scholarly journals Topography of the respiratory tract bacterial microbiota in cattle

2020 ◽  
Author(s):  
Christopher McMullen ◽  
Trevor W. Alexander ◽  
Renaud Léguillette ◽  
Matthew Workentine ◽  
Edouard Timsit
Keyword(s):  
Respiratory Tract ◽  
Pathogenic Bacteria ◽  
Primary Source ◽  
Alpha Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Upper Respiratory Tract ◽  
Bacterial Microbiota ◽  
Sampling Locations ◽  
Healthy Cattle

Abstract Background Bacterial bronchopneumonia (BP) is the leading cause of morbidity and mortality in cattle. The nasopharynx is generally accepted as the primary source of pathogenic bacteria that cause BP. However, it has recently been shown in humans that the oropharynx may act as the primary reservoir for pathogens that reach the lung. The objective was therefore to describe the bacterial microbiota present along the entire cattle respiratory tract to determine which upper respiratory tract (URT) niches may contribute the most to the composition of the lung microbiota. Methods Seventeen upper and lower respiratory tract locations were sampled from 15 healthy feedlot steer calves. Samples were collected using a combination of swabs, protected specimen brushes, and saline washes. DNA was extracted from each sample and the 16S rRNA gene (V3-V4) was sequenced. Community composition, alpha-diversity, and beta-diversity were compared among sampling locations. Results Microbiota composition differed across sampling locations, with physiologically and anatomically distinct locations showing different relative abundances of 1,137 observed sequence variants (SVs). An analysis of similarities showed that the lung was more similar to the nasopharynx (R-statistic = 0.091) than it was to the oropharynx (R-statistic = 0.709) or any other URT sampling location. Five distinct metacommunities were identified across all samples after clustering at the genus level using Dirichlet multinomial mixtures. This included a metacommunity found primarily in the lung and nasopharynx that was dominated by Mycoplasma . Further clustering at the SV level showed a shared metacommunity between the lung and nasopharynx that was dominated by Mycoplasma dispar . Other metacommunities found in the nostrils, tonsils, and oral microbiotas were dominated by Moraxella , Fusobacterium , and Streptococcus , respectively. Conclusions The nasopharyngeal bacterial microbiota is most similar to the lung bacterial microbiota in healthy cattle and therefore may serve as the primary source of bacteria to the lung. This finding indicates that the nasopharynx is likely the most important location that should be targeted when doing bovine respiratory microbiota research.

scholarly journals Topography of the respiratory tract bacterial microbiota in cattle

2020 ◽  
Author(s):  
Christopher McMullen ◽  
Trevor W. Alexander ◽  
Renaud Léguillette ◽  
Matthew Workentine ◽  
Edouard Timsit
Keyword(s):  
Respiratory Tract ◽  
Pathogenic Bacteria ◽  
Primary Source ◽  
Alpha Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Upper Respiratory Tract ◽  
Bacterial Microbiota ◽  
Sampling Locations

Abstract Background Bacterial bronchopneumonia (BP) is the leading cause of morbidity and mortality in cattle. While the bacterial composition of the bovine upper respiratory tract (URT) has not been studied in detail, the nasopharynx is generally accepted as the primary source of pathogenic bacteria that cause BP. However, it has recently been shown in humans that the oropharynx may act as the primary reservoir for pathogens that reach the lung. The objective was therefore to describe the bacterial microbiota present along the entire cattle respiratory tract to determine which URT niches may contribute the most to the composition of the lung microbiota. Methods Seventeen upper and lower respiratory tract locations were sampled from 15 healthy feedlot steer calves. Samples were collected using a combination of swabs, protected specimen brushes, and saline washes. DNA was extracted from each sample and the 16S rRNA gene (V3-V4) was sequenced. Community composition, alpha-diversity, and beta-diversity were compared among sampling locations. Results Microbiota composition differed across sampling locations, with physiologically and anatomically distinct locations showing different relative abundances of 1,137 observed sequence variants (SVs). An analysis of similarities showed that the lung was more similar to the nasopharynx (R-statistic = 0.091) than it was to the oropharynx (R-statistic = 0.709) or any other URT sampling location. Five distinct metacommunities were identified across all samples after clustering at the genus level using Dirichlet multinomial mixtures. This included a metacommunity found primarily in the lung and nasopharynx that was dominated by Mycoplasma . Further clustering at the SV level showed a shared metacommunity between the lung and nasopharynx that was dominated by Mycoplasma dispar . Other metacommunities found in the nostrils, tonsils, and oral microbiotas were dominated by Moraxella , Fusobacterium , and Streptococcus , respectively. Conclusions The nasopharyngeal bacterial microbiota is most similar to the lung bacterial microbiota and therefore may serve as the primary source of bacteria to the lung. This finding confirms that the nasopharyngeal microbiota should be the focus of research as it relates to the role of the URT microbiota in BP. As well, this microbiota should be the main target for future interventions and pharmaceuticals aimed at controlling and preventing BP.

