scholarly journals Use of 16s rRNA to identify non-lactose-fermenting bacilli and molecular detection of ESBL resistance genes associated with hospital-acquired infection in Soba University Hospital, Sudan

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1311
Author(s):  
Wissam Ahmed Al Hag ◽  
Hana Elbadawi ◽  
Muzamil Mahdi Abdel Hamid
Keyword(s):  
Pseudomonas Aeruginosa ◽  
16S Rrna ◽  
Resistance Genes ◽  
University Hospital ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Biochemical Tests ◽  
Gram Negative ◽  
Hospital Acquired Infections ◽  
Hospital Acquired

Background: Non-lactose-fermenting gram-negative bacilli (NLFGNB) have become significant nosocomial pathogens and often exhibit intrinsic multidrug resistance. Sequencing of 16s rRNA genes could be utilized for robust identification of NLFGNB. This study aimed to identify resistant NLFGNB associated with hospital-acquired infections using 16s rRNA sequencing and to detect the extended-spectrum β-lactamase (ESBL) genes of isolates in Soba Hospital, Khartoum State, Sudan. Methods: A prospective, cross-sectional, laboratory-based study was conducted from October 2017 to March 2018 at the Microbiology Department of Soba University Hospital. A total of 100 randomly selected NLFGNB samples were isolated from blood and urine during the time of the study. All the isolates were identified using standard biochemical tests and antimicrobial sensitivity testing, 16s rRNA gene sequencing, and bioinformatics techniques. Results: The biochemical tests revealed that, out of the 100 NLFGNB isolates, the Pseudomonas species was predominant (57 isolates), followed by gram-negative bacilli (33 isolates), Coccobacilli (9 isolates) and Coliform (1 isolate) species. Sequencing of 16s rRNA genes identified all the resistant isolates at the species level: Pseudomonas aeruginosa (26%), Acinetobacter baumannii (22%), Burkholderia cepacia (13%), Stenotrophomonas maltophilia (10%), Enterococcus species (E. faecalis, E. faecium) (10%), and other GNB (Acinetobacter variabilis, Klebsiella pneumoniae, Morganella morganii, Escherichia fergusonii, Enterobacter hormaechei and Pseudomonas stutzeri) (19%). The antimicrobial susceptibility tests indicated that 31 isolates were resistant to at least three classes of antibiotics and contain the highest level of ESBL resistance genes. Conclusions: Pseudomonas aeruginosa and Acinetobacter baumannii were the most widely recognized NLFGNB identified from hospital-acquired infections in Soba hospital. Among the NLFGNB, antimicrobial resistance and ESBL resistance genes were observed at a high frequency.

scholarly journals High-Quality Complete Genome Sequences of Three Pseudomonas aeruginosa Isolates Retrieved from Patients Hospitalized in Intensive Care Units

2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Bárbara Magalhães ◽  
Laurence Senn ◽  
Dominique S. Blanc
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Intensive Care ◽  
Intensive Care Units ◽  
Genome Sequences ◽  
High Quality ◽  
Gram Negative ◽  
Content Type ◽  
Hospital Acquired Infections ◽  
Hospital Acquired ◽  
High Quality Genome

Pseudomonas aeruginosa is one of the major Gram-negative pathogens responsible for hospital-acquired infections. Here, we present high-quality genome sequences of isolates from three P. aeruginosa genotypes retrieved from patients hospitalized in intensive care units.

scholarly journals Cultivation-Independent Examination of Horizontal Transfer and Host Range of an IncP-1 Plasmid among Gram-Positive and Gram-Negative Bacteria Indigenous to the Barley Rhizosphere

2006 ◽  
Vol 72 (10) ◽  
pp. 6687-6692 ◽  
Author(s):  
Sanin Musovic ◽  
Gunnar Oregaard ◽  
Niels Kroer ◽  
Søren J. Sørensen
Keyword(s):  
16S Rrna ◽  
Host Range ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gram Positive ◽  
Gram Negative ◽  
Indigenous Bacteria ◽  
Transfer Frequency

