Colony Polymerase Chain Reaction Research Articles

Resistance Genes and Mortality in Carbapenem-resistant Klebsiella pneumoniae Bacteremias: Effects of the COVID-19 Pandemic

Emerging carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) (CRKP) bacteremias are presenting significant public health risks due to limited treatment options and increased mortality. K. pneumoniae isolates exhibit carbapenem resistance rates that vary from 25% to 50% throughout the European continent, including our country. To assess the characteristics of CRKP bacteremia, a condition that has recently demonstrated an increasing prevalence in our center. We sought to ascertain the resistance rates of isolated strains to antibiotics other than carbapenems, identify the responsible carbapenemase genes, evaluate the efficacy of antibiotics, determine mortality rates, explore clonality among strains, and investigate the influence of the COVID-19 pandemic on all these factors. Retrospective observational study. This study included patients aged 18 and older who had experienced meropenem-resistant K. pneumoniae bacteremia. Meropenem resistance was confirmed by employing the Kirby-Bauer disk diffusion method. Meropenem minimum inhibitory concentration (MIC) levels were determined using the gradient test, while colistin MIC levels were ascertained using the disk elution technique. Carbapenemase genes were evaluated via colony polymerase chain reaction (PCR), and clonality analysis was performed using the arbitrarily primed PCR technique. The study comprised 230 patients, with a mean age of 63.1 ± 15.9 years, of whom 58.7% were male. Oxacillinase-48 (OXA-48) was detected in 74.8% of the patients, New Delhi metallo-beta-lactamase (NDM) in 12.6%, OXA-48 + NDM in 7.8%, and KPC in 4.8%. The 14-day and 30-day mortality rates were 57% and 69.6%, respectively. Multivariate analysis of the 30-day mortality revealed several crucial factors, including bacteremia development in the intensive care unit, the occurrence of bacteremia during the COVID-19 pandemic, polymicrobial bacteremia, the use of indwelling intravenous catheters, a platelet count of ≤ 140,000/μl, procalcitonin levels of ≥ 6 μg/l, and a Charlson comorbidity score ≥ 3. Notably, the OXA-48 and KPC genes were upregulated significantly during the COVID-19 pandemic, while the NDM gene groups were downregulated. Additionally, both 14-day and 30-day mortality rates increased significantly. In this study, the most prevalent carbapenemase gene was OXA-48; however, there has been a recent increase in KPC genes. No dominant epidemic strain was identified through clonality analysis. The clustering rate was 68% before the pandemic, increasing to 85.7% during the pandemic. The significance of infection control measures is underscored by the rise in both clustering and mortality rates during the COVID-19 pandemic.

First report of Alternaria crassa causing yellow spots on Daturastramonium in China.

