The Genus Ochrobactrum as Major Opportunistic Pathogens

Misidentification of Brucella melitensis as Ochrobactrum species: potential pitfalls in the diagnosis of brucellosis

We describe a case of brucellosis in a man in his 20s, who presented to the emergency department with a 1-month history of fevers, dry cough and knee pain. Blood cultures were positive after 55 hours and Ochrobactrum daejeonense was identified on matrix-assisted laser desorption/ionisation time of flight (MALDI-TOF) mass spectrometry. Ochrobactrum spp are Gram-negative organisms that are phylogenetically related to Brucella spp but commercially available MALDI-TOF libraries cannot distinguish between the two genera. Further positive blood cultures for O. daejeonense combined with characteristic growth patterns for Brucella spp led to targeted questioning of the patient regarding potential exposure risks, which revealed a history of consumption of unpasteurised camel milk in the Middle East 3 months earlier. Treatment of brucellosis was initiated and subsequent whole genome sequencing identified the blood culture isolate as Brucella melitensis confirming the diagnosis of brucellosis. This case highlights the challenges in the diagnosis of brucellosis in low-incidence settings.

"Phylogenomic insights into brucellaceae: The Pseudochrobactrum algeriensis case"

The genus Pseudochrobactrum encompasses free-living bacteria phylogenetically close to Ochrobactrum opportunistic pathogens and to Brucella, facultative intracellular parasites causing brucellosis, a worldwide-extended and grave zoonosis. Recently, Pseudochrobactrum strains were isolated from Brucella natural hosts on Brucella selective media, potentially causing diagnostic confusions. Strikingly, P. algeriensis was isolated from cattle lymph nodes, organs that are inimical to bacteria. Here, we analyse P. algeriensis potential virulence factors in comparison with Ochrobactrum and Brucella. Consistent with genomic analyses, Western-Blot analyses confirmed that P. algeriensis lacks the ability to synthesize the N-formylperosamine O-polysaccharide characteristic of the lipopolysaccharide (LPS) of smooth Brucella core species. However, unlike other Pseudochrobactrum but similar to some early diverging brucellae, P. algeriensis carries genes potentially synthetizing a rhamnose-based O-polysaccharide LPS. Lipid A analysis by MALDI-TOF demonstrated that P. algeriensis LPS bears a lipid A with a reduced pathogen-associated molecular pattern, a trait shared with Ochrobactrum and Brucella that is essential to generate a highly stable outer membrane and to delay immune activation. Also, although not able to multiply intracellularly in macrophages, the analysis of P. algeriensis cell lipid envelope revealed the presence of large amounts of cationic aminolipids, which may account for the extremely high resistance of P. algeriensis to bactericidal peptides and could favor colonization of mucosae and transient survival in Brucella hosts. However, two traits critical in Brucella pathogenicity are either significantly different (T4SS [VirB]) or absent (erythritol catabolic pathway) in P. algeriensis. This work shows that, while diverging in other characteristics, lipidic envelope features relevant in Brucella pathogenicity are conserved in Brucellaceae. The constant presence of these features strongly suggests that reinforcement of the envelope integrity as an adaptive advantage in soil was maintained in Brucella because of the similarity of some environmental challenges, such as the action of cationic peptide antibiotics and host defense peptides. This information adds knowledge about the evolution of Brucellaceae, and also underlines the taxonomical differences of the three genera compared.

Evaluation of a Multilocus Variable-Number Tandem-Repeat Analysis Scheme for Typing Ochrobactrum anthropi

Ochrobactrum anthropi (O. anthropi) is found in water, soil, plants and animals. Even though it has low virulence, it has increasingly been found to cause a number of infectious diseases in people with low immunity. The identification of O. anthropi mainly uses biochemical methods, such as the API 20NE or Vitek-2. The typing studies of O. anthropi have mainly utilized PFGE, rep-PCR, AFLP, 16s rDNA sequencing, RecA-PCR RFLP, and MALDI-TOF MS. This study aims to evaluate the polymorphisms of variable-number tandem-repeats (VNTRs) within genomic DNA of O. anthropi strains. The tandem repeats (TRs) in genomic DNA are discovered using Tandem Repeat Finder software (version 4.09). Twelve different VNTRs are designated and assigned to the nomenclature. The primers for PCR of 12 loci are designed. The PCR product size is converted to the number of tandem repeats in every locus. The relatedness of 65 O. anthropi strains from geographically different countries are analyzed by means of 12-variable-number tandem-repeat analysis(MLVA-12). A total of 51 different genotypes are found in 65 O. anthropi strains. These strains, which were collected from the same environmental samples, hospitals, and countries, are clustered within the same or closely genotypes. The MLVA-12 assay has a good discriminatory power for species determination, typing of O. anthropi, and inferring the origin of bacteria.

Brucella pituitosa strain BU72, a new hydrocarbonoclastic bacterium through exopolysaccharide-based surfactant production

Hydrocarbon and heavy metal pollution are amongst the most severe and prevalent environmental problems due to their toxicity and persistence. Bioremediation using microorganisms is considered one of the most effective ways to treat polluted sites. In the present study, we unveil the bioremediation potential of Brucella pituitosa strain BU72. Besides its ability to grow on multiple hydrocarbons as the sole carbon source and highly tolerant to several heavy metals, BU72 produces different exopolysaccharide-based surfactants (EBS) when grown with glucose or with crude oil as sole carbon source. These EBS demonstrated particular and specific functional groups as determined by Fourier transform infrared (FTIR) spectral analysis that showed a strong absorption peak at 3250 cm-1 generated by the -OH group for both EBS. The FTIR spectra of the produced EBS revealed major differences in functional groups and protein content. To better understand the EBS production coupled with the degradation of hydrocarbons and heavy metal resistance, the genome of strain BU72 was sequenced. Annotation of the genome revealed multiple genes putatively involved in EBS production pathways coupled with resistance to heavy metals genes such as arsenic tolerance and cobalt-zinc-cadmium resistance. The genome sequence analysis showed the potential of BU72 to synthesise secondary metabolites and the presence of genes involved in plant growth promotion. Here, we describe the physiological, metabolic, and genomic characteristics of Brucella pituitosa strain BU72, indicating its potential as a bioremediation agent.

Ochrobactrum anthropi sepsis in a 15-month-old child: A case report

Key Clinical Message

Ochrobactrum anthropi (O. anthropi), a rare opportunistic pathogen, caused sepsis in a malnourished 15-month-old African child. Early detection and appropriate antibiotics led to full recovery, highlighting the importance of robust surveillance for emerging pathogens in vulnerable populations.

Abstract

While rarely causing infections, O. anthropi, a non-fermenting, obligately aerobic, flagellated gram-negative bacillus, demonstrates oxidase positivity and indole negativity. Traditionally, Ochrobactrum spp is considered a low threat due to its environmental abundance and mild virulence. It is, however, a multidrug-resistant bacteria known for causing opportunistic infections in humans. O. anthropi is typically associated with catheter-related bloodstream infections. The first documented case was in 1998; most cases have been reported in developed countries. We present a case of O. anthropi sepsis in a malnourished child in sub-Saharan Africa. We report a case involving a 15-month-old African female who presented with symptoms and signs of protein-energy malnutrition and sepsis. The blood culture revealed O.anthropi. We treated the child with the empirical first-line antibiotics per the national guidelines, intravenous ampicillin and gentamicin for a week, and the child fully recovered. This report describes a rare case of O. anthropi sepsis with malnutrition in an African female child. O. anthropi is an emerging pathogen causing opportunistic infections in both immunocompetent and immunocompromised patients. We report that early bacterial detection, appropriate antibiotic susceptibility and antimicrobial management based on local antibiogram data may be essential for excellent patient outcomes. Additionally, we recommend more robust surveillance to detect such rare emerging pathogens.

Latent Tuberculosis Infection Is Associated with an Enrichment of Short-Chain Fatty Acid-Producing Bacteria in the Stool of Women Living with HIV

Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high-TB-burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI in PLHIV. We characterised the stool microbiota of PLHIV with [interferon-γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST-negative) LTBI (n = 25 per group). The 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet-Multinomial Mixtures, DESeq2, and PICRUSt2. No α- or β-diversity differences occurred by LTBI status; however, LTBI-positive people were Faecalibacterium-, Blautia-, Gemmiger-, and Bacteroides-enriched and Moryella-, Atopobium-, Corynebacterium-, and Streptococcus-depleted. Inferred metagenome data showed that LTBI-negative-enriched pathways included several metabolite degradation pathways. Stool from LTBI-positive people demonstrated differential taxa abundance based on a quantitative response to antigen stimulation. In LTBI-positive people, older people had different β-diversities than younger people, whereas in LTBI-negative people, no differences occurred across age groups. Amongst female PLHIV, those with LTBI were, vs. those without LTBI, Faecalibacterium-, Blautia-, Gemmiger-, and Bacteriodes-enriched, which are producers of short-chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.

