Mycobacterium avium complex (MAC) genomics and transmission in a London hospital

Non-tuberculous mycobacteria (NTM) are ubiquitous environmental microorganisms and opportunistic pathogens in individuals with pre-existing lung conditions such as cystic fibrosis (CF) and non-CF bronchiectasis (BX). Whilst recent studies of Mycobacterium abscessus have identified transmission within single CF centres as well as nationally and globally, transmission of other NTM species is less well studied. We sequenced 1000 Mycobacterium avium complex (MAC) isolates from CF and non-CF patients at the Royal Brompton Hospital (RBH), London. Epidemiological links were identified from patient records. Previously published genomes were used to characterise global population structures. Analysis of the three most predominant MAC species identified putative transmission clusters that contained patients with CF, BX and other lung conditions, although few epidemiological links could be identified. For M. avium, lineages were largely limited to single countries, whilst for M. chimaera, global transmission clusters previously associated with heater cooler units (HCUs) were found. However, the origin of the major HCU-associated outbreak was a lineage already circulating in patients with pre-existing lung conditions. CF and non-CF patients share transmission chains even in the presence of CF patient-focussed hospital control measures, although the lack of epidemiological links suggests that most transmission is indirect and may be due to environmental foci or else asymptomatic carriage in the wider population. The major HCU-associated M. chimaera lineage being derived from an already circulating lineage, suggests that HCUs are not the sole vector nor the ultimate source of this lineage. Future studies should include sampling of environmental reservoirs and potential asymptomatic carriers.

The Protective Role of 1,8-Dihydroxynaphthalene–Melanin on Conidia of the Opportunistic Human Pathogen Aspergillus fumigatus Revisited: No Role in Protection against Hydrogen Peroxide and Superoxides

Opportunistic pathogens like Aspergillus fumigatus have strategies to protect themselves against reactive oxygen species like hydrogen peroxides and superoxides that are produced by immune cells. DHN-melanin is the green pigment on conidia of Aspergillus fumigatus and more than 2 decades ago was reported to protect conidia against hydrogen peroxide.

Influence of cow reproductive tract microbiota on formation of calf upper respiratory tract microbiota

Diagnosis of latent endometritis and predicting the effect of the inflammatory process on the course of pregnancy and its outcome is a necessary measure when conducting clinical examination of animals. Lack of diagnostic criteria, including microbiological one, cause difficulties for veterinarians in assessing latent endometritis. Often, animals suffering from latent inflammation of the reproductive tract are infertile and cannot be treated. And from cows with dysbiosis of the genital tract, sick young animals are born, lagging behind in growth and development. The aim of the work was to establish the relationship between the genital tract microbiome, the number and species composition of commensals and opportunistic microorganisms on the ability to carry pregnancy. Washes from the oral and nasal cavities were taken from the young born to study the microbiome: lactic acid microorganisms in combination with opportunistic pathogens. As a result of the research, it was found that animals with a low number of lactic acid microorganisms and an increased titer of opportunistic microorganisms were infertile, which led to their culling. In young animals, they are present in the respiratory tract in all samples, together with coccal microorganisms. The study of lactic acid microorganisms is advisable in the diagnosis of inflammatory processes of the reproductive tract and upper respiratory tract.

The Impact of Extreme Weather Events on Bacterial Communities and Opportunistic Pathogens in a Drinking Water Treatment Plant

Drinking water treatment processes are highly effective at improving water quality, but pathogens can still persist in treated water, especially after extreme weather events. To identify how extreme weather events affected bacterial populations in source and treated water, water samples were collected from the Yangtze River Delta area and a local full-scale drinking water treatment plant. Bacterial community structure and the occurrence of pathogens were investigated in samples using 16S rRNA sequencing and qPCR techniques. In this study, the results show that intense rainfall can significantly increase levels of bacteria and opportunistic pathogens in river and drinking water treatment processes (p < 0.05); in particular, the relative abundance of Cyanobacteria increased after a super typhoon event (p < 0.05). The biological activated carbon (BAC) tank was identified as a potential pathogen reservoir and was responsible for 52 ± 6% of the bacteria released downstream, according to Bayesian-based SourceTracker analysis. Our results provide an insight into the challenges faced by maintaining finished water quality under changing weather conditions.

