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2.
Int J Infect Dis ; 80: 115-117, 2019 Mar.
Article in English | MEDLINE | ID: mdl-30634044

ABSTRACT

OBJECTIVES: Mycoplasma pneumoniae is a common cause of community-acquired pneumonia in humans. Treatment of infections can be complicated by the occurrence of macrolide resistant strains. The study was conducted to evaluate the presence of resistant strains in Cuba and to determine the corresponding genotypes. METHODS: DNA of M. pneumoniae isolates and positive respiratory tract specimens collected in the years 2012 and 2017 were tested for resistance-associated mutations of 23S rRNA. In addition, strain types (P1 and MLVA) were determined. RESULTS: Macrolide resistance mutations were confirmed in 5 out of 27 strains (18.5%). Whereas both P1 subtypes 1 and 2 as well variants V2a and V2c were identified, only two MLVA types (4/5/7/2 and 3/5/6/2) could be found. CONCLUSIONS: During both sampling years, circulation of macrolide resistant strains was demonstrated. No association of resistance with a particular P1/MLVA type was found. Future longitudinal sampling to monitor prevalence of macrolide resistance of M. pneumoniae is recommended to verify the resistance pattern of this important pathogen of human respiratory tract infections.


Subject(s)
Anti-Bacterial Agents/pharmacology , Drug Resistance, Bacterial , Macrolides/pharmacology , Mycoplasma pneumoniae/isolation & purification , Community-Acquired Infections/drug therapy , Community-Acquired Infections/microbiology , Cuba , DNA, Bacterial/isolation & purification , Genotyping Techniques , Humans , Mycoplasma pneumoniae/drug effects , Pneumonia, Mycoplasma , RNA, Ribosomal, 23S/isolation & purification , Respiratory Tract Infections/drug therapy , Respiratory Tract Infections/microbiology , Specimen Handling
3.
Int J Food Microbiol ; 293: 53-59, 2019 Mar 16.
Article in English | MEDLINE | ID: mdl-30640000

ABSTRACT

The heavy use or abuse of antimicrobials in food animals has caused an increase in antimicrobial resistance in enterococci of animal origin, which could get transmitted to those of human origin via the food chain. Since duck meat consumption has been on the rise in Korea, we conducted this study to provide information about the antimicrobial resistance of the enterococci obtained from healthy ducks and their carcasses. A total of 82 Enterococcus faecium and 174 E. faecalis isolated from duck fecal and carcass samples were investigated for antimicrobial resistance to 16 agents, using broth dilution method, and were further characterized using molecular methods. Most of E. faecium (84.1%) and E. faecalis (87.9%) isolates were resistant to one or more antimicrobials. Multi-drug resistant (MDR) isolates were observed in both E. faecium (40.2%) and E. faecalis (33.9%) with high frequencies. High rate of resistance was observed for tetracycline, ciprofloxacin, chloramphenicol, and erythromycin in both E. faecium and E. faecalis. Resistance to gentamicin, vancomycin, and daptomycin, in both E. faecium and E. faecalis, was, if at all, very rare. However, linezolid resistance was observed in nine E. faecium (11.0%) and one E. faecalis (0.6%). All, but one, Linezolid resistant (LR) isolates were also resistant to chloramphenicol and florfenicol. The novel transferable oxazolidinone and phenicol resistant gene, optrA, was found in six E. faecium isolates. All of them co-carried phenicol exporter gene fexA. None of the LR isolates had mutation in the 23S ribosomal RNA and in the ribosomal protein L3. Six LR E. faecium isolates had Asn130Lys mutation in the ribosomal protein L4, of which five also carried optrA gene. None of the isolates carried the multi-resistance gene cfr. Transfer of oxazolidinone and phenicol resistance was observed in five among the 10 LR isolates; two of them had optrA and fexA genes. Multi-drug resistant Enterococcus that also carried the resistance gene to a last-resort antimicrobial is a major concern for public health. Thus, to prevent the introduction of last-resort antimicrobial resistance into food chain, continuous surveillance of antimicrobial resistance in duck is imperative.