ABSTRACTThe host range and transfer frequency of an IncP-1 plasmid (pKJK10) among indigenous bacteria in the barley rhizosphere was investigated. A new flow cytometry-based cultivation-independent method for enumeration and sorting of transconjugants for subsequent 16S rRNA gene classification was used. Indigenous transconjugant rhizosphere bacteria were collected by fluorescence-activated cell sorting and identified by cloning and sequencing of 16S rRNA genes from the sorted cells. The host range of the pKJK10 plasmid was exceptionally broad, as it included not only bacteria belonging to the alpha, beta, and gamma subclasses of theProteobacteria, but alsoArthrobactersp., a gram-positive member of theActinobacteria. The transfer frequency (transconjugants per donor) from thePseudomonas putidadonor to the indigenous bacteria was 7.03 × 10−2± 3.84 × 10−2. This is the first direct documentation of conjugal transfer between gram-negative donor and gram-positive recipient bacteria in situ.

scholarly journals Draft Genome Sequences of Pseudomonas aeruginosa Isolates from Wounded Military Personnel: TABLE 1 

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Brock A. Arivett ◽  
Dave C. Ream ◽  
Steven E. Fiester ◽  
Destaalem Kidane ◽  
Luis A. Actis
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Military Personnel ◽  
Draft Genome ◽  
Multidrug Resistant ◽  
Negative Bacterium ◽  
Genome Sequences ◽  
Gram Negative ◽  
Hospital Acquired Infections ◽  
Extensive Drug Resistance ◽  
Hospital Acquired

Pseudomonas aeruginosa , a Gram-negative bacterium that causes severe hospital-acquired infections, is grouped as an ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa , and Enterobacter species) pathogen because of its extensive drug resistance phenotypes and effects on human health worldwide. Five multidrug resistant P. aeruginosa strains isolated from wounded military personnel were sequenced and annotated in this work.

scholarly journals Intracellular Symbionts and Other Bacteria Associated with Deer Ticks (Ixodes scapularis) from Nantucket and Wellfleet, Cape Cod, Massachusetts

2004 ◽  
Vol 70 (1) ◽  
pp. 616-620 ◽  
Author(s):  
Micah J. Benson ◽  
Jeffrey D. Gawronski ◽  
Douglas E. Eveleigh ◽  
David R. Benson
Keyword(s):  
16S Rrna ◽  
Ixodes Scapularis ◽  
Pcr Amplification ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cape Cod ◽  
Intracellular Bacteria ◽  
Cloning And Sequencing ◽  
Gram Negative ◽  
Insect Symbionts

ABSTRACT The diversity of bacteria associated with the deer tick (Ixodes scapularis) was assessed using PCR amplification, cloning, and sequencing of 16S rRNA genes originating from seven ticks collected from Nantucket Island and Wellfleet, Cape Cod, Mass. The majority of sequences obtained originated from gram-negative proteobacteria. Four intracellular bacteria were detected including strains of Ehrlichia, Rickettsia, and Wolbachia and an organism related to intracellular insect symbionts from the Cytophaga-Flavobacterium-Bacteroides group. Several strains of members of the Sphingomonadaceae were also detected in all but one tick. The results provide a view of the diversity of bacteria associated with I. scapularis ticks in the field.

scholarly journals Carriage of two carbapenem-resistance genes in Pseudomonas aeruginosa isolated from hospital-acquired infections in children from Costa Rica: the importance of local epidemiology

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Cristian Pérez-Corrales ◽  
Valeria Peralta-Barquero ◽  
Christopher Mairena-Acuña
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Costa Rica ◽  
Resistance Genes ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Middle Income ◽  
Hospital Acquired Infections ◽  
Antimicrobial Resistance Genes ◽  
Hospital Acquired

