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We report the draft genome assembly of strain 4866-2_S43 isolated from a eucalyptus lesion in Argentina and what until recently was caused by Xanthomonas citri pv. eucalyptorum (Xce). The genome size is 5 188 607 bp, with a G+C content of 64.66%. Comparative analysis reveals that the closest relative of strain 4866-2_S43 is Xce LPF 602, isolated in Brazil. Comparison of the whole genome sequences revealed an average nucleotide identity (ANI) of 99.96% between the two strains. ANIs were determined between the whole genome sequence of strain 4866-2_S43 and the genomes of all currently validated Xanthomonas spp. These results revealed that strain 4866-2_S43 shared >95% similarity with X. citri pv. citri and X. citri pv. phaseoli, and <95% with X. euvesicatoria pv. alfalfae, X. euvesicatoria pv. perforans, and X. euvesicatoria pathovars euvesicatoria and eucalyptii.

Ribosomal RNA gene amplicon sequencing is commonly used to evaluate microbiome profiles in health and disease and document the impact of interventional treatments. Nanopore sequencing is attractive since it can provide greater classification at the species level. However, optimized protocols to target marker genes for bacterial and fungal profiling are needed. To achieve an increased taxonomic resolution, we developed extraction and full-length amplicon PCR-based approaches using Nanopore sequencing. Three lysis conditions were applied to a mock microbial community, including known bacterial and fungal species: ZymoBIOMICS lysis buffer (ML) alone, incorporating bead-beating (MLB) or bead-beating plus MetaPolyzyme enzymatic treatment (MLBE). In profiling of bacteria in comparison to reference data, MLB had more statistically different bacterial phyla and genera than the other two conditions. In fungal profiling, MLB had a significant increase of Ascomycota and a decline of Basidiomycota, subsequently failing to detect Malassezia and Cryptococcus. Also, a principal coordinates analysis plot by the Bray-Curtis metric showed a significant difference among groups for bacterial (P=0.033) and fungal (P=0.012) profiles, highlighting the importance of understanding the biases present in pretreatment. Overall, microbial profiling and diversity analysis revealed that ML and MLBE are more similar than MLB for both bacteria and fungi; therefore, using this specific pipeline, bead-beating is not recommended for whole gene amplicon sequencing. However, ML alone was suggested as an optimal approach considering DNA yield, taxonomic classification, reagent cost and hands-on time. This could be an initial proof-of-concept study for simultaneous human bacterial and fungal microbiome studies.

Introduction. Hepatitis B infection causes a spectrum of clinical diseases varying from asymptomatic infection to severe or fulminant acute hepatitis, chronic liver disease, cirrhosis and hepatocellular carcinoma. Hepatitis B virus (HBV) genotypes appear to influence transmission dynamics, clinical outcomes and responses to antiviral therapy. However, hepatitis B genotyping has been poorly investigated in Sri Lanka. This study intended to determine hepatitis B genotypes in a group of HBV-infected people in central and northern Sri Lanka. Methodology. The study was a laboratory-based descriptive cross-sectional study. Initial detection of HBV DNA in 100 EDTA blood samples was done by using a commercially validated quantitative real-time PCR kit. Hepatitis B genotyping was performed by in-house conventional semi-nested multiplex PCR using genotype-specific primers (for genotypes A-F). The serological profile was determined using a commercially validated ELISA/chemiluminescence immunoassay. The results were evaluated for genotype prevalence, viral load association and hepatitis B e antigen (HBeAg) expression in the study population. Results and conclusion. The study detected that genotype C (n=38) is most prevalent and infections with multiple genotypes (n=52, 52%) were commoner than mono-genotype (n=23, 23%) infections. In total, 25% of patients had no detectable genotype among genotypes A-F. The mean viral load in asymptomatic patients with a single genotype was 3.28 log₁₀ copies ml^-1 and in multiple genotypes was 4.18 log₁₀ copies ml^-1 before treatment. Statistical significance was not detected in mean viral loads and HBeAg expression in these two groups. In the future, chronic HBV infection may be effectively treated and managed according to the infected genotype.