Subject(s)
Drug Resistance, Multiple, Bacterial/genetics , Ducks/microbiology , Enterococcus faecalis/isolation & purification , Enterococcus faecium/isolation & purification , Oxazolidinones/pharmacology , Animals , Anti-Bacterial Agents/pharmacology , Anti-Infective Agents/pharmacology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Chloramphenicol/pharmacology , Ciprofloxacin/pharmacology , Enterococcus faecalis/drug effects , Enterococcus faecalis/genetics , Enterococcus faecium/drug effects , Enterococcus faecium/genetics , Erythromycin/pharmacology , Feces/microbiology , Genes, Bacterial , Linezolid/pharmacology , Microbial Sensitivity Tests , Multilocus Sequence Typing , RNA, Ribosomal, 23S/isolation & purification , Republic of Korea , Ribosomal Protein L3 , Tetracycline/pharmacology , Thiamphenicol/analogs & derivatives , Thiamphenicol/pharmacology
4.
Indian J Med Res ; 150(5): 458-467, 2019 11.
Article in English | MEDLINE | ID: mdl-31939389

ABSTRACT

Background & objectives: The burden of non-tuberculous mycobacterial (NTM) disease is increasing worldwide. The disease shares clinicoradiological features with tuberculosis (TB), Nocardia and several fungal diseases, and its diagnosis is frequently delayed. The present study was performed to determine the frequency of NTM disease among TB suspects in a tertiary care centre in north India. Methods: In this prospective study, mycobacterial culture isolates from pulmonary and extrapulmonary specimens among TB suspects were tested with immunochromatographic assay (ICA). All ICA-negative isolates were considered as NTM suspects and further subjected to 16S-23S rRNA internal transcribed spacer gene sequencing for confirmation and species identification. Patients with active disease were treated with drug regimen as per the identified NTM species. Follow up of patients was done to determine clinical, radiological and microbiological outcomes. Results: Of the 5409 TB suspects, 42 (0.77%) were diagnosed with NTM disease. Patients with active disease consenting for treatment were treated and followed up. Thirty four patients had NTM pulmonary disease (NTM-PD) and the remaining eight had extrapulmonary NTM (EP-NTM) disease. Mycobacterium intracellulare and M. abscessus, respectively, were most frequently isolated from NTM-PD and EP-NTM patients. Fifteen NTM-PD and seven EP-NTM patients successfully completed the treatment. Ten patients died due to unrelated causes, five were lost to follow up and another four declined the treatment. Interpretation & conclusions: Our study showed that the frequency of NTM disease was low among TB suspects at a large tertiary care centre in north India and this finding was similar to other Indian studies. More studies need to be done in other parts of the country to know the geographical variation in NTM disease, if any.


Subject(s)
Diagnostic Tests, Routine , Mycobacterium Infections, Nontuberculous/diagnosis , Nontuberculous Mycobacteria/isolation & purification , Tuberculosis, Pulmonary/diagnosis , Adult , Female , Humans , India/epidemiology , Male , Mycobacterium Infections, Nontuberculous/epidemiology , Mycobacterium Infections, Nontuberculous/genetics , Mycobacterium Infections, Nontuberculous/microbiology , Nontuberculous Mycobacteria/genetics , Nontuberculous Mycobacteria/pathogenicity , Prospective Studies , RNA, Ribosomal, 16S/genetics , RNA, Ribosomal, 16S/isolation & purification , RNA, Ribosomal, 23S/genetics , RNA, Ribosomal, 23S/isolation & purification , Sputum/microbiology , Tertiary Care Centers , Tuberculosis, Pulmonary/epidemiology , Tuberculosis, Pulmonary/genetics , Tuberculosis, Pulmonary/microbiology
5.
Pediatr Infect Dis J ; 37(6): e145-e148, 2018 06.
Article in English | MEDLINE | ID: mdl-29088029

ABSTRACT

BACKGROUND: A pertussis outbreak was studied in a primary school in Xi'an, China, in March 2016. The school consisted of 536 pupils 6-12 years of age who were divided into 12 classes of 6 grades (2 classes for each grade). The identified index case was an 11-year-old girl at class 2 of grade 5. METHODS: Interview was conducted and nasopharyngeal swabs were taken from all pupils (N = 94) in the 2 classes of grade 5. Nasopharyngeal swabs were tested by both culture and polymerase chain reaction (PCR). RESULTS: Four culture- and 17 PCR-positive cases were identified in 94 pupils. Infection rate was significantly higher in class 2 compared with that in class 1 [37.0% (17/46) vs. 14.6% (7/48), χ(2) = 4.26, P < 0.05]. All Bordetella pertussis isolates were macrolide-resistant, harbored prn1/ptxP1/fim3-1 as previously reported and belonged to multilocus variable tandem repeat analysis type MLVA 195. Of the 17 DNAs positive for diagnostic PCR, 12 were also positive for 23S ribosomal RNA PCR. All the 12 DNAs had the A2047G mutation of 23S rRNA gene of B. pertussis. CONCLUSIONS: This study described a pertussis outbreak caused by macrolide-resistant B. pertussis in a primary school and indicated that close contact of index case causes the bacterial transmission.