scholarly journals Bacterial communities of the upper respiratory tract of turkeys

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Olimpia Kursa ◽  
Grzegorz Tomczyk ◽  
Anna Sawicka-Durkalec ◽  
Aleksandra Giza ◽  
Magdalena Słomiany-Szwarc
Keyword(s):  
Respiratory Tract ◽  
Bacterial Communities ◽  
Pathogenic Bacteria ◽  
Viral Infections ◽  
Rrna Gene ◽  
Respiratory Pathogens ◽  
Upper Respiratory Tract ◽  
Genus Level ◽  
Upper Respiratory ◽  
And Performance

AbstractThe respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplification of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identified in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Differences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identified, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey flocks.

scholarly journals Characterization of the upper respiratory tract microbiome of turkeys

2020 ◽  
Author(s):  
Olimpia Kursa ◽  
Grzegorz Tomczyk ◽  
Anna Sawicka-Durkalec ◽  
Aleksandra Giza ◽  
Magdalena Słomiany-Szwarc
Keyword(s):  
16S Rrna ◽  
Respiratory Tract ◽  
Pathogenic Bacteria ◽  
Rrna Gene ◽  
Upper Respiratory Tract ◽  
Bacterial Phyla ◽  
Sequencing Technologies ◽  
Upper Respiratory ◽  
Commercial Turkey

Abstract Background: The respiratory tracts of turkeys are the main route of infection therefore plays important roles in the overall health and performance of the birds. Understanding the poultry microbiome has the potential to offer better diagnosis and rational management of many poultry diseases. Characterization of microbial communities in the upper respiratory tract of turkeys could help better understand the role of pathogenic bacteria and other commensal or symbiotic microorganisms in the infection. The aim of this study was microbiome characterization of upper respiratory tracks of commercial turkeys using next-generation sequencing technologies. Results: The microbiome from samples collected from commercial turkey flocks was determined using 16S rRNA metagenomic approach. Taxonomic analysis of the microbiome was done by of the V3 and V4 regions of 16S rRNA gene (MiSeq, Illumina) amplification. The phylogenetic analysis identified the 10 bacterial phyla in turkey, the most abundant were phyla Firmicutes and Proteobacteria, accounting for >99% of all the sequences. The turkey sequences represent 144 established bacterial genera. Differences between bacterial abundances were found at the family and genus level. Several defining markers of microbiome succession were identified, including the presence of Ornithobacterium and Mycoplasma. Conclusions: Understanding the turkey’s respiratory microbiome is very important. Unique informations about microbiome representing members of the four major phyla of the respiratory tract in turkeys was assembled. These results obtained in this study supply information about turkey microbiome and can be useful in controlling, diagnosing and treating commercial turkey flocks. Our study significantly broaden the knowledge of the upper respiratory tract microbiome of turkeys.

scholarly journals Effect of hay type on cecal and fecal microbiome and fermentation parameters in horses

2020 ◽  
Author(s):  
Rachel J Sorensen ◽  
James S Drouillard ◽  
Teresa L Douthit ◽  
Qinghong Ran ◽  
Douglas G Marthaler ◽  
...  
Keyword(s):  
Fixed Effects ◽  
Volatile Fatty Acids ◽  
Random Effect ◽  
Alpha Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Fecal Microbiome ◽  
Β Diversity ◽  
Fermentation Parameters

