Jamie Harrison, Rana Muhammad Fraz Hussain, Shannon F Greer, Vardis Ntoukakis, Andrew Aspin, Joana G Vicente, Murray Grant, David J Studholme
{"title":"Draft genome sequences for ten strains of <i>Xanthomonas</i> species that have phylogenomic importance.","authors":"Jamie Harrison, Rana Muhammad Fraz Hussain, Shannon F Greer, Vardis Ntoukakis, Andrew Aspin, Joana G Vicente, Murray Grant, David J Studholme","doi":"10.1099/acmi.0.000532.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000532.v3","url":null,"abstract":"<p><p>Here we report draft-quality genome sequences for pathotype strains of eight plant-pathogenic bacterial pathovars: <i>Xanthomonas campestris</i> pv. <i>asclepiadis</i>, <i>X. campestris</i> pv. <i>cannae</i>, <i>X. campestris</i> pv. <i>esculenti</i>, <i>X. campestris</i> pv. <i>nigromaculans</i>, <i>X. campestris</i> pv. <i>parthenii</i>, <i>X. campestris</i> pv. <i>phormiicola</i>, <i>X. campestris</i> pv. <i>zinniae</i> and <i>X. dyei</i> pv. <i>eucalypti</i> (= <i>X. campestris</i> pv. <i>eucalypti</i>). We also sequenced the type strain of species <i>X. melonis</i> and the unclassified <i>Xanthomonas</i> strain NCPPB 1067. These data will be useful for phylogenomic and taxonomic studies, filling some important gaps in sequence coverage of <i>Xanthomonas</i> phylogenetic diversity. We include representatives of previously under-sequenced pathovars and species-level clades. Furthermore, these genome sequences may be useful in elucidating the molecular basis for important phenotypes, such as biosynthesis of coronatine-related toxins and degradation of fungal toxin cercosporin.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10424806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"BactoBattle: a game-based learning companion for medical bacteriology.","authors":"Korakrit Imwattana, Areeya Methawirune, Isara Voralakkulchai, Popchai Ngamskulrungroj","doi":"10.1099/acmi.0.000608.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000608.v3","url":null,"abstract":"<p><p>A card game called BactoBattle has been developed to help medical students who have just started learning medical bacteriology to improve their learning efficacy and satisfaction, especially on the topic of antimicrobial resistance. Copies of the game were placed in the students' study room (approximately 1 set per 12 students) and made available to the students throughout the study period so that they could choose to play the game during their free time if desired. After the study period had ended, the students were asked to complete a questionnaire and a post-test. In total, 33 students completed the questionnaire, and were split into 2 groups: the player group, comprising 12 (36.4 %) students who had played the game, and the non-player group. The player group perceived that they could memorize more knowledge compared to the non-player group and indeed recorded higher post-test scores than the non-player group (10.4 vs 8.3 out of 15 points, <i>P</i>=0.031). However, there was no difference in learning motivation (<i>P</i>=0.441) or enjoyment (<i>P</i>=0.562) between the two groups. A majority of the players said they would continue playing the game after the study period and would recommend the game to other students. In short, the BactoBattle game can be a useful tool to improve the learning efficacy of students, but its effect on learning satisfaction remains unclear.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9799122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zeeshan Mustafa, Haris Manzoor Khan, Mohd Azam, Hiba Sami, Syed Ghazanfar Ali, Islam Ahmad, Adil Raza, Mohammad Azam Khan
{"title":"Insight into the seroepidemiology and dynamics of circulating serotypes of dengue virus over a 4 year period in western Uttar Pradesh, India.","authors":"Zeeshan Mustafa, Haris Manzoor Khan, Mohd Azam, Hiba Sami, Syed Ghazanfar Ali, Islam Ahmad, Adil Raza, Mohammad Azam Khan","doi":"10.1099/acmi.0.000567.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000567.v4","url":null,"abstract":"<p><p>An important public health problem in India is dengue infection, with every year seeing an increase in cases of dengue fever. Dengue affects all individuals irrespective of their gender and age, although the infection rate is higher among males and younger people. Despite low severity in general, dengue virus can cause severe health conditions in some individuals. Genetic characterization of circulating endemic dengue virus (DENV) serotypes plays a significant role in providing epidemiological knowledge and subsequent vaccine development. In the present study, over a 4 year period, we assessed DENV transmission dynamics in major regions of western Uttar Pradesh in North India. ELISA tests were used to diagnose dengue, and PCRs were used to determine the circulating serotype. We found that dengue infection peaks after the rainy season and affects all sexes and ages. A total of 1277 individuals were found positive for dengue; among them, 61.7 % were male and 38.3 % were female. DEN-1 was found in 23.12 %, DEN-2 in 45 %, DEN-3 in 29.06 % and DEN-4 in 1.5 % of the dengue-infected individuals. All four DENV serotypes were circulating in the study area, and DENV serotype-2 (DEN-2) was the most prevalent serotype.