First Report of Kosakonia radicincitans Bacteraemia from Europe (Austria) - Identification and Whole-Genome Sequencing of Strain DSM 107547

Kosakonia radicincitans with hypervirulent lON genes causes human bloodstream infections

Kosakonia radicincitans is a species within the new genus Kosakonia, which is typically a plant pathogen, with rare reports of human infection. The number of human infections may be underestimated because this new genus is under-represented among diagnostic tools. This report describes a case of bloodstream infection caused by K. radicincitans. The pathogen was identified by matrix-assisted laser desorption/ionization-TOF mass spectrometry and 16S rRNA gene sequencing. The hypervirulent human pathogenicity gene LON, which has not been described before, was detected in the bacterial genome by gene annotation. Thus, this discovery provides a new reference for studying the pathogenic mechanism of this rare pathogen.

Insights into the Bacterial Diversity and Detection of Opportunistic Pathogens in Mexican Chili Powder

Chili powder is the most frequently consumed spice in Mexican diets. Thus, the dissemination of microorganisms associated with chili powder derived from Capsicum annuum L. is significant during microbial quality analysis, with special attention on detection of potential pathogens. The results presented here describe the initial characterization of bacterial community structure in commercial chili powder samples. Our results demonstrate that, within the domain Bacteria, the most abundant family was Bacillaceae, with a relative abundance of 99% in 71.4% of chili powder samples, while 28.6% of samples showed an average relative abundance of 60% for the Enterobacteriaceae family. Bacterial load for aerobic mesophilic bacteria (AMB) ranged from 10⁴ to 10⁶ cfu/g, while for sporulated mesophilic bacteria (SMB), the count ranged from 10² to 10⁵ cfu/g. Bacillus cereus sensu lato (s.l.) was observed at ca. ˂600 cfu/g, while the count for Enterobacteriaceae ranged from 10³ to 10⁶ cfu/g, Escherichia coli and Salmonella were not detected. Fungal and yeast counts ranged from 10² to 10⁵ cfu/g. Further analysis of the opportunistic pathogens isolated, such as B. cereus s.l. and Kosakonia cowanii, using antibiotic-resistance profiles and toxinogenic characteristics, revealed the presence of extended-spectrum β-lactamases (ESBLs) and Metallo-β-lactamases (MBLs) in these organisms. These results extend our knowledge of bacterial diversity and the presence of opportunistic pathogens associated with Mexican chili powder and highlight the potential health risks posed by its use through the spread of antibiotic-resistance and the production of various toxins. Our findings may be useful in developing procedures for microbial control during chili powder production.

Transitions in bacterial communities across two fermentation-based virgin coconut oil (VCO) production processes

Despite being one of the most used methods of virgin coconut oil (VCO) production, there is no metagenomic study that details the bacterial community shifts during fermentation-based VCO production. The identification and quantification of bacteria associated with coconut milk fermentation is useful for detecting the dominant microbial genera actively involved in VCO production which remains largely undescribed. Describing the constitutive microbial genera involved in this traditional fermentation practice can be used as a preliminary basis for improving industrial practices and developing better fermentation procedures. In this study, we utilized 16S rRNA metagenomic sequencing to trace the transitions in microbial community profiles as coconut milk is fermented to release VCO in two VCO production lines. The results show that difference in the microbiome composition between the different processing steps examined in this work was mainly due to the abundance of the Leuconostoc genus in the raw materials and its decline and transition into the lactic acid bacteria groups Weissella, Enterococcus, Lactobacillus, Lactococcus, and Streptococcus during the latter stages of fermentation. A total of 17 genera with relative abundances greater than 0.01% constitute the core microbiome of the two processing lines and account for 74%–97% of the microbial abundance in all coconut-derived samples. Significant correlations were shown through an analysis of the Spearman’s rank between and within the microbial composition and pH at the genus level. The results of the present study show that the dynamics of VCO fermentation rely on the shifts in abundances of various members of the Lactobacillales order.

