Utilización de diferentes técnicas de biología molecular integradas en un algoritmo de identificación de micobacterias no tuberculosas

Introduction

The aim of the present work was to demonstrate the utility of a non-tuberculous mycobacteria (NTM) identification algorithm, which integrates different PCR-based techniques and basic phenotypic features. Moreover, the algorithm for pattern restriction analysis of hsp65 (hsp65 PRA) interpretation has been updated.

Methods

The workflow chosen consisted of the identification by a DNA hybridization probe method, followed by PCR-restriction enzyme analysis of hsp65 (hsp65 PRA) in those isolates that cannot be identified by hybridization probes. If necessary, 16S rRNA gene and hsp65 gene sequencing were used for speciation.

Results

A total of 236 NTM were collected, in which 102 (43.2%) isolates were identified by DNA specific probes and 76 (32.2%) isolates were identified with hsp65 PRA. Partial sequencing of the 16S rRNA gene was used for species identification of the remaining 58 (24.5%) isolates. Fifty-three (22.4%) were identified using this method. Five isolates (2.1%) were submitted for partial sequencing of hsp65 gene and one isolate was identified with this method. Four strains (1.7%) could not be identified at species level. Three new PRA patterns were found. Seven isolates tested positive with the AccuProbe Mycobacterium avium complex identification test but did not test positive with the M. avium or Mycobacterium intracellulare specific probes. Five and two of these isolates were identified as M. intracellulare and Mycobacterium colombiense, respectively.

Conclusion

This approach allowed us to identify almost all NTM isolates found in this study, including some recently described species.     

Identification and characterization of nontuberculous mycobacteria isolated from suspected pulmonary tuberculosis patients in eastern china from 2009 to 2019 using an identification array system

ObjectiveNontuberculous mycobacteria (NTM) species are increasingly being isolated and have become a key factor affecting public health by causing pulmonary diseases. Most NTM species do not respond to conventional tuberculosis (TB) drugs. This study aimed to identify NTM isolated from suspected pulmonary TB patients from the Zhejiang province and analyze their distribution in the region.MethodsA total of 1,113 NTM isolates from patients suspected to be suffering from acid-fast bacilli-positive tuberculosis were identified at the species level, using the CapitalBio Mycobacterium identification array and polymerase chain reaction amplification and sequencing of 16S-23S gene internal transcribed spacer (ITS), 16S rRNA, and hsp65.ResultsOf the 23,138 isolates, we identified 1,102 NTM (4.8%), mainly including Mycobacterium intracellulare (54.81%, 604/1,102), M. chelonae-M. abscessus (16.52%, 182/1,102), M. avium (13.16%, 145/1,102), M. kansasii (8.17%, 90/1,102), and M. gordonae (3.27%, 36/1,102).ConclusionThe distribution of NTM species observed in patients with suspected pulmonary tuberculosis provides guidance for the diagnosis and treatment of NTM pulmonary diseases.     

某高级中学结核病爆发分离菌株的实验室鉴定

目的鉴定从某中学结核病爆发分离菌株的种属。方法对2006年5—8月,辽宁省某高级中学发生的10例痰检阳性病例中的3份痰标本分离的菌株经表型鉴定方法;传统生化方法;扩增hupB基因、dnaA-dnaN 和NTF-1区;Spoligotyping 以及MIRU基因分型;16S rRNA基因、16S-23S ITS和hsp65基因测序以及hsp65基因限制性酶切分析进行鉴定。结果临床分离株经生化方法初步鉴定1份为结核分枝杆菌复合群和2份为非结核分枝杆菌,随后经表型鉴定和扩增hupB基因、dnaA-dnaN 和NTF-1区;Spoligotyping 以及MIRU基因分型,说明属于结核分枝杆菌复合群的菌株为结核分枝杆菌北京基因型现代株,MIRU基因型为223325173533。经16S rRNA基因、16S-23S ITS和hsp65基因测序以及hsp65基因限制性酶切分析说明属于非结核分枝杆菌的菌株为猪分枝杆菌。结论本次从结核病爆发累及病人的标本中分离出结核分枝杆菌北京基因型现代株和猪分枝杆菌,猪分枝杆菌在暴发流行中的意义尚需进一步研究。     

Clinical features and treatment outcomes of Mycobacterium chimaera lung disease and antimicrobial susceptibility of the mycobacterial isolates