Subject(s)
Bordetella pertussis/isolation & purification , Drug Resistance, Bacterial , Macrolides/pharmacology , Whooping Cough/epidemiology , Whooping Cough/transmission , Bordetella pertussis/drug effects , Child , China/epidemiology , DNA, Bacterial/isolation & purification , Disease Outbreaks , Female , Humans , Male , Nasopharynx/microbiology , RNA, Ribosomal, 23S/isolation & purification , Schools , Students
6.
J Med Microbiol ; 66(12): 1730-1735, 2017 Dec.
Article in English | MEDLINE | ID: mdl-29111969

ABSTRACT

PURPOSE: To investigate linezolid-resistance mechanisms in linezolid-nonsusceptible enterococci (LNSE) isolated from a tertiary hospital in Korea. METHODOLOGY: Enterococcal isolates exhibiting linezolid MICs ≥4 mg l-1 that were isolated between December 2011 and May 2016 were investigated by PCR and sequencing for mutations in 23S rRNA or ribosomal proteins (L3, L4 and L22) and for the presence of cfr, cfr(B) and optrA genes.Results/Key findings. Among 135 LNSE (87 Enterococcus faecium and 48 Enterococcus faecalis isolates), 39.1 % (34/87) of E. faecium and 18.8 % (9/48) of E. faecalis isolates were linezolid-resistant. The optrA carriage was the dominant mechanism in E. faecalis: 13 isolates, including 10 E. faecalis [70 % (7/10) linezolid-resistant and 30 % (3/10) linezolid-intermediate] and three E. faecium [33.3 % (1/3) linezolid-resistant and 66.7 % (2/3) linezolid-intermediate], contained the optrA gene. G2576T mutations in the 23S rRNA gene were detected only in E. faecium [14 isolates; 71.4 % (10/14) linezolid-resistant and 28.6 % (4/14) linezolid-intermediate]. One linezolid-intermediate E. faecium harboured a L22 protein alteration (Ser77Thr). No isolates contained cfr or cfr(B) genes and any L3 or L4 protein alterations. No genetic mechanism of resistance was identified for 67.6 % (23/34) of linezolid-resistant E. faecium. CONCLUSION: A low rate of 23S rRNA mutations and the absence of known linezolid-resistance mechanisms in the majority of E. faecium isolates suggest regional differences in the mechanisms of linezolid resistance and the possibility of additional mechanisms.


Subject(s)
Drug Resistance, Multiple, Bacterial/genetics , Enterococcus faecalis/genetics , Enterococcus faecium/genetics , Linezolid/pharmacology , Anti-Bacterial Agents/pharmacology , Enterococcus faecalis/drug effects , Enterococcus faecium/drug effects , Humans , Microbial Sensitivity Tests , Multilocus Sequence Typing , Mutation , RNA, Ribosomal, 23S/isolation & purification , Republic of Korea , Sequence Analysis, DNA
7.
Org Biomol Chem ; 15(40): 8535-8543, 2017 Oct 18.
Article in English | MEDLINE | ID: mdl-28959821

ABSTRACT

Development of antibiotics that target new regions of functionality is a possible way to overcome antibiotic resistance. In this study, the interactions of aminoglycoside antibiotics with helix 69 of the E. coli 23S rRNA in the context of complete 70S ribosomes or the isolated 50S subunit were investigated by using chemical probing and footprinting analysis. Helix 69 is a dynamic RNA motif that plays major roles in bacterial ribosome activity. Neomycin, paromomycin, and gentamicin interact with the stem region of helix 69 in complete 70S ribosomes, but have diminished binding to the isolated 50S subunit. Pseudouridine modifications in helix 69 were shown to impact the aminoglycoside interactions. These results suggest a requirement for a specific conformational state of helix 69 for efficient aminoglycoside binding, and imply that this motif may be a suitable target for mechanism-based therapeutics.


Subject(s)
Aminoglycosides/chemistry , Anti-Bacterial Agents/chemistry , Escherichia coli/chemistry , Pseudouridine/chemistry , RNA, Ribosomal, 23S/chemistry , Aminoglycosides/pharmacology , Anti-Bacterial Agents/pharmacology , Binding Sites/drug effects , Crystallography, X-Ray , Escherichia coli/drug effects , Models, Molecular , Molecular Conformation , RNA, Ribosomal, 23S/drug effects , RNA, Ribosomal, 23S/isolation & purification
8.
Article in Japanese | MEDLINE | ID: mdl-28817941