DaturastramoniumL.(jimson weed)is an invasiveweedin agricultural fieldsand a medicinalplant. In April 2022, a leaf disease on D. stramonium was observed in Zhanjiang (21.17 N, 110.18 E), Guangdong province, China. Early symptoms were small yellow spots on leaves. Later, the spots gradually expanded and turned becoming necrotic with a clear yellow halo and a white center. The disease incidence in the field was 85% (n= 50, about 1 ha). Twenty diseased leaves were collected from the field. The margin of the diseased tissues was cut into 2 mm × 2 mm pieces, surface disinfected with 75% ethanol and 2% sodium hypochlorite for 30 and 60 s, respectively, and rinsed twice with sterile water before isolation. The tissues were plated onto potato dextrose agar (PDA) medium and incubated at 28 ℃. After 2-day incubation, grayish fungal colonies appeared on the PDA, then pure cultures were produced by transferring hyphal tips to new PDA plates. Single-spore isolation method was used to recover pure cultures for three isolates (DSAC-1, DSAC-2, and DSAC-3). The isolates were morphologically identical.They colonies were gray to brownish black. Conidiophores were branched, brown. Conidia were brown, long ellipsoid, had 4-12 transverse and 0-3 longitudinal septa; measured within 67.5-127.8 (average =105.6) × 12.5-27.8 (average=20.4) µm (n=30). Apical beak was longer than conidia body. measured within 40.5-423.5 (average =365.2) × 2.5-5.8 (average=3.2) µm (n=30). Based on morphological characteristics, the three isolates were identified asAlternariacrassa(Sacc.) Rands (Simmons 2007). Molecular identification was performed using the colony polymerase chain reaction method with MightyAmp DNA Polymerase (Takara-Bio, Dalian, China) (Lu et al. 2012) to amplify internal transcribed spacer (ITS) region, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), RNA polymerase second largest subunit (RPB2) and translation elongation factor (TEF1) with primers of ITS1/ITS4, GDF1/GDR1, RPB2-5F2/fRPB2-7cR, and EF-1α-F/EF-1α-R, respectively (Walther et al. 2013; Woudenberg et al. 2015; Nishikawa and Nakashima. 2020). Amplicons of the isolates were sequenced and submitted to GenBank (ITS, ON430524-ON430526; GAPDH, ON500656-ON500658; RPB2, ON500659-ON500661; TEF1, ON500662-ON500664). The sequences were 100% identical with those of Alternaria crassa strain CBS 116647 upon BLAST analysis. The sequences were also concatenated for phylogenetic analysis by maximum likelihood. The isolates clustered withA. crassa (CBS 116647, CBS 116648, CBS CBS-110.38, and CBS_103.18 ).Thus, the fungus associated with leafyellow spoton D. stramonium was identified asA. crassa.Pathogenicity tests were conducted in a greenhouse at 24℃-30℃ with 80% relative humidityusing 3 isolates. Individual plants were grown in pots (n = 5, 1 month old). The unwounded leaflets were inoculated using three isolates (DSAC-1, DSAC-2, and DSAC-3). The fungal mycelium on 5 mm-diameter PDA plugs were placed faced down to the leaves. Sterile PDA was used for mock inoculated comtrols.. The test was performed three times. Disease symptoms were observed on the leaves after 7 days, whereas the controls remained healthy. The pathogen was re-isolated from infected leaves and was morphologically identical to the original isolates, fulfilling Koch's postulates.A. crassa was reported causing leaf spot on D. stramonium in Algeria (Nabahat et al. 2020). To our knowledge, this report is the first report of A. crassa causing leaf yellow spot on D. stramonium in China. This pathogen possessespotential biocontrol properties on the invasiveweed, while this study also provides an important reference for the control of the diseaseof the medicinalplant.

Anticancer and bioactivity effect of the AraA-IL13 fusion protein on the glioblastoma cell line

Background and purpose: Glioblastoma (GBM) is an aggressive and malignant brain cancer with the highest mortality and low survival rates. To discover a more specific and efficient treatment for GBM, we synthesized and examined the cytotoxic effect of arazyme-interleukin-13 (Ara-IL13) fusion protein on GBM cells. Experimental approach: At first, the araA-IL13 chimeric gene in the pET28a (+) vector was designed and synthesized. After transformation into Escherichia coli BL21 (DE3), the chimeric gene was verified by colony polymerase chain reaction. Expression optimization and purification of the AraA-IL13 fusion protein was performed and subsequently evaluated by 10% SDS-PAGE. The protein was purified and concentrated using the Amicon® Ultra- 15 centrifugal filter unit. The presence of AraA-IL13 was investigated by the western blotting technique. The enzyme was evaluated for proteolytic activity after purification on skim milk agar. The cytotoxic effect of the AraA-IL13 fusion protein was evaluated by MTT assay on U251 and T98G cell lines in vitro. Findings/Results: The chimeric protein had no proteolytic activity on skim milk agar despite high expression. Furthermore, no cytotoxic effect of this fusion protein (up to 400 μg/mL) was observed on the U251 and T98G cell lines. Conclusion and implications: The lack of proteolytic activity and cytotoxic effect of AraA-IL13 may be due to the disruption of the three-dimensional structure of the protein or the large structure of the arazyme coupled with the ligand and the lack of proper folding of the arazyme to make the active site of the enzyme inaccessible.

Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer.