Abstract The effect of hay type on the microbiome of the equine gastrointestinal tract is relatively unexplored. Our objective was to characterize the cecal and fecal microbiome of mature horses consuming alfalfa or Smooth Bromegrass (brome) hay. Six cecally cannulated horses were used in a split plot design run as a crossover in 2 periods. Whole plot treatment was ad libitum access to brome or alfalfa hay fed over two 21-d acclimation periods with subplots of sampling location (cecum and rectum) and sampling hour. Each acclimation period was followed by a 24-h collection period where cecal and fecal samples were collected every 3 h for analysis of pH and volatile fatty acids (VFA). Fecal and cecal samples were pooled and sent to a commercial lab (MR DNA, Shallowater, TX) for amplification of the V4 region of the 16S rRNA gene and sequenced using Illumina HiSeq. Main effects of hay on VFA, pH, and taxonomic abundances were analyzed using the MIXED procedure of SAS 9.4 with fixed effects of hay, hour, location, period, all possible interactions and random effect of horse. Alpha and β diversity were analyzed using the R Dame package. Horses fed alfalfa had greater fecal than cecal pH (P ≤ 0.05) whereas horses fed brome had greater cecal than fecal pH (P ≤ 0.05). Regardless of hay type, total volatile fatty acid (VFA) concentrations were greater (P ≤ 0.05) in the cecum than in feces, and alfalfa resulted in greater (P ≤ 0.05) VFA concentrations than brome in both sampling locations. Alpha diversity was greater (P ≤ 0.05) in fecal compared to cecal samples. Microbial community structure within each sampling location and hay type differed from one another (P ≤ 0.05). Bacteroidetes were greater (P ≤ 0.05) in the cecum compared to the rectum, regardless of hay type. Firmicutes and Firmicutes:Bacteroidetes were greater (P ≤ 0.05) in the feces compared to cecal samples of alfalfa-fed horses. In all, fermentation parameters and bacterial abundances were impacted by hay type and sampling location in the hindgut.

scholarly journals Absence of Mycoplasma spp. in nightingales (Luscinia megarhynchos) and blue (Cyanistes caeruleus) and great tits (Parus major) in Germany and its potential implication for evolutionary studies in birds

2021 ◽  
Vol 68 (1) ◽  
Author(s):  
Luisa Fischer ◽  
Franca Möller Palau-Ribes ◽  
Silke Kipper ◽  
Michael Weiss ◽  
Conny Landgraf ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Bird Species ◽  
Respiratory Pathogen ◽  
Economic Losses ◽  
Rrna Gene ◽  
Upper Respiratory Tract ◽  
Healthy Individuals ◽  
Cyanistes Caeruleus ◽  
Potential Implication ◽  
Free Ranging

AbstractMycoplasma spp. are important pathogens in poultry and cause high economic losses for poultry industry worldwide. In other bird species (e.g. white storks, birds of prey, and several waterfowl species), Mycoplasma spp. are regularly found in healthy individuals, hence, considered apathogenic or part of the microbiota of the upper respiratory tract. However, as Mycoplasma spp. are absent in healthy individuals of some wild bird species, they might play a role as respiratory pathogen in these bird species, e.g. Mycoplasma gallisepticum in house finches. The knowledge on the occurrence of Mycoplasma spp. in wild birds is limited. To evaluate the relevance of Mycoplasma spp. in free-ranging nightingales and tits, 172 wild caught birds were screened for the presence of mycoplasmas. The birds were sampled via choanal swabs and examined via molecular methods (n = 172) and, when possible, via culture (n = 142). The Mycoplasma sp. was determined by sequencing the 16S rRNA gene and 16S-23S Intergenic Transcribed Spacer Region. All birds were tested negative for mycoplasmas via PCR and/or mycoplasmal culture. Hence, free-ranging nightingales and tits do not show any mycoplasma in their microbial flora of the respiratory tract. Therefore, these songbird species may suffer from clinical mycoplasmosis when being infected. We hypothesize that birds relying on their vocal ability for reproduction have excluded mycoplasmas from their respiratory flora compared to other bird species.

scholarly journals Antibiotic resistance in bacteria associated with equine respiratory disease in the United Kingdom