The Mexican giant maize of Jala landrace harbour plant-growth-promoting rhizospheric and endophytic bacteria

The giant landrace of maize Jala is a native crop cultured in Nayarit and Jalisco States in the occident of México. In this study, after screening 374 rhizospheric and endophytic bacteria isolated from rhizospheric soil, root, and seed tissues of maize Jala, a total of 16 bacterial strains were selected for their plant-growth-promoting potential and identified by 16S rRNA phylogenetic analysis. The isolates exhibited different combinations of phenotypic traits, including solubilisation of phosphate from hydroxyapatite, production of a broad spectrum of siderophores such as cobalt, iron, molybdenum, vanadium, or zinc (Co²⁺, Fe³⁺, Mo^2 +, V⁵⁺, Zn²⁺), and nitrogen fixation capabilities, which were detected in both rhizospheric and endophytic strains. Additional traits such as production of 1-aminocyclopropane-1-carboxylate deaminase and a high-rate production of Indoleacetic Acid were exclusively detected on endophytic isolates. Among the selected strains, the rhizospheric Burkholderia sp., and Klebsiella variicola, and the endophytic Pseudomonas protegens significantly improved the growth of maize plants in greenhouse assays and controlled the infection against Fusarium sp. 50 on fresh maize cobs. These results present the first deep approach on handling autochthonous microorganisms from native maize with a potential biotechnological application in sustainable agriculture as biofertilizers or biopesticides.

Novel Viruses That Lyse Plant and Human Strains of Kosakonia cowanii

Kosakonia cowanii (syn. Enterobacter cowanii) is a highly competitive bacterium that lives with plant, insect, fish, bird, and human organisms. It is pathogenic on some plants and an opportunistic pathogen of human. Nine novel viruses that lyse plant pathogenic strains and/or human strains of K. cowanii were isolated, sequenced, and characterized. Kc166A is a novel kayfunavirus, Kc261 is a novel bonnellvirus, and Kc318 is a new cronosvirus (all Autographiviridae). Kc237 is a new sortsnevirus, but Kc166B and Kc283 are members of new genera within Podoviridae. Kc304 is a new winklervirus, and Kc263 and Kc305 are new myoviruses. The viruses differ in host specificity, plaque phenotype, and lysis kinetics. Some of them should be suitable also as pathogen control agents.

Genomic Insight into Pediococcus acidilactici HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang

Pediococcus acidilactici HN9 is a beneficial lactic acid bacterium isolated from Nhang, a traditional Thai-style fermented beef. In this study, the molecular properties of P. acidilactici HN9 were characterized to provide insights into its potential probiotic activity. Specifically, this work sought to report the complete genome of P. acidilactici HN9 and perform a comparative genome analysis with other bacterial strains belonging to the genus Pediococcus. Genomic features of HN9 were compared with those of all other bacterial Pediococcus strains to examine the adaptation, evolutionary relationships, and diversity within this genus. Additionally, several bioinformatic approaches were used to investigate phylogenetic relationships, genome stability, virulence factors, bacteriocin production, and antimicrobial resistance genes of the HN9 strain, as well as to ensure its safety as a potential starter culture in food applications. A 2,034,522 bp circular chromosome and two circular plasmids, designated pHN9-1 (42,239-bp) and pHN9-2 (30,711-bp), were detected, and used for pan-genome analysis, as well as for identification of bacteriocin-encoding genes in 129 strains belonging to all Pediococcus species. Two CRISPR regions were identified in P. acidilactici HN9, including type II-A CRISPR/CRISPR-associated (Cas). This study provides an in-depth analysis on P. acidilactici HN9, facilitating a better understanding of its adaptability to different environments and its mechanism to maintain genome stability over time.

Bacteremia Due to Kosakonia cowanii in a Preterm Neonate

Objective Low-birthweight infants admitted to neonatal intensive care units are at high risk of hospital-acquired infections by opportunistic pathogens. The gut microbiota of preterm neonates lacks commensal bacteria providing a barrier against pathogens. We report a case of bacteremia due to Kosakonia cowanii in a preterm neonate.

Case Report A female baby of 680 g was delivered through a cesarean-section at 28 weeks of gestation due to intrauterine growth retardation and fetal rhythm abnormalities. On day 27, two blood cultures grew gram-negative bacilli in a context of functional ileus. No reliable identification could be obtained using matrix assisted laser desorption ionization-time of flight, biochemical reactions with the VITEK 2 GN ID card, or 16S rDNA sequencing. K. cowanii was finally identified by gyrB sequencing. The source of infection may have been either the central venous catheter or translocation from the gut microbiota. Evolution was favorable after 14 days of cefepime (combined with amikacin for 5 days) and central venous catheter removal.

Conclusion K. cowanii is a member of the Enterobacteriaceae family that was recently reclassified from the Enterobacter genus. Human infections due to K. cowanii are scarce and have mainly been associated with traumatic inoculation from plants or transient gut colonization. K. cowanii may be an underestimated opportunistic pathogen in susceptible populations such as preterm neonates.