Structural characteristics of lower respiratory tract microflora in patients with pneumoconiosis / 中华劳动卫生职业病杂志

Objective: To explore the composition of bacteria in lower respiratory tract of patients with pneumoconiosis and dust exposure, and to compare and analyze the difference and correlation between them. Methods: From May 2020 to January 2021, a prospective multicenter cross-sectional study was conducted to select patients with pneumoconiosis who underwent bronchoalveolar lavage treatment at the Respiratory and Critical Care Medical Department of the 920th Hospital of the Joint Support Force and the Respiratory Department of Tongren Hospital in Kunming, as well as the population of dust recipients. A total of 24 patients with pneumoconiosis (pneumoconiosis group) were included, and 16 dust exposed individuals (dust exposed group) were used as controls. Two groups of patients' alveolar lavage fluid were collected. The 16SrRNA gene V3-V4 sequencing technology and bioinformatics analysis platform were used to measure and analyze the differences in microbial structure composition and associations between bacterial communities. Results: Compared with the dust exposed group, the top 5 bacterial phyla in the alveolar lavage fluid level of patients with pneumoconiosis were the same, followed by Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria. Compared with the dust exposure group, the pneumoconiosis group patients belong to the top 5 genera of horizontal flora abundance, which are different. The dust exposure group is respectively: Pseudomonas, Proctor, Streptococcus, Achromobacter, and Neisseria. The pneumoconiosis group is respectively: Pseudomonas, Achromobacter, Streptococcus, Ralstonia, and Proctor. The Alpha diversity analysis results showed that compared with the dust exposed group, the level of bacterial diversity in the pneumoconiosis group was difference (P<0.05), and there was no statistically significant difference in bacterial evenness (P>0.05) ; Beta diversity showed differences in microbial community structure between the two groups (P<0.05 ). Single factor microbial association network analysis showed that there was a high correlation between Firmicutes and Bacteroidetes in the pneumoconiosis and dust exposed groups and other species, showing a positive correlation; The correlation between Proteobacteria and other species is high, showing a negative correlation. Conclusion: The structure and relative abundance of bacteria in lower respiratory tract were different between patients with pneumoconiosis and dust exposure, and the diversity of bacteria in lower respiratory tract increased in patients with pneumoconiosis, which may be related to disease status.

Toxinotyping of Clostridium perfringens in Poultry from Necrotic Enteritis Cases

Clostridium perfringens is well known causative agent of necrotic enteritis in poultry and is mainly caused by Type A toxin. NetB toxin is found to be one of the newly emerging virulent toxin gene which is also responsible for necrotic enteritis. The present study was carried out to characterize and to type the different toxins associated with C. perfringens in NE cases of poultry. For the present study total 125 samples were collected from poultry birds, out of which 50 samples were of intestinal content from diseased birds, 50 cloacal swabs and 25 intestinal content from healthy birds. These samples were further processed for isolation, identification, and toxinotyping of Clostridium perfringens isolates. Onisolation of C. perfringens on blood agar total 43 isolates were found positive showing a pattern of double hemolysis on blood agar. The positive isolates of C. perfringens were further confirmed by using 16S rRNA species specific PCR. After confirmation isolates were processed for toxinotyping mainly targeting cpa, cpb and cpb2 toxins by using multiplex PCR. On toxinotyping it was found that NE in poultry birds were mainly caused by C. perfringens type A. On virulent gene detection of netB toxin, total 4 isolates were found positive for netB toxin. This study pointed out that C. perfringens type A is responsible for development of NE in poultry along with net B toxin which is a new key virulent factor. Further studies of netB toxoid and C. perfringens type A for vaccine production could minimize the clostridial problems in broiler farms

In Vitro Antibacterial Activities Of Marine Sponge-Associated Bacteria Against Pathogenic Vibrio Spp. Causes Vibriosis In Shrimps

Objective: This study was aimed to isolate and screen marine sponge-associated bacteria producing anti-Vibrio compounds and to identify their compounds from the bacterial extract. Methods: Sponge-associated bacteria were isolated by spread plate method. Their anti-Vibrio activity against Vibrio parahaemolyticus, V. harveyi, and V. vulnificus was determined by dual culture test. Three potential isolates were identified based on 16S-rRNA gene analysis. All isolates producing anti-Vibrio compounds was tested for their haemolytic characters in blood agar medium. Anti-Vibrio activity of the most potential isolate was also tested by using its supernatant, extract, and concentrated culture. Chemical composition of crude extract derived from that isolate was identified by GC-MS analysis. Results: 68 bacterial isolates have been isolated from the marine sponge, Spongia sp., Svenzea sp., Ircinia sp., and Igernella sp. Of 68 isolates, 15 (22%) isolates had anti-Vibrio activities in various spectra against three Vibrio species, including V. harveyi, V. parahaemolyticus, and V. vulnificus. All isolates producing anti-Vibrio compounds were non-haemolytic. Bacterial isolates coded as D6.6, D6.19, and P4.17 have broad spectra. They could inhibit at least two Vibrio species as indicated by the clear zone formed around bacterial colonies. Based on 16S-rRNA, these isolates were closely related (similarity ≥ 99%) to Brevibacterium casei strain M Sw oHS, Bacillus altitudinis strain FJAT 47750, and Bacillus altitudinis strain PgBe190, respectively. D6.6 isolate was the most potential isolate, which could inhibit three Vibrio species. Consistently, its anti-Vibrio activity also confirmed by their supernatant, concentrated culture, and crude extract of that isolate. The crude extract derived from this isolate contained 10 major compounds that are biologically active. Conclusion: This study suggests that 15 bacteria strains isolated from marine sponges were potentially could inhibit Vibrio’s growth in vitro. These isolate could be further explored as anti-Vibrio agent.