Coronaviruses (CoVs), including severe acute respiratory syndrome coronavirus 2, can infect a variety of mammalian and avian hosts with significant medical and economic consequences. During the life cycle of CoV, a coordinated series of subgenomic RNAs, including canonical subgenomic messenger RNA and non-canonical defective viral genomes (DVGs), are generated with different biological implications. Studies that adopted the Nanopore sequencer (ONT) to investigate the landscape and dynamics of viral RNA subgenomic transcriptomes applied arbitrary bioinformatics parameters without justification or experimental validation. The current study used bovine coronavirus (BCoV), which can be performed under biosafety level 2 for library construction and experimental validation using traditional colony polymerase chain reaction and Sanger sequencing. Four different ONT protocols, including RNA direct and cDNA direct sequencing with or without exonuclease treatment, were used to generate RNA transcriptomic libraries from BCoV-infected cell lysates. Through rigorously examining the k-mer, gap size, segment size, and bin size, the optimal cutoffs for the bioinformatic pipeline were determined to remove the sequence noise while keeping the informative DVG reads. The sensitivity and specificity of identifying DVG reads using the proposed pipeline can reach 82.6% and 99.6% under the k-mer size cutoff of 15. Exonuclease treatment reduced the abundance of RNA transcripts; however, it was not necessary for future library preparation. Additional recovery of clipped BCoV nucleotide sequences with experimental validation expands the landscape of the CoV discontinuous RNA transcriptome, whose biological function requires future investigation. The results of this study provide the benchmarks for library construction and bioinformatic parameters for studying the discontinuous CoV RNA transcriptome.IMPORTANCEFunctional defective viral genomic RNA, containing all the cis-acting elements required for translation or replication, may play different roles in triggering cell innate immune signaling, interfering with the canonical subgenomic messenger RNA transcription/translation or assisting in establishing persistence infection. This study does not only provide benchmarks for library construction and bioinformatic parameters for studying the discontinuous coronavirus RNA transcriptome but also reveals the complexity of the bovine coronavirus transcriptome, whose functional assays will be critical in future studies.

The Incidence and Risk Factors for Enterotoxigenic E. coli Diarrheal Disease in Children under Three Years Old in Lusaka, Zambia.

This study aimed to estimate the incidence and risk factors for Enterotoxigenic Escherichia coli (ETEC) diarrhea. This was a prospective cohort study of children recruited in a household census. Children were enrolled if they were 36 months or below. A total of 6828 children were followed up passively for 12 months to detect episodes of ETEC diarrhea. Diarrheal stool samples were tested for ETEC using colony polymerase chain reaction (cPCR). Among the 6828 eligible children enrolled, a total of 1110 presented with at least one episode of diarrhea. The overall incidence of ETEC diarrhea was estimated as 2.47 (95% confidence interval (CI): 2.10-2.92) episodes per 100 child years. Children who were HIV-positive (adjusted Hazard ratio (aHR) = 2.14, 95% CI: 1.14 to 3.99; p = 0.017) and those whose source of drinking water was public tap/borehole/well (aHR = 2.45, 95% CI: 1.48 to 4.06; p < 0.002) were at increased risk of ETEC diarrhea. This study found that children whose mothers have at least senior secondary school education (aHR = 0.49, 95% CI: 0.29 to 0.83; p = 0.008) were at decreased risk of ETEC diarrhea. Our study emphasizes the need for integrated public health strategies focusing on water supply improvement, healthcare for persons living with HIV, and maternal education.

Engineering probiotic bacteria to express tcdB antigen as an oral vaccine carrier against Clostridium difficile infection

Background Clostridium (now known as Clostridioides) difficile (C. difficile) is a spore-forming, gram-positive organism that can pose serious public health complications. The elderly are especially vulnerable to C. difficile infections, which can be fatal. C. difficile strains cause symptomatic diseases via the release of two toxins; tcdA and tcdB, that induce inflammation and tissue damage. Vaccines targeting any of these toxins may offer an effective strategy against C. difficile infections. Objective This study aimed to use live probiotics as oral vaccines to express the C. difficile toxin B gene. Oral vaccination has many advantages over intramuscular injection, as it has higher compliance, feasibility, and simpler administration. In addition, oral vaccines can stimulate both mucosal and systemic immunity against the target antigen. Probiotic bacteria were chosen as they present ideal candidates for this goal in terms of safety and health promotion. Materials and methods We chose two probiotic strains: Lactobacillus gasseri ATCC 33323 in addition to Enterococcus faecium NM1015, which had previously been identified in our lab and is capable of suppressing C. difficile colonization. The C-terminal of the tcdB gene was amplified by polymerase chain reaction (PCR) from C. difficile, cloned, and transformed into an E. coli EZ strain. The tcdB fragment was digested with BamHI and XhoI (NEB, UK) and subcloned into the bile salt-inducible expression plasmid pLB210 (obtained from INRA, France). The transformation and electroporation procedures were employed to insert cloning and expression plasmids into the target bacteria. Colony PCR was used to confirm the engineering strains. Reverse transcription PCR was used to confirm the expression of the C. difficile tcdB fragment. Results and conclusion The expression vector ‘p210-tcdB’ was constructed, then introduced into the selected probiotic strains by electroporation and confirmed by colony PCR and plasmid extraction. The reverse transcription (RT)-PCR confirmed the expression of the gene by the engineered strains. No significant difference in the survival rate was observed between the engineered strains and their parental types at pH 2.00 and 1% oxygen. Moreover, the strains showed satisfactory plasmid stability for 210 generations. Future work will involve the in vivo evaluation of the engineered probiotic strains as oral vaccines against C. difficile using an animal model.