Lactiplantibacillus pentosus is a probiotic bacterium reported to be present in various fermented foods, such as fermented olives, and it significantly influences human health. The present study concerns a lactic acid bacterial strain designated L. pentosus krglsrbmofpi2, isolated from traditional fermented rice, and which has been shown to have an assortment of beneficial attributes. Using Illumina technologies, we have sequenced and investigated the whole genome sequence of L. pentosus krglsrbmofpi2 to understand its functionality and safety. The chromosomal genome was 3.7 Mb in size with 46% GC content and 3192 protein-coding genes. Additional extensive bioinformatics investigations were carried out involving whole genome sequence assembly and annotation.

Background. Macrolide-induced resistance to clindamycin is a well-described mechanism leading to treatment failure. Herein, we determined the frequency and associated factors of inducible clindamycin resistance in Gram-positive cocci in a tertiary care hospital. Methods. A cross-sectional descriptive study was carried out between January and December 2022. d-tests were performed as recommended by EUCAST 2021 guidelines on 100 non-duplicate clinical isolates of Gram-positive cocci to determine the prevalence of methicillin resistance and inducible clindamycin resistance among the collected isolates. Results. Of the 100 Gram-positive cocci isolates, 56 (56.0%), 17 (17.0%) and 27 (27.0%) were respectively coagulase-negative staphylococci, Staphylococcus aureus and Streptococcus spp. Among Streptococcus spp., Group D Streptococci (15.0%) were the most isolated. Methicillin-resistant Staphylococcus aureus (MRSA) represented nine (53.0%) of the S. aureus isolates. Constitutive (cMLSb) and inducible clindamycin resistance (iMLSb) phenotypes were detected in 36 (36.0%) and 14 (14.0 %) of the isolates, respectively. S. aureus exhibited 38.4% of cMLSb and 13.7% of iMLSb. The result of multivariate analysis showed that age groups, gender, type of samples, provenance, and bacteria, were not significantly associated with Gram-positive cocci iMLSb phenotype. Conclusion. The study reported for the first time a high prevalence of inducible resistance of Gram-positive cocci strains to clindamycin in Niger Republic. This suggests the urgent need for the implementation of regular screening of these isolates and the wise use of clindamycin in clinical practice.

Introduction. There are many multidrug-resistant isolates of the nosocomial pathogen, Acinetobacter baumannii, causing severe healthcare-acquired infections in terminally ill patients with high mortality and morbidity rates. Aim. This study aims to retrospectively analyse A. baumannii bacteraemia (ABB) cases in Saudi Arabia, where the information is sparse regarding the prevalence, risk factors, clinical disease, antibiotic regimen, antibiotic susceptibility, treatment outcomes and mortality associated with this infection. Methods. A retrospective chart review was conducted between 1 January 2015 and 31 December 2022 to identify all patients aged 14 years and above with ABB. Demographic and clinical data, as well as results from laboratory analyses, were collected from patients' electronic charts. Statistical analyses were performed on the data to identify factors associated with 90-day mortality. Results. Of the 122 ABB cases, 71 (63.4%) died. The factors that were found to be associated with 90-day mortality were the Charlson Comorbidity Index, Pitt bacteraemia score, quick Sequential Organ Failure Assessment score (P<0.001 for each), hospital ward (P<0.02), short duration of antibiotic treatment (P<0.01) and higher age (P<0.05). The most common source of infection was central line-associated bloodstream infection in 52.7%. Also associated with mortality were inappropriate antimicrobial therapy (P<0.02) and empirical use of colistin (P<0.05). In many patients, ABB was caused by carbapenem-resistant A. baumannii [(CRAB), 69.6%], and 74.4% of those patients died. Conclusion. To prevent ABB-associated mortality, an appropriate regimen and duration of treatment are necessary. Hospitals should also practice proper hygiene to prevent the spread of ABB. CRAB is a growing threat in hospitals in Saudi Arabia, especially in the critical care setting, and carries a very high risk of mortality.