Pulmonary Mycobacterium kyorinense disease: A case report and review of literature

We report here the first case of pulmonary infection due to Mycobacterium kyorinense in a 55-year-old hypertensive woman treated for pulmonary tuberculosis earlier on two occasions. She presented with productive cough, intermittent episode of left-sided chest pain, loss of appetite, low-grade fever, and breathlessness. Sputum cultures revealed non-tuberculous mycobacteria (NTM). She remained persistently symptomatic with sputum cultures positive for acid-fast bacilli even after 6 months of treatment. Hence, a 16SrRNA gene amplification and sequencing were done that revealed M. kyorinense. Based on the guidelines of the American Thoracic Society, she was started on weight-based dosing of clarithromycin, levofloxacin, ethambutol, isoniazid and injection amikacin daily. The patient improved symptomatically and became culture-negative after 3 months of therapy with the above regimen and continued to be culture negative for 12 months of treatment. She continues to remain symptom-free without evidence of any clinical or bacteriological relapse.

Phylogenic Characteristics of a Unique Antagonistic Micromonospora Sp. Rc5 to S. aureus Isolated from Sinai Desert of Egypt

A distinct strain named Micromonospora sp. Rc5 was isolated from Sinai desert of Egypt and recorded high antagonistic activities against some food and bloodborne pathogens. Morphological and chemotaxonomy characterization confirmed that this isolate belongs to genus Micromonospora. Sequencing of partial 16S rDNA and BLASTN showed that isolate Rc5 is identical to Micromonospora haikouensis (99%) but with low bootstrap value in NJ phylogenetic tree. Comprehensive optimization of several growth factors was performed including initial pH, incubation periods, and different sources of carbon and nitrogen. The highest yield of antimicrobial agent production was obtained after 8 days of incubation at 30°C, pH 6.0, 3 x 105CFU/ml in soya bean meal broth media with agitation of 150 rpm. A dramatic proportional decrease occurred with 0.3, 0.6, 0.9 µg active fraction /ml against Staphylococcus aureus culture and reached to complete inhibition at a minimum inhibitory concentration of (1.5 µg /ml). The physicochemical characterization of the purified fraction was identified as phthalate derivative. Our results indicated that Rc5 generated potential antimicrobial compounds against foodborne pathogens and   may combat resistant strains of Staphylococcus aureus.

First phylogenetic analysis of Ehrlichia canis in dogs and ticks from Mexico. Preliminary study / Primer análisis filogenético de Ehrlichia canis en perros y garrapatas de México. Estudio preliminar

ABSTRACT Objective. Phylogenetic characterization of Ehrlichia canis in dogs naturally infected and ticks, diagnosed by PCR and sequencing of 16SrRNA gene; compare different isolates found in American countries. Materials and methods. Were collected Blood samples from 139 dogs with suggestive clinical manifestations of this disease and they were infested with ticks; part of 16SrRNA gene was sequenced and aligned, with 17 sequences reported in American countries. Two phylogenetic trees were constructed using the Maximum likelihood method, and Maximum parsimony. Results. They were positive to E. canis 25/139 (18.0%) dogs and 29/139 (20.9%) ticks. The clinical manifestations presented were fever, fatigue, depression and vomiting. Rhipicephalus sanguineus Dermacentor variabilis and Haemaphysalis leporis-palustris ticks were positive for E. canis. Phylogenetic analysis showed that the sequences of dogs and ticks in Mexico form a third group diverging of sequences from South America and USA. Conclusions. This is the first phylogenetic analysis of E. canis in Mexico. There are differences in the sequences of Mexico with those reported in South America and USA. This research lays the foundation for further study of genetic variability.