Long-read 16S-seq reveals nasopharynx microbial dysbiosis and enrichment of Mycobacterium and Mycoplasma in COVID-19 patients: A source of co-infection

Background The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is a major global health concern. This virus infects the upper respiratory tract and causes pneumonia-like symptoms. So far, few studies have shown alterations in nasopharyngeal (NP) microbial diversity, enrichment of opportunistic pathogens and their role in co-infections during respiratory infections. Therefore, we hypothesized that microbial diversity changes, with increase in the population of opportunistic pathogens, during SARS-CoV2 infection in the nasopharynx which may be involved in co-infection in COVID-19 patients. Methods The 16S rRNA variable regions, V1-V9, of NP samples of control and COVID-19 (symptomatic and asymptomatic) patients were sequenced using the Oxford Nanopore™ technology. Comprehensive bioinformatics analysis for determining alpha/beta diversities, non-metric multidimensional scaling, correlation studies, canonical correspondence analysis, linear discriminate analysis, and dysbiosis index were used to analyze the control and COVID-19-specific NP microbiomes. Results We observed significant dysbiosis in COVID-19 NP microbiome with increase in abundance of opportunistic pathogens at genus and species levels in asymptomatic/symptomatic patients. The significant abundance of Mycobacteria spp. and Mycoplasma spp. in symptomatic patients suggest their association and role in co-infections in COVID-19 patients. Furthermore, we found strong correlation of enrichment of Mycobacteria and Mycoplasma with the occurrences of chest pain and fever in symptomatic COVID-19 patients. Conclusion This is the first study from India to show the abundance of Mycobacteria and Mycoplasma opportunistic pathogens in non-hospitalized COVID-19 patients and their relationship with symptoms, indicating the possibility of co-infections.

Evaluation of Selected Parameters of the Specific Immune Response against Pseudomonas aeruginosa Strains

The immune response to Pseudomonas aeruginosa strains could be influenced by differences in antibiotic resistance and virulence. At the present time, it is unclear which type of immune responses enables uncontrolled invasion of opportunistic pathogens. The conditional pathogenicity of Pseudomonas aeruginosa served as an inspiration to begin a study on this bacterium. The aim of this study was to gain insight into selected parameters describing immune responses with regards to the adaptable agents of this pathogen. For the analysis of the specific immune response, the potential of Pseudomonas aeruginosa to stimulate lymphocytes, including Th17 lymphocytes, dendritic cells and other components of the adaptive immune response, was examined. The highest percentage of CD83+CD1a-HLA-DR++ cells was found after stimulation with lysates of strains isolated from the patients with severe systemic infection. We found statistically significant differences in percentages of HLA-DR+ PBMCs and MFI of HLA-DR between groups of Pseudomonas aeruginosa strains isolated from the patients with different clinical courses of infection. Our results suggest that the clinical course and outcomes of Pseudomonas aeruginosa infections are not associated with impairment of the specific immune response.

The Impact of Pre-Slaughter Fasting on the Ruminal Microbial Population of Commercial Angus Steers

Diet impacts the composition of the ruminal microbiota; however, prior to slaughter, cattle are fasted, which may change the ruminal microbial ecosystem structure and lead to dysbiosis. The objective of this study was to determine changes occurring in the rumen after pre-slaughter fasting, which can allow harmful pathogens an opportunity to establish in the rumen. Ruminal samples were collected before and after pre-slaughter fasting from seventeen commercial Angus steers. DNA extraction and 16S rRNA gene sequencing were performed to determine the ruminal microbiota, as well as volatile fatty acid (VFA) concentrations. Microbial richness (Chao 1 index), evenness, and Shannon diversity index all increased after fasting (p ≤ 0.040). During fasting, the two predominant families Prevotellaceae and Ruminococcaceae decreased (p ≤ 0.029), whereas the remaining minor families increased (p < 0.001). Fasting increased Blautia and Methanosphaera (p ≤ 0.003), while Campylobacter and Treponema tended to increase (p ≤ 0.086). Butyrate concentration tended to decrease (p = 0.068) after fasting. The present findings support that fasting causes ruminal nutrient depletion resulting in dysbiosis, allowing opportunistic pathogens to exploit the void in the ruminal ecological niche.

