Comparative Genomic Analysis of Streptococcus dysgalactiae subspecies dysgalactiae Isolated From Bovine Mastitis in China

Streptococcus dysgalactiae subsp. dysgalactiae (SDSD) is one of the most prevalent pathogens causing bovine mastitis worldwide. However, there is a lack of comprehensive information regarding genetic diversity, complete profiles of virulence factors (VFs), and antimicrobial resistance (AMR) genes for SDSD associated with bovine mastitis in China. In this study, a total of 674 milk samples, including samples from 509 clinical and 165 subclinical mastitis cases, were collected from 17 herds in 7 provinces in China from November 2016 to June 2019. All SDSD isolates were included in phylogenetic analysis based on 16S rRNA and multi-locus sequence typing (MLST). In addition, whole genome sequencing was performed on 12 representative SDSD isolates to screen for VFs and AMR genes and to define pan-, core and accessory genomes. The prevalence of SDSD from mastitis milk samples was 7.57% (51/674). According to phylogenetic analysis based on 16S rRNA, 51 SDSD isolates were divided into 4 clusters, whereas based on MLST, 51 SDSD isolates were identified as 11 sequence types, including 6 registered STs and 5 novel STs (ST521, ST523, ST526, ST527, ST529) that belonged to 2 distinct clonal complexes (CCs) and 4 singletons. Based on WGS information, 108 VFs genes in 12 isolates were determined in 11 categories. In addition, 23 AMR genes were identified in 11 categories. Pan-, core and accessory genomes were composed of 2,663, 1,633 and 699 genes, respectively. These results provided a comprehensive profiles of SDSD virulence and resistance genes as well as phylogenetic relationships among mastitis associated SDSD in North China.

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Mycoplasmal mastitis in dairy cows in the Moghan region of Ardabil State, Iran : short communication

Journal of the South African Veterinary Association ◽

10.4102/jsava.v77i4.382 ◽

2006 ◽

Vol 77 (4) ◽

Cited By ~ 5

Author(s):

C. Ghazaei

Keyword(s):

Dairy Cows ◽

Short Communication ◽

Bovine Mastitis ◽

Subclinical Mastitis ◽

Clinical Mastitis ◽

Mycoplasma Bovis ◽

Bulk Tank Milk ◽

Milk Samples ◽

The World ◽

Bulk Tank

Mycoplasmas are an important and economically significant cause of mastitis in dairy cows in various parts of the world. The organisms are highly contagious, with the main reservoir of infection originating from cows with subclinical mastitis. In 1998 the 1st cases of bovine mastitis due to Mycoplasma bovis were diagnosed in Ardabil State, Iran. An investigation was carried out with the aim of establishing the extent of mycoplasma infections in dairy cows in Ardabil State. Milk samples obtained from 80 cows with clinical mastitis were cultured in the laboratory for the presence of mycoplasmas. Similarly, 48 bulk-tank milk samples were examined for the presence of mycoplasmas. A modified Hayflick broth was used to isolate the mycoplasmas and an immunoperoxidase test used for the species identification of the isolates. Mycoplasma bovis was isolated from 39 (48.75 %) of the clinical mastitis samples and from 48 of the bulk-tank milk samples tested. This indicated that mycoplasma udder infections were more prevalent in dairy cows in Ardabil State than previously thought.

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Risk factors associated with the occurrence of multiresistant Staphylococcus spp. isolated from bovine subclinical mastitis in northern Brazil

Semina Ciências Agrárias ◽

10.5433/1679-0359.2022v43n2p901 ◽

2022 ◽

Vol 43 (2) ◽

pp. 901-910

Author(s):

Lilian Bernardina Ferreira ◽

◽

Larissa de Freitas Santiago Israel ◽

Renata Fernandes Rabello ◽

Guilherme Nunes de Souza ◽

...

