Accurate species-level identification of Enterobacter cloacae complex (ECC) is crucial for related research. The classification of ECC is based on strain-to-strain phylogenetic congruence, as well as genomic features including average nucleotide identity (ANI) and digitalized DNA-DNA hybridization (dDDH). ANI and dDDH derived from whole-genome sequencing have emerged as a reliable metric for assessing genetic relatedness between genomes and are increasingly recognized as a standard for species delimitation. Up to now, there are two different classification methods for ECC. The first one categorizes E. hormaechei, a species within ECC, into five subspecies (E. hormaechei subsp. steigerwaltii, subsp. oharae, subsp. xiangfangensis, subsp. hoffmannii, and subsp. hormaechei). The second classifies E. hormaechei as three species: E. hormaechei, \"E. xiangfangensis,\" \"E. hoffmanii.\" While the former is well-accepted in the academic area, the latter may have a greater ability to distinguish different species of ECC. To assess the suitability of these identification criteria for clinical ECC isolates, we conducted a comprehensive analysis involving phylogenetic analysis, ANI and dDDH value alignment, virulence gene identification, and capsule typing on 256 clinical ECC strains isolated from the bloodstream. Our findings indicated that the method of categorizing E. hormaechei into five subspecies has better correlation and consistency with the molecular characteristics of clinical ECC isolates, as evidenced by phylogenetic analysis, virulence genes, and capsule typing. Therefore, the subspecies-based classification method appears more suitable for taxonomic assignments of clinical ECC isolates.
OBJECTIVE: Standardizing taxonomy of the Enterobacter cloacae complex (ECC) is necessary for data integration across diverse studies. The study utilized whole-genome data to accurately identify 256 clinical ECC isolated from bloodstream infections using average nucleotide identity (ANI), digitalized DNA-DNA hybridization (dDDH), and phylogenetic analysis. Through comprehensive assessments including phylogenetic analysis, ANI and dDDH comparisons, virulence gene, and capsule typing of the 256 clinical isolates, it was concluded that the classification method based on subspecies exhibited better correlation and consistency with the molecular characteristics of clinical ECC isolates. In summary, this research contributes to the precise identification of clinical ECC at the species level and expands our understanding of ECC.

BACKGROUND: Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS).
RESULTS: We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently.
CONCLUSIONS: Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.

Mycobacterium tuberculosis genotyping has impacted evolutionary studies worldwide. Nonetheless, its application and the knowledge generated depend on the genetic marker evaluated and the detection technologies that have evolved over the years. Here we describe the timeline of main genotypic methods related to M. tuberculosis in Latin America and the main findings obtained.
Systematic searches through the PubMed database were performed from 1993 to May 2021. A total of 345 articles met the inclusion criteria and were selected.
Spacer oligonucleotide typing (spoligotyping) was the most widely used method in Latin America, with decreasing use in parallel with increasing use of mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) and whole genome sequencing (WGS). Among the countries, Brazil, Mexico, and Argentina had the most publications, and a considerable part of the articles were in collaboration with Latin American or non-Latin American institutions; a small proportion of studies needed partnerships to perform the genotypic methods. The genotypic methods allowed the identification of M. tuberculosis genotypes with greater capacity for clonal expansion and revealed the predominance of the Euro-American lineage in Latin America. There was a notable presence of the Beijing family in Peru and Colombia.
The data obtained demonstrated the importance of expanding collaborative networks of tuberculosis (TB) research groups to countries with low productivity in this area, the commitment of the few Latin American countries to advance TB research, as well as the inestimable value of building a Latin America database, considering ease of population mobility between countries.