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9809091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Application of a sepsis flow chip (SFC) assay for the molecular diagnosis of paediatric sepsis.","authors":"Dimas Seto Prasetyo, Mulya Rahma Karyanti, Irene Yuniar, Yulia Rosa Saharman, Livya Holiwono","doi":"10.1099/acmi.0.000474.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000474.v4","url":null,"abstract":"<p><p>A delay in detecting sepsis pathogens is a problematic issue for determining definitive antibiotic therapy for the causative pathogens. The gold standard method for sepsis is blood culture but this requires 3 days to detect the definitive pathogen. Molecular methods offer rapid identification of pathogens. We evaluated the use of sepsis flow chip (SFC) assay for identifying pathogens from children with sepsis. Blood samples from children with sepsis were collected and incubated in a culture device. Positive samples were subjected to amplification-hybridization using SFC assay and culture. A total of 94 samples from 47 patients were recovered, from which 25 isolates were recovered, including <i>Klebsiella pneumoniae</i> (11) and <i>Staphylococcus epidermidis</i> (6). From 25 positive blood culture bottles subjected to SFC assay, 24 genus/species and 18 resistance genes were detected. The sensitivity, specificity and conformity was 80, 94.2 and 94.68 % respectively. SFC assay offers promise to identify pathogens from positive blood culture in paediatric patients with sepsis and may support the antimicrobial stewardship programme in hospitals.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10202402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Acquiring bifidobacteria species from formula-fed and breast-fed newborns: identifying, quantifying and creating an antibiogram.","authors":"Rajagopal Kammara, Anagha Nellikka","doi":"10.1099/acmi.0.000590.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000590.v3","url":null,"abstract":"<p><p>After examining the <i>Bifidobacterium</i> spp. population in faeces samples from breast-fed and formula-fed infants, an antibiogram was created. The prevalence of <i>Bifidobacterium</i> spp. in faeces was determined using common bacterial growth media, including Man Rogos Sharpe (MRS), Brain Heart Infusion (BHI), Luria Bertani (LB) broth and Bifidobacteria agar. According to the findings, formula-fed babies had a low population of <i>Bifidobacterium</i> spp. in their stools while breast-fed babies had a high population. By using phylogenetic analysis of the 16S rRNA and <i>xfp</i> (xylose/fructose 6-phosphate phosphoketolase) genes, and RFLP mapping of <i>Bifidobacterium</i> isolates, it was possible to identify a new and unique <i>Bifidobacterium</i> species. The intensity of the reddish brown colour produced during the F6PPK (fructose 6-phosphate phosphoketolase) assay is an accurate indicator of the proportion of various bifidobacteria present. Bifidobacteria agar media produced the greatest amounts of bifidobacteria diversity and recovery. Small (SCV) and Big colony variations (BCV) were formed during growth on different media. The various antibiotic MIC values changed depending on the use of different media, growth circumstances, bile salt treatment and low pH. The findings of this study demonstrate that test conditions also impact the diversity of microbiological conditions that distinguish between resistant and susceptible bacteria.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10484311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10569874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Case Report: <i>Kingella kingae</i> causing prosthetic joint infection in an adult.","authors":"Katherine Wensley, Damian McClelland, Natalie Grocott, Gopikanthan Manoharan, Seema Desai","doi":"10.1099/acmi.0.000559.