ABSTRACT

Urinary antigen test is frequently used as a routine laboratory test for early diagnosis of Legionella infection, which is especially suitable for ordinary Legionella pneumophila serogroup 1, but not for other types of Legionella. We report a case of severe pneumonia caused by Legionella longbeachae, where a method of loop-mediated isothermal amplification (LAMP) assay contributed an important role for the early detection. This case involved an 83-year-old man who developed fever, dyspnea, and productive cough. Since the medication of prescribed ceftriaxone had not been effective, he visited the emergency room of our hospital, where an X-ray revealed a severe pneumonia harboring a consolidation with air bronchogram in his right lower lung. His sputum and urine were subjected to the routine bacterial culture or the urinary antigen test for Legionella, which initially brought negative results. However, a positive result of LAMP assay enabled early diagnosis of Legionella pneumonia. Later, the bacterial cultures of sputum made some progress and 16S rRNA sequencing provided a proof of L. longbeachae. This LAMP assay may bring a benefit for the patients with Legionella pneumonia by enabling early detection of not only specific L. pneumophila serogroup 1, but also of the other Legionella species.


Subject(s)
Legionella longbeachae/isolation & purification , Legionellosis/diagnostic imaging , Microbiological Techniques , Pneumonia/diagnostic imaging , Pneumonia/microbiology , Aged, 80 and over , Humans , Legionella longbeachae/genetics , Legionellosis/drug therapy , Male , Pneumonia/drug therapy , RNA, Ribosomal, 23S/isolation & purification , Tomography, X-Ray Computed
9.
Am J Trop Med Hyg ; 97(5): 1319-1322, 2017 Nov.
Article in English | MEDLINE | ID: mdl-28820698

ABSTRACT

Coxiella-like bacteria have been recently proposed as human pathogens. Using molecular techniques, we detected Coxiella-like bacteria in the blood and serum samples of a patient with a scalp eschar, neck lymphadenopathy, severe urticaria, edema, fever, and arthralgia indicating that this organism can provide systemic complications.


Subject(s)
Coxiella/isolation & purification , Lymphadenopathy/diagnosis , Neck/pathology , Scalp/pathology , Bacteremia/diagnosis , Bacteremia/drug therapy , Coxiella/classification , Coxiella/drug effects , DNA, Bacterial/isolation & purification , Doxycycline/therapeutic use , Humans , Lymphadenopathy/drug therapy , Lymphadenopathy/microbiology , Male , Neck/microbiology , Phylogeny , RNA, Ribosomal, 23S/isolation & purification , Scalp/microbiology , Young Adult
10.
Foodborne Pathog Dis ; 14(2): 96-102, 2017 02.
Article in English | MEDLINE | ID: mdl-27854542

ABSTRACT

This study was conducted to determine the prevalence of antimicrobial resistance in Campylobacter spp. isolates from broilers in live bird markets (LBMs). A total of 209 Campylobacter spp. isolates (84 Campylobacter jejuni; 125 Campylobacter coli) were recovered from 364 broiler cecum samples collected from five LBMs in Shanghai, China. Minimum inhibitory concentrations of 13 antimicrobials were determined using agar dilution method. More than 96% of the Campylobacter spp. isolates were resistant to quinolones and tetracyclines. A high prevalence of macrolide resistance (erythromycin, 84.0%; azithromycin, 80.8%) was observed in C. coli, but not in C. jejuni (erythromycin, 6.0%; azithromycin, 2.4%). C. coli also showed significantly higher resistance than C. jejuni to clindamycin, gentamicin, and kanamycin. In contrast, C. coli isolates had lower resistance to florfenicol than the C. jejuni isolates. The majority of the C. jejuni (88.1%) and C. coli (97.6%) isolates exhibited multidrug resistance (MDR) to three or more classes of antimicrobials. All of the 208 ciprofloxacin-resistant Campylobacter spp. isolates were positive for the C257T mutation of the gyrA gene. In addition, the tet(O) gene was identified in all of the 202 doxycycline-resistant Campylobacter spp. isolates. Furthermore, 75.7% and 20.4% of the 103 azithromycin-resistant Campylobacter spp. isolates were positive for the A2075G mutation of the 23S rRNA gene and the presence of the erm(B) gene, respectively. Moreover, the cat gene was found in 14.3% (8/56) and 76.8% (73/95) of the chloramphenicol-resistant C. jejuni and C. coli isolates, respectively. To the best of our knowledge, this is the first report of the prevalence of antimicrobial resistance among Campylobacter spp. isolates originating from LBMs. The high prevalence of MDR Campylobacter spp. isolates in LBMs highlights the need to implement efficient intervention measures to control not only Campylobacter contamination in LBMs but also dissemination of antimicrobial resistance among Campylobacter spp. in poultry production.