OPTIMIZATION OF COLONY POLYMERASE CHAIN REACTION FOR THE 16SRRNA OF DIFFERENT STRAINS OF ESCHERICHIA COLI

Objective: This work aimed to enhance colony polymerase chain reaction (PCR) for the 16S rRNA of several Escherichia coli strains. Methods: The isolation of E. coli is done from the gut of the chicken and soil. Then, we optimized the condition for colony PCR for the amplification of 16s ribosomal RNA. We successfully designed primer 3 for 16s ribosomal RNA and made the dilution solution with PCR grade water that is 1:10. Moreover, finally, we made a 20 μL solution that contains the master mix of our isolated colony and forward and reverse base primer for amplification. After the conventional PCR, the amplified 16s ribosomal RNA was then run on Gel to obtain the desired bands. And finally saw the bands in the Gel Doc picture. Results: Our result shows that the technique of colony PCR is an efficient and quick method than other existing methods that are too costly, tedious, and time-consuming procedures that deter their exploitation in various experimentations and for the identification of E. coli strains. Conclusion: This study concluded that 16s ribosomal RNA can be amplified without the extraction and purification of total genomic DNA from a bacterial colony using colony PCR. Therefore, by designing rRNA primers for E. coli species, we can evaluate their various types of mutations, strain detection, and antibiotic resistance.

Biosensor for PCR amplicons by combining split trehalase and DNA-binding proteins: A proof of concept study

The use of polymerase chain reaction (PCR) technology in low-cost settings has gained significant attention due to its ability to amplify and detect specific bacterial pathogen genes, aiding in the diagnosis of infectious diseases. PCR amplicons can be visualized by conventional endpoint agarose gel electrophoresis and fluorochrome-enabled real-time PCR. However, this is not practical in on-field tests due to cumbersome instrumentation, labor-intensive reaction preparation, and long time-to-results. Many studies have combined microfluidic devices or electrochemical dyes with PCR technology to enhance in-field operability. However, the high cost of manufacturing high-precision microfluidic chips and the dependence on non-portable readout equipment limit their further development. In this paper, we present a proof-of-principle study of a novel method combining split enzyme technology and DNA-binding proteins for the convenient and efficient detection of amplified genetic material from bacterial pathogens. The amplicon binding split trehalase assay (ABSTA) relies on incorporating specific recognition sequences of DNA-binding protein SpoIIID in tandem within one of the PCR primers. Applied by a Gram-type specific PCR assay, ABSTA was capable of discriminating Staphylococcus devriesei and Escherichia coli in <90 min after colony PCR amplicons bound split trehalase fragments-fused SpoIIID and triggered split enzyme complementation. The salt concentration, protein reagents versus DNA substrate ratio, direction and linker length of tandem recognition sites required for the complementation were optimized. The glucose produced by restored enzymatic activity was detectable by glucometer. With limited requirements for reaction preparation and the compatibility of ABSTA with commercially available handheld glucometers, this test platform has substantial potential to be implemented into a future point-of-care (POC) diagnostic tool for detecting pathogen specific genes with further improvement.

First report of Neopestalotiopsis clavispora Causing Leaf Spots on Garcinia mangostana in China.