A novel Neisseria strain, designated CSL10203-ORH2T, was isolated from the oropharynx of a wild California sea lion (Zalophus californianus) that was admitted to The Marine Mammal Center in California, USA. The strain was originally cultured from an oropharyngeal swab on BD Phenylethyl Alcohol (PEA) agar with 5% sheep blood under aerobic conditions. Phylogenetic analyses based on 16S rRNA, rplF, and rpoB gene sequences and the core genome sequences indicated that the strain was most closely related to only N. zalophi CSL 7565T. The average nucleotide identity and digital DNA-DNA hybridization values between strain CSL10203-ORH2T and the closely related species N. zalophi CSL 7565T were 89.84 and 39.70%, respectively, which were significantly lower than the accepted species-defined thresholds for describing novel prokaryotic species at the genomic level. Both type strains were phenotypically similar but can be easily and unambiguously distinguished between each other by the analysis of their housekeeping genes, e.g., rpoB, gyrB, or argF. The major fatty acids in both type strains were C12:0, C16:0, C16:1-c9, and C18:1-c11. Based on the genomic, phenotypic, and phylogenetic properties, the novel strain represents a novel species of the genus Neisseria, for which the name Neisseria montereyensis sp. nov. with the type strain CSL10203-ORH2T (= DSM 114706T = CCUG 76428T = NCTC 14721T) is proposed. The genome G + C content is 45.84% and the complete draft genome size is 2,310,535 bp.

In this study, three lactic acid bacteria, namely, HBUAS51963T, HBUAS51964 and HBUAS51965, were isolated from Chinese rice wine starter sampled in Fangxian County, PR China. All were non-motile, non-spore-forming and Gram-positive spherical cells. Their taxonomic status was characterized using a polyphasic approach. Genome-based analysis revealed that all three strains were phylogenomically related to Weissella thailandensis KCTC 3751T and Weissella paramesenteroides ATCC 33313T. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the three strains and the phylogenetically related type strains were less than 54.8 and 93.8 %, respectively, and thus, they were below the thresholds of dDDH and ANI for species definition. The genomic DNA G+C content was 38.6 mol %. The predominant fatty acid methyl esters (>10 %) were C16 : 0, C19 : 0 cyc11 and summed feature 10 (C18 : 1 cyc11 and/or ECL 17.834). The polar lipids in the cells of strain HBUAS51963T were mainly phosphatidylglycerol, diphosphatidylglycerol, unidentified glycolipids, phospholipids and lipids. Finally, the three strains were capable of producing d-lactic acid (4.29 g l-1) and various organic acids such as tartaric, acetic, lactic and succinic acids. Overall, the results of genotypic, phenotypic and genomic analyses suggest that the three strains represent a new species of the genus Weissella, for which the name Weissella fangxianis sp. nov. is proposed. The type strain is HBUAS51963T (=GDMCC 1.3506T= JCM 35803T).

Members of the genus Marinomonas are known for their environmental adaptation and metabolically versatility, with abundant proteins associated with antifreeze, osmotic pressure resistance, carbohydrase and multiple secondary metabolites. Comparative genomic analysis focusing on secondary metabolites and orthologue proteins was conducted with 30 reference genome sequences in the genus Marinomonas. In this study, a Gram-stain-negative, rod-shaped, non-flagellated and strictly aerobic bacterium, designated as strain E8T, was isolated from the red algae (Gelidium amansii) in the coastal of Weihai, China. Optimal growth of the strain E8T was observed at temperatures 25-30 °C, pH 6.5-8.0 and 1-3% (w/v) NaCl. The DNA G + C content was 42.8 mol%. The predominant isoprenoid quinone was Q-8 and the major fatty acids were C16:0, summed feature 3 and summed feature 8. The major polar lipids were phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). Based on data obtained from this polyphasic taxonomic study, strain E8T should be considered as a novel species of the genus Marinomonas, for which the name Marinomonas algarum is proposed. The type strain is E8T (= KCTC 92201T = MCCC 1K07070T).

Despite the worldwide use of 16S rRNA to identify bacterial species, the use of this gene does not discriminate the 750 species in the genus Streptomyces. A MLST scheme was constructed with rpoB, gyrB, recA, trpB and atpD genes to access the genomic variances in Streptomyces species evolution. We analyze the housekeeping genes in 49 Streptomyces isolates from Antarctic soil. It was used two different databases, GenBank and EzBioCloud to compare the 16S sequences. The species founded in both databases are not the same, but in both cases, a few isolates achieve the necessary high percentage to consider the identification. There is a lack of deposited sequences in the other genes, as the data in GenBank proved to be insufficient. Isolate LMA323St_9 has the potential to be studied as a novel species. Besides that, the use of housekeeping genes gives robust phylogenetic information to understand in group relationships.