Due to consumer demand, many conventional poultry farms are now growing poultry without antibiotics or synthetic chemicals. In addition to this, pasture/organic poultry farms have increased significantly in the USA, and they are also antibiotic- and chemical-free. According to recent reports, both antibiotic-free conventional and pasture poultry farmers are facing the re-emergence of bacterial diseases. Bacterial diseases cause higher mortality rates in birds and lead to non-profitable poultry farming. This study investigated the prevalence of Salmonella enterica subsp. enterica serovar Gallinarum biovars Gallinarum (S. Gallinarum), the causative agent of fowl typhoid, and Salmonella enterica subsp. enterica serovar Gallinarum biovars Pullorum (S. Pullorum), the causative agent of pullorum disease, within integrated crop-livestock/pasture farm environments and their processed products. Specifically, the study focused on both the pre-harvest period, which includes the conditions and practices on the farm before the crops and livestock are harvested, and the post-harvest period, which encompasses the handling, processing, and storage of the products after harvest. A total of 1286 samples were collected from six farms and adjacent 13 markets to determine the prevalence of S. Gallinarum and S. Pullorum by using both microbiological culture and molecular techniques, specifically PCR. Antimicrobial susceptibility testing was performed using the agar dilution method for the recommended antibiotics as described in the Clinical Laboratory Standards Institute (CLSI). S. Pullorum was detected in 11 samples (2.7%), while S. Gallinarum was found in six samples (1.5%) out of a total of 403 samples at the pre-harvest level. At the post-harvest level, only S. Gallinarum was identified in 14 meat samples out of 883(1.6%) recovered from samples collected from retail markets. Antibiogram showed S. Gallinarum and S. Pullorum to be highly resistant to cephradine, trimethoprim-sulfamethoxazole, amoxicillin, streptomycin, and ampicillin. This data demonstrates that both S. Pullorum and S. Gallinarum are commonly present in farm poultry environments as well as the products sold in the markets, which warrants implementation of regular surveillance and monitoring programmes, as well as potentially requiring future control strategies to reduce S. Pullorum and S. Gallinarum transmission.

We describe the whole-genome sequences of seven diverse marine bacteria isolated from Portuguese environments that presented the ability to promote the growth of the model diatom, Phaeodactylum tricornutum. The bacterial genome sequences will contribute to the study of genetic and molecular mechanisms involved in diatom-bacteria interactions.

The rat is a useful laboratory model for respiratory diseases. SARS-CoV-2 proteins, such as the spike (S) protein, can induce inflammation. This study has investigated the ability of the Q498Y, P499T (QP-YT) amino acid change, described in the S-protein of the mouse-adapted laboratory SARS-CoV-2 MA strain, to interact with rat angiotensin converting enzyme-2 (ACE2) and stimulate responses in rat lungs. A real-time S-ACE2 quantitative fusion assay shows that ancestral and L452R S-proteins fuse with human but not rat ACE2 expressed on HEK293 (human embryonic kidney-293) cells. The QP-YT S-protein retains the ability to fuse with human ACE2 and increases the binding to rat ACE2. Although lower lung of the rat contains both ACE2 and TMPRSS2 (transmembrane serine protease 2) target cells, intratracheal delivery of ancestral or QP-YT S-protein pseudotyped lentivirus did not induce measurable respiratory changes, inflammatory infiltration or innate mRNA responses. Isolation of primary cells from rat alveoli demonstrated the presence of cells expressing ACE2 and TMPRSS2. Infection of these cells, however, with ancestral or QP-YT S-protein pseudotyped lentivirus was not observed, and the QP-YT S-protein pseudotyped lentivirus poorly infected HEK293 cells expressing rat ACE2. Analysis of the amino acid changes across the S-ACE2 interface highlights not only the Y498 interaction with H353 as a likely facilitator of binding to rat ACE2 but also other amino acids that could improve this interaction. Thus, rat lungs contain cells expressing receptors for SARS-CoV-2, and the QP-YT S-protein variant can bind to rat ACE2, but this does not result in infection or stimulate responses in the lung. Further, amino acid changes in S-protein may enhance this interaction to improve the utility of the rat model for defining the role of the S-protein in driving lung inflammation.