Garcinia mangostana L. is a famous tropical fruit in Asia. In April 2021, a leaf disease on G. mangostana cv. Huazhu was observed in Zhanjiang (21.17° N, 110.18° E), Guangdong province, China. Symptoms was on new leaves of 2 year old plants. The spots were circular to irregular, gray in the center, and brown on the lesion margin. The disease incidence was estimated 25% (n = 500 investigated plants from about 50-ha). Twenty diseased leaves were collected from the orchard. The margin of the diseased tissues was cut into 2 mm × 2 mm pieces; surface disinfected with 75% ethanol and 2% sodium hypochlorite for 30 and 60 s, respectively; and rinsed thrice with sterile water. The tissues were plated onto potato dextrose agar (PDA) medium and incubated at 28 ℃. Twenty-eight isolates were obtained (isolation frequency = 28/4×20 = 35%). Single-spore isolation method was used to recover pure cultures for three isolates (GMN-1, GMN-2, and GMN-3) (Liu et al. 2021). The colonies were initially white with cottony aerial mycelium at 7 days on PDA. Then, they developed black acervular conidiomata at 10 days. Conidia were clavate to fusiform, four-septate, straight or slightly curved, and measured 16.5 to 21.4 µm long (average 19.5 µm; n = 40) × 4.5 to 6.5 µm wide (average 5.2 µm; n = 40). The three median cells were versicolored, whereas the basal and apical cells were hyaline. Conidia had a single basal appendage (4.5 to 5.5 µm long; n = 40) and three apical appendages (19.2 to 24.5 µm long; n = 40). The morphological characteristics of the isolates are comparable with those of the genus Neopestalotiopsis(Sajeewa et al. 2012). Molecular identification was performed using the colony polymerase chain reaction method with MightyAmp DNA Polymerase (Takara-Bio, Dalian, China) (Lu et al. 2012). Sequences were generated from the isolates using primers for the rDNA ITS (ITS1/ITS4), TEF1-α (EF1-728F/EF1-986R), and β-tubulin (T1/βt2b) loci (Sajeewa et al. 2012). The sequences of the isolates were submitted to GenBank (ITS, MZ026535-MZ026537; TEF, MZ032203-MZ032205; β-tubulin, MZ032206-MZ032208). The sequences of the isolates were 100% identical to the type strain MFLUCC12-0281 (accession nos. JX398979, JX399014, and JX399045) through BLAST analysis. The isolates clustered with N. clavispora (MFLUCC12-0280 and MFLUCC12-0281). The pathogenicity was tested in vivo. Individual plants (cv. Huazhu) were grown (n = 2, 1-1.5 year old) in a greenhouse at 24℃-30℃ with 80% relative humidity. Wounded leaflets were inoculated with 5-mm-diameter mycelial plugs or agar plugs (as control). Besides, sterile cotton balls were immersed in the spore suspension (1 × 105 per mL) and sterile distilled water (control) for about 15 s before they were fixed on the leaves for 3 days. One plant employed for each isolate with nine leaves. The test was performed thrice. Disease symptoms were found on the leaflets after 10 days, whereas the controls remained healthy. The pathogen was re-isolated from infected leaves and phenotypically identical to the original isolates to fulfill Koch's postulates. Neopestalotiopsis clavispora and Pestalotiopsis clavispora are synonyms. The fungus appeared to have a wide host range and distribution including in Thailand, Malaysia, North Queensland, and Australia (Sajeewa et al. 2012;Shahriar et al. 2022). Thus, this is the first report of N. clavispora causing leaf spot on G. mangostana in China. This finding will help improve management strategies against the leaf spots on G. mangostana in China.

Staphylococcus aureus Colony Polymerase Chain Reaction.

Here, we describe a protocol for a colony polymerase chain reaction (PCR) method for Staphylococcus aureus The methodology involves the preparation of small S. aureus lysates by using the enzyme lysostaphin to degrade the peptidoglycan layer. These lysates are prepared using a small patch of bacteria grown on LB agar plates, and the lysates can subsequently be used for PCR analyses.

Development of Leishmania Species Strains with Constitutive Expression of eGFP.

Protozoan parasites of the genus Leishmania cause leishmaniasis, a disease with variable clinical manifestations that affects millions of people worldwide. Infection with L. donovani can result in fatal visceral disease. In Panama, Colombia, and Costa Rica, L. panamensis is responsible for most of the reported cases of cutaneous and mucocutaneous leishmaniasis. Studying a large number of drug candidates with the methodologies available to date is quite difficult, given that they are very laborious for evaluating the activity of compounds against intracellular forms of the parasite or for performing in vivo assays. In this work, we describe the generation of L. panamensis and L. donovani strains with constitutive expression of the gene that encodes for an enhanced green fluorescent protein (eGFP) integrated into the locus that encodes for 18S rRNA (ssu). The gene encoding eGFP was obtained from a commercial vector and amplified by polymerase chain reaction (PCR) to enrich it and add restriction sites for the BglII and KpnI enzymes. The eGFP amplicon was isolated by agarose gel purification, digested with the enzymes BglII and KpnI, and ligated into the Leishmania expression vector pLEXSY-sat2.1 previously digested with the same set of enzymes. The expression vector with the cloned gene was propagated in E. coli, purified, and the presence of the insert was verified by colony PCR. The purified plasmid was linearized and used to transfect L. donovani and L. panamensis parasites. The integration of the gene was verified by PCR. The expression of the eGFP gene was evaluated by flow cytometry. Fluorescent parasites were cloned by limiting dilution, and clones with the highest fluorescence intensity were selected using flow cytometry.

