5.82, 95% CI=2.85 to 11.92, p<0.001) were significantly associated with poorer survival outcomes. However, only DS (adjusted HR=5.55, 95% CI=2.63 to 11.75, p<0.001) independently predicted worse outcomes by multivariable analysis. Conclusions: Our analysis of the hospital discharge database found that the prevalence of gastrointestinal anomalies in Thailand was lower than that reported in other countries, except for HSCR and anorectal malformations. Associated Down syndrome and cardiac defects influence the survival outcomes of these anomalies.

BacSeq: A User-Friendly Automated Pipeline for Whole-Genome Sequence Analysis of Bacterial Genomes.

Whole-genome sequencing (WGS) of bacterial pathogens is widely conducted in microbiological, medical, and clinical research to explore genetic insights that could impact clinical treatment and molecular epidemiology. However, analyzing WGS data of bacteria can pose challenges for microbiologists, clinicians, and researchers, as it requires the application of several bioinformatics pipelines to extract genetic information from raw data. In this paper, we present BacSeq, an automated bioinformatic pipeline for the analysis of next-generation sequencing data of bacterial genomes. BacSeq enables the assembly, annotation, and identification of crucial genes responsible for multidrug resistance, virulence factors, and plasmids. Additionally, the pipeline integrates comparative analysis among isolates, offering phylogenetic tree analysis and identification of single-nucleotide polymorphisms (SNPs). To facilitate easy analysis in a single step and support the processing of multiple isolates, BacSeq provides a graphical user interface (GUI) based on the JAVA platform. It is designed to cater to users without extensive bioinformatics skills.

Combination of genetically diverse Pseudomonas phages enhances the cocktail efficiency against bacteria.

Phage treatment has been used as an alternative to antibiotics since the early 1900s. However, bacteria may acquire phage resistance quickly, limiting the use of phage treatment. The combination of genetically diverse phages displaying distinct replication machinery in phage cocktails has therefore become a novel strategy to improve therapeutic outcomes. Here, we isolated and studied lytic phages (SPA01 and SPA05) that infect a wide range of clinical Pseudomonas aeruginosa isolates. These relatively small myophages have around 93 kbp genomes with no undesirable genes, have a 30-min latent period, and reproduce a relatively high number of progenies, ranging from 218 to 240 PFU per infected cell. Even though both phages lyse their hosts within 4 h, phage-resistant bacteria emerge during the treatment. Considering SPA01-resistant bacteria cross-resist phage SPA05 and vice versa, combining SPA01 and SPA05 for a cocktail would be ineffective. According to the decreased adsorption rate of the phages in the resistant isolates, one of the anti-phage mechanisms may occur through modification of phage receptors on the target cells. All resistant isolates, however, are susceptible to nucleus-forming jumbophages (PhiKZ and PhiPA3), which are genetically distinct from phages SPA01 and SPA05, suggesting that the jumbophages recognize a different receptor during phage entry. The combination of these phages with the jumbophage PhiKZ outperforms other tested combinations in terms of bactericidal activity and effectively suppresses the emergence of phage resistance. This finding reveals the effectiveness of the diverse phage-composed cocktail for reducing bacterial growth and prolonging the evolution of phage resistance.