We investigated the 16S-23S rRNA intergenic spacer region (ISR)-PCR and the phylogenetic PCR analyses of 150 Escherichia coli isolates as tools to explore their diversity, according to their sampling origins, and their relative dominance in these sampling sources. These genetic markers are used to explore phylogenetic and genetic relationships of these 150 E. coli isolates recovered from different environmental sources (water, food, animal, human and vegetables). These isolates are tested for their biochemical pattern and later genotyped through the 16S-23S rRNA intergenic spacer PCR amplification and their polymorphism investigation of PCR-amplified 16S-23S rDNA ITS. The main results of the pattern band profile revealed one to four DNA fragments. Distributing 150 E. coli isolates according to their ITS and using RS-PCR, revealed four genotypes and four subtypes. The DNA fragment size ranged from 450 to 550 bp. DNA band patterns analysis revealed considerable genetic diversity in interspecies. Thus, the 450 and 550 bp sizes of the common bands in all E. coli isolates are highly diversified. Genotype I appeared as the most frequent with 77.3% (116 isolates), genotype II with 12% (18 isolates); genotype III with 9.7% (14 isolates), and the IV rarely occurred with 4% (2 isolates). Distributing the E. coli phylogroups showed 84 isolates (56%) of group A, 35 isolates (23.3%) of group B1, 28 isolates (18.7%) of group B2 and only three isolates (2%) of group D.

BACKGROUND: Globally, surgical site infections are the most reported healthcare-associated infection and common surgical complication. In developing countries such as Ethiopia, there is a paucity of published reports on the microbiologic profile and resistance patterns of an isolates.
OBJECTIVE: This study aimed at assessing the bacterial profile and antimicrobial susceptibility patterns of isolates among patients diagnosed with surgical site infection at Jimma Medical Center in Ethiopia.
METHODS: A prospective cohort study was employed among adult patients who underwent either elective or emergency surgical procedures. All the eligible patients were followed for 30 days for the occurrence of surgical site infection (SSI). From those who developed SSI, infected wound specimens were collected and studied bacteriologically.
RESULTS: Of 251 study participants, 126 (50.2%) of them were females. The mean ± SD age of the patients was 38 ± 16.30 years. The overall postoperative surgical site infection rate was 21.1% and of these 71.7% (38/53) were culture positive. On gram stain analysis, 78% of them were Gram-negative, 11.5% were Gram-positive and 10.5% were a mixture of two microbial growths. Escherichia coli accounted for (21.43%), followed by Pseudomonas aeruginosa (19.05%), Proteus species (spp.) 14.29%), Staphylococcus aureus (11.90%), Klebsiella species (11.90%), Citrobacter spp. (9.5%), streptococcal spp. (7.14%), Coagulase-negative S. aureus (CoNS) (2.38%) CONCLUSION: Gram-negative bacteria were the most dominant isolates from surgical sites in the study area. Among the Gram-negative bacilli, Escherichia coli were the most common bacteria causing surgical site infection. As there is high antibiotic resistance observed in the current study, it is necessary for routine microbial analysis of samples and their antibiogram.

Streptococcus suis naturally colonizes the upper respiratory tract of pigs and can lead to severe disease conditions. Although there are several serotypes associated with disease, untypable isolates have also been observed. The objective of this study was to investigate the relatedness of untypable S. suis isolates detected in clinical cases and healthy pigs in Ontario, Canada, and their relation to typing serotypes. One hundred fifty-six isolates obtained from 33 cases and 26 farm-and-pen-matched control pigs were sequenced using Illumina HiSeq sequencing. Protein sequences of the capsular polysaccharide genes (cps) were identified and analyzed using a maximum likelihood tree. Among the 27 untypable isolates, 3 were from systemic sites of cases and 13 and 11 were from upper respiratory sites of cases and controls, respectively. One hundred fifty-six isolates were grouped into 17 distinct groups based on the cps gene tree. Isolates from these 17 distinct individual cps groups were distributed among a minimum of one farm and maximum of eight farms. Untypable isolates were detected in 12 of those groups and each cps group had untypable isolates present amongst multiple farms. Interestingly, the three systemic untypable isolates not only coexisted with other serotypes found in the same location of the same pigs but were also found among different cps groups. These isolates are of interest and warrant further investigation. Overall, a wide diversity of S. suis among untypable isolates was observed in this study.