Abstract Background The assessment of Hospital-acquired infections due to multidrug-resistant bacteria involves the use of a variety of commercial and laboratory-developed tests to detect antimicrobial resistance genes in bacterial pathogens; however, few are evaluated for use in low- and middle-income countries. Methods We used whole-genome sequencing, rapid commercial molecular tests, laboratory-developed tests and routine culture testing. Results We identified the carriage of the metallo-β-lactamase blaVIM-2 and blaIMP-18 alleles in Carbapenem-Resistant Pseudomonas aeruginosa infections among children in Costa Rica. Conclusions The blaIMP-18 allele is not present in the most frequently used commercial tests; thus, it is possible that the circulation of this resistance gene may be underdiagnosed in Costa Rica.

scholarly journals Isolation, biochemical characterization and phylogeny of a cellulose-degrading ruminal bacterium

2019 ◽  
Vol 32 (2) ◽  
pp. 117-125
Author(s):  
Lorena Luna ◽  
David Hernández ◽  
Hilda V Silva ◽  
Mario A Cobos ◽  
Sergio S González ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Congo Red ◽  
Biochemical Characterization ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cellulolytic Activity ◽  
Cellulolytic Bacteria ◽  
Biochemical Tests ◽  
Culture Techniques

Background: The isolation of cellulolytic bacteria, which hydrolyze cellulose to cellobiose and glucose, can provide useful information about rumen diversity. Objective: To identify and characterize a microorganism capable of hydrolyzing cellulose, isolated from a cow rumen. Methods: Anaerobic culture techniques were used for isolating cellulose-degrading rumen bacteria. Congo red staining was used to evaluate β-D-glucanase activity, and carbohydrate fermentation pattern was obtained with the kit API 50CHB/E. DNA extraction was performed and the 16S rDNA gene was amplified using 8F (5'-AGA GTT TGA TCC TGG CTC AG-3'), and 1492R (5' GGT TAC CTT GTT ACG ACT T 3') primers. The phylogenetic tree was reconstructed with the algorithm of maximum parsimony (bootstrap 5000), and 16S rDNA sequence was deposited in the NCBI database (accession number: KM094184). Results: The isolated bacterium showed cellulolytic activity detected with Congo red; besides, glycerol, ribose, xylose, sucrose, galactose and glucose were fermented by this bacterium. However, biochemical tests did not identify the bacteria because no match was found at database of API WEB Software. The phylogenetic inference indicated that this bacterium belongs to Shigella genus, with 98% maximal identity respect to the other taxonomic species. Conclusions: Phylogenetic analysis of 16S rRNA genes showed that the rumen isolated bacterium was a member of the genus Shigella, which, under mesophilic conditions, is an interesting candidate for obtaining oligosaccharides from lignocellulosic biomass.Keywords: cellulolytic, fermentation, monophyletic, rumen, Shigella. Resumen Antecedentes: El aislamiento de las bacterias celulolíticas, que hidrolizan la celulosa a celobiosa y glucosa, proporciona valiosa información sobre la diversidad del rumen,. Objetivo: Identificar y caracterizar un microorganismo capaz de hidrolizar celulosa, aislado de un rumen vacuno. Métodos: Se utilizaron técnicas de cultivo anaeróbico para aislar bacterias ruminales que degradan celulosa. La tinción con rojo Congo se usó para evaluar la actividad β-D-glucanasa y el patrón de fermentación