scholarly journals Association between 16S rRNA gene mutations and susceptibility to amikacin in Mycobacterium avium Complex and Mycobacterium abscessus clinical isolates

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Su-Young Kim ◽  
Dae Hun Kim ◽  
Seong Mi Moon ◽  
Ju Yeun Song ◽  
Hee Jae Huh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Mycobacterium Avium ◽  
Inhibitory Concentration ◽  
Gene Mutations ◽  
Mycobacterium Abscessus ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
High Level ◽  
Culture Conversion

AbstractWe evaluated the association between 16S rRNA gene (rrs) mutations and susceptibility in clinical isolates of amikacin-resistant nontuberculous mycobacteria (NTM) in NTM-pulmonary disease (PD) patients. Susceptibility was retested for 134 amikacin-resistant isolates (minimum inhibitory concentration [MIC] ≥ 64 µg/ml) from 86 patients. Amikacin resistance was reconfirmed in 102 NTM isolates from 62 patients with either Mycobacterium avium complex-PD (MAC-PD) (n = 54) or M. abscessus-PD (n = 8). MICs and rrs mutations were evaluated for 318 single colonies from these isolates. For the 54 MAC-PD patients, rrs mutations were present in 34 isolates (63%), comprising all 31 isolates with amikacin MICs ≥ 128 µg/ml, but only three of 23 isolates with an MIC = 64 µg/ml. For the eight M. abscessus-PD patients, all amikacin-resistant (MIC ≥ 64 µg/ml) isolates had rrs mutations. In amikacin-resistant isolates, the A1408G mutation (n = 29) was most common. Two novel mutations, C1496T and T1498A, were also identified. The culture conversion rate did not differ by amikacin MIC. Overall, all high-level and 13% (3/23) of low-level amikacin-resistant MAC isolates had rrs mutations whereas mutations were present in all amikacin-resistant M. abscessus isolates. These findings are valuable for managing MAC- and M. abscessus-PD and suggest the importance of phenotypic and genotypic susceptibility testing.

scholarly journals Association Between 16S rRNA Gene Mutations and Susceptibility to Amikacin in Mycobacterium avium Complex and Mycobacterium Abscessus Clinical Isolates

2020 ◽  
Author(s):  
Su-Young Kim ◽  
Dae Hun Kim ◽  
Seong Mi Moon ◽  
Ju Yeun Song ◽  
Hee Jae Huh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Mycobacterium Avium ◽  
Inhibitory Concentration ◽  
Gene Mutations ◽  
Mycobacterium Abscessus ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
Novel Mutations ◽  
Culture Conversion

Abstract We evaluated the association between 16S rRNA gene (rrs) mutations and susceptibility in amikacin-resistant nontuberculous mycobacterial (NTM) clinical isolates in NTM- pulmonary disease (PD) patients. Susceptibility was retested for 134 amikacin-resistant isolates (minimum inhibitory concentration [MIC] ≥64 µg/ml) from 86 patients. Amikacin resistance was reconfirmed in 102 NTM isolates from 62 patients with either Mycobacterium avium complex-PD (MAC-PD) (n=54) or M. abscessus-PD (n=8). MIC and rrs mutations were evaluated for 318 single colonies from these isolates. For the 54 MAC-PD patients, rrs mutations were present in all isolates (obtained from 31 patients) with an amikacin MIC ≥128 µg/ml, but only in a few isolates (from three of 23 patients) with an MIC=64 µg/ml. For the eight M. abscessus-PD patients, all amikacin-resistant isolates (MIC ≥64 µg/ml) had rrs mutations. Of amikacin resistance isolates, A1408G mutation (n=29) was most common. Two novel mutations, C1496T and T1498A, were also identified. The culture conversion rate did not differ by amikacin MIC (20% for MIC=64µg/ml vs. 7% for MIC ≥128 µg/ml, p=0.468). In conclusion, all amikacin-resistant M. abscessus isolates had rrs mutations, but in MAC isolates showing relatively low resistance (MIC=64µg/ml), rrs mutations were infrequently identified.

scholarly journals Effects of 16S rRNA Gene Mutations on Tetracycline Resistance in Helicobacter pylori

2003 ◽  
Vol 47 (9) ◽  
pp. 2984-2986 ◽  
Author(s):  
Monique M. Gerrits ◽  
Marco Berning ◽  
Arnoud H. M. Van Vliet ◽  
Ernst J. Kuipers ◽  
Johannes G. Kusters
Keyword(s):  
Helicobacter Pylori ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Base Pair ◽  
Gene Mutations ◽  
Tetracycline Resistance ◽  
Rrna Gene ◽  
H Pylori ◽  
High Level ◽  
Double Base

ABSTRACT The triple-base-pair 16S rDNA mutation AGA926-928→TTC mediates high-level tetracycline resistance in Helicobacter pylori. In contrast, single- and double-base-pair mutations mediated only low-level tetracycline resistance and decreased growth rates in the presence of tetracycline, explaining the preference for the TTC mutation in tetracycline-resistant H. pylori isolates.