Abundance and diversity of methicillin-resistant bacteria from bathroom surfaces at workplaces using CHROMagar media, 16S, and dnaJ gene sequence typing

University campus communities consist of dynamic and diverse human populations originated from different regions of the country or the world. Their national/global movement to and from campus may contribute to the spread and buildup of methicillin-resistant (MR) bacteria, including MR Staphylococci (MRS) on high-touch surfaces, sinks, and toilets. However, studies on MR bacteria contamination of surfaces, sinks, and toilets are scarce in workplaces outside of healthcare settings. Hence, little is known whether university communities contaminate campus bathrooms by MR bacteria. This study evaluated the abundance, identity, and phylogenetics of MR bacteria grown on CHROMagar MRSA media from bathrooms at workplaces. We collected 21 sink and 21 toilet swab samples from 10 buildings on campus and cultured them on CHROMagar MRSA media, extracted DNA from MR bacteria colonies, sequenced PCR products of 16S and dnaJ primers, determined the sequence identities by BLAST search, and constructed a phylogenetic tree. Of 42 samples, 57.1% (24/42) harbored MR bacteria. MR bacteria were more prevalent on the sink (61.9%) than in the toilet (52.2%) and in male bathrooms (54.2%) than in female bathrooms (41.7%). The colony count on the bathroom surfaces of 42 samples varied in that 42.9% (18/42), 33.3, 14.3, and 9.5% of samples harbored 0, 100, and > 1000 MR bacteria colonies, respectively. Of MR bacteria sequenced, BLAST search and phylogenetic analysis showed that Staphylococcus accounted for 60% of the MR bacteria and the rest were non-Staphylococci. Of Staphylococcus carrying MR (n = 15), 53.3% were S. hemolyticus followed by S. lugdunensis (26.7%), S. epidermidis (8%), and a newly discovered S. borealis in 2020 (4%). Of non-Staphylococci MR bacteria, 20% accounted for Sphingomonas koreensis. Campus bathrooms serve as a reservoir for diverse bacteria carrying MR, which pose a direct risk of infection and a potential source of horizontal gene transfer. To reduce the health risk posed by MR bacteria in high traffic areas such as bathrooms additional environmental monitoring and improved decontamination practices are needed.

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

Latent tuberculosis infection is associated with an enrichment of short chain fatty acid producing bacteria in the stool of women living with HIV

Background

Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high TB burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI, including in PLHIV.

Method

Within a parent study that recruited adult females with HIV from Cape Town, South Africa into predefined age categories (18-25, 35-60 years), we characterised the stool microbiota of those with [interferon-γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST- negative) LTBI (n=25 per group). 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet Multinomial Mixtures, DESeq2 and PICRUSt2.

Results

No α- or β-diversity differences occurred by LTBI status; however, LTBI-positives were Faecalibacterium-, Blautia-, Gemmiger-, Bacteroides-enriched and Moryella-, Atopobium-, Corynebacterium-, Streptococcus-depleted. Inferred metagenome data showed LTBI-negative-enriched pathways included several involved in methylglyoxal degradation, L-arginine, putrescine, 4-aminobutanoate degradation and L-arginine and ornithine degradation. Stool from LTBI-positives demonstrated differential taxa abundance based on a quantitative response to antigen stimulation (Acidaminococcus-enrichment and Megamonas-, Alistipes-, and Paraprevotella-depletion associated with higher IGRA or TST responses, respectively). In LTBI-positives, older people had different β-diversities than younger people whereas, in LTBI-negatives, no differences occurred across age groups.

Conclusion

Amongst female PLHIV, those with LTBI had, vs. those without LTBI, Faecalibacterium, Blautia, Gemmiger, Bacteriodes-enriched, which are producers of short chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.

Two Case Reports of Ochrobactrum anthropi Bacteremia in a Tertiary Care Hospital in Northeast India

Ochrobactrum anthropi is a non-fermenting, Gram-negative bacillus and an emerging opportunistic pathogen. We have isolated this organism from the blood cultures of two patients, a 53-year-old immunocompetent male presenting with an episode of mild fever post craniotomy and an 85-year-old male with chronic obstructive pulmonary disease (COPD) and urinary retention on an indwelling catheter. The organism was identified using VITEK 2 (bioMérieux, France). Both the isolates were resistant to most of the β-lactams, including cephalosporins, and sensitive to quinolones, aminoglycosides, and carbapenems.

In vitro model of human mammary gland microbial colonization (MAGIC) demonstrates distinctive cytokine response to imbalanced human milk microbiota

Despite the established concept of the human mammary gland (MG) as a habitat with its own microbiota, the exact mechanism of MG colonization is still elusive and a well-characterized in vitro model would reinforce studies of the MG microbiota development. We aimed to establish and characterize an in vitro cell model for studying MAmmary Gland mIcrobial Colonization (MAGIC) model. We used the immortalized cell line MCF10A, which expresses the strong polarized phenotype similar to MG ductal epithelium when cultured on a permeable support (Transwell). We analyzed the surface properties of the MAGIC model by gene expression analysis of E-cadherin, tight junction proteins, and mucins and by scanning electron microscopy. To demonstrate the applicability of the model, we tested the adhesion capability of the whole human milk (HM) microbial community and the cellular response of the model when challenged directly with raw HM samples. MCF10A on permeable supports differentiated and formed a tight barrier, by upregulation of CLDN8, MUC1, MUC4, and MUC20 genes. The surface of the model was covered with mucins and morphologically diverse with at least two cell types and two types of microvilli. Cells in the MAGIC model withstood the challenge with heat-treated HM samples and responded differently to the imbalanced HM microbiota by distinctive cytokine response. The microbial profile of the bacteria adhered on the MAGIC model reflected the microbiological profile of the input HM samples. The well-studied MAGIC model could be useful for studies of bacterial attachment to the MG and for in vitro studies of biofilm formation and microbiota development.IMPORTANCEThe MAGIC model may be particularly useful for studies of bacterial attachment to the surface of the mammary ducts and for in vitro studies of biofilm formation and the development of the human mammary gland (MG) microbiota. The model is also useful for immunological studies of the interaction between bacteria and MG cells. We obtained pioneering information on which of the bacteria present in the raw human milk (HM) were able to attach to the epithelium treated directly with raw HM, as well as on the effects of bacteria on the MG epithelial cells. The MAGIC cell model also offers new opportunities for research in other areas of MG physiology, such as the effects of bioactive milk components on microbial colonization of the MG, mastitis prevention, and studies of probiotic development. Since resident MG bacteria may be an important factor in breast cancer development, the MAGIC in vitro tool also offers new opportunities for cancer research.

Pneumonia due to Ochrobactrum intermedium in an ICU patient

Ochrobactrum intermedium is recognized as a rare emerging opportunistic pathogen mostly related with bloodstream infections. In this report, we describe the first clinical case of pneumonia due to O. intermedium. The case involved a 71-year old tetraplegic man hospitalized for vertebral fractures after falling from a ladder.

The Roles of Plant-Growth-Promoting Rhizobacteria (PGPR)-Based Biostimulants for Agricultural Production Systems

The application of biostimulants has been proven to be an advantageous tool and an appropriate form of management towards the effective use of natural resources, food security, and the beneficial effects on plant growth and yield. Plant-growth-promoting rhizobacteria (PGPR) are microbes connected with plant roots that can increase plant growth by different methods such as producing plant hormones and molecules to improve plant growth or providing increased mineral nutrition. They can colonize all ecological niches of roots to all stages of crop development, and they can affect plant growth and development directly by modulating plant hormone levels and enhancing nutrient acquisition such as of potassium, phosphorus, nitrogen, and essential minerals, or indirectly via reducing the inhibitory impacts of different pathogens in the forms of biocontrol parameters. Many plant-associated species such as Pseudomonas, Acinetobacter, Streptomyces, Serratia, Arthrobacter, and Rhodococcus can increase plant growth by improving plant disease resistance, synthesizing growth-stimulating plant hormones, and suppressing pathogenic microorganisms. The application of biostimulants is both an environmentally friendly practice and a promising method that can enhance the sustainability of horticultural and agricultural production systems as well as promote the quantity and quality of foods. They can also reduce the global dependence on hazardous agricultural chemicals. Science Direct, Google Scholar, Springer Link, CAB Direct, Scopus, Springer Link, Taylor and Francis, Web of Science, and Wiley Online Library were checked, and the search was conducted on all manuscript sections in accordance with the terms Acinetobacter, Arthrobacter, Enterobacter, Ochrobactrum, Pseudomonas, Rhodococcus, Serratia, Streptomyces, Biostimulants, Plant growth promoting rhizobactera, and Stenotrophomonas. The aim of this manuscript is to survey the effects of plant-growth-promoting rhizobacteria by presenting case studies and successful paradigms in various agricultural and horticultural crops.

