scholarly journals Prevalence, Molecular Identification, Antimicrobial Resistance, and Disinfectant Susceptibility of Listeria innocua Isolated from Ready-to-Eat Foods Sold in Johannesburg, South Africa

2021 ◽  
Author(s):  
H.H. Makumbe ◽  
F.T. Tabit ◽  
B.C. Dlamini
Keyword(s):  
South Africa ◽  
Antimicrobial Resistance ◽  
16S Rrna ◽  
Molecular Identification ◽  
Food Contamination ◽  
Food Samples ◽  
Listeria Innocua ◽  
Food Sources ◽  
Rrna Gene ◽  
Search Tool

Background: Food contamination with Listeria spp. can occur at all stages of the food chain. The aim of this research was to investigate the prevalence, molecular identification, antimicrobial resistance, and disinfectant susceptibility of Listeria innocua isolated from Ready-To-Eat (RTE) foods sold in Johannesburg, South Africa. Methods: Eighty RTE foods were collected from Johannesburg, South Africa. The 16S rRNA region of L. innocua isolates was amplified, sequenced, and identified using Basic Alignment Search Tool (BLAST). The antimicrobial resistance and disinfectant susceptibility (against four commercial disinfectants) of the isolates were evaluated using disk diffusion and microdilution assays. Data were statistically analyzed using SPSS v. 23.0. Results: Listeria strains revealed a high 16S rRNA gene sequence analogy to L. innocua of between 98-99%. The overall prevalence of L. innocua was 21.3% (17 out of 80) in the RTE food samples. Most isolates were susceptible to the studied commercial disinfectants. All the L. innocua isolates from food sources were found to be resistant to ampicillin and cephalothin, while 83 and 74% of isolates were resistant to colistin sulphate and sulphatriad. Conclusion: Prevalence of L. innocua was considerable in the RTE food samples sold in Johannesburg, South Africa. The L. innocua isolates showed high antibiotic resistance against ampicillin, cephalothin, colistin sulphate, and sulphatriad.

scholarly journals Three novel lineages of ‘Candidatus Liberibacter africanus’ associated with native rutaceous hosts of Trioza erytreae in South Africa

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 723-731 ◽  
Author(s):  
Ronel Roberts ◽  
Emma T. Steenkamp ◽  
Gerhard Pietersen
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Nucleotide Sequence Data ◽  
Trioza Erytreae

Greening disease of citrus in South Africa is associated with ‘Candidatus Liberibacter africanus’ (Laf), a phloem-limited bacterium vectored by the sap-sucking insect Trioza erytreae (Triozidae). Despite the implementation of control strategies, this disease remains problematic, suggesting the existence of reservoir hosts to Laf. The current study aimed to identify such hosts. Samples from 234 trees of Clausena anisata, 289 trees of Vepris lanceolata and 231 trees of Zanthoxylum capense were collected throughout the natural distribution of these trees in South Africa. Total DNA was extracted from samples and tested for the presence of liberibacters by a generic Liberibacter TaqMan real-time PCR assay. Liberibacters present in positive samples were characterized by amplifying and sequencing rplJ, omp and 16S rRNA gene regions. The identity of tree host species from which liberibacter sequences were obtained was verified by sequencing host rbcL genes. Of the trees tested, 33 specimens of Clausena, 17 specimens of Vepris and 10 specimens of Zanthoxylum tested positive for liberibacter. None of the samples contained typical citrus-infecting Laf sequences. Phylogenetic analysis of 16S rRNA gene sequences indicated that the liberibacters obtained from Vepris and Clausena had 16S rRNA gene sequences identical to that of ‘Candidatus Liberibacter africanus subsp. capensis’ (LafC), whereas those from Zanthoxylum species grouped separately. Phylogenetic analysis of the rplJ and omp gene regions revealed unique clusters for liberibacters associated with each tree species. We propose the following names for these novel liberibacters: ‘Candidatus Liberibacter africanus subsp. clausenae’ (LafCl), ‘Candidatus Liberibacter africanus subsp. vepridis’ (LafV) and ‘Candidatus Liberibacter africanus subsp. zanthoxyli’ (LafZ). This study did not find any natural hosts of Laf associated with greening of citrus. While native citrus relatives were shown to be infected with Laf-related liberibacters, nucleotide sequence data suggest that these are not alternative sources of Laf to citrus orchards, per se.

scholarly journals Morphological and molecular identification of hairtail (Trichiurus spp.) caught in Pangandaran Waters