2020 ◽  
Vol 187 (5) ◽  
pp. 189-189 ◽  
Author(s):  
Joana D Fonseca ◽  
Daphne E Mavrides ◽  
Alice L Morgan ◽  
Jea G Na ◽  
Peter A Graham ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Respiratory Disease ◽  
Pathogenic Bacteria ◽  
Multiple Drug Resistance ◽  
Clinical Signs ◽  
Multiple Drug ◽  
Upper Respiratory Tract ◽  
Sensitivity Testing ◽  
Commercial Laboratory ◽  
First Choice

IntroductionRespiratory diseases account for the highest number of clinical problems in horses compared with other body systems. While microbiological culture and sensitivity testing is essential for certain cases, knowledge of the most likely bacterial agents and their susceptibilities is necessary to inform empirical antibiotic choices.MethodsA retrospective study of microbiological and cytological results from upper and lower respiratory samples (n=615) processed in a commercial laboratory between 2002 and 2012 was carried out. A further study of lower respiratory samples from horses with clinical signs of lower respiratory disease from May to June 2012 was undertaken.ResultsBoth studies revealed Streptococcus equi subspecies zooepidemicus, Pseudomonas aeruginosa, Pasteurella species, Escherichia coli and Bordetella bronchiseptica as the most frequently isolated species. S equi subspecies zooepidemicus and subspecies equi were susceptible to ceftiofur (100 per cent) and erythromycin (99 per cent). Resistance to penicillin (12.5 per cent of S equi subspecies equi from upper respiratory tract samples) and tetracycline (62.7 per cent) was also detected. Gram-negative isolates showed resistance to gentamicin, trimethoprim-sulfamethoxazole and tetracycline but susceptibility to enrofloxacin (except Pseudomonas species, where 46.2 per cent were resistant). Multiple drug resistance was detected in 1 per cent of isolates.ConclusionResistance to first-choice antibiotics in common equine respiratory tract bacteria was noted and warrants continued monitoring of their susceptibility profiles. This can provide information to clinicians about the best empirical antimicrobial choices against certain pathogenic bacteria and help guide antibiotic stewardship efforts to converse their efficacy.

scholarly journals Community-Acquired Pneumonia in Children: Myths and Facts

2019 ◽  
Vol 36 (S 02) ◽  
pp. S54-S57 ◽  
Author(s):  
Ki Wook Yun ◽  
Rebecca Wallihan ◽  
Alexis Juergensen ◽  
Asuncion Mejias ◽  
Octavio Ramilo
Keyword(s):  
Respiratory Tract ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Bacterial Pathogen ◽  
Transcriptome Profiling ◽  
Antibiotic Use ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Prognostic Indicators ◽  
Upper Respiratory Tract

AbstractCommunity-acquired pneumonia (CAP) is the leading cause of death in children < 5 years of age worldwide. It is also one of the most frequent infectious diseases in children, leading to large antibiotic use and hospitalization even in the industrialized countries. However, the optimal management of CAP in children is still not well defined. Currently, respiratory viruses are considered the most frequent etiologic agents, but detection of viruses in the upper respiratory tract does not guarantee causation of pneumonia, nor precludes the presence of a bacterial pathogen. In both the upper and lower respiratory tract, respiratory viruses and pathogenic bacteria interact. Emerging evidence indicates that dual viral–bacterial infections function synergistically in many cases and together likely enhance the severity of CAP. Therefore, new and advanced technologies capable of sensitively and specifically discriminating viral, bacterial, and viral–bacterial coinfections are needed. Instead of focusing on the pathogen, analysis of host immune transcriptome profiles from children with CAP can potentially offer diagnostic signatures, help to assess disease severity, and eventually, prognostic indicators. An optimized management strategy by using molecular pathogen testing and transcriptome profiling will facilitate prompt, more appropriate, and targeted therapies, which in turn will lead to improved clinical outcomes in children with CAP.

scholarly journals Ciliates as bioindicators of environmental pressure in a karstic river 

2021 ◽  
Vol 4 ◽  
Author(s):  
Antonija Kulaš ◽  
Vesna Gulin ◽  
Renata Matoničkin Kepčija ◽  
Petar Žutinić ◽  
Mirela Sertić Perić ◽  
...  
Keyword(s):  
Alpha Diversity ◽  
Freshwater Ecosystems ◽  
Central Position ◽  
Rrna Gene ◽  
Molecular Approach ◽  
Indicator Organisms ◽  
Ecological Sensitivity ◽  
Clear Separation ◽  
Ciliate Community ◽  
Sampling Locations