Swinging between the beneficial and harmful microbial community in biofloc technology: A paradox

Biofloc Technology (BFT) is proven to be the fulcrum of sustainable recirculating aquaculture system especially under zero water discharge condition. The efficiency of BFT system is reinforced by an unswerving microbial community in the system. Several researchers have made copious reports on the microorganisms in BFT and identified heterotrophic bacteria predominant in the microbial composition. A summary of these researches considers these microorganisms playing the role of chemo-photosynthetic autotrophs, organic detoxifiers, probiotic, decomposers/bioflocculants, bio-leachers and pathogens. Although these functional roles are well identified, the reports have failed to sufficiently illustrate the borderline at which these microbial communities fail to serve their beneficial roles in BFT system. This review paper firstly presents a snapshot of some indispensable water quality conditions and zootechnical variables aided by the microbial community in floc as well as the amphibolic process that synthesizes nutrient from the organic deposit in BFT. Furthermore, information on the microbial community in BFT is evaluated to have Bacillus sp., Lecane sp. and Pseudomonas sp. serving all-encompassing role in BFT while Vibrio sp. and Enterobacter sp. are pathogenic under unsuitable water quality conditions. Functional characterisation of the commonly reported microorganisms in BFT categorised 21.95 % as most critical, whose abundance indicates an efficient BFT.

Ochrobactrum Anthropi; an Unusual Cause of Bacteremia and Pneumonia: A Case Report and a Brief Review of the Literature

Background: Ochrobactrum anthropi spp. is a non-enteric, aerobic gram-negative bacillus that has been reported to cause sepsis and occasionally bacteremia in both immunocompetent and immunocompromised hosts. This bacterium is capable of surviving in various habitats, but due to its affinity for aqueous environments, O. anthropi is hypothesized to have an affinity for indwelling plastic devices and other foreign bodies.

Case Presentation: We report a case of a 66 y/o male with a history of polysubstance abuse disorder admitted for toxic metabolic encephalopathy and found to have bronchopneumonia and bacteremia secondary to O. anthropi infection resulting in sepsis and cardiopulmonary arrest.

Discussion: Ochrobactrum spp. is an unusual pathogen of low virulence and has been noted to cause bacteremia and occasionally sepsis in both immunocompetent and immunosuppressed patients. Isolation of this pathogen in the appropriate setting should be considered a true pathogen and treated as such to avoid sequela of this infection.

Conclusion: This case report and literature review suggest that Ochrobactrum anthropi appears more frequently as a pathogen in nosocomial infections than suggested in the literature.

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Influence of the Antibiotic Oxytetracycline on the Morphometric Characteristics and Endophytic Bacterial Community of Lettuce (Lactuca sativa L.)

Antibiotics enter the soil with compost prepared from livestock manures and other sources. There is concern that they may influence plant growth and cause antibiotic resistance in soil and plant endospheric microbiomes. In the present work, lettuce plants were cultivated in soil and hydroponics spiked with oxytetracycline (0, 15, and 300 mg × kg-1 and 0, 15, and 50 mg × L-1, respectively) during a 28-day greenhouse experiment. It was revealed that the antibiotic reduced the chlorophyll content, the biomass, and the length of the roots and stems by 1.4-4.7, 1.8-39, 2.5-3.2, and 1.8-6.3 times in soil and in hydroponics. The copy numbers of the tet(A) and tet(X) genes were revealed to be 4.51 × 103-1.58 × 105 and 8.36 × 106-1.07 × 108 copies × g-1, respectively, suggesting the potential migration of these genes from soil/hydroponics to plant roots and leaves. According to a non-metric multidimensional scaling (NMDS) analysis of the 16S rRNA amplicon sequencing data, endospheric bacterial communities were similar in leaves and roots independent of the growing substrate and antibiotic concentration. While soil bacterial communities were unaffected by the presence of antibiotics, hydroponic communities exhibited dependency, likely attributable to the absence of the mitigating effect of soil particle absorption.

Correlation Between Microbial Community and Hatching Failure in Loggerhead Sea Turtle Caretta caretta

Microbial communities provide essential information about host ecology and could be helpful as a tool to improve species conservation efforts. However, microbes can also infect and compromise the host development process and viability. Caretta caretta is the most widespread marine turtle species in the Mediterranean basin and is the only species of sea turtle nesting along the Italian coasts. Little is known about the microbiota composition of the nest of sea turtles and its correlation with hatching failures. In this study, the microbial composition of two nests of C. caretta featuring different rates of hatching success from a nesting beach in Lampedusa (Italy) was analyzed and compared. The bacterial community was determined using culture-dependent methods and next-generation sequencing based on 16S rRNA gene metabarcoding analysis. Our results showed five dominant bacterial phyla (Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, and Firmicutes) and indicated different bacterial families (Pseudomonadaceae and Brucellaceae) as likely causes of hatching failures. Besides, our findings demonstrated the nests' active role in modulating the sand's bacterial communities. This study suggests microbiological analysis could be a valuable tool in monitoring nests to take preventive actions and reduce hatching failures.

Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD

In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.

Molecular docking and antibacterial activity of Sargassum fusiforme extracts against major coral pathogens

The present study evaluates the antibacterial properties of alkaloids and the crude extracts (ethanol, n-hexane and ethyl acetate) from seaweed Sargassum fusiforme against coral pathogens (Photobacterium galatheae, Vibrio harveyi, Bordetella trematum, and Ochrobactrum pseudogrignonese) isolated from coral Porites lutea. To our knowledge, this is the first in vitro assay for such extracts on Porites lutea coral pathogens. Bacterial pathogens have been identified using 16S RNA and BankIt into gene bank and given the accession numbers (OR401000; OR401001; OR401336, and OR400998 respectively). GC-Mass profiling conducted for n-hexane compounds confirmed the presence of thirty-eight molecules, twelve of which have been previously reported for their bioactivity. The results revealed that alkaloids and n-hexane extract demonstrated eminent antibacterial activity compared to the other extracts against the tested coral pathogenic bacteria. Molecular docking was conducted to evaluate the twelve previously mentioned bioactive molecules to get a full understanding of the interaction of those bioactive molecules on vital bacterial proteins (Hemolysin protein (PDB ID: 1XEZ) and Cytoplasmic proteins (PDB ID: 3TZC)). Docked twelve molecules against hemolysin protein (PDB ID: 1XEZ) came exactly in line with the docked result of the same molecules with cytoplasmic proteins (PDB ID: 3TZC), proving the bioactivity of 6-O-Palmitoyl-L-ascorbic acid, 3TMS derivative; Glycerol monostearate, 2TMS derivative and Eicosanoic acid complexes in antibacterial activity action and score higher than reference ligand. Those three compounds will be investigated separately in future in vitro assay soon. Our conclusions align with the study's antibacterial in vitro assay results. The present study reports the novelty of different extracts of S. fusiforme as an antibacterial agent against coral pathogenic bacteria that trigger diseases in Porites lutea.

Fine Particulate Matter Perturbs the Pulmonary Microbiota in Broiler Chickens

(1) Fine particulate matter (PM2.5) seriously affects the respiratory tract health of both animals and humans. Growing evidence indicates that the pulmonary microbiota is involved in the development of respiratory tract health; however, there is still much that is unknown about the specific changes of pulmonary microbiota caused by PM2.5 in broilers. (2) In this experiment, a total of 48 broilers were randomly divided into a control group and PM-exposure group. The experiment lasted for 21 days. Microbiota, inflammation biomarkers, and histological markers in the lungs were determined. (3) On the last day of the experiment, PM significantly disrupted the structure of lung tissue and induced chronic pulmonary inflammation by increasing IL-6, TNFα, and IFNγ expression and decreasing IL-10 expression. PM exposure significantly altered the α and β diversity of pulmonary microbiota. At the phylum level, PM exposure significantly decreased the Firmicutes abundance and increased the abundance of Actinobacteria and Proteobacteria. At the genus level, PM exposure significantly increased the abundance of Rhodococcus, Achromobacter, Pseudomonas, and Ochrobactrum. We also observed positive associations of the above altered genera with lung TNFα and IFNγ expression. (4) The results suggest that PM perturbs the pulmonary microbiota and induces chronic inflammation, and the pulmonary microbiota possibly contributes to the development of lung inflammation.