Subject(s)
Bacterial Proteins/genetics , Campylobacter coli/drug effects , Campylobacter jejuni/drug effects , Chickens/microbiology , Drug Resistance, Multiple, Bacterial/genetics , Animals , Anti-Bacterial Agents/pharmacology , Campylobacter coli/genetics , Campylobacter coli/isolation & purification , Campylobacter jejuni/genetics , Campylobacter jejuni/isolation & purification , Carrier Proteins/genetics , China , Ciprofloxacin/pharmacology , Clindamycin/pharmacology , DNA Gyrase/genetics , Erythromycin/pharmacology , Food Contamination/analysis , Food Contamination/prevention & control , Food Microbiology , Gentamicins/pharmacology , Kanamycin/pharmacology , Methyltransferases/genetics , Microbial Sensitivity Tests , Poultry/microbiology , Quinolones/pharmacology , RNA, Ribosomal, 23S/isolation & purification , Tetracyclines/pharmacology
11.
J Microbiol Methods ; 131: 130-134, 2016 12.
Article in English | MEDLINE | ID: mdl-27789313

ABSTRACT

The prevalence of macrolide-resistant Mycoplasma pneumoniae harboring a mutation in the 23S rRNA gene is increasing, and rapid detection assays are needed for clinical management. We developed an endpoint genotyping assay to detect the M. pneumoniae 23S rRNA gene and determine the existence of macrolide resistance-associated mutations at position 2063 (A2063G, A2063T and A2063C mutations). This A2063B genotyping assay detected more than 50 copies/reaction of the M. pneumoniae gene in every nucleotide mutation at position 2063. Of 42 clinical specimens, 3 were positive without mutation, 6 were positive with the A2063G mutation, and 33 were negative. The results were confirmed using nested PCR with the sequencing of the M. pneumoniae 23S rRNA gene, and a high sensitivity (90%), specificity (100%), and coincidence ratio (kappa coefficient=0.93) were obtained. Therefore, the A2063B genotyping assay is useful for the rapid discrimination of macrolide resistance mutations at position 2063.


Subject(s)
Drug Resistance, Bacterial/genetics , Endpoint Determination/methods , Genotype , Macrolides/pharmacology , Mutation , Mycoplasma pneumoniae/genetics , RNA, Ribosomal, 23S/genetics , RNA, Ribosomal, 23S/isolation & purification , Anti-Bacterial Agents/pharmacology , DNA, Bacterial/genetics , Humans , Mycoplasma pneumoniae/pathogenicity , Pneumonia, Mycoplasma/microbiology , Polymerase Chain Reaction/methods , Prevalence , RNA Probes , RNA, Bacterial/genetics , Sensitivity and Specificity
12.
Clin Microbiol Infect ; 22(12): 1002.e1-1002.e8, 2016 Dec.
Article in English | MEDLINE | ID: mdl-27542334

ABSTRACT

Our whole genome sequence (WGS) pipeline was assessed for accurate prediction of antimicrobial phenotypes. For 2316 invasive pneumococcal isolates recovered during 2015 we compared WGS pipeline data to broth dilution testing (BDT) for 18 antimicrobials. For 11 antimicrobials categorical discrepancies were assigned when WGS-predicted MICs and BDT MICs predicted different categorizations for susceptibility, intermediate resistance or resistance, ranging from 0.9% (tetracycline) to 2.9% (amoxicillin). For ß-lactam antibiotics, the occurrence of at least four-fold differences in MIC ranged from 0.2% (meropenem) to 1.0% (penicillin), although phenotypic retesting resolved 25%-78% of these discrepancies. Non-susceptibility to penicillin, predicted by penicillin-binding protein types, was 2.7% (non-meningitis criteria) and 23.8% (meningitis criteria). Other common resistance determinants included mef (475 isolates), ermB (191 isolates), ermB + mef (48 isolates), tetM (261 isolates) and cat (51 isolates). Additional accessory resistance genes (tetS, tet32, aphA-3, sat4) were rarely detected (one to three isolates). Rare core genome mutations conferring erythromycin-resistance included a two-codon rplD insertion (rplD69-KG-70) and the 23S rRNA A2061G substitution (six isolates). Intermediate cotrimoxazole-resistance was associated with one or two codon insertions within folP (238 isolates) or the folA I100L substitution (38 isolates), whereas full cotrimoxazole-resistance was attributed to alterations in both genes (172 isolates). The two levofloxacin-resistant isolates contained parC and/or gyrA mutations. Of 11 remaining isolates with moderately elevated MICs to both ciprofloxacin and levofloxacin, seven contained parC or gyrA mutations. The two rifampin-resistant isolates contained rpoB mutations. WGS-based antimicrobial phenotype prediction was an informative alternative to BDT for invasive pneumococci.