de carbohidratos se obtuvo con el kit API 50CHB/E. Se realizó la extracción de DNA y se amplificó el gen de 16S rDNA utilizando los cebadores 8F (5'-AGA GTT TGA TCC TGG CTC AG-3'), y 1492R (5' GGT TAC CTT GTT ACG ACT T 3'). El árbol filogenético se reconstruyó con el algoritmo de máxima parsimonia (replicas 5000) y la secuencia 16S rDNA se depositó en la base de datos del NCBI (número de acceso: KM094184). Resultados: La bacteria aislada mostró actividad celulolítica detectada con la tinción de rojo Congo; además, esta bacteria fermenta glicerol, ribosa, xilosa, sacarosa, galactosa y glucosa. Sin embargo, las pruebas bioquímicas no permitieron identificar a la bacteria aislada, por no encontrar coincidencias en la base de datos del software API WEB. La inferencia filogenética indicó que esta bacteria pertenece al género Shigella, con 98% de identidad máxima respecto a las otras especies taxonómicas. Conclusiones: El análisis filogenético del gen 16S rRNA mostró que la bacteria aislada del rumen es un miembro del género Shigella que, en condiciones mesófilas, es un candidato interesante para obtener oligosacáridos a partir de biomasa lignocelulósica.Palabras clave: celulolítica, fermentación, monofilético, rumen, Shigella. ResumoAntecedentes: As bactérias celulolíticas hidrolizam a celulosa em celobiose e glicose, e o isolamento desses microrganismos fornece informações sobre a diversidade do rúmen. Objetivo: Identificar e caracterizar um microorganismo isolada do rúmen de uma vaca, com capacidade para hidrolisar a celulose. Métodos: Técnicas de cultura anaeróbica foram utilizadas para isolar bactérias ruminais que degradam a celulose. A atividade β-D-glucanase foi mostrada utilizando mancha de vermelho Congo, e o padrão de fermentação de carbohidratos foi obtida com o kit API 50CHB/E. A extracção foi realizada de DNA e amplificou-se os genes 16S rDNA utilizando os iniciadores 8F (AGA GTT TGA 5'-TCC TGG CTC AG-3'), e 1492R (5' CTT GGT TAC GTT ACG TCA T 3'). A árvore filogenética foi reconstruída com o algoritmo de máxima parcimônia (réplicas 5000). A sequência de rDNA 16S foi depositada no banco de dados do NCBI (número de acesso: KM094184). Resultados: O isolado mostrou uma atividade celulolítica com coloração vermelho Congo; además esta bactéria fermentação de glicerol, ribose, xilose, sacarose, galactose e glicose. No entanto, com as provas bioquímicas não se identificou a bactérias isolada, já que não se encontrou na base de dados do software API WEB. A inferência filogenética indicou que esta bactéria pertence ao género Shigella, com 98% de identidade de máximo respeito para outras espécies taxonômicas. Conclusão: A análise filogenética do gene 16S rRNA mostrou as bactérias isoladas do ambiente ruminal como um membro do género Shigella, que condições mesofilicas é um candidato atraente para obter oligossacarídeos da biomassa lignocelulósica.Palavras-chave: celulolítica, fermentação, monofilético, rúmen, Shigella.

scholarly journals 16S rRNA Mutation-Mediated Tetracycline Resistance in Helicobacter pylori

2002 ◽  
Vol 46 (9) ◽  
pp. 2996-3000 ◽  
Author(s):  
Monique M. Gerrits ◽  
Marcel R. de Zoete ◽  
Niek L. A. Arents ◽  
Ernst J. Kuipers ◽  
Johannes G. Kusters
Keyword(s):  
Helicobacter Pylori ◽  
16S Rrna ◽  
Resistance Genes ◽  
Base Pair ◽  
Tetracycline Resistance ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Tetracycline Resistance Genes ◽  
Base Pair Substitution ◽  
H Pylori