Comparison of automatic methods MALDI-TOF, VITEK2 and manual methods for the identification of intestinal microbial communities on the example of samples from alpacas (Vicugna pacos)

Introduction

Universally, in microbiological diagnostics the detection of live bacteria is essential. Rapid identification of pathogens enables appropriate remedial measures to be taken. The identification of many bacteria simultaneously facilitates the determination of the characteristics of the accompanying microbiota and/or the microbiological complexity of a given environment.

Material and Methods

The effectiveness of the VITEK2 Compact automated microbial identification system and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS), analytical profile index (API) and Remel RapID tests were compared in identification of bacteria isolated from the alpaca gastrointestinal tract.

Results

Most isolates were Gram-positive, such as Bacillus cereus, Bacillus flexus, Bacillus licheniformis, Bacillus pumilus and Bacillus subtilis; Enterococcus faecium, Enterococcus gallinarum, Enterococcus hirae and Enterococcus casseliflavus; Staphylococcus aureus, Staphylococcus equorum, Staphylococcus lentus, Staphylococcus pseudintermedius and Staphylococcus sciuri; Paenibacillus amylolyticus; Cellulosimicrobium cellulans; Leuconostoc mesenteroides; Clostridium perfringens; Corynebacterium stationis, Corynebacterium xerosis, and Corynebacterium diphtheriae (the last only isolated manually by API Coryne and the VITEK2 system and Corynebacteria (CBC) card). Corynebacterium diphtheriae was misidentified by MALDI-TOF MS as Candida lipolytica (currently Yarrowia lipolytica). Gram-positive and Gram-variable Micrococcus luteus were also isolated. Gram-negative Enterobacter cloacae, Enterobacter gergoviae, Enterobacter hormaechei and Enterobacter ludwigii; E. coli; Klebsiella pneumoniae subsp. pneumoniae; Citrobacter braakii and Citrobacter freundii; Serratia liquefaciens, Serratia odorifera and Serratia marcescens; Morganella morganii subsp. morganii; Providencia alcalifaciens; Pseudomonas aeruginosa; Stenotrophomonas maltophilia; Moraxella osloensis; and Ochrobactrum intermedium were also found. The yeasts Candida albicans, Candida haemulonii and Candida ciferrii were also present.

Conclusion

MALDI-TOF MS enabled the identification of pathogens and opportunistic pathogens from the alpaca gut which may represent a high risk to human and animal health.

If You're Not Confused, You're Not Paying Attention: Ochrobactrum Is Not Brucella

Bacteria of the genus Brucella are facultative intracellular parasites that cause brucellosis, a severe animal and human disease. Recently, a group of taxonomists merged the brucellae with the primarily free-living, phylogenetically related Ochrobactrum spp. in the genus Brucella. This change, founded only on global genomic analysis and the fortuitous isolation of some opportunistic Ochrobactrum spp. from medically compromised patients, has been automatically included in culture collections and databases. We argue that clinical and environmental microbiologists should not accept this nomenclature, and we advise against its use because (i) it was presented without in-depth phylogenetic analyses and did not consider alternative taxonomic solutions; (ii) it was launched without the input of experts in brucellosis or Ochrobactrum; (iii) it applies a non-consensus genus concept that disregards taxonomically relevant differences in structure, physiology, population structure, core-pangenome assemblies, genome structure, genomic traits, clinical features, treatment, prevention, diagnosis, genus description rules, and, above all, pathogenicity; and (iv) placing these two bacterial groups in the same genus creates risks for veterinarians, medical doctors, clinical laboratories, health authorities, and legislators who deal with brucellosis, a disease that is particularly relevant in low- and middle-income countries. Based on all this information, we urge microbiologists, bacterial collections, genomic databases, journals, and public health boards to keep the Brucella and Ochrobactrum genera separate to avoid further bewilderment and harm.

Polyethylene and polyvinyl chloride microplastics promote soil nitrification and alter the composition of key nitrogen functional bacterial groups

Microplastics (MPs) contamination in soils seriously threatens agroecosystems globally. However, very few studies have been done on the effects of MPs on the soil nitrogen cycle and related functional microorganisms. To assess MP's impact on the soil nitrogen cycle and related functional bacteria, we carried out a one-month soil incubation experiment using typical acidic soil. The soil was amended with alfalfa meal and was spiked with 1% and 5% (mass percentage) of low-density polyethylene (LDPE) and polyvinyl chloride (PVC) MPs. Our results showed that both LDPE and PVC addition significantly increased soil nitrification rate and nitrate reductase activity, which could further promote soil denitrification. The relative abundance of diazotrophs, ammonium oxidizing, and denitrifying bacterial groups were significantly altered with MPs addition. Moreover, the MPs treatments greatly enhanced denitrifying bacteria richness. Redundancy analysis showed that nitrate reductase activity was the most significant factor affecting the soil functional bacterial community. Correlation analysis shows that Nitrosospira genus might be for the improvement of soil nitrification rate. Our results implied that MPs exposure could significantly affect the soil nitrogen cycling in farmland ecosystems by influencing essential nitrogen functional microorganisms and related enzymatic activities.

Association of gut microbial dysbiosis with disease severity, response to therapy and disease outcomes in Indian patients with COVID-19

BACKGROUND

Severe coronavirus disease 2019 (COVID-19) is associated with systemic hyper-inflammation. An adaptive interaction between gut microbiota and host immune systems is important for intestinal homeostasis and systemic immune regulation. The association of gut microbial composition and functions with COVID-19 disease severity is sparse, especially in India. We analysed faecal microbial diversity and abundances in a cohort of Indian COVID-19 patients to identify key signatures in the gut microbial ecology in patients with severe COVID-19 disease as well as in response to different therapies. The composition of the gut microbiome was characterized using 16Sr RNA gene sequences of genomic DNA extracted from faecal samples of 52 COVID-19 patients. Metabolic pathways across the groups were predicted using PICRUSt2. All statistical analyses were done using Vegan in the R environment. Plasma cytokine abundance at recruitment was measured in a multiplex assay.

RESULTS

The gut microbiome composition of mild and severe patients was found to be significantly different. Immunomodulatory commensals, viz. Lachnospiraceae family members and Bifidobacteria producing butyrate and short-chain fatty acids (SCFAs), were under represented in patients with severe COVID-19, with an increased abundance of opportunistic pathogens like Eggerthella. The higher abundance of Lachnoclostridium in severe disease was reduced in response to convalescent plasma therapy. Specific microbial genera showed distinctive trends in enriched metabolic pathways, strong correlations with blood plasma cytokine levels, and associative link to disease outcomes.

CONCLUSION

Our study indicates that, along with SARS-CoV-2, a dysbiotic gut microbial community may also play an important role in COVID-19 severity through modulation of host immune responses.

Structure of the O-specific polysaccharide of Ochrobactrum endophyticum KCTC 42485T containing 3-(3-hydroxy-2,3-dimethyl-5-oxoprolyl)amino-3,6-dideoxy-d-galactose

Ochrobactrum endophyticum (syn. Brucella endophytica) is an aerobic species of Alphaproteobacteria isolated from healthy roots of Glycyrrhiza uralensis. Here we report the structure of the O-specific polysaccharide obtained by mild acid hydrolysis of the lipopolysaccharide of the type strain KCTC 42485:→3)-α-l-FucpNAc-(1→3)-β-d-QuipNAc-(1→2)-β-d-Fucp3NAcyl-(1→ where Acyl is 3-hydroxy-2,3-dimethyl-5-oxoprolyl. The structure was elucidated using chemical analyses along with ¹H and ¹³C NMR spectroscopy (including ¹H,¹H COSY, TOCSY, ROESY and ¹H,¹³C HSQC, HMBC, HSQC-TOCSY and HSQC-NOESY experiments). To our knowledge the OPS structure is novel and has not been previously published.