Ciliates (protozoa) are a very large and diverse group of microeukaryotes that occupy a central position in the trophic web of freshwater ecosystems. Ciliates exhibit high ecological sensitivity and have tremendous bioindicator potential, but they are largely ignored in routine biomonitoring, mainly due to limitations in morphological diagnosis, which is both time-consuming and costly. In this study, we combined molecular (Illumina sequencing of the hypervariable V9 region of the SSU rRNA gene) and morphological approaches to get a detailed insight into the periphytic ciliate community structure and function within a karst, tufa-precipitating hydrosystem (National Park Krka, Croatia). Periphyton (biofilm) was sampled from light- and dark-exposed lithified tufa/stones at four representative locations within the Krka River, including upstream, midstream, and downstream river sections. We identified hydrological parameters and saprobiological classification of the sampling locations as the main structuring factors for ciliate communities. The molecular approach showed a clear separation of sampling locations in beta diversity analyses, as confirmed by PERMANOVA test. In contrast, alpha diversity was mostly affected by light exposition of the lithified tufa/stones, as confirmed by morphological approach. Environmental conditions consistently affected ciliate community composition at all locations, resulting in clear separation of periphyton samples. Our results indicate that ciliates should be considered as important bioindicators in monitoring tufa-forming rivers and streams, and the molecular approach (V9 region) proved to be applicable because as it efficiently captured the diversity of ciliates in periphyton. Validation of such an approach would lead to significant progress in extending monitoring to a broader range of indicator organisms than those now included in standard monitoring.

scholarly journals Antibiotic Susceptibility Profiling of Gram-Negative Bacteria Causing Upper Respiratory Tract Infections in Hyderabad, Sindh

2020 ◽  
Vol 1 (1) ◽  
pp. 12-15
Author(s):  
Ghulam Maka ◽  
Samreen Shah ◽  
Shaista Bano ◽  
Sarfraz Ali Tunio
Keyword(s):  
Respiratory Tract ◽  
Antibiotic Susceptibility ◽  
Respiratory Tract Infections ◽  
Pathogenic Bacteria ◽  
Diffusion Method ◽  
Upper Respiratory Tract ◽  
Isolation And Identification ◽  
Gram Negative ◽  
Upper Respiratory ◽  
Tract Infections

Respiratory tract infections (RTIs) are important clinical problems and among the commonest infectious diseases throughout the world. Several factors including gender, age and season have been shown to influence the prevalence rates of RTIs. The current study aimed to isolate and identify bacteria causing of upper respiratory tract (URT) infections and to determine the antibiotic susceptibility patterns of the isolated bacteria. A total of 201 sputum and swab samples were collected from patients from August 2015 to March 2016 and investigated for Gram-negative pathogenic bacteria. The antibiotic sensitivity of isolated bacteria was performed using Kirby Bauer Disc diffusion method. Isolation and identification of the bacteria were carried out using conventional methods including microscopic, cultural and biochemical testing. Out of 201 samples, 29.85% (n=60) yielded bacterial growth in which 20.9% (n=42) belonged to male while 8.96% (n=18) were from female patients. Among the isolates, Pseudomonas aeruginosa was the most frequent bacteria accounting 48.33% (n=29), followed by Klebsiella pneumoniae 45% (n=27) and E. coli 6.67% (n=04). The data of antibiotic susceptibility profiling demonstrated that Cefoperazone sulbactam, Meropenem, Piperacillin Tazobactam and Amikacin were highly effective against all isolated bacteria. However, Ampicillin, Cephradine, Ofloxacin and Co-trimoxazole were found the least effective antibiotics against all isolated bacteria. In summary, an increasing trend in the resistance against antibiotics which are more frequently prescribed, such as Cephradine, Ampicillin and Co-trimoxazole was observed. Therefore, a continuous surveillance of antibiotic resistance trends of pathogens is needed to ensure appropriate recommendations for the treatment of the URTIs.

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