Identification of non-tuberculous mycobacteria: utility of the GenoType Mycobacterium CM/AS assay compared with HPLC and 16S rRNA gene sequencing

2009 ◽  
Vol 58 (7) ◽  
pp. 900-904 ◽  
Author(s):  
Andie S. Lee ◽  
Peter Jelfs ◽  
Vitali Sintchenko ◽  
Gwendolyn L. Gilbert
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Rapid Identification ◽  
Mycobacterium Abscessus ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Clinically Significant ◽  
Species Specific

Non-tuberculous mycobacteria (NTM) causing clinical disease have become increasingly common and more diverse. A new reverse line probe assay, GenoType Mycobacterium CM/AS (Hain Lifescience), was evaluated for identification of a broad range of NTM. It was compared with phenotypic (HPLC) and molecular (DNA probes, in-house real-time multiplex species-specific PCR, 16S rRNA gene PCR and sequencing) identification techniques, which together provided the reference ‘gold standard’. A total of 131 clinical isolates belonging to 31 Mycobacterium species and 19 controls, including 5 non-Mycobacterium species, was used. Concordant results between the GenoType Mycobacterium assay and the reference identification were obtained in 119/131 clinical isolates (90.8 %). Identification of Mycobacterium abscessus and Mycobacterium lentiflavum by the assay was problematic. The GenoType Mycobacterium assay enables rapid identification of a broad range of potentially clinically significant Mycobacterium species, but some species require further testing to differentiate or confirm ambiguous results.

Rapid macrolide and amikacin resistance testing for Mycobacterium abscessus in people with cystic fibrosis

2021 ◽  
Vol 70 (4) ◽  
Author(s):  
Amanda Bordin ◽  
Sushil Pandey ◽  
Christopher Coulter ◽  
Melanie Syrmis ◽  
Carolyn Pardo ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Real Time ◽  
Real Time Pcr ◽  
Gene Mutations ◽  
Mycobacterium Abscessus ◽  
Molecular Methods ◽  
Rrna Gene ◽  
The Real

Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively. Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation. Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC. Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing. Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples. Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.

scholarly journals Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3965-3970 ◽  
Author(s):  
Estelle Jumas-Bilak ◽  
Philippe Bouvet ◽  
Emma Allen-Vercoe ◽  
Fabien Aujoulat ◽  
Paul A. Lawson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Clinical Isolates ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5–91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).

scholarly journals Mycobacterium parascrofulaceum sp. nov., novel slowly growing, scotochromogenic clinical isolates related to Mycobacterium simiae

2004 ◽  
Vol 54 (5) ◽  
pp. 1543-1551 ◽  
Author(s):  
C. Y. Turenne ◽  
V. J. Cook ◽  
T. V. Burdz ◽  
R. J. Pauls ◽  
L. Thibert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Great Part ◽  
16S Rrna Gene Sequencing ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
Culture Collections ◽  
Clinical Specimens ◽  
Mycobacterium Simiae ◽  
Reference Strains

A group of pigmented, slowly growing mycobacteria identified by 16S rRNA gene sequencing as ‘MCRO 33’ (GenBank accession no. AF152559) have been isolated from several clinical specimens in various laboratories across Canada. Genotypically, the organism is most closely related to Mycobacterium simiae. However, it presents with a similar phenotypic profile to Mycobacterium scrofulaceum. Several reference strains obtained from ATCC and TMC culture collections, previously identified as M. scrofulaceum or M. simiae, have also been found to possess the MCRO 33 16S rRNA gene sequence. Biochemical testing, susceptibility testing, HPLC, hsp65 gene and 16S–23S spacer (ITS1) sequencing were performed on clinical and reference strains to characterize further this unique species. Of the clinical strains, one was isolated from a cervix biopsy whereas all other clinical isolates were obtained from respiratory samples. In one patient, symptoms, imaging and repeat clinical specimens positive on culture for this organism were suggestive of active clinical disease. The description of this species, for which the name Mycobacterium parascrofulaceum sp. nov. is proposed, follows the present trend of a large number of novel Mycobacterium species identified due in great part to sequence-based methods. The type strain is HSC68T (=ATCC BAA-614T=DSM 44648T).

scholarly journals High-Level Congruence of Myrionecta rubra Prey and Dinophysis Species Plastid Identities as Revealed by Genetic Analyses of Isolates from Japanese Coastal Waters

2010 ◽  
Vol 76 (9) ◽  
pp. 2791-2798 ◽  
Author(s):  
Goh Nishitani ◽  
Satoshi Nagai ◽  
Katsuhisa Baba ◽  
Susumu Kiyokawa ◽  
Yuki Kosaka ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Coastal Waters ◽  
Primary Source ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Myrionecta Rubra ◽  
High Level ◽  
Almost All