2020 ◽  
Vol 147 ◽  
pp. 02021
Author(s):  
Tia Aprianti Lestari ◽  
Murwantoko Murwantoko ◽  
Eko Setyobudi
Keyword(s):  
Principal Component Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Identification ◽  
Principal Component ◽  
Component Analysis ◽  
Rrna Gene ◽  
Morphometric Variation ◽  
Dorsal Fin ◽  
Fish Samples

This study aimed to identify the species of hairtail caught in Pengandaran waters based on morphological, meristic character and molecular approach. In total 135 fish samples were collected from Pangandaran Waters, during March-April 2017. Each sample was identified, measured on 22 morphometric and 4 meristic characters, then analyzed using Principal Component Analysis (PCA). Molecular identification was conducted by sequenced of 16S rRNA gene. The result of the research showed that hairtail characterized by III spines and 125-140 soft rays of dorsal fin (D.III, 125-140), the anal fin situated below 38th to 41th of dorsal-fin soft ray, I spine and 10 soft rays of pectoral fin (P.I.10), and I spine and 91 to 112 spinules of anal fin (A.I.91-112). Based on the morphological identification, the hairtail was belonged to Trichiurus lepturus. Principal Component Analysis showing the morphometric variation was presented in the caudal peduncle length. Molecular analysis of mitochondrial DNA of the partial 16S rRNA gene confirmed the hairtail as T. lepturus with similarity 98-99% based on previously published data. Phylogenetic analysis showed that T. lepturus from Pangandaran were closely similar to related species caught from the Southern Coast of Yogyakarta Special Territory (Indian Ocean) and Hainan China (Pacific Ocean).

scholarly journals Colony morphology and molecular identification of Vibrio spp. on green mussels (Perna viridis) in Yogyakarta, Indonesia tourism beach areas

2019 ◽  
Vol 20 (10) ◽  
Author(s):  
FARIDA HIKMAWATI ◽  
Ari Susilowati ◽  
RATNA SETYANINGSIH
Keyword(s):  
16S Rrna ◽  
Molecular Identification ◽  
Pathogenic Bacteria ◽  
Morphological Characteristics ◽  
Vibrio Species ◽  
Colony Morphology ◽  
Perna Viridis ◽  
Rrna Gene ◽  
Coastal Tourism ◽  
Vibrio Spp

Abstract. Hikmawati F, Susilowati A, Setyaningsih R. 2019. Colony morphology and molecular identification of Vibrio spp. on green mussels (Perna viridis) in Yogyakarta, Indonesia tourism beach areas. Biodiversitas 20: 2891-2899. Green mussels (Perna viridis) have filter feeder properties that allow pathogenic bacteria from the water environment to accumulate in relatively high levels. About 20% of foodborne diseases are caused by large quantities of seafood contaminated with bacteria. The purpose of this study is to determine the morphological characteristics, pathogenicity, identity, and the kinship of Vibrio species on green mussels in Yogyakarta coastal tourism areas. Vibrio spp. were grown on selective differential TCBS media. In this media, the suspected Vibrio spp. would produce yellow or green colonies. The ability of hemolysis of Vibrio was blood agar media, the species was molecularly identified using 16S rRNA gene sequence, and the phylogenetic relationship of the Vibrio spp., was analyzed using MEGA X Neighbor-Joining program. Based on morphological analysis, we obtained 23 bacterial isolates suspected to be Vibrio spp. Two Isolates (L1K2 6 and L2K2 13) were positive for α-hemolysis activity and 4 isolates (L1K1 3, L2K1 8, L2K2 16, and L3K2 22) were positive for β-hemolysis activity. The molecular analysis involved 18 Vibrio species, and 4 of them represented the Vibrio genus and 14 species represented 97-99% similarity species in accordance with the 16S rRNA sequence in database, namely: Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio cholerae, Vibrio neocaledonicus, Vibrio mimicus, Vibrio azureus, Vibrio diabolicus, Vibrio tapetis, Vibrio natriegens, and Vibrio owensii. The most dominant number of Vibrio isolates was V. alginolyticus, while the lowest was V. owensii. The highest number of Vibrio species in green mussels was found in Goa Cemara beach while the lowest was in Kwaru beach. Vibrio spp bacteria found in green clams in coastal tourism areas in Yogyakarta have close phylogenetic relationships with other Vibrio in seafood in Indonesian coastal waters.

scholarly journals THE 16S rRNA GENE MARKER-BASED MOLECULAR IDENTIFICATION OF CULTURABLE COLIFORM BACTERIA ISOLATED FROM FORAMINIFERA CALCARINA DERIVED FROM PRAMUKA ISLAND WATERS, THE SERIBU ISLAND DISTRICT, JAKARTA PROVINCE