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000559.v3","url":null,"abstract":"<p><strong>Introduction: </strong><i>Kingella kingae</i> is a Gram-negative micro-organism that is rarely isolated as a pathogen in the adult population. Although widely reported to affect prosthetic heart valves, there have been no previously reported cases of <i>K. kingae</i> infecting prosthetic joints in adults.</p><p><strong>Case presentation: </strong>A 61-year-old patient with a history of rheumatoid arthritis presented with insidious onset of pain and swelling in her right shoulder, which had progressed to a discharging sinus. The patient had undergone a total shoulder replacement 11 years previously and had not developed any prior post-operative infections. She had been taking anti-TNF medication for 5 years prior to review for her rheumatoid disease. The patient underwent a two-stage revision replacement procedure, including implant removal, sinus excision and debridement. Deep tissue samples grew <i>K. kingae</i> post-operatively. The patient was commenced on intravenous ceftriaxone for 14 days, followed by a further 28 days of oral ciprofloxacin. A second-stage custom shoulder replacement was undertaken 10 months following the first stage and the patient made a good functional recovery.</p><p><strong>Conclusion: </strong>The authors suggest that clinicians should be attuned to <i>K. kingae</i> as a potential pathogen for prosthetic joint infection, particularly in patients who are immunosuppressed. Two-stage revision procedures can ensure a favourable outcome and eradication of this pathogen from the joint. Beta lactams remain the principal antibiotic of choice.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10484313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10219985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shivanand Hegde, Hallie E Rauch, Grant L Hughes, Nikki Shariat
{"title":"Identification and characterization of two CRISPR/Cas systems associated with the mosquito microbiome.","authors":"Shivanand Hegde, Hallie E Rauch, Grant L Hughes, Nikki Shariat","doi":"10.1099/acmi.0.000599.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000599.v4","url":null,"abstract":"<p><p>The microbiome profoundly influences many traits in medically relevant vectors such as mosquitoes, and a greater functional understanding of host-microbe interactions may be exploited for novel microbial-based approaches to control mosquito-borne disease. Here, we characterized two novel clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems in <i>Serratia</i> sp. Ag1, which was isolated from the gut of an <i>Anopheles gambiae</i> mosquito. Two distinct CRISPR/Cas systems were identified in <i>Serratia</i> Ag1, CRISPR1 and CRISPR2. Based on <i>cas</i> gene composition, CRISPR1 is classified as a type I-E CRISPR/Cas system and has a single array, CRISPR1. CRISPR2 is a type I-F system with two arrays, CRISPR2.1 and CRISPR2.2. RT-PCR analyses show that all <i>cas</i> genes from both systems are expressed during logarithmic growth in culture media. The direct repeat sequences of CRISPRs 2.1 and 2.2 are identical and found in the arrays of other <i>Serratia</i> spp., including <i>S. marcescens</i> and <i>S. fonticola</i> , whereas CRISPR1 is not. We searched for potential spacer targets and revealed an interesting difference between the two systems: only 9 % of CRISPR1 (type I-E) targets are in phage sequences and 91 % are in plasmid sequences. Conversely, ~66 % of CRISPR2 (type I-F) targets are found within phage genomes. Our results highlight the presence of CRISPR loci in gut-associated bacteria of mosquitoes and indicate interplay between symbionts and invasive mobile genetic elements over evolutionary time.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10484321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10587653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sophie L Nixon, Alvaro M Plominsky, Natali Hernandez-Becerra, Christopher Boothman, Douglas H Bartlett
{"title":"Microbial communities in freshwater used for hydraulic fracturing are unable to withstand the high temperatures and pressures characteristic of fractured shales.","authors":"Sophie L Nixon, Alvaro M Plominsky, Natali Hernandez-Becerra, Christopher Boothman, Douglas H Bartlett","doi":"10.1099/acmi.0.000515.