BackgroundMycobacterium chimaera, one of the Mycobacterium avium complex (MAC) members, was recently identified using modern gene sequencing analysis. Unlike M. avium and M. intracellulare, little is known about the clinical features, antimicrobial susceptibilities, and treatment outcomes of M. chimaera lung disease.MethodsThis study was conducted in a medical center from December 2012 to July 2015. Patients who fulfilled the 2007 ATS/IDSA diagnostic criteria for nontuberculous mycobacterial lung disease were enrolled. M. chimaera isolates were identified based on the findings of sequencing of rpoB gene, the internal transcribed spacer (ITS) region of the 16S–23S rRNA gene, and the heat-shock protein 65 gene (hsp65). Minimum inhibitory concentrations (MICs) of 13 antimicrobial agents were determined.ResultsDuring the study period, 247 patients with MAC lung disease were identified, and 11.3% (28/247) of the patients had lung disease caused by M. chimaera. Among these patients, 17 (60.7%) were female, and their median age was 72.5 (40–100) years. All M. chimaera isolates were susceptible to clarithromycin and rifabutin. All the isolates were resistant to moxifloxacin and only 10 (35.7%) and 2 (7.1%) were susceptible to amikacin and linezolid, respectively. Of the nine patients who received macrolide-based regimens, more achieved radiographic resolution than those treated with non-macrolide-based regimens (66.7% vs. 15.8%, P = 0.013), and they tended to have better survival (P = 0.10).ConclusionsA substantial portion (11.3%) of MAC lung disease cases were caused by M. chimaera, and treatment with macrolide-based regimens resulted in better clinical outcomes for patients with M. chimaera lung disease.     

Mycobacterium heckeshornense lung infection that was diagnosed as Mycobacterium xenopi disease by DNA-DNA hybridization (DDH)

The DNA sequencing analyses of the 16S rRNA gene, rpoB and hsp65 were conducted to characterize six strains that had been identified as Mycobacterium xenopi by DNA-DNA hybridization (DDH) for past ten years in our hospital. The results revealed Mycobacterium heckeshornense infection in one of the six cases. A 47-year-old man, who had been treated for pneumonia, had pulmonary nontuberculous mycobacterial disease. The sputa from the patient were culture positive for mycobacterium in three times. And it was diagnosed as M. xenopiby DDH method. Chest X-ray showed fibrocavitary lesion in right upper lobe was successfully treated with clarithromycin for four weeks.     

43株甘肃临床分离非结核分枝杆菌分类鉴定

目的了解甘肃当前临床流行的非结核分枝杆菌(NTM)的病原谱特点及其主要NTM种类,为指导临床诊疗、有效防治NTM肺病提供参考依据。方法收集2012年~2014年来源于甘肃省不同地区的875株临床分离分枝杆菌菌株,经PNB/TCH方法初步鉴定为疑似NTM菌株,采用16SrRNA基因测序技术进行菌种鉴定。结果 875株分枝杆菌临床分离菌株中分离出疑似NTM菌株46株。经16SrRNA基因序列分析鉴定,43株为NTM,3株为诺卡氏菌。43株NTM菌株分别为胞内分枝杆菌、堪萨斯分枝杆菌、塞内加尔分枝杆菌、鸟分枝杆菌、戈登氏分枝杆菌、楚尔盖分枝杆菌、罕见分枝杆菌、偶然分枝杆菌和脓肿分枝杆菌。其中,胞内分枝杆菌有31株,占总NTM菌株数的72.09%。结论甘肃省非结核分枝杆菌群以胞内分枝杆菌为主,应用16SrRNA基因序列分析鉴定方法能准确鉴定出NTM菌种,为临床诊治提供依据。     

福建省肺非结核分枝杆菌临床分离株的菌种鉴定

目的 对2005-2011年间,福建省福州市胸科医院分离获得的非结核分枝杆菌临床菌株进行菌种鉴定.方法 分别使用传统鉴别培养基法和多位点PCR、hsp65-PRA与rpoB-PRA,以及hsp65、rpoB、16s rRNA和ITS基因测序等分子生物学方法,对全部菌株进行菌种鉴定.结果 450株被初步鉴定为非结核分枝杆菌的临床分离菌株中,有45株被鉴定为结核分枝杆菌,其余405株被鉴定为23种不同的非结核分枝杆菌和1株支气管戈登菌.结论 在该地区有多种非结核分枝杆菌传播和流行,其中,6种非结核分枝杆菌和支气管戈登菌为在福建省内首次发现.     