Keyword(s):

Risk Factors ◽

Multidrug Resistance ◽

Phenotypic Expression ◽

Bovine Mastitis ◽

Subclinical Mastitis ◽

Isolation And Identification ◽

Phenotypic Profile ◽

Milk Samples ◽

California Mastitis Test ◽

Staphylococcus Spp

Staphylococcus bacteria are often associated with subclinical bovine mastitis. This study aimed to identify multiresistant Staphylococcus spp. associated with subclinical mastitis and the associated risk factors. Twenty-three dairy farms with a history of decrease in milk production, located in the lower Acre region, Brazil, were selected. An epidemiological questionnaire was provided in all farms. All animals were examined using the California Mastitis Test (CMT) and their milk samples were collected for bacterial culture. After isolation and identification, the disk diffusion antimicrobial susceptibility test was performed against nine classes of antimicrobials. Of the 339 cows examined using the CMT, 108 had mastitis. A total of 229 milk samples were collected from individual teats. MALDI-TOF MS found isolates belonging to eight species of Staphylococcus, in 101 of these samples. S. chromogenes (58.4%) demonstrated strongest resistance to the nine classes of antimicrobial active principles. Nineteen isolates with multidrug resistance phenotypic profile were identified. This phenotypic expression indicates wide circulation of resistant genes in this species. The presence of multidrug resistance in Staphylococcus spp. in this study was correlated with lack of water for cleaning the corral, which is a preventive factor, minimizing the transmission and persistence of pathogens in the farms.

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Asgard archaea are diverse, ubiquitous, and transcriptionally active microbes

10.1101/374165 ◽

2018 ◽

Cited By ~ 5

Author(s):

Mingwei Cai ◽

Yang Liu ◽

Zhichao Zhou ◽

Yuchun Yang ◽

Jie Pan ◽

...

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Genomic Analysis ◽

Phylogenetic Position ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Group D ◽

Origin Of Eukaryotes

AbstractAsgard is a newly proposed archaeal superphylum. Phylogenetic position of Asgard archaea and its relationships to the origin of eukaryotes is attracting increasingly research interest. However, in-depth knowledge of their diversity, distribution, and activity of Asgard archaea remains limited. Here, we used phylogenetic analysis to cluster the publicly available Asgard archaeal 16S rRNA gene sequences into 13 subgroups, including five previously unknown subgroups. These lineages were widely distributed in anaerobic environments, with the majority of 16S rRNA gene sequences (92%) originating from sediment habitats. Co-occurrence analysis revealed potential relationships between Asgard, Bathyarchaeota, and Marine Benthic Group D archaea. Genomic analysis suggested that Asgard archaea are potentially mixotrophic microbes with divergent metabolic capabilities. Importantly, metatranscriptomics confirmed the versatile lifestyles of Lokiarchaeota and Thorarchaeota, which can fix CO2using the tetrahydromethanopterin Wood-Ljungdahl pathway, perform acetogenesis, and degrade organic matters. Overall, this study broadens the understandings of Asgard archaea ecology, and also provides the first evidence to support a transcriptionally active mixotrophic lifestyle of Asgard archaea, shedding light on the potential roles of these microorganisms in the global biogeochemical cycling.

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Prevalence, Etiology, and Risk Factors of Mastitis in Dairy Cattle in Embu and Kajiado Counties, Kenya

Veterinary Medicine International ◽

10.1155/2020/8831172 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12

Author(s):

Christine M. Mbindyo ◽

George C. Gitao ◽

Charles M. Mulei

Keyword(s):