RESUMEN Objetivos. Caracterizar filogenéticamente Ehrlichia canis a partir de perros naturalmente infectados y sus garrapatas, mediante PCR y secuenciación del gene 16SrRNA para compararlos con diferentes aislados encontrados en el continente Americano. Material y métodos. Se colectaron muestras sanguíneas de 139 perros con manifestaciones clínicas sugestivas a Ehrlichiosis, y que estuvieran infestados con garrapatas; una parte del gene 16SrRNA, fue secuenciada y alineada junto con las 17 secuencias reportadas en los países de América. Se construyeron dos árboles filogenéticos utilizando el método de Máxima verosimilitud compuesta, y Máxima parsimonia. Resultados. Fueron positivos a E. canis 25/139 (18.0%) perros y 29/139 (20.9%) garrapatas colectadas sobre los perros. Las manifestaciones clínicas presentadas fueron fiebre, astenia, depresión y vómito. Las garrapatas Rhipicephalus sanguineus, Dermacentor variabilis y Haemaphysalis leporis-palustris fueron positivas para E. canis. El análisis filogenético mostró que las secuencias 16SrRNA de Ehrlichia canis aisladas de perros y garrapatas en este estudio forman un tercer grupo que diverge de las secuencias de Sudamérica y EUA. Conclusiones. Es el primer análisis filogenético de E. canis en México. Hay diferencias entre las secuencias de este estudio, con las reportadas en otros países de Sudamérica y en EUA. Esta investigación sienta las bases para profundizar en el estudio de la variabilidad genética.

Acute myonecrosis in horse caused by Clostridium novyi type A

The objective of this study was to describe the first report involving a case of equine acute myonecrosis caused by C. novyi type A with an emphasis on clinical signs, the pathological and bacteriological analysis, and molecular identification of the microorganisms as the key of the definitive diagnosis.

Universal primer V3 coupled with multiplex PCR for the pathogen detection of infective endocarditis / 中国小儿急救医学

Objective To investigate the pathogen of 21 infective endocarditis (IE) cases treated with operation in Shanghai Children's Medical Center from 2007 to 2010.Methods Blood culture,vegetation culture and vegetation PCR assay(target gene to the conserved region V3 in 16SrRNA gene) were detected in 21 IE patients; multiplex PCR amplification of staphylococci for methicillin-resistant staphylococcus was performed.Results Of 21 IE cases,20 cases were detected positive by vegetation PCR with the detection rate of 95.2％,12 IE cases were detected positive by blood culture with the detection rate of 57.1％,2 IE cases were detected positive by vegetation culture with the detection rate of 9.5％.The difference of the positive rates of the three methods was statistically significant (P ＜ 0.0001).The vegetation PCR of one case was actinobacillus actinomycetemcomitans,while the blood culture was haemolysis pasteurell which was inconsistent with the vegetation PCR result.Howerver,the PCR result of colony obtained by blood culture was consistent with vegetation PCR that was confirmed as actinobacillus actinomycetemcomitans.The endocardium PCR results of 11 IE cases were consistent with the results of blood culture.MecA gene was detected by multiplex PCR,which could identify methicillin-resistant staphylococcus quickly,sensitively and accurately and could also effectively identify methicillin resistant staphylococcus aureus,when coupled with femA gene detection,thus glycopeptides antibiotic could be prescribed promptly.All the 21 patients recovered and discharged without infection recurrence in the follow-up.Conclusion Universal primer V3 coupled with multiplex PCR can improve vegetation pathogen detection rate of IE patients and is minimally influenced by antibiotic therapy.Multiplex PCR can be applied for etiological diagnosis of IE patients with indication of surgery and negative blood culture or difficult diagnosis,contributing to post-surgery antibiotics selection and improvement of recovery rate of IE patients.

Simultaneous detection of Legionella species and Legionella pneumophila by duplex PCR (dPCR) assay in cooling tower water samples from Jakarta, Indonesia.

Aim: Since culture method is time-consuming and has low sensitivity, we developed a duplex PCR (dPCR) assay for the detection of Legionella sp. and L. pneumophila in cooling tower samples. We used culture method as a gold standard. Methods: Optimization of dPCR method was performed to obtain an assay with high sensitivity and specifi city. The optimized method was used to detect Legionella sp. dan L. pneumophila in 9 samples obtained from 9 buildings in Jakarta. For culture method, the bacteria were grown or isolated on selective growth factor supplemented-buffered charcoal yeast extract (BCYE) media. Results: Of 9 samples tested by dPCR assay, 6 were positive for Legionella species,1 was positive for L. pneumophila, and 2 showed negative results. For the same samples, no Legionella sp. was detected by the culture method. Conclusion: dPCR assay was much more sensitive than the culture method and was potentially used as a rapid, specifi c and sensitive test for routine detection of Legionella sp. dan for L. pneumophila in water samples.

Cavitary pneumonia caused by nocardia otitidiscaviarum

We report a case of cavitary pneumonia caused by N. otitidiscaviarum in a man with diabetes mellitus and thrombocytopenia treated with systemic corticosteroid. Taxonomic identification involved phenotypic testing and molecular identification that was carried out by DNA sequencing of the 16SrRNA gene.

A Case of Bacteremia Caused by Arthrobacter woluwensis / 대한임상미생물학회지

Arthrobacter spp. are coryneform bacteria known as a soil flora and also part of normal flora of human. Since coryneform bacteria are often reported to be a cause of life-threatening diseases, and especially the human infections of Arthrobacter spp. are reported recently, it is important to identify them to the genus and species levels by additional studies including molecular tests. We report a case of bacteremia caused by Arthrobacter woluwensis, which was misidentified initially as Leifsonia aquatica by commercial kits and conventional tests, but correctly identified by 16S rRNA sequencing.