2020 ◽  
Vol 13 (1) ◽  
pp. 10-18
Author(s):  
Mochamad Untung Kurnia - Agung ◽  
Agus Tri Askar ◽  
Yuli Andriani ◽  
Lintang Permatasari Yuliadi
Keyword(s):  
Coral Reef ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Identification ◽  
Bay Of Bengal ◽  
Coliform Bacteria ◽  
Gene Marker ◽  
Rrna Gene ◽  
Gene Markers ◽  
The 16S Rrna Gene

Contamination of coliform bacteria in benthic foraminifera has been reported due to pollution of organic wastes in the aquatic environment around coral reef ecosystems and this event was known to interfere the process of foraminifera shell formation which in turn resulted the disruption of the role of foraminifera in the process of formation of coral reef bottom sediments. The aim of this research is to identify the isolates of culturable coliform bacteria that contaminate foraminifera Calcarina species isolated from the waters of the Pramuka Island, the Seribu Island district, Jakarta Province using the 16S rRNA gene markers. Foraminifera sampling was carried out in the waters of Pramuka Island, the Seribu Island district, Jakarta Province in 5 (five) stations, while the process of bacterial isolation and molecular identification were carried out at the Laboratory of Microbiology and Molecular Biotechnology (MICROMOL), Faculty of Fisheries and Marine Sciences (FPIK), University Padjadjaran. Molecular identification was carried out using the Polymerase Chain Reaction (PCR) method based on the 16S rRNA gene markers. Sequencing is done by sending PCR results to 1st Base, sequencing service company, in Singapore and then, the aligning of sequencing results with databases in genBank was done using  the Basic Local Alignment Search Tool (BLASTTM) program available on the National Center for Biotechnology Information (NCBI) website. The results of 16S rRNA gene amplification from the five isolates produced amplicons of ± 1400 bp length with concentrations ranging from 157.5 µg / mL-230 µg / mL and with a purity ratio ranging from 1.477-1.769. While the results of BLAST and phylogenetic analysis showed that the five isolates were closely related to the isolate Eschericia coli strain inspire99 (Acc No. JQ315935.1), which was isolated from the waters of the Bay of Bengal, India. These results also indicate the existence of ecological connectivity between the waters of the Bay of Bengal in India and the waters of Pramuka Island in Indonesia.

scholarly journals Evaluasi Deteksi Berbasis PCR untuk Bakteri Bifidobacterium longum dalam Sampel Feses Bayi dari Kota Manado

2020 ◽  
Vol 20 (1) ◽  
pp. 18
Author(s):  
Beivy Jonathan Kolondam
Keyword(s):  
Polymerase Chain Reaction ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Detection Method ◽  
Bifidobacterium Longum ◽  
Local Alignment ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Search Tool ◽  
Polymerase Chain

Bifidobakteria merupakan mikroflora yang umum hidup dalam usus manusia sejak bayi. Peran Bifidobacterium longum yang positif sebagai salah satu bakteri yang menunjang kesehatan inangnya membuat bakteri ini menjadi objek studi yang menarik. Salah satu instrumen dalam penelitian adalah adalah metode deteksi bakteri B. longum yang berbasis PCR (Polymerase Chain Reaction) gen 16S rRNA. Dengan mempertimbangkan bahwa perancangan primer untuk deteksi ini sudah lebih dari 20 tahun, penelitian ini bertujuan mengevaluasi hasil deteksi melalui PCR terhadap B. longum dalam feses bayi. Akurasi hasil dilihat melalui sekuensing terhadap hasil PCR sampel yang terdeteksi positif. Dua sampel feses bayi di Manado yang diperiksa menunjukkan hasil positif dan produk PCR tersebut dilakukan sekuensing. Panjang DNA yang nyata dari hasil deteksi ini yaitu 829 bp dan bukan 831 bp. Sekuens DNA kedua sampel ini identik satu sama lain. Hasil BLAST (Basic Local Alignment Search Tool) mengonfirmasi kesamaan 100% (identik) dari kedua specimen dari Kota Manado dengan sekuens gen 16S rRNA specimen bakteri B. longum yang telah ada dalam GenBank.Kata-kata kunci: Bifidobacterium longum, Polymerase Chain Reaction, deteksi, feses, bayi. Evaluation of PCR-Based Detection for Bifidobacterium longum in Infant Fecal Samples from Manado City ABSTRACTBifidobacteria are common members of the gut microflora of humans since infant. The Bifidobacterium longum has positive roles and one of supportive bacteria to the host, which made interesting as a study object. One instrument in studying this bacterial species is the detection method based on PCR of 16S rRNA gene. In consideration of the design of primers for this detection method is already more than 20 years, this research aimed to evaluate the PCR-based detection of B. longum in infant feces. The accuracy of the method was evaluated from sequencing of DNA fragment from positive results. Two fecal samples in Manado City shown positive result were sent for sequencing. The actual length of DNA amplified by PCR was 829 bp, not 831 bp. The DNA sequence of both samples were identical to each other. The BLAST (Basic Local Alignment Search Tool) result confirmed the similarity of both samples from Manado with 16S rRNA gene sequence of B. longum specimens in GenBank.Keywords: Bifidobacterium longum, Polymerase Chain Reaction, detection, feces, infant.