Management Practices ◽

Health Hazard ◽

Previous History ◽

Bovine Mastitis ◽

Subclinical Mastitis ◽

Control Measures ◽

Economic Losses ◽

Isolation And Identification ◽

Cross Sectional ◽

Milk Samples

Bovine mastitis continues to be a leading cause of heavy economic losses in the dairy industry and a public health hazard globally. This cross-sectional study investigated the prevalence, etiologies of clinical and subclinical mastitis, and associated predisposing factors in Embu and Kajiado counties in Kenya. A semistructured questionnaire was administered to 154 smallholder dairy farmers to collect data on management practices, animal factors, and disease history. A total of 395 dairy cows were initially screened for subclinical mastitis using the California mastitis test (CMT), and milk samples were aseptically collected. Both CMT positive and CMT negative samples were analyzed using conventional bacteriological isolation and identification procedures. In the present study, the overall prevalence of mastitis based on CMT and clinical examination was 80% (316/395), out of which 6.8% (27/395) was clinical mastitis, while 73.1% (289/395) was subclinical mastitis. Based on culture, the overall prevalence of clinical and subclinical mastitis was 51.6% (815/1580), 74.4% (294/395), and 76.6% (118/154) at the quarter, cow, and farm level, respectively. From the 1574 milk samples analyzed by cultured, 1016 bacteria were yielded. The predominant bacteria were coagulase-negative Staphylococcus (CNS), 42.8% (435/1016), and in decreasing order, Streptococcus species, 22.2% (226/1016), Staphylococcus aureus, 15.7% (160/1016), and Pseudomonas aeruginosa, 5.1% (52/1016), and the least was Enterobacter species, 0.7% (7/1016), while 23.7% of the sample yielded no bacterial growth. Risk factor analysis revealed that milking mastitic cows last (p=0.002), using a clean udder drying towel for each cow (p=0.033) and previous history of mastitis (p=0.046) were significantly associated with presence of mastitis. The current study has shown a relatively high prevalence of subclinical mastitis with CNS as predominant bacteria. Therefore, control measures are urgently warranted. Management factors such as milking mastitic cows last, using a clean towel for udder drying for each cow, and culling mastitic cows should be considered and included in the Kenyan mastitis control programs.

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Using milk leukocyte differentials for diagnosis of subclinical bovine mastitis

Journal of Dairy Research ◽

10.1017/s0022029917000267 ◽

2017 ◽

Vol 84 (3) ◽

pp. 309-317 ◽

Cited By ~ 10

Author(s):

Juliano Leonel Gonçalves ◽

Roberta L. Lyman ◽

Mitchell Hockett ◽

Rudy Rodriguez ◽

Marcos Veiga dos Santos ◽

...

Keyword(s):

Bovine Mastitis ◽

Dairy Herd ◽

Inflammatory Cells ◽

Subclinical Mastitis ◽

Absolute Number ◽

Dairy Herds ◽

Milk Samples ◽

Lactating Cows ◽

Automated Instrument ◽

Culture Positive

This research study aimed to evaluate the use of the milk leukocyte differential (MLD) to: (a) identify quarter milks that are culture-positive; and (b) characterize the milk leukocyte responses to specific groups of pathogens causing subclinical mastitis. The MLD measures the absolute number and relative percentage of inflammatory cells in milk samples. Using the MLD in two dairy herds (170 and 172 lactating cows, respectively), we studied all lactating cows with a most recent monthly Dairy Herd Improvement Association somatic cell count (SCC) >200 × 103 cells/ml. Quarter milk samples from 78 cows meeting study criteria were analysed by MLD and aseptically collected milk samples were subjected to microbiological culture (MC). Based upon automated instrument evaluation of the number and percentage of inflammatory cells in milk, samples were designated as either MLD-positive or – negative for subclinicial mastitis. Positive MC were obtained from 102/156 (65·4%) of MLD-positive milk samples, and 28/135 (20·7%) of MLD-negative milk samples were MC-positive. When MC was considered the gold standard for mastitis diagnosis, the calculated diagnostic Se of the MLD was 65·4% (IC95% = 57·4 to 72·8%) and the Sp was 79·3% (IC95% = 71·4 to 85·7%). Quarter milks positive on MC had higher absolute numbers of neutrophils, lymphocytes and macrophages, with higher neutrophils% and lymphocytes% but lower macrophages%. The Log10 (N/L) ratios were the most useful ratio to differentiate specific subclinical mastitis quarters from healthy quarters. Use of the MLD on cows with monthly composite SCC > 200 × 103 cells/ml for screening at quarter level identified quarters more likely to be culture-positive.In conclusion, the MLD can provide an analysis of mammary quarter status more detailed than provided by SCC alone; however, the MLD response to subclinical mastitis was not found useful to specifically identify the causative pathogen.