The Development of Diagnostic and Vaccine Strategies for Early Detection and Control of Human Brucellosis, Particularly in Endemic Areas

Brucellosis is considered one of the most serious zoonotic diseases worldwide. This disease affects both human and animal health, in addition to being one of the most widespread zoonotic illnesses in the Middle East and Northern Africa. Human brucellosis generally presents in a diverse and non-specific manner, making laboratory confirmation of the diagnosis critical to the patient’s recovery. A coordinated strategy for diagnosing and controlling brucellosis throughout the Middle East is required, as this disease cannot be known to occur without reliable microbiological, molecular, and epidemiological evidence. Consequently, the current review focuses on the current and emerging microbiological diagnostic tools for the early detection and control of human brucellosis. Laboratory assays such as culturing, serology, and molecular analysis can frequently be used to diagnose brucellosis. Although serological markers and nucleic acid amplification techniques are extremely sensitive, and extensive experience has been gained with these techniques in the laboratory diagnosis of brucellosis, a culture is still considered to be the “gold standard” due to the importance of this aspect of public health and clinical care. In endemic regions, however, serological tests remain the primary method of diagnosis due to their low cost, user-friendliness, and strong ability to provide a negative prediction, so they are commonly used. A nucleic acid amplification assay, which is highly sensitive, specific, and safe, is capable of enabling rapid disease diagnosis. Patients who have reportedly fully healed may continue to have positive molecular test results for a long time. Therefore, cultures and serological methods will continue to be the main tools for diagnosing and following up on human brucellosis for as long as no commercial tests or studies demonstrate adequate interlaboratory reproducibility. As there is no approved vaccine that prevents human brucellosis, vaccination-based control of animal brucellosis has become an important part of the management of human brucellosis. Over the past few decades, several studies have been conducted to develop Brucella vaccines, but the problem of controlling brucellosis in both humans and animals remains challenging. Therefore, this review also aims to present an updated overview of the different types of brucellosis vaccines that are currently available.

Gut Microbiota Composition Can Predict Colonization by Multidrug-Resistant Bacteria in SARS-CoV-2 Patients in Intensive Care Unit: A Pilot Study

The SARS-CoV-2 infection has increased the number of patients entering Intensive Care Unit (ICU) facilities and antibiotic treatments. Concurrently, the multi-drug resistant bacteria (MDRB) colonization index has risen. Considering that most of these bacteria are derived from gut microbiota, the study of its composition is essential. Additionally, SARS-CoV-2 infection may promote gut dysbiosis, suggesting an effect on microbiota composition. This pilot study aims to determine bacteria biomarkers to predict MDRB colonization risk in SARS-CoV-2 patients in ICUs. Seventeen adult patients with an ICU stay >48 h and who tested positive for SARS-CoV-2 infection were enrolled in this study. Patients were assigned to two groups according to routine MDRB colonization surveillance: non-colonized and colonized. Stool samples were collected when entering ICUs, and microbiota composition was determined through Next Generation Sequencing techniques. Gut microbiota from colonized patients presented significantly lower bacterial diversity compared with non-colonized patients (p < 0.05). Microbiota in colonized subjects showed higher abundance of Anaerococcus, Dialister and Peptoniphilus, while higher levels of Enterococcus, Ochrobactrum and Staphylococcus were found in non-colonized ones. Moreover, LEfSe analysis suggests an initial detection of Dialister propionicifaciens as a biomarker of MDRB colonization risk. This pilot study shows that gut microbiota profile can become a predictor biomarker for MDRB colonization in SARS-CoV-2 patients.

Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential

Although it is clinically important for acute respiratory tract (co)infections to have a rapid and accurate diagnosis, it is critical that respiratory medicine understands the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n = 29) with a commercially available PCR assay and compared the results with those of a hybridization-capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct < 35 and for mNGS samples it was >40% target coverage, median depth of 1X and RPKM > 10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positively 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterized the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify^® Platform (Illumina^® Inc, San Diego, CA, USA) for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompromised or immunocompetent with comorbidity respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndrome-based tests, and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration-with promise to reduce morbidity and mortality.

Profiling Microbial Communities in Idiopathic Granulomatous Mastitis

Idiopathic granulomatous mastitis (IGM) is a rare and benign inflammatory breast disease with ambiguous aetiology. Contrastingly, lactational mastitis (LM) is commonly diagnosed in breastfeeding women. To investigate IGM aetiology, we profiled the microbial flora of pus and skin in patients with IGM and LM. A total of 26 patients with IGM and 6 patients with LM were included in the study. The 16S rRNA sequencing libraries were constructed from 16S rRNA gene amplified from total DNA extracted from pus and skin swabs in patients with IGM and LM controls. Constructed libraries were multiplexed and paired-end sequenced on HiSeq4000. Metagenomic analysis was conducted using modified microbiome abundance analysis suite customised R-resource for paired pus and skin samples. Microbiome multivariable association analyses were performed using linear models. A total of 21 IGM and 3 LM paired pus and skin samples underwent metagenomic analysis. Bray−Curtis ecological dissimilarity distance showed dissimilarity across four sample types (IGM pus, IGM skin, LM pus, and LM skin; PERMANOVA, p < 0.001). No characteristic dominant genus was observed across the IGM samples. The IGM pus samples were more diverse than corresponding IGM skin samples (Shannon and Simpson index; Wilcoxon paired signed-rank tests, p = 0.022 and p = 0.07). Corynebacterium kroppenstedtii, reportedly associated with IGM in the literature, was higher in IGM pus samples than paired skin samples (Wilcoxon, p = 0.022). Three other species and nineteen genera were statistically significant in paired IGM pus−skin comparison after antibiotic treatment adjustment and multiple comparisons correction. Microbial profiles are unique between patients with IGM and LM. Inter-patient variability and polymicrobial IGM pus samples cannot implicate specific genus or species as an infectious cause for IGM.

First record of the human infection of Brucella melitensis in Kyrgyzstan: evidence from whole-genome sequencing-based analysis

BACKGROUND

Brucellosis, a zoonosis mainly transmitted by consumption of unpasteurized dairy products as well as direct contact with infected animals, is endemic in Kyrgyzstan. However, Brucella species in humans have not been investigated and the origin of the disease remains poorly known in wide parts of Сentral Asia. Thus, molecular characterization of the circulating strains is a critical first step in understanding Brucella diversity in the country.

METHODS

In this study, isolates were collected from patients with suspected brucellosis from different regions in Kyrgyzstan between 2019 and 2020. The detection and identification of Brucella was carried out by Bruce-ladder PCR. Next generation sequencing was used to sequence the 89 Brucella isolates, which were genotyped by cgSNP and cgMLST to identify epidemiological connection between Brucella isolates as well as placing them in the context of the global Brucella phylogeny.

RESULTS

The Brucella strains isolated from all regions of Kyrgyzstan were identified as B. melitensis. Based on cgSNP analysis, 18 sequence types were differentiated. The highest numbers of different sequence types were found in Batken (n = 8), Osh (n = 8) and Jalal-Abad (n = 6) oblasts. According to cgSNP and cgMLST analyses, different B. melitensis lineages circulate in Kyrgyzstan, all of them belonging to the Eastern Mediterranean group of the global Brucella phylogeny with the highest similarity to strains from Turkmenistan, Iran and Turkey.

CONCLUSION

In the present study, B. melitensis was identified as a causative agent of human brucellosis in Kyrgyzstan and different lineages could be identified. Since this study focused on isolates of human origin, the identity of Brucella species and lineages circulating among animal populations remains elusive. Implementing culture techniques and use of most recent molecular, bioinformatic and epidemiological tools are needed to set up a One Health approach to combat brucellosis in Kyrgyzstan. Further, other Сentral Asian countries need to take part in this effort as brucellosis is a transboundary disease in these regions.

Pathogenic bacteria significantly increased under oxygen depletion in coastal waters: A continuous observation in the central Bohai Sea

The spread of pathogenic bacteria in coastal waters endangers the health of the local people and jeopardizes the safety of the marine environment. However, their dynamics during seasonal hypoxia in the Bohai Sea (BHS) have not been studied. Here, pathogenic bacteria were detected from the 16S rRNA gene sequencing database and were used to explore their dynamics and driving factors with the progressively deoxygenating in the BHS. Our results showed that pathogenic bacteria were detected in all samples, accounting for 0.13 to 24.65% of the total number of prokaryotic sequences in each sample. Pathogenic Proteobacteria was dominated in all samples, followed by Firmicutes, Actinobacteria, Tenericutes, and Bacteroidetes, etc. β-diversity analysis showed that pathogenic bacteria are highly temporally heterogeneous and regulated by environmental factors. According to RDA analysis, these variations may be influenced by salinity, ammonia, DO, phosphate, silicate, and Chl a. Additionally, pathogenic bacteria in surface water and hypoxia zone were found to be significantly separated in August. The vertical distribution of pathogenic bacterial communities is influenced by several variables, including DO and nutrition. It is noteworthy that the hypoxia zones increase the abundance of certain pathogenic genera, especially Vibrio and Arcobacter, and the stability of the pathogenic bacterial community increased from May to August. These phenomena indicate that the central Bohai Sea is threatened by an increasingly serious pathogenic community from May to August. And the developing hypoxia zone in the future may intensify this phenomenon and pose a more serious threat to human health. This study provides new insight into the changes of pathogenic bacteria in aquatic ecosystems and may help to make effective policies to control the spread of pathogenic bacteria.