ABSTRACT We analyzed cryptophyte nucleomorph 18S rRNA gene sequences retained in natural Myrionecta rubra cells and plastid 16S rRNA gene and psbA sequences retained in natural cells of several Dinophysis species collected from Japanese coastal waters. A total of 715 nucleomorph sequences obtained from 134 M. rubra cells and 564 plastid 16S rRNA gene and 355 psbA sequences from 71 Dinophysis cells were determined. Almost all sequences in M. rubra and Dinophysis spp. were identical to those of Teleaulax amphioxeia, suggesting that M. rubra in Japanese coastal waters preferentially ingest T. amphioxeia. The remaining sequences were closely related to those of Geminigera cryophila and Teleaulax acuta. Interestingly, 37 plastid 16S rRNA gene sequences, which were different from T. amphioxeia and amplified from Dinophysis acuminata and Dinophysis norvegica cells, were identical to the sequence of a D. acuminata cell found in the Greenland Sea, suggesting that a widely distributed and unknown cryptophyte species is also preyed upon by M. rubra and subsequently sequestered by Dinophysis. To confirm the reliability of molecular identification of the cryptophyte Teleaulax species detected from M. rubra and Dinophysis cells, the nucleomorph and plastid genes of Teleaulax species isolated from seawaters were also analyzed. Of 19 isolates, 16 and 3 clonal strains were identified as T. amphioxeia and T. acuta, respectively, and no sequence variation was confirmed within species. T. amphioxeia is probably the primary source of prey for M. rubra in Japanese coastal waters. An unknown cryptophyte may serve as an additional source, depending on localities and seasons.

scholarly journals 16S rRNA Gene Mutations Associated with Decreased Susceptibility to Tetracycline in Mycoplasma bovis

2014 ◽  
Vol 59 (2) ◽  
pp. 796-802 ◽  
Author(s):  
E. Amram ◽  
I. Mikula ◽  
C. Schnee ◽  
R. D. Ayling ◽  
R. A. J. Nicholas ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
16S Rrna ◽  
Molecular Mechanisms ◽  
Gene Mutations ◽  
Binding Pocket ◽  
Clinical Isolates ◽  
Mycoplasma Bovis ◽  
Rrna Gene ◽  
Content Type ◽  
Encoding Genes

ABSTRACTMycoplasma bovisisolates with decreased susceptibilities to tetracyclines are increasingly reported worldwide. The acquired molecular mechanisms associated with this phenomenon were investigated in 70 clinical isolates ofM. bovis. Sequence analysis of the two 16S rRNA-encoding genes (rrs3andrrs4alleles) containing the primary binding pocket for tetracycline (Tet-1 site) was performed on isolates with tetracycline hydrochloride MICs of 0.125 to 16 μg/ml. Mutations at positions A965T, A967T/C (Escherichia colinumbering) of helix 31, U1199C of helix 34, and G1058A/C were identified. Decreased susceptibilities to tetracycline (MICs, ≥2 μg/ml) were associated with mutations present at two (A965 and A967) or three positions (A965, A967, and G1058) of the tworrsalleles. Notet(M),tet(O), ortet(L) determinants were found in the genome of any of the 70M. bovisisolates. The data presented correlate (P< 0.0001) the mutations identified in the Tet-1 site of clinical isolates ofM. boviswith decreased susceptibility to tetracycline.

Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella: implications for phylogeny and taxonomy

Microbiology ◽  
2003 ◽  
Vol 149 (6) ◽  
pp. 1493-1501 ◽  
Author(s):  
Hélène Marchandin ◽  
Corinne Teyssier ◽  
Michèle Siméon de Buochberg ◽  
Hélène Jean-Pierre ◽  
Christian Carriere ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Clinical Isolates ◽  
Clinical Strain ◽  
Species Differentiation ◽  
Rrna Gene ◽  
Rdna Sequences ◽  
Gene Copies ◽  
High Level ◽  
Human Flora

Among the seven species characterized within the genus Veillonella, three (Veillonella dispar, Veillonella parvula and Veillonella atypica) have so far been isolated from human flora and during infectious processes. Sequencing and analysis of 16S rDNA (rrs) has been described as the best method for identification of Veillonella strains at the species level since phenotypic characteristics are unable to differentiate between species. rrs sequencing for the three species isolated from humans showed more than 98 % identity between them. Four rrs copies were found in the reference strains and in all the clinical isolates studied. The sequences of each rrs were determined for the clinical strain ADV 360.1, and they showed a relatively high level of heterogeneity (1·43 %). In the majority of cases, polymorphic positions corresponded to nucleotides allowing differentiation between the three species isolated from humans. Moreover, variability observed between rrs copies was higher than that between 16S rDNA sequences of V. parvula and V. dispar. Phylogenetic analysis showed that polymorphism between rrs copies affected the position of strain ADV 360.1 in the tree. Variable positions occurred in stems and loops belonging to variable and hypervariable regions of the 16S rRNA secondary structure but did not change the overall structure of the 16S rRNA. PCR-RFLP experiments performed on 27 clinical isolates of Veillonella sp. suggested that inter-rrs heterogeneity occurs widely among the members of the genus Veillonella. These results, together with the lack of phenotypic criteria for species differentiation, give preliminary arguments for unification of V. dispar and V. parvula.

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