scholarly journals Molecular identification of genus Pipistrellus (Mammalia: Chiroptera) from Fata region, Pakistan

2023 ◽  
Vol 83 ◽  
Author(s):  
M. Idnan ◽  
A. Javid ◽  
M. Tayyab ◽  
A. Hussain ◽  
S. Mansoor ◽  
...  
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Molecular Identification ◽  
Dna Sequences ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Morphometric Measurements ◽  
Tree Analysis ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Abstract A total of 10 specimens were captured from selected sites of Bajaur Agency FATA, Pakistan using mist nets. The captured specimens were morphologically identified and various morphometric measurements were taken. The head and Body length (HB) of Pipistrellus coromondra and Pipistrellus kuhlii lepidus (n=10) was 43±0.11 mm and 45±1.1 respectively. Morphologically identified Pipistrellus kuhlii confirmed as Pipistrellus kuhlii lepidus based on 16S rRNA sequences. The DNA sequences were submitted to GenBank and accession numbers were obtained (MN 719478 and MT430902). The available 16S rRNA gene sequences of Pipistrellus coromondra and Pipistrellus kuhlii lepidus were retrieved from NCBI and incorporated in N-J tree analysis. Overall, the interspecific genetic variations among Pipistrellus coromondra and Pipistrellus kuhlii lepidus were 8% and 1% respectively. In our recommendation, a comprehensive molecular identification of bats is need of hour to report more cryptic and new species from Pakistan.

Isolation and Molecular Characterization of Riemerella anatipestifer from Domesticated Ducks of Assam, India

2021 ◽  
Author(s):  
M.K. Doley ◽  
S. Das ◽  
R.K. Sharma ◽  
P. Borah ◽  
D.K. Sarma ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Molecular Identification ◽  
Rrna Gene ◽  
Eastern Region ◽  
Riemerella Anatipestifer ◽  
Field Samples ◽  
Apparently Healthy

Background: Riemerella anatipestifer (R. anatipestifer) is a gram negative, microaerophilic, non-motile, bipolar bacteria. High genetic diversity and molecular differentiation were reported among field isolates. Although the bacterium causes one of the most economically important duck diseases in the north-eastern region of India, little work has been done on isolation, identification and molecular characterization of the bacteria. Hence, the present investigation was undertaken with a view to characterize the R. anatipestifer isolates from ducks of Assam.Methods: Phenotypic and molecular identification of R. anatipestifer isolates from domesticated ducks of Assam, India were carried out during the period from February, 2019 to January 2020. A total of 624 samples (Ocular swab, throat swab, liver, spleen, kidney, brain, heart, lung) from ducks comprising of apparently healthy, ailing and dead ducks were collected from five districts of Assam, India were processed to isolate and identify the bacteria. The tentative identification of the bacteria was done based on phenotypic characteristics viz., colony morphology, growth characteristics and biochemical reactions. All the phenotypically positive isolates were further subjected to molecular identification based on PCR assay targeting 16S rRNA gene and ERIC sequence.Result: The bacteria could be isolated from different field samples. The highest percentage of the samples that yielded the bacteria are from brain (76%) followed by spleen (74%) of dead ducks and less number of ocular swab (33%) from apparently healthy ducks were found positive. Sequencing of the amplified product of the selected R. anatipestifer isolates targeting 16S rRNA gene revealed homology percentage of 96.5-100%. Further, sequences representing five geographical locations were submitted to NCBI gene bank. Phylogenetic studies of the isolates indicated that there is prevalence of at least two genetically different strains of R. anatipestifer in the study area. The study suggested that the R. anatipestifer infection is endemic in Assam causing varying rate of morbidity (39%) and mortality (53%) and molecular based confirmation is necessary besides phenotypic identification.

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