The Emergence of the Genus Comamonas as Important Opportunistic Pathogens

Comamonas spp. are non-fermenting Gram-negative bacilli. They were first discovered in 1894, and since then, twenty-four species have been characterized. The natural habitat of these bacteria is soil, wastewater/sludge, fresh water such as ponds and rivers, and the animal intestinal microbiome. They were also isolated from industrial settings, such as activated sludge and polluted soil, and from the hospital environment and clinical samples, such as urine, pus, blood, feces, and kidney. Comamonas spp. are associated with environmental bioremediation and are considered an important environmental bacterium rather than a human pathogen. However, in the 1980s, they became a concern when several human infections associated with these species were reported. Here, the Comamonas genus was examined in terms of its members, identification techniques, and pathogenicity. Seventy-seven infection cases associated with these microorganisms that have been discussed in the literature were identified and investigated in this project. All relevant information regarding year of infection, country of origin, patient information such as age, sex, underlying medical conditions if any, type of infection caused by the Comamonas species, antibiotic susceptibility testing, treatment, and outcomes for the patient were extracted from case reports. The findings suggest that even though Comamonas spp. are thought of as being of low virulence, they have caused harmful health conditions in many healthy individuals and even death in patients with underlying conditions. Antimicrobial treatment of infections associated with these species, in general, was not very difficult; however, it can become an issue in the future because some strains are already resistant to different classes of antibiotics. Therefore, these pathogens should be considered of such importance that they should be included in the hospital screening programs.

Development of the degradation bacteria in household food waste and analysis of the microbial community in aerobic composting

By screening the strains and testing different combinations of diverse bacteria, we developed a compound bacteria agent composing of 5 g Bacillus amyloliquefacien (B2), 10 g Pseudomonas aeruginosa (F4), 5 g Paenibacillus lautus (303), and 10 mL composite strains (DOD) for the degradation of household food waste (HFW). The final mass loss of HFW in aerobic composting with the compound bacteria agent B2+F4+303+DOD (group C) was 84.52%, increased by 20.83% over that loss in natural composting (group A). Analysis of 16S rRNA high-throughput sequencing showed that the phyla in the group A and the group C mainly included Firmicutes, Proteobacteria and Cyanobacteria. At the genus level, Pediococcus was the dominant genus in the group A, of which the microbial community performed better to maintain microbial system stable in the later stage of composting, while Weissella accounted for a larger proportion of the group C that acted well in reducing final mass of composting. The Ochrobactrum was closely related to the removal of odours in the early stage of the group C. The relative abundance of compound bacteria agent was always at a rather low level, suggested that it affected the composting process by changing the proportion of dominant bacteria in the compost. This article is protected by copyright. All rights reserved.

Lactobacillus salivarius SNK-6 Activates Intestinal Mucosal Immune System by Regulating Cecal Microbial Community Structure in Laying Hens

The production performance and disease resistance of laying hens decrease obviously with age. This study aimed to investigate the effects of supplementary Lactobacillus salivarius (L. salivarius) SNK-6 on laying performance, the immune-related gene expression in cecal tonsil, and the cecal microbial composition of laying hens. Here, 384 Xinyang black commercial hens (55 weeks old) were randomly allocated to three groups under the same husbandry and dietary regimes: basal diet (Con), the low L. salivarius SNK-6 group (T1: 1.0 × 106 CFU/g), and the high L. salivarius SNK-6 group (T2: 1.0 × 107 CFU/g). The results showed that the feed intake and broken-egg rate in the T1 group were significantly higher than the Con group (p < 0.05). Meanwhile, expressions of intestinal mucosal immune-related genes were significantly upregulated. The 16S rRNA gene sequencing indicated that supplementary L. salivarius SNK-6 had no significant difference in α -diversity and only displayed a trend difference in the β-diversity of cecal microbiota (p = 0.07). LEfSe and random forest were further used to identify bacteria family Enterobacteriaceae, order RF39, genera Ochrobactrum, and Eubacterium as biomarkers between the Con and T1 groups. Genera Ochrobactrum, which had high relative abundance and nodal degree in the T1 and T2 groups, showed a significant positive correlation with the expression of TLR-6, IL-10, MHC-II, and CD40 in cecal tonsils and might play a critical role in activating the host intestinal mucosal immune responses. Overall, dietary supplementary L. salivarius SNK-6 can display an immunomodulatory function, possibly by regulating cecal microbial composition. However, the changes in immune responses may be at the expenditure of corresponding production performance, which needs to be weighed up in practical application.

Recombinant Muscovy Duck Parvovirus Led to Ileac Damage in Muscovy Ducklings

Waterfowl parvovirus (WPFs) has multiple effects on the intestinal tract, but the effects of recombinant Muscovy duck parvovirus (rMDPV) have not been elucidated. In this study, 48 one-day-old Muscovy ducklings were divided into an infected group and a control group. Plasma and ileal samples were collected from both groups at 2, 4, 6, and 8 days post-infection (dpi), both six ducklings at a time. Next, we analyzed the genomic sequence of the rMDPV strain. Results showed that the ileal villus structure was destroyed seriously at 4, 6, 8 dpi, and the expression of ZO-1, Occludin, and Claudin-1 decreased at 4, 6 dpi; 4, 6, 8 dpi; and 2, 6 dpi, respectively. Intestinal cytokines IFN-α, IL-1β and IL-6 increased at 6 dpi; 8 dpi; and 6, 8 dpi, respectively, whereas IL-2 decreased at 6, 8 dpi. The diversity of ileal flora increased significantly at 4 dpi and decreased at 8 dpi. The bacteria Ochrobactrum and Enterococcus increased and decreased at 4, 8 dpi; 2, 4 dpi, respectively. Plasma MDA increased at 2 dpi, SOD, CAT, and T-AOC decreased at 2, 4, 8 dpi; 4, 8 dpi; and 4, 6, 8 dpi, respectively. These results suggest that rMDPV infection led to early intestinal barrier dysfunction, inflammation, ileac microbiota disruption, and oxidative stress.

The Retrospective on Atypical Brucella Species Leads to Novel Definitions

The genus Brucella currently comprises twelve species of facultative intracellular bacteria with variable zoonotic potential. Six of them have been considered as classical, causing brucellosis in terrestrial mammalian hosts, with two species originated from marine mammals. In the past fifteen years, field research as well as improved pathogen detection and typing have allowed the identification of four new species, namely Brucella microti, Brucella inopinata, Brucella papionis, Brucella vulpis, and of numerous strains, isolated from a wide range of hosts, including for the first time cold-blooded animals. While their genome sequences are still highly similar to those of classical strains, some of them are characterized by atypical phenotypes such as higher growth rate, increased resistance to acid stress, motility, and lethality in the murine infection model. In our review, we provide an overview of state-of-the-art knowledge about these novel Brucella sp., with emphasis on their phylogenetic positions in the genus, their metabolic characteristics, acid stress resistance mechanisms, and their behavior in well-established in cellulo and in vivo infection models. Comparison of phylogenetic classification and phenotypical properties between classical and novel Brucella species and strains finally lead us to propose a more adapted terminology, distinguishing between core and non-core, and typical versus atypical brucellae, respectively.

Pathogenicity and Its Implications in Taxonomy: The Brucella and Ochrobactrum Case

The intracellular pathogens of the genus Brucella are phylogenetically close to Ochrobactrum, a diverse group of free-living bacteria with a few species occasionally infecting medically compromised patients. A group of taxonomists recently included all Ochrobactrum organisms in the genus Brucella based on global genome analyses and alleged equivalences with genera such as Mycobacterium. Here, we demonstrate that such equivalencies are incorrect because they overlook the complexities of pathogenicity. By summarizing Brucella and Ochrobactrum divergences in lifestyle, structure, physiology, population, closed versus open pangenomes, genomic traits, and pathogenicity, we show that when they are adequately understood, they are highly relevant in taxonomy and not unidimensional quantitative characters. Thus, the Ochrobactrum and Brucella differences are not limited to their assignments to different “risk-groups”, a biologically (and hence, taxonomically) oversimplified description that, moreover, does not support ignoring the nomen periculosum rule, as proposed. Since the epidemiology, prophylaxis, diagnosis, and treatment are thoroughly unrelated, merging free-living Ochrobactrum organisms with highly pathogenic Brucella organisms brings evident risks for veterinarians, medical doctors, and public health authorities who confront brucellosis, a significant zoonosis worldwide. Therefore, from taxonomical and practical standpoints, the Brucella and Ochrobactrum genera must be maintained apart. Consequently, we urge researchers, culture collections, and databases to keep their canonical nomenclature.