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Clinical and subclinical bovine mastitis in area of Kilkis

Journal of the Hellenic Veterinary Medical Society ◽

10.12681/jhvms.15791 ◽

2018 ◽

Vol 48 (1) ◽

pp. 32 ◽

Cited By ~ 1

Author(s):

N. ILIADIS (Ν. ΗΛΙΑΔΗΣ) ◽

E. N. PETRIDOU (Ε.N.ΠΕΤΡΙΔΟΥ) ◽

A. FOUKOS (Α. ΦΟΥΚΟΣ)

Keyword(s):

Bovine Mastitis ◽

Subclinical Mastitis ◽

Sensitivity Test ◽

Coagulase Negative Staphylococci ◽

Milk Samples ◽

Microbiological Examination

In this study 216 milk samples from equal number of quarters were examined. The results from microbiological examination and the performed California test revealed that 82 samples (38%) were collected from quartres with subclinical mastitis. Coagulase-negative staphylococci were the most frequent pathogens isolated from the examined milk samples, representing 47.5% of the total isolated strains. Sensitivity test of the strains to certain antimicrobials showed higher performance of gentamycine (90.9% of the cases). On a descending sequence cephalotin (75%), oxalinique acid (63.6%) and ampicilline (54.2%) were the antimicrobials to which sensitivity of the strains was higher than 50%. On the contrary, tetracycline, tincomycine, erythromycine and penicilline G performance was lower than 50%.

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Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

10.21203/rs.2.21773/v1 ◽

2020 ◽

Author(s):

Benwen Liu ◽

Yu Xin Hu ◽

Zheng Yu Hu ◽

Guo Xiang Liu ◽

Huan Zhu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Genomic Analysis ◽

Comparative Genomic ◽

Rdna Sequences ◽

Chloroplast Genomes ◽

Basal Clade

Abstract Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

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Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

10.21203/rs.2.20588/v4 ◽

2020 ◽

Author(s):

Eiseul Kim ◽

Seung-Min Yang ◽

Bora Lim ◽

Si Hong Park ◽

Bryna Rackerby ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Genomic Analysis ◽

23S Rrna ◽

Lactobacillus Species ◽

Comparative Genomic ◽

Rrna Gene ◽

Gene Sequences ◽

23S Rrna Gene ◽

Species Specific

Abstract Background Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the simultaneous identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods. Results To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label. Conclusions The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus , and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.

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Comparative Genomic Analysis and Phenotypic Characterization of Bronchoscope-Associated Klebsiella aerogenes

Polish Journal of Microbiology ◽

10.33073/pjm-2021-038 ◽

2021 ◽

Vol 70 (3) ◽

pp. 409-412

Author(s):

FANG HUANG ◽

SHUANG LI ◽

LAN LOU ◽

JUNJUN MO ◽

HAO XU

Keyword(s):

Antimicrobial Agents ◽

Genomic Analysis ◽

Phenotypic Characterization ◽

Comparative Genomic ◽

Klebsiella Aerogenes ◽

Clinical Procedures ◽

First Time ◽

Sequence Types ◽

Level Resistance

Bronchoscopes have been linked to outbreaks of nosocomial infections. The phenotypic and genomic profiles of bronchoscope-associated Klebsiella aerogenes isolates are largely unknown. In this work, a total of 358 isolates and 13 isolates were recovered from samples after clinical procedures and samples after decontamination procedures, respectively, over the five months. Antimicrobial susceptibility testing found seven K. aerogenes isolates exhibiting a low-level resistance to antimicrobial agents. Among seven K. aerogenes isolates, we found five sequence types (STs) clustered into three main clades. Collectively, this study described for the first time the phenotypic and genomic characteristics of bronchoscope-associated K. aerogenes.

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