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000515.v3","url":null,"abstract":"<p><p>Natural gas is recovered from shale formations by hydraulic fracturing, a process known to create microbial ecosystems in the deep subsurface. Microbial communities that emerge in fractured shales include organisms known to degrade fracturing fluid additives and contribute to corrosion of well infrastructure. In order to limit these negative microbial processes, it is essential to constrain the source of the responsible micro-organisms. Previous studies have identified a number of potential sources, including fracturing fluids and drilling muds, yet these sources remain largely untested. Here, we apply high-pressure experimental approaches to assess whether the microbial community in synthetic fracturing fluid made from freshwater reservoir water can withstand the temperature and pressure conditions of hydraulic fracturing and the fractured shale environment. Using cell enumerations, DNA extraction and culturing, we show that the community can withstand high pressure or high temperature alone, but the combination of both is fatal. These results suggest that initial freshwater-based fracturing fluids are an unlikely source of micro-organisms in fractured shales. These findings indicate that potentially problematic lineages, such as sulfidogenic strains of <i>Halanaerobium</i> that have been found to dominate fractured shale microbial communities, likely derive from other input sources into the downwell environment, such as drilling muds.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10202394/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christian Heryakusuma, Eric F Johnson, Endang Purwantini, Biswarup Mukhopadhyay
{"title":"Nitrite reductase activity in F<sub>420</sub>-dependent sulphite reductase (Fsr) from <i>Methanocaldococcus jannaschii</i>.","authors":"Christian Heryakusuma, Eric F Johnson, Endang Purwantini, Biswarup Mukhopadhyay","doi":"10.1099/acmi.0.000482.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000482.v3","url":null,"abstract":"<p><p><i>Methanocaldococcus jannaschii</i> (<i>Mj</i>), a hyperthermophilic and evolutionarily deeply rooted methanogenic archaeon from a deep-sea hydrothermal vent, produces F<sub>420</sub>-dependent sulphite reductase (Fsr) in response to exposure to sulphite. This enzyme allows <i>Mj</i> to detoxify sulphite, a potent inhibitor of methyl coenzyme-M reductase (Mcr), by reducing it to sulphide with reduced coenzyme F<sub>420</sub> (F<sub>420</sub>H<sub>2</sub>) as an electron donor; Mcr is essential for energy production for a methanogen. Fsr allows <i>Mj</i> to utilize sulphite as a sulphur source. Nitrite is another potent inhibitor of Mcr and is toxic to methanogens. It is reduced by most sulphite reductases. In this study, we report that <i>Mj</i>Fsr reduced nitrite to ammonia with F<sub>420</sub>H<sub>2</sub> with physiologically relevant <i>K</i> <sub>m</sub> values (nitrite, 8.9 µM; F<sub>420</sub>H<sub>2</sub>, 9.7 µM). The enzyme also reduced hydroxylamine with a <i>K</i> <sub>m</sub> value of 112.4 µM, indicating that it was an intermediate in the reduction of nitrite to ammonia. These results open the possibility that <i>Mj</i> could use nitrite as a nitrogen source if it is provided at a low concentration of the type that occurs in its habitat.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10202398/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9521520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genetic Engineering of <i>Escherichia coli</i> BL21 (DE3) with a codon-optimized insecticidal toxin complex gene <i>tccZ</i>.","authors":"Mosibudi Thabiki Malomane, Kulsum Kondiah, Mahloro Hope Serepa-Dlamini","doi":"10.1099/acmi.0.000426","DOIUrl":"https://doi.org/10.1099/acmi.0.000426","url":null,"abstract":"<p><p>A toxin complex consists of a high-molecular-weight group of toxins that exhibits insecticidal activity against insect pests. These toxins are a promising alternative to <i>Bacillus thuringiensis</i> (<i>Bt</i>) toxins that have been extensively utilized in insect pest control. Herein, a codon-optimized insecticidal gene (<i>tccZ</i>) (381 bp) identified in <i>Pantoea ananatis</i> strain MHSD5 (a bacterial endophyte previously isolated from <i>Pellaea calomelanos</i>) was ligated into the pET SUMO expression vector and expressed in <i>Escherichia coli</i> BL21 (DE3). We report the success of cloning the <i>tccZ</i> gene into the pET SUMO vector and ultimately the transformation into <i>E. coli</i> BL21 (DE3) competent cells. However, despite conducting a time course of expression as well as isopropyl β-d-1-thiogalactopyranoside (IPTG) dosage optimization to determine optimal conditions for expression, TccZ protein expression could not be detected on Stain-Free and Coomassie-stained SDS-PAGE gels.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 1","pages":"acmi000426"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9968953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10824027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}