First Report of Fire Blight Caused by Erwinia amylovora on Korean Mountain Ash (Sorbus alnifolia) in Korea

During the nationwide survey of fire blight, the typical shoot blight symptoms were found on Korean mountain ash (Sorbus alnifolia) which was located near an orchard that produced fire blight on pear trees in Eumseong, Korea, May 2021. To identify the causal agent, we progressed isolation from the symptomatic leaves and shoots. Two white and mucoid colonies were isolated into the pure culture. Two isolates were identified as Erwinia amylovora according to the colony–polymerase chain reaction (PCR) with amsB primers and the phylogenetic tree using 16S rRNA sequences. To test of pathogenicity of two isolates, we inoculated immature pear fruits and understock of apple. We observed necrosis and oozes on immature pear fruits and shoot blight resulting in necrosis on apple shoots six days after inoculation. Colonies were recovered from the inoculated pears and apples, and identity was confirmed through colony PCR for amsB genes. To our knowledge, E. amylovora was first reported on Korean mountain ash native to South Korea.

First Report of Fire Blight Caused by Erwinia amylovora on Korean Mountain Ash (Sorbus alnifolia) in Korea

During the nationwide survey of fire blight, the typical shoot blight symptoms were found on Korean mountain ash (Sorbus alnifolia) which was located near an orchard that produced fire blight on pear trees in Eumseong, Korea, May 2021. To identify the causal agent, we progressed isolation from the symptomatic leaves and shoots. Two white and mucoid colonies were isolated into the pure culture. Two isolates were identified as Erwinia amylovora according to the colony–polymerase chain reaction (PCR) with amsB primers and the phylogenetic tree using 16S rRNA sequences. To test of pathogenicity of two isolates, we inoculated immature pear fruits and understock of apple. We observed necrosis and oozes on immature pear fruits and shoot blight resulting in necrosis on apple shoots six days after inoculation. Colonies were recovered from the inoculated pears and apples, and identity was confirmed through colony PCR for amsB genes. To our knowledge, E. amylovora was first reported on Korean mountain ash native to South Korea.

Molecular identification of Ralstonia pseudosolanacearum causing bacterial wilt in tomatoes from Da Nang by using Colony PCR

Ralstonia solanacearum species complex (RSSC) is the main pathogen causing bacterial wilt disease in tomatoes. This study applied the colony polymerase chain reaction (PCR) technique to rapidly screen and select RSSC strains from isolated bacteria of diseased tomatoes. This method directly used bacterial colonies on the Petri plate as templates to amplify with RSSC’s specific and multiplex primers. The results showed that the Vietnamese isolates were identified as R. pseudosolanacearum, phylotype I. Phylogenetic analysis of the 16S-23S rDNA sequencing also confirmed these results. Therefore, this is the first report to recognize R. pseudosolanacearum phylotype I as the cause of bacterial wilt disease in tomatoes from Danang.

In Vitro Site Directed Mutagenesis.

Site-Directed Mutagenesis (SDM) allows for changes in the DNA sequence of plasmids using polymerase chain reaction (PCR). It is a reliable, accessible, and rapid method which is the common initial step of many biochemial or genetic experiments. Here we describe the various different forms of SDM before giving a detailed method for the introduction of substitutions, insertions, or deletions using a fast, ligation-free protocol, followed by colony PCR to screen for mutated sequences.

First report of Alternaria alternata causing leaf yellow spot on Heteropanax fragrans in China.