Subject(s)
Anti-Bacterial Agents/pharmacology , Drug Resistance, Multiple, Bacterial/genetics , Pneumococcal Infections/epidemiology , Streptococcus pneumoniae/genetics , Chloramphenicol/pharmacology , Ciprofloxacin/pharmacology , Clindamycin/pharmacology , Erythromycin/pharmacology , Genes, Bacterial , Humans , Microbial Sensitivity Tests , Mutation , Penicillin-Binding Proteins/genetics , Penicillins/pharmacology , Pneumococcal Infections/microbiology , RNA, Ribosomal, 23S/genetics , RNA, Ribosomal, 23S/isolation & purification , Streptococcus pneumoniae/classification , Streptococcus pneumoniae/isolation & purification , Tetracycline/pharmacology , Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology , United States/epidemiology
13.
Hum Gene Ther Methods ; 27(4): 159-70, 2016 08.
Article in English | MEDLINE | ID: mdl-27440556

ABSTRACT

Gene therapy products are very complex advanced therapy medicinal products produced using different processes that require many chemical and biological reagents and production intermediates, such as producing cells. The quantification of residual impurities in gene therapy vectors is a major quality control step when these vectors are used for therapeutic purposes, whether or not they are derived from viruses. Indeed, in nonviral gene therapy products, particularly plasmid vectors used to transfer genetic material, the presence of host-cell DNA (HCDNA) from the bacterial cells used for the vector production is an important concern because of the risk of immunogenicity and insertional mutagenesis. Several methods have been developed to quantify residual HCDNA, but real-time quantitative polymerase chain reaction (qPCR) seems to be most suitable because it allows detecting traces of "contaminating" DNA. The French National Agency for Medicines and Health Products Safety (ANSM) ensures the quality and safety of gene transfer medicinal products and must be able to quantify, in its own laboratories, the amount of HCDNA present in plasmid vector batches. Therefore, we developed and validated a qPCR method to quantify at the femtogram level the presence of Escherichia coli residual DNA in plasmid vectors. This approach uses the capillary-based LightCycler 1.5 System (Roche) with SYBR Green I, a primer pair against the E. coli 23S ribosomal RNA gene and different concentrations of a linearized plasmid that contains the 23S target sequence, as standard. This qPCR method is linear on an 8-decade logarithmic scale, accurate, reproducible, and sensitive (quantification of up to 10 copies of 23S target sequence per reaction, or 1.4 E. coli genome, or 7 fg of bacterial DNA). This technique allows ensuring that batches of plasmid vectors to be used in clinical trials comply with the specifications on HCDNA content.


Subject(s)
Genetic Therapy , Genetic Vectors , Plasmids/genetics , RNA, Ribosomal, 23S/genetics , DNA, Bacterial/genetics , DNA, Bacterial/isolation & purification , Escherichia coli/genetics , Escherichia coli/isolation & purification , Humans , Plasmids/isolation & purification , RNA, Ribosomal, 23S/isolation & purification , Real-Time Polymerase Chain Reaction
14.
Nan Fang Yi Ke Da Xue Xue Bao ; 36(2): 190-4, 2016 Feb.
Article in Chinese | MEDLINE | ID: mdl-26922014

ABSTRACT

OBJECTIVE: To explore the value of detecting bacterial 16S rRNA with 23S rRNA in the diagnosis of periprosthetic joint infection (PJI). METHODS: A prospective study was conducted among 67 patients with previous total hip arthroplasty (THA) undergoing a reoperation for infection (23 patients) or aseptic loosening (44 patients). Bacterial 16S rRNA and 23S rRNA in the interface membrane were detected by real-time PCR and their value in diagnosis of PJI was assessed. RESULTS: The 16S rRNA and 23S rRNA showed no significant difference in their power in the diagnosis of PJI. The detection of 16S rRNA/23S rRNA showed a higher sensitivity and a greater negative predictive value in PJI diagnosis than the detection of 16S rRNA+23S rRNA (95.7% vs 52.2%, P<0.01; 97.6% vs 79.6%, P=0.01). The specificity, positive predictive value, and accuracy of the 4 diagnostic strategies were not significantly different. CONCLUSIONS: The diagnostic power of 16S rRNA and 23S rRNA was similar in detecting PJI. Compared with the diagnostic strategy with 16S rRNA+23S rRNA, 16S rRNA/23S rRNA is more sensitive in detecting PJI.


Subject(s)
Arthritis, Infectious/diagnosis , Prosthesis-Related Infections/diagnosis , RNA, Bacterial/isolation & purification , RNA, Ribosomal, 16S/isolation & purification , RNA, Ribosomal, 23S/isolation & purification , Arthritis, Infectious/microbiology , Arthroplasty, Replacement, Hip , Humans , Prospective Studies , Prosthesis-Related Infections/microbiology , Real-Time Polymerase Chain Reaction , Reoperation , Sensitivity and Specificity
15.
Nucleic Acids Res ; 43(5): e32, 2015 Mar 11.
Article in English | MEDLINE | ID: mdl-25539917

ABSTRACT

A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria.