ABSTRACT Most Helicobacter pylori strains are susceptible to tetracycline, an antibiotic commonly used for the eradication of H. pylori. However, an increase in incidence of tetracycline resistance in H. pylori has recently been reported. Here the mechanism of tetracycline resistance of the first Dutch tetracycline-resistant (Tetr) H. pylori isolate (strain 181) is investigated. Twelve genes were selected from the genome sequences of H. pylori strains 26695 and J99 as potential candidate genes, based on their homology with tetracycline resistance genes in other bacteria. With the exception of the two 16S rRNA genes, none of the other putative tetracycline resistance genes was able to transfer tetracycline resistance. Genetic transformation of the Tets strain 26695 with smaller overlapping PCR fragments of the 16S rRNA genes of strain 181, revealed that a 361-bp fragment that spanned nucleotides 711 to 1071 was sufficient to transfer resistance. Sequence analysis of the 16S rRNA genes of the Tetr strain 181, the Tets strain 26695, and four Tetr 26695 transformants showed that a single triple-base-pair substitution, AGA926-928→TTC, was present within this 361-bp fragment. This triple-base-pair substitution, present in both copies of the 16S rRNA gene of all our Tetr H. pylori transformants, resulted in an increased MIC of tetracycline that was identical to that for the Tetr strain 181.

scholarly journals Molecular Survey of the Occurrence of Legionella spp., Mycobacterium spp., Pseudomonas aeruginosa, and Amoeba Hosts in Two Chloraminated Drinking Water Distribution Systems

2012 ◽  
Vol 78 (17) ◽  
pp. 6285-6294 ◽  
Author(s):  
Hong Wang ◽  
Marc Edwards ◽  
Joseph O. Falkinham ◽  
Amy Pruden
Keyword(s):  
Pseudomonas Aeruginosa ◽  
16S Rrna ◽  
Distribution Systems ◽  
Water Distribution ◽  
Opportunistic Pathogen ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Drinking Water Distribution Systems ◽  
Drinking Water Distribution

ABSTRACTThe spread of opportunistic pathogens via public water systems is of growing concern. The purpose of this study was to identify patterns of occurrence among three opportunistic pathogens (Legionella pneumophila,Mycobacterium avium, andPseudomonas aeruginosa) relative to biotic and abiotic factors in two representative chloraminated drinking water distribution systems using culture-independent methods. Generally, a high occurrence ofLegionella(≥69.0%) and mycobacteria (100%), lower occurrence ofL. pneumophila(≤20%) andM. avium(≤33.3%), and rare detection ofPseudomonas aeruginosa(≤13.3%) were observed in both systems according to quantitative PCR. Also,Hartmanella vermiformiswas more prevalent thanAcanthamoeba, both of which are known hosts for opportunistic pathogen amplification, the latter itself containing pathogenic members. Three-minute flushing served to distinguish distribution system water from plumbing in buildings (i.e., premise plumbing water) and resulted in reduced numbers of copies ofLegionella, mycobacteria,H. vermiformis, and 16S rRNA genes (P< 0.05) while yielding distinct terminal restriction fragment polymorphism (T-RFLP) profiles of 16S rRNA genes. Within certain subgroups of samples, some positive correlations, including correlations of numbers of mycobacteria and total bacteria (16S rRNA genes),H. vermiformisand total bacteria, mycobacteria andH. vermiformis, andLegionellaandH. vermiformis, were noted, emphasizing potential microbial ecological relationships. Overall, the results provide insight into factors that may aid in controlling opportunistic pathogen proliferation in real-world water systems.

scholarly journals Simulated Winter Incubation of Soil With Swine Manure Differentially Affects Multiple Antimicrobial Resistance Elements

2020 ◽  
Vol 11 ◽  
Author(s):  
Daniel N. Miller ◽  
Madison E. Jurgens ◽  
Lisa M. Durso ◽  
Amy M. Schmidt
Keyword(s):  
Antibiotic Resistance ◽  
16S Rrna ◽  
Relative Abundance ◽  
Resistance Genes ◽  
Swine Manure ◽  
The United States ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Manure Application ◽  
Background Soil