Heteropanax fragrans (Roxb.) Seem is a common garden landscape tree in China. In December 2020, a leaf disease on H. fragrans was observed in a 2 ha field in Zhanjiang (20.85° N, 109.28° E), Guangdong province, China. Early symptoms were small yellow spots on leaves. Later, the spots gradually expanded and turned into necrotic tissues with a clear yellow halo and a white center. The disease incidence on plants was 100%. Twenty diseased leaves were collected from the field. The margin of the diseased tissues was cut into 2 mm × 2 mm pieces, surface disinfected with 75% ethanol and 2% sodium hypochlorite for 30 and 60 s, respectively, and rinsed thrice with sterile water before isolation. The tissues were plated onto potato dextrose agar (PDA) medium and incubated at 28 ℃. After 2-day incubation, grayish fungal colonies appeared on the PDA, then pure cultures were produced by transferring hyphal tips to new PDA plates. Single-spore isolation method was used to recover pure cultures for three isolates (HFA-1, HFA-2, and HFA-3). The colonies first produced a light-grayish aerial mycelia, which turned dark grayish upon maturity. Conidiophores were branched. Conidia numbered from two to four in chains, were dark brown, ovoid, or ellipsoid and mostly beakless; had 1-4 transverse and 0-3 longitudinal septa; measured within 7.2-17.8 (average =10.2) × 2.5-7.5 (average=4.3) µm (n=30). Molecular identification was performed using the colony polymerase chain reaction method with MightyAmp DNA Polymerase (Takara-Bio, Dalian, China) (Lu et al. 2012) to amplify the large subunit (LSU), internal transcribed spacer (ITS) region, translation elongation factor (TEF) , and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with NL1/LR3, ITS1/ITS4, EF-1α-F/EF-1α-R, and GDF1/GDR1 (Walther et al. 2013;Woudenberg et al. 2015; Nishikawa and Nakashima. 2020). Amplicons of the isolates were sequenced and submitted to GenBank (LSU, ON088978-ON088980; ITS, MW629797, ON417005 and ON417006; TEF, MW654167, ON497264,and ON497265;GAPDH, MW654166, ON497262,and ON497263). The obtained sequences were 100% identical with those of Alternaria alternata strain CBS 102600 upon BLAST analysis . The sequences were also concatenated for phylogenetic analysis by maximum likelihood. The isolates clustered withA. alternata (CBS 102600, CBS 102598, CBS 118814, CBS 918.96,CBS 106.24, CBS 119543, CBS 916.96).The fungus associated with leaf yellow spot on H. fragrans was thus identified asA. alternata.Pathogenicity tests were conducted in a greenhouse at 24℃-30℃ with 80% relative humidity. Individual plants were grown in pots (n = 5, 1 month old). The unwounded leaflets were inoculated with 5 mm-diameter mycelial plugs of the isolates or agar plugs (as control). The test was performed thrice. Disease symptoms were found on the leaves after 7 days, whereas the controls remained healthy. The pathogen was re-isolated from infected leaves and phenotypically identical to the original isolates to fulfill Koch's postulates.To our knowledge, this report is the first one on A. alternata causing leaf yellow spot on H. fragrans. Thus, this work provides an important reference for the control of this disease in the future.

A novel and improved selective media for the isolation and enumeration of Klebsiella species

Bacterial pathogens are fostered in and transmitted through wastewater. Hence, monitoring their impact on sanitation and hygiene is imperative. As part of the monitoring process, culture-based methodologies are primarily used, which centre on the use of selective and differential media. Media available today are, at best, difficult to formulate and, at worst, prohibitively expensive. To address this lacuna, the study proposes a selective and differential medium for Klebsiella spp. Klebsiella blue agar (KBA) is completely selective against selected gram-positive bacteria (Bacillus spp., Staphylococcus aureus) and a few gram-negative bacteria (Acinetobacter baumanii, Serratia marcescens). On the other hand, it supports the growth of the chosen members of the Klebsiella pneumoniae species-complex with a characteristic green colouration. Methylene blue, tryptophan, and bile salt make up the selective components of KBA. Moreover, methylene blue, 0.6% NaCl, and glycerol render it differential. KBA was more selective than HiCrome™ Klebsiella Selective Agar Base (KSA) in replica plating experiments. KBA promoted only 157 CFUs against 209 CFUs in KSA when stamped with 253 CFUs grown on LB. The colonies so isolated were predominantly Klebsiella spp., on identification through colony polymerase chain reaction. Moreover, the differential nature of KBA distinguished Klebsiella aerogenes from other species. On the contrary, KSA lodged colonies indistinguishable from each other and Klebsiella spp. Due to its ease of formulation, high selectivity, differential nature, and cost-effective composition, KBA is a viable option for the routine culture of Klebsiella spp. in environmental and clinical settings.Key points• Formulated a novel selective and differential media for Klebsiella spp., named Klebsiella Blue agar• Facile formulation methodology• Can be employed to isolate Klebsiella spp. from complex sources such as wastewater