The perspective of antibiotic therapeutic challenges of brucellosis in the Middle East and North African (MENA) countries: Current situation and therapeutic management

Brucellosis is among the most prevalent zoonotic infections in Middle Eastern and North African (MENA) countries, critically impacting human and animal health. A comprehensive review of studies on antibiotic susceptibility and therapeutic regimes for brucellosis in ruminants and humans in the MENA region was conducted to evaluate the current therapeutic management in this region. Different scientific databases were searched for peer-reviewed original English articles published from January 1989 to February 2021. Reports from research organizations and health authorities have been taken into consideration. Brucella melitensis and Brucella abortus have been reported from the majority of MENA countries, suggesting a massive prevalence particularly of B. melitensis across these countries. Several sporadic cases of brucellosis relapse, therapeutic failure, and antibiotic resistance of animal and human isolates have been reported from the MENA region. However, several studies proved that brucellae are still in-vitro susceptible to the majority of antibiotic compounds and combinations in current recommended WHO treatment regimens, e.g. levofloxacin, tetracyclines, doxycycline, streptomycin, ciprofloxacin, chloramphenicol, gentamicin, tigecycline, and trimethoprim/sulfamethoxazole. The current review presents an overview on resistance development of brucellae and highlights the current knowledge on effective antibiotics regimens for treating human brucellosis. This article is protected by copyright. All rights reserved.

Ochrobactrum anthropi - An Emerging Opportunistic Pathogen in Musculoskeletal Disorders - A Case Report and Review of Literature

INTRODUCTION

Ochrobactrum anthropi is an opportunistic and rare human pathogen, which is seen widely in the environment. O. anthropi infections have been reported in both immunocompetent and immunocompromised individuals. There is no proper consensus on the diagnosis and management of O. anthropi related infections.

CASE REPORT

We report a case of O. anthropi related left distal clavicular osteomyelitis in an immunocompetent individual with an elaborative diagnostic and treatment algorithm for its effective management.

CONCLUSION

A comprehensive management strategy with a combination of implant removal (if present) with extensive surgical debridement of bone and soft tissue and intravenous antibiotics results in successful eradication of O. anthropi infection.

Pseudochrobactrum algeriensis sp. nov., isolated from lymph nodes of Algerian cattle

Three Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile strains (C130915_07^T, C150915_16 and C150915_17) were isolated from lymph nodes of Algerian cows. On the basis of 16S rRNA gene and whole genome similarities, the isolates were almost identical and clearly grouped in the genus Pseudochrobactrum. This allocation was confirmed by the analysis of fatty acids (C_19:cyclo, C_18 : 1, C_18 : 0, C_16 : 1 and C_16 : 0) and of polar lipids (major components: phosphatidylethanolamine, ornithine-lipids, phosphatidylglycerol, cardiolipin and phosphatidylcholine, plus moderate amounts of phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and other aminolipids). Genomic, physiological and biochemical data differentiated these isolates from previously described Pseudochrobactrum species in DNA relatedness, carbon assimilation pattern and growth temperature range. Thus, these organisms represent a novel species of the genus Pseudochrobactrum, for which the name Pseudochrobactrum algeriensis sp. nov. is proposed (type strain C130915_07^T=CECT30232^T=LMG 32378^T).

Gegen Qinlian Decoction Alleviates Experimental Colitis and Concurrent Lung Inflammation by Inhibiting the Recruitment of Inflammatory Myeloid Cells and Restoring Microbial Balance

Objective

Ulcerative colitis (UC) as one of the intractable diseases in gastroenterology seriously threatens human health. Respiratory pathology is a representative extraintestinal manifestation of UC affecting the quality of life of patients. Gegen Qinlian Decoction (GQD) is a classical traditional Chinese medicine prescription for UC or acute lung injury. This study was aimed to reveal the therapeutic effect of GQD on UC and its pulmonary complications and uncover its molecular mechanism mediated by myeloid cells and microbiota.

Methods

Mice with DSS-induced colitis were orally administrated with GQD. Overall vital signs were assessed by body weight loss and disease activity index (DAI). Pulmonary general signs were evaluated by pulmonary pathology and lung function. The mechanism of GQD relieving UC was characterized by detecting myeloid cells (neutrophils, macrophages, inflammatory monocytes, and resident monocytes) in colonic and lung tissues, related inflammatory cytokines, as well as the microbiota in bronchoalveolar lavage fluid (BALF) and feces.

Results

GQD significantly reduced weight loss, DAI scores, and lung injury but improved the lung function of colitis mice. The DSS-induced colonic and concurrent pulmonary inflammation were also alleviated by GQD, as indicated by the down-regulated expressions of inflammatory cytokines (TNF-α, IL-1β, IL-6, CCR2, and CCL2) and the suppressed recruitment of neutrophils and inflammatory monocytes. Meanwhile, GQD greatly improved intestinal microbiota imbalance by enriching Ruminococcaceae UCG-013 while decreasing Parabacteroides, [Eubacterium]_fissicatena_group, and Akkermansia in the feces of colitis mice. Expectantly, GQD also restored lung microbiota imbalance by clearing excessive Coprococcus 2 and Ochrobactrum in the BALF of colitis mice. Finally, significant correlations appeared between GQD-mediated specific bacteria and inflammatory cytokines or immune cells.

Conclusion

GQD could alleviate UC by decreasing excessive inflammatory myeloid cells and cytokines, and reshaping the microbiota between the colon and lung, which contributes to clarifying the mechanism by which GQD ameliorates colitis-associated pulmonary inflammation.

Deciphering Cadmium (Cd) Tolerance in Newly Isolated Bacterial Strain, Ochrobactrum intermedium BB12, and Its Role in Alleviation of Cd Stress in Spinach Plant (Spinacia oleracea L.)

A cadmium (Cd)-tolerant bacterium Ochrobactrum intermedium BB12 was isolated from sewage waste collected from the municipal sewage dumping site of Bhopal, India. The bacterium showed multiple heavy metal tolerance ability and had the highest minimum inhibitory concentration of 150 mg L-1 of Cd. Growth kinetics, biosorption, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Fourier transform infrared (FTIR) spectroscopy studies on BB12 in the presence of Cd suggested biosorption as primary mode of interaction. SEM and TEM studies revealed surface deposition of Cd. FTIR spectra indicated nitrogen atom in exopolysaccharides secreted by BB12 to be the main site for Cd attachment. The potential of BB12 to alleviate the impact of Cd toxicity in spinach plants (Spinacia oleracea L.) var. F1-MULAYAM grown in the soil containing Cd at 25, 50, and 75 mg kg-1 was evaluated. Without bacterial inoculation, plants showed delayed germination, decrease in the chlorophyll content, and stunted growth at 50 and 75 mg kg-1 Cd content. Bacterial inoculation, however, resulted in the early germination, increased chlorophyll, and increase in shoot (28.33%) and root fresh weight (72.60%) at 50 mg kg-1 of Cd concentration after 75 days of sowing. Due to bacterial inoculation, elevated proline accumulation and lowered down superoxide dismutase (SOD) enzyme activity was observed in the Cd-stressed plants. The isolate BB12 was capable of alleviating Cd from the soil by biosorption as evident from significant reduction in the uptake/translocation and bioaccumulation of Cd in bacteria itself and in the plant parts of treated spinach. Potential PGP prospects and heavy metal bioremediation capability of BB12 can make the environmental application of the organism a promising approach to reduce Cd toxicity in the crops grown in metal-contaminated soils.