Subject(s)
Mycobacterium bovis/genetics , RNA, Bacterial/genetics , RNA, Ribosomal, 5S/genetics , RNA, Untranslated/genetics , Chromatography, Gel , Chromatography, High Pressure Liquid/methods , RNA Processing, Post-Transcriptional , RNA, Bacterial/isolation & purification , RNA, Ribosomal, 16S/genetics , RNA, Ribosomal, 16S/isolation & purification , RNA, Ribosomal, 23S/genetics , RNA, Ribosomal, 23S/isolation & purification , RNA, Ribosomal, 5S/isolation & purification , RNA, Transfer/genetics , RNA, Transfer/isolation & purification , RNA, Untranslated/isolation & purification , Reproducibility of Results , Ribonucleosides/genetics
16.
Article in English | MEDLINE | ID: mdl-23722841

ABSTRACT

RlmM is an AdoMet-dependent methyltransferase that is responsible for 2'-O-methylation of C2498 in the peptidyl-transferase loop of bacterial 23S rRNA. This modification occurs before assembly of the 50S ribosomal subunit, and lack of C2498 methylation can cause a slight reduction in bacterial fitness. Here, the purification and crystallization of RlmM from Escherichia coli as well as its preliminary crystallographic analysis are presented. Cocrystallization of RlmM with AdoMet was carried out and X-ray diffraction data were collected to a resolution of 2.30 Å on beamline BL17U at the SSRF. However, electron density for AdoMet cannot be observed by comprehensive crystallographic analysis, indicating that it is not bound by RlmM during the cocrystallization process. The structure was solved by molecular replacement and refinement is in progress. The crystal contained one molecule in the asymmetric unit and belonged to space group P2(1), with unit-cell parameters a = 56.07, b = 59.38, c = 54.35 Å, ß = 94.84°, which differs from the P3(1) or P3(1)21 space groups of previously reported RlmM structures (PDB entries 4auk, 4atn and 4b17).


Subject(s)
Crystallography, X-Ray , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/isolation & purification , Escherichia coli , Methyltransferases/chemistry , Methyltransferases/isolation & purification , RNA, Ribosomal, 23S/chemistry , RNA, Ribosomal, 23S/isolation & purification , X-Ray Diffraction
17.
Foodborne Pathog Dis ; 10(3): 250-5, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23379282

ABSTRACT

BACKGROUND: Arcobacter species, primarily Arcobacter butzleri, are widely distributed among animals, infrequently isolated from humans, and previously not associated with outbreaks of foodborne illness. We report results of an investigation of a foodborne outbreak that occurred among attendees of a wedding reception in Wisconsin, United States, and was likely caused by A. butzleri. METHODS: We conducted a case-control study among reception attendees and a laboratory investigation to determine the extent, source, and cause of the outbreak. A clinical case was defined as diarrhea in an attendee with illness onset ≤7 days following the wedding reception. RESULTS: The case-control study included 47 of 51 case patients and 43 non-ill attendees. Results demonstrated that consuming broasted chicken was the only factor significantly associated with illness (odds ratio 10.51; 95% confidence interval 1.28, 476.4). Five patients provided stool specimens. Comprehensive culture and polymerase chain reaction (PCR) testing did not detect common bacterial or viral pathogens. Subsequent testing with PCRs targeting 16S/23S rDNA of the three most clinically relevant Arcobacter spp. and the rpoB/C gene of A. butzleri provided products confirmed as A. butzleri (four patients) and A. cryaerophilus (one patient) by sequence analysis. CONCLUSIONS: The results of this investigation suggest that A. butzleri should be considered an agent that can cause outbreaks of foodborne illness. Rigorous investigation of outbreaks of undetermined etiology is valuable for incrementally increasing our understanding of emerging agents causing foodborne illnesses.


Subject(s)
Arcobacter/isolation & purification , Disease Outbreaks , Foodborne Diseases/epidemiology , Meat/microbiology , Adult , Aged , Animals , Arcobacter/classification , Arcobacter/pathogenicity , Case-Control Studies , Chickens , Female , Foodborne Diseases/microbiology , Humans , Male , Middle Aged , Polymerase Chain Reaction , RNA, Ribosomal, 16S/isolation & purification , RNA, Ribosomal, 23S/isolation & purification , Sequence Analysis, DNA , Wisconsin/epidemiology , Young Adult
18.
Emerg Infect Dis ; 19(1): 129-32, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23260390
19.
Elife ; 1: e00102, 2012 Oct 30.
Article in English | MEDLINE | ID: mdl-23110254