Gastrointestinal bacteria that harbor antibiotic resistance genes (ARG) become enriched with antibiotic use. Livestock manure application to cropland for soil fertility presents a concern that ARG and bacteria may proliferate and be transported in the environment. In the United States, manure applications typically occur during autumn with slow mineralization until spring planting season. A laboratory soil incubation study was conducted mimicking autumn swine manure application to soils with concentrations of selected ARG monitored during simulated 120-day winter incubation with multiple freeze-thaw events. Additionally, the effects of two soil moistures [10 and 30% water holding capacity (WHC)] and two manure treatments [raw versus hydrated lime alkaline stabilization (HLAS)] were assessed. Fourteen tetracycline resistance genes were evaluated; tet(D), tet(G), and tet(L) were detected in background soil while swine manure contained tet(A), tet(B), tet(C), tet(G), tet(M), tet(O), tet(Q), and tet(X). By day 120, the manure-borne tet(M) and tet(O) were still detected while tet(C), tet(D), tet(L), and tet(X) genes were detected less frequently. Other tet resistance genes were detected rarely, if at all. The sum of unique tet resistance genes among all treatments decreased during the incubation from an average of 8.9 to 3.8 unique tet resistance genes. Four resistance elements, intI1, blactx–m–32, sul(I), erm(B), and 16s rRNA genes were measured using quantitative PCR. ARG abundances relative to 16S abundance were initially greater in the raw manure compared to background soil (−1.53 to −3.92 log abundance in manure; −4.02 to &lt;−6.7 log abundance in soil). In the mixed manure/soil, relative abundance of the four resistance elements decreased (0.87 to 1.94 log abundance) during the incubation largely because 16S rRNA genes increased by 1.21 log abundance. Throughout the incubation, the abundance of intI1, blactx–m–32, sul(I), and erm(B) per gram in soil amended with HLAS-treated manure was lower than in soil amended with raw manure. Under low initial soil moisture conditions, HLAS treatment reduced the abundance of intI1 and resulted in loss of blactx–m–32, sul(I), and erm(B)] compared to other treatment-moisture combinations. Although one might expect antibiotic resistance to be relatively unchanged after simulated winter manure application to soil, a variety of changes in diversity and relative abundance can be expected.

Chromosomal Arsenic Resistance Genes from Sulfobacillus Thermosulfidooxidans and a Demonstration that the Genetic Diversity of arsB among the Sulfobacilli is Similar to that of their 16S rRNA Genes

2009 ◽  
Vol 71-73 ◽  
pp. 171-174 ◽  
Author(s):  
J. Arrie van der Merwe ◽  
Shelly M. Deane ◽  
Douglas E. Rawlings
Keyword(s):  
Escherichia Coli ◽  
16S Rrna ◽  
Resistance Genes ◽  
Southern Hybridization ◽  
Sequence Data ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Arsenic Resistance ◽  
Moderately Thermophilic ◽  
Sulfobacillus Thermosulfidooxidans

Arsenic resistance genes were isolated from the moderately thermophilic, Gram-positive iron and sulfur-oxidizing bacterium, Sulfobacillus thermosulfidooxidans. Only arsR and arsB genes were present and attempts to identify an arsC using degenerate PCR primers or dependent arsC genes as probes in Southern hybridization experiments were unsuccessful. Although enhanced resistance to arsenite was not detected when the ars genes were cloned in Escherichia coli, the kumamolisin-As and arsRB genes were induced by arsenite. RT-PCR experiments suggested that transcription of the cloned kumamolisin-As-like and arsRB genes is linked in Escherichia coli, but not in Sb. thermosulfidooxidans. The gene order kumamolisin-As precursor, arsR and arsB was maintained among three strains of Sb. thermosulfidooxidans isolated from three continents. Southern hybridization using a Sb. thermosulfidooxidans arsB gene fragment as a probe gave a positive hybridization signal using S. acidophilus but not with S. thermotolerans genomic DNA. Comparison of partial sequence data of the arsB and 16S rRNA genes suggested that the two types of genes have undergone a similar evolutionary history and therefore that the arsB genes were present in the ancestral Sulfobacillus before its divergence into species.

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