Induction of TLR4/TLR2 Interaction and Heterodimer Formation by Low Endotoxic Atypical LPS

The Toll-like receptor 4 (TLR4)/myeloid differentiation protein-2 (MD-2) complex is considered the major receptor of the innate immune system to recognize lipopolysaccharides (LPSs). However, some atypical LPSs with different lipid A and core saccharide moiety structures and compositions than the well-studied enterobacterial LPSs can induce a TLR2-dependent response in innate immune cells. Ochrobactrum intermedium, an opportunistic pathogen, presents an atypical LPS. In this study, we found that O. intermedium LPS exhibits a weak inflammatory activity compared to Escherichia coli LPS and, more importantly, is a specific TLR4/TLR2 agonist, able to signal through both receptors. Molecular docking analysis of O. intermedium LPS predicts a favorable formation of a TLR2/TLR4/MD-2 heterodimer complex, which was experimentally confirmed by fluorescence resonance energy transfer (FRET) in cells. Interestingly, the core saccharide plays an important role in this interaction. This study reveals for the first time TLR4/TLR2 heterodimerization that is induced by atypical LPS and may help to escape from recognition by the innate immune system.

The first case of Ochrobactrum intermedium bacteremia in a pediatric patient with malignant tumor

BACKGROUND

Ochrobactrum spp. are non-fermenting, Gram-negative bacilli that are regarded as emerging human pathogens of low virulence that can cause infections. The first identified case of Ochrobactrum intermedium was reported in 1998 in a liver transplantation patient with liver abcess. There are no reports of infections in pediatric patients. Here, we report the first case of O. intermedium bacteremia in a pediatric patient.

CASE PRESENTATION

A two and a half years old male was admitted with fever, chills and nausea. He had been diagnosed as pineoblastoma and underwent surgical resection and chemotherapy. O. intermedium was isolated from his blood cultures and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), however, the Vitek II automated system failed to identify the organism. Then the pathogen was confirmed by 16S rDNA sequencing and average nucleotide identity result (ANI) confirmed the precise identification of O. intermedium at genomic level. In addition, the patient recovered well after antibiotic combined therapy.

CONCLUSIONS

This, to our knowledge, is the first case of O. intermedium bacteremia in a pediatric patient with malignant tumor. Traditional biochemical identification methods such as API 20NE or VITEK2 system cannot differentiate O. anthropi and O. intermedium. MALDI-TOF may be a promising tool for rapid identification of microorganisms such as O. intermedium.

Genomics of Ochrobactrum pseudogrignonense (newly named Brucella pseudogrignonensis) reveals a new bla OXA subgroup

Ochrobactrum pseudogrignonense (newly named Brucella pseudogrignonensis) is an emerging pathogen in immunodeficient and immunocompetent patients. Most documented cases associated with Ochrobactrum are frequently catheter-related and exhibit wide-spectrum β-lactam resistance. Misidentification of this pathogen using commercial bacterial identification kits is common. We identified a case of O. pseudogrignonense infection associated with cholelithiasis. The O. pseudogrignonense genome was sequenced and reconstructed using a Nanopore and Illumina hybrid strategy. A novel bla _OXA-919 divergent from existing OXA members was identified and subsequent analysis revealed its existence in all available O. pseudogrignonense genomes, which forms a new phylogenetic subgroup distinct from other OXA clusters. Further analysis demonstrated the presence of the novel bla _OXA-919 in the chromosome of several other Ochrobactrum species. Our study indicated that Ochrobactrum chromosomes may be a reservoir of bla _OXA-919 β-lactamases.

Isolation, characterization, and interaction of lignin-degrading bacteria from rumen of buffalo (Bubalus bubalis)

The purpose of this study was to isolate lignin-degrading bacteria from buffalo rumen and to explore their interactions further. Using lignin as the carbon source, three bacteria, B-04 (Ochrobactrum pseudintermedium), B-11 (Klebsiella pneumoniae), and B-45 (Bacillus sonorensis), which have shown lignin degradation potential, were successfully isolated and identified from the rumen fluid of buffalo by colony morphology, 16S ribosomal RNA gene sequencing, and biochemical and physiological analyses. The degradation rates of lignin were determined, and the maximum values were 4.86%, 11.1%, and 7.68% for B-04, B-11, and B-45, respectively. The maximum laccase activities were 0.65, 0.93, and 1.15 U/ml, while the maximum lignin peroxidase activities were 5.72, 8.29, and 18.69 U/ml, respectively. Pairwise interaction studies showed inhibitory interaction between B-04 and B-45, inhibitory interaction between B-04 and B-11, and symbiotic interaction between B-11 and B-45. This is the first report on the lignin degradation ability of bacteria isolated from the buffalo's rumen, which provides a new understanding for revealing the mechanism of roughage tolerance of buffalo.

Comprehensive characterization of stress tolerant bacteria with plant growth-promoting potential isolated from glyphosate-treated environment

The application of plant growth-promoting bacteria in agricultural systems is an efficient and environment-friendly strategy to improve crop yields and maintain soil quality. However, as different soils have diverse and specific ecological characteristics and may represent adverse abiotic conditions, in vivo application requires the careful selection of the desired beneficial microorganisms. In this study we report Ensifer adhaerens SZMC 25856 and Pseudomonas resinovorans SZMC 25875 isolates recovered from glyphosate-treated soil to possess yet undiscovered plant growth-enhancing potential. The strains were found to promote the growth of tomato seedlings significantly, to have the ability of synthesizing indole-3-acetic acid and siderophores, to tolerate pH in the range of 6.59-7.96, salinity up to 12.5 g L-1 NaCl and drought up to 125 g L-1 polyethylene glycol 6000, as well as to survive in the presence of various pesticides including glyphosate, diuron, chlorotoluron, carbendazim and thiabendazole, and heavy metals such as Al, Fe, Mn, Zn, Pb and Cu. The plant growth-promoting traits of the examined E. adhaerens and P. resinovorans isolates and their tolerance to numerous abiotic stress factors make them promising candidates for application in different agricultural environments, including soils polluted with glyphosate.

A Case of Ochrobactrum intermedium Bacteremia Secondary to Cholangitis With a Literature Review

Ochrobactrum species are gram-negative, non-lactose fermenting, aerobic bacilli closely related to Brucella genus. Ochrobactrum intermedium (O. intermedium) is an emergent human pathogen that is difficult to differentiate from other Ochrobactrum species by conventional methods. It is known to infect immunocompromised hosts, has the propensity for abscess formation, and is known for its multidrug resistance. We describe the case of an 84-year-old woman with a background of primary sclerosing cholangitis who presented with fatigue, fever, and syncope. Blood cultures grew O. intermedium. Magnetic resonance cholangiopancreatography and endoscopic retrograde cholangiopancreatography were consistent with cholangitis. Cultures from the biliary duct confirmed the same microorganism. The patient was successfully treated with minocycline. Although rare, O. intermedium should be considered as a differential diagnosis in patients with biliary and gut pathology, particularly in immunocompromised patients.

An Update on Wastewater Multi-Resistant Bacteria: Identification of Clinical Pathogens Such as Escherichia coli O25b:H4-B2-ST131-Producing CTX-M-15 ESBL and KPC-3 Carbapenemase-Producing Klebsiella oxytoca

Wastewater treatment plants (WWTPs) are significant reservoirs of bacterial resistance. This work aims to identify the determinants of resistance produced by Gram-negative bacteria in the influent and effluent of two WWTPs in Portugal. A total of 96 wastewater samples were obtained between 2016 and 2019. The numbers of total aerobic and fecal contamination bacteria were evaluated, and genomic features were searched by polymerase chain reaction (PCR) and Next-Generation Sequencing (NGS). Enterobacteriaceae corresponded to 78.6% (n = 161) of the 205 isolates identified by 16sRNA. The most frequent isolates were Escherichia spp. (57.1%, n = 117), followed by Aeromonas spp. (16.1%, n = 33) and Klebsiella spp. (12.7%, n = 26). The remaining 29 isolates (14.1%) were distributed across 10 different genera. Among the 183 resistant genes detected, 54 isolates produced extended spectrum β-lactamases (ESBL), of which bla_CTX-M-15 was predominant (37 isolates; 68.5%). A KPC-3 carbapenemase-producing K. oxytoca was identified (n = 1), with bla_KPC-3 included in a transposon Tn4401 isoform b. A higher number of virulence genes (VG) (19 genes) was found in the E. coli 5301 (O25b-ST131-B2) isolate compared with a commensal E. coli 5281 (O25b-ST410-A) (six genes). Both shared five VG [Enterobactin; Aerobactin, CFA/1 (clade α); Type1 (clade γ1); Type IV]. In conclusion, this work highlights the role of relevant clinical bacteria in WWTPs, such as KPC-3-producing K. oxytoca, and, for the first time, a CTX-M-15-producing Ochromobactrum intermedium, a human opportunistic pathogen, and a SED-1-producing Citrobacter farmeri, an uncommon CTX-M-type extended-spectrum beta-lactamase.