ABSTRACT

Toll-like receptors (TLRs) detect microbial infections and trigger innate immune responses. Among vertebrate TLRs, the role of TLR13 and its ligand are unknown. Here we show that TLR13 detects the 23S ribosomal RNA of both gram-positive and gram-negative bacteria. A sequence containing 13 nucleotides near the active site of 23S rRNA ribozyme, which catalyzes peptide bond synthesis, was both necessary and sufficient to trigger TLR13-dependent interleukin-1ß production. Single point mutations within this sequence destroyed the ability of the 23S rRNA to stimulate the TLR13 pathway. Knockout of TLR13 in mice abolished the induction of interleukin-1ß and other cytokines by the 23S rRNA sequence. Thus, TLR13 detects bacterial RNA with exquisite sequence specificity.DOI:http://dx.doi.org/10.7554/eLife.00102.001.


Subject(s)
Dendritic Cells/immunology , Macrophages/immunology , RNA, Bacterial/metabolism , RNA, Ribosomal, 23S/metabolism , Toll-Like Receptors/genetics , Animals , Base Sequence , Cells, Cultured , Dendritic Cells/cytology , Dendritic Cells/drug effects , Escherichia coli/chemistry , Gene Expression , Immunity, Innate , Interleukin-1beta/biosynthesis , Interleukin-1beta/metabolism , Lactobacillus/chemistry , Macrophages/cytology , Macrophages/drug effects , Mice , Mice, Knockout , Molecular Sequence Data , RNA, Bacterial/isolation & purification , RNA, Ribosomal, 23S/isolation & purification , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , Toll-Like Receptors/antagonists & inhibitors , Toll-Like Receptors/immunology
20.
Foodborne Pathog Dis ; 9(10): 902-6, 2012 Oct.
Article in English | MEDLINE | ID: mdl-22924522

ABSTRACT

Antimicrobial treatment of animals may select resistance in Campylobacter to antimicrobial agents belonging to several classes of compounds. We investigated the effect of widely used aminopenicillin therapy on the minimum inhibitory concentration (MIC) levels in porcine Campylobacter coli isolates and investigated the presence of a ß-lactamase gene and ß-lactamase production. Epidemiological cut-off values (ECOFFs) were applied to detect decreased susceptibility. Fifty-three isolates were obtained from aminopenicillin-treated (ampicillin or amoxicillin) sows and piglets during and up to 3 weeks post-treatment. All isolates had ampicillin MICs below the ECOFF (≤ 8 µg/mL). An additional 63 isolates were sampled before treatment or from other untreated sows and piglets. Of these isolates, four had ampicillin MICs above the ECOFF. All ciprofloxacin MICs were below the ECOFF (≤ 1 µg/mL), except for three isolates from untreated sows and four isolates after aminopenicillin therapy. One isolate originating from an untreated sow had an erythromycin MIC above the ECOFF (> 16 µg/mL). None of the isolates had MICs above the ECOFFs for two or three studied antimicrobials simultaneously. Of the 116 C. coli isolates, 90 (77.6%) isolates carried the bla(OXA-61) ß-lactamase gene, and 63 (70.0%) of those produced ß-lactamase. The isolates producing ß-lactamase had higher ampicillin MICs than those without the bla(OXA-61) gene and production of ß-lactamase. Proportion of the bla(OXA-61)-positive C. coli isolates was similar among untreated animals or during and after the treatment. In conclusion, C. coli isolates did not acquire high ampicillin MICs even though aminopenicillins were administered at therapeutic levels for several days. The bla(OXA-61) gene and production of ß-lactamase increased ampicillin MICs in C. coli, but the values remained mainly under the ECOFF. We also demonstrated that aminopenicillin therapy did not select simultaneously resistance to the major antimicrobials used in human therapy against campylobacteriosis (i.e., erythromycin and ciprofloxacin).


Subject(s)
Amoxicillin/pharmacology , Ampicillin/pharmacology , Campylobacter coli/drug effects , Campylobacter coli/isolation & purification , beta-Lactamases/biosynthesis , Animals , Anti-Bacterial Agents/pharmacology , Campylobacter Infections/drug therapy , Campylobacter Infections/veterinary , Campylobacter coli/genetics , Ciprofloxacin/pharmacology , DNA Gyrase/genetics , DNA Gyrase/isolation & purification , Drug Resistance, Bacterial , Erythromycin/pharmacology , Finland , Microbial Sensitivity Tests , RNA, Ribosomal, 23S/genetics , RNA, Ribosomal, 23S/isolation & purification , Swine/microbiology , Swine Diseases/drug therapy , Swine Diseases/microbiology , beta-Lactamases/genetics
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