Trichosporon inkin fungemia case report: clinical and laboratory management

Trichosporon species are emerging as opportunistic pathogens that mainly affect immunocompromised patients. Patients with onco-hematological diseases usually present with fungemia by Trichosporon species, especially by T. asahii. Reports of this infection by other species of the genus are uncommon. Thus, in this paper, we present a case of T. inkin fungemia in a 39-year-old female patient with intestinal obstruction and absence of malignant hematological diseases. The late mycological diagnosis, the ineffective control of her pre-existing conditions and consequent failure to start antifungal therapy were the contributing factors for the patient's death.

Detección de Pasteurella multocida, Mannhemia haemolytica, Histophilus somni y Mycoplasma bovis en pulmón de bovinos

In this study, it was aimed to determine of P. multocida, M. haemolytica, H. somni and M. bovis in macroscopically healthy cattle lungs by PCR. The study was carried out on 82 macroscopically healthy cattle lung. DNA extraction was performed to the lung samples. PCR was then performed using all specific primers. By molecular evaluation, positive results were achieved for P. multocida, M. haemolytica, H. somni and M. bovis in 4 (4.8 %), 4 (4.8 %), 6 (7.3 %) and 3 (3.6 %) of the samples, respectively. Mix infections were detected in five samples. Of the samples, two were positive for both P. multocida and M. haemolytica, two were positive for both M. haemolytica and H. somni and one was positive for both P. multocida and H. somni. However, a positive sample, which carried all of pathogens, was not detected. In conclusion, P. multocida, M. haemolytica, H. somni and M. bovis are the important opportunistic pathogens of respiratory tract in cattle and these pathogens have a major role during infections. But multifactorial nature of bovine respiratory disease and immune system affected the formation of the disease. Hence, firstly cattle’s immunity should be strengthened and other conditions should be kept under control.

Correlation between faecal microbial taxa and ulcerative colitis in different phases of disease activity in a north Indian cohort

Objective: A link between gut microbiota and Ulcerative Colitis (UC) has been established in several studies. However, a few studies have examined specific changes in microbiota associated with different phases of disease activity in UC. In this study, we investigated phenotypic variability underlying genetically distinct north Indian (NI) UC patients by identifying differentially abundant taxa between (i) UC patients and healthy controls and (ii) different disease phases of disease activity. Design: 16S rRNA (V3,V4) sequencing of 105 patients with UC [newly diagnosed (n=14); patients in remission (n=36) and active disease (relapse, n=55)]; and 36 healthy controls was performed. The faecal microbiota composition in different phases of UC disease activity and healthy controls was analysed. Results: Lower gut microbial diversity; enrichment of lactate-producing bacteria namely Streptococcus, Bifidobacterium and Lactobacillus; and depletion of butyrate-producing bacteria (e.g., Lachnospiraceae and Ruminococcaceae), was observed among UC patients. Subgroup analysis revealed differential abundance of Escherichia-Shigella, Streptococcus, Enterococcus and Faecalibacterium in newly diagnosed UC patients. No discrete microbial features were observed between patients in remission and those with active disease. Co-occurrence network analysis revealed a mutualistic association between opportunistic pathogens and Bifidobacterium and Lactobacillus and antagonistic relationship with butyrate-producers. Conclusion: This first faecal microbiome study elucidated dysanaerobiosis; loss of short chain fatty acid producers and enrichment of inflammation associated microbes; population specific differential microbial genera; and microbial signature for early dysbiosis, among NI UC cohort.