The prevalence and species of Mycoplasma identified from dairy goats in Taiwan

Except for Mycoplasma capricolum subsp. capripneumoniae, which only causes pneumonia, Mycoplasma species can cause otitis, arthritis, septicemia, mastitis, pneumonia and encephalitis in goats. After a mycoplasma outbreak was recorded in Taiwan in 2016, an increasing number of mycoplasma infection cases have been observed. It is important to understand how many Mycoplasma species are currently prevalent in Taiwan. In this study, 57–61 bulk milk samples were collected from dairy goats in Taiwan every year from 2017 to 2020 to identify the presence of mycoplasma DNA fragments by polymerase chain reaction (PCR). The mycoplasma species were identified based on colony characteristics, PCR, and DNA sequences. In total, 39 out of 236 samples (16.52%) tested mycoplasma positive. The annual mycoplasma prevalence rates from 2017 to 2020 were 24.59% (15/61), 8.20% (5/61), 17.54% (10/57) and 15.79% (9/57), respectively. Mycoplasma mycoides subsp. capri (n = 19), Mycoplasma putrefaciens (n = 10), Mycoplasma ovipneumoniae (n = 5) and Mycoplasma bovis (n = 5) were present in Taiwan. No M. capricolum subsp. capripneumoniae was detected. Except for the large drop in 2018, the prevalence of mycoplasma infection declined to a consistent level for the final two years of the study. However, the seasonal pattern is still worth investigating. This is the first survey of mycoplasma infection in goats, and we believe that a larger survey is still needed to understand the pathogenicity and diversity of these mycoplasma isolates.

The optimal combination of Nile red identification, colony polymerase chain reaction, and gas chromatography detection methods in screening for polyhydroxyalkanoicate-producing bacteria.

The study devised a detection process combining Nile red-containing media, polymerase chain reaction (PCR), and gas chromatography (GC) to evaluate the possibility of microbes becoming polyhydroxyalkanoate (PHA) producers. The Nile red and PCR detection steps of designating PHA producers had true positive rates of 39.4% and 40%, respectively, and the use of GC analysis as the final step yielded accurate results for the production types and yields of PHAs. When the number of screening samples was up to 102, connecting all three inspection methods in tandem generated economic benefits. When up to 105 samples were screened, the use of all three detection methods reduced the cost to 3% of the cost and the time consumed 6% of using just Nile red plus GC or PCR plus GC. However, when the sum of samples exceeded 108, the cost of combining the three methods exceeds 1 million US dollars and was excessive; here, the combination of Nile red plus PCR could be considered, even though the true positive rate was only 30.7%.

Genetic diversity analysis of grapevine rupestris stem pitting-associated virus from grapevine by colony PCR-SSCP and -RFLP.

We have developed methods for detecting the genetic diversity of grapevine rupestris stem pitting-associated virus (GRSPaV) based on restriction fragment length polymorphism (RFLP) and single stranded conformational polymorphism (SSCP) in the 905 nt 3' sequence. The amplicons were cloned from six grapevine cultivars, and colony polymerase chain reaction (colony PCR) using recombination bacteria was subsequently analyzed by RFLP and SSCP. Four haplotypes of SSCP and six haplotypes of Sac IRFLPs were defined. The two methods had a40% discrepancy rate in showing the degree of diversity. All clones were sequenced and were used to construct aphylogenetic tree with seven previously reported GRSPaV sequences. In the tree, all the newly acquired sequences were divided into three clusters, I, II, and III, which corresponded to haplotypes I, II, and III of SSCP, respectively. Haplotype IV of SSCP was grouped into cluster II. Arecombination analysis showed that haplotype IV has undergone arecombination event. Together, these results indicate that the SSCP assay is useful for the rapid identification of genetic diversity of GRSPaV. This is the first report of an analysis of the large fragment of GRSPaV by colony PCR-SSCP. Keywords: grapevine; grapevine rupestris stem pitting-associated virus (GRSPaV); RFLP; SSCP; genetic diversity analysis.