山东省非结核分枝杆菌感染的菌种分布研究

目的研究山东省13个哨点县2004—2007年非结核分枝杆菌临床分离率和菌种分布情况。方法对山东省13个哨点县2004—2007年送到汉光中心的2625株分枝杆菌菌株,进行分枝杆菌菌群鉴定试验,鉴定为非结核分枝杆菌的菌株应用16SrDNA测序方法进行菌种鉴定。结果2625株菌株分枝杆菌菌群鉴定39株为非结核分枝杆菌菌群,39株菌株16SrDNA序列分析结果有36株是非结核分枝杆菌,其中29株为胞内分枝杆菌株（80.6%）, 其余分别为堪萨斯分枝杆菌、偶然分枝杆菌各2株、戈登分枝杆菌、龟脓肿分枝杆菌复合物、瘰疬分枝杆菌各1株;结核分枝杆菌复合群2株;鼻疽诺卡氏菌1株。山东地区非结核分枝杆菌临床分离率占分枝杆菌培养阳性菌株的1.4%。结论山东地区流行的非结核分枝杆菌以慢生长分枝杆菌的胞内分枝杆菌为主。     

Altered Methylation of Ribosomal RNA in an Erythromycin-Resistant Strain of Staphylococcus aureus

In certain strains of Staphylococcus aureus, a concentration of erythromycin between 10^-8 and 10^-7 M can induce resistance to concentrations of this drug as high as 10^-4 M. In one such strain studied, S. aureus (1206), N⁶-dimethyladenine is not normally present in 23S rRNA; however, a compound presumptively identified (on the basis of paper chromatography in three different solvents) as N⁶-dimethyladenine appears in the 23S rRNA of growing cells that have been incubated in a medium containing 10^-7 M erythromycin. It has been shown previously that the induction of the erythromycin-resistant phenotype that occurs under these conditions requires 10^-8-10^-7 M erythromycin for maximal expression within 1 hr and that induction results in modified 50S ribosomal subunits, which are then unable to bind erythromycin or lincomycin. Methylated adenine is also found in the 16S rRNA from the strain of S. aureus studied; however, in contrast to the situation with 23S rRNA, the amount in 16S rRNA is not affected by erythromycin. These findings provide the first example of a correlation between the methylation of rRNA and altered ribosomal function.     

Comparison of Drug Resistance of Helicobacter pylori Between Children and Adults in Jilin,China

Background: The drug resistance of Helicobacter pylori in children is gaining more and more attention.Methods: Polymerase chain reaction-reverse dot blot was used to analyze main virulence genes and drug resistance of H. pylori.Results: (1) The main H. pylori vacA virulence genotypes were s1/m1 and s1/m2 in Jilin, China. There was no significant difference in H. pylori virulence genotypes between children and adults. (2) The resistance rates of H. pylori to clarithromycin, metronidazole, and levofloxacin were high, the resistance rate to tetracycline and amoxicillin were relatively low. The drug-resistance rate of clarithromycin in children was significantly higher than that in adults. The single drug-resistance rate of metronidazole in adults was significantly higher than that in children. (3) The mutation sites of clarithromycin resistance in H. pylori were mainly A2143G of 23S rRNA gene, G616A of rdxA gene in metronidazole, N81K and D91G/N/Y of gyrA gene in levofloxacin, T556S and N562D/Y of PBP1 gene in amoxicillin, AGA926-928TTC and AG926-927GT of 16S rRNA gene in tetracycline. There was significant difference in D91Y of gyrA gene in levofloxacin between children and adults. (4) In different groups, the drug-resistance rate of clarithromycin in male children was higher than that in male adults. The drug-resistance rate of clarithromycin in children with peptic ulcers was higher than that in adults.Conclusion: There are some differences in drug resistance of H. pylori between children and adults, which indicated us to pay attention to the infection of H. pylori in children.     

Mycobacterium neoaurum bacteremia in a hemodialysis patient

Bacteremia due to Mycobacterium neoaurum, a rapidly growing mycobacterium, is described in a diabetic woman on hemodialysis. This is the first reported case of M neoaurum bacteremia in Canada. The organism initially grew on standard BacT/Alert SA aerobic blood cultures, and was subsequently positively identified using 16S rRNA sequence analysis. The present case serves to reinforce the need for a high index of clinical suspicion of infections caused by unusual microorganisms in the context of an immunocompromised hostKey Words: 16S rRNA sequencing, Hemodialysis infection, Mycobacterium neoaurum The present report describes a case of Mycobacterium neoaurum bacteremia and arteriovenous shunt infection in a hemodialysis patient. M neoaurum, a member of the Mycobacterium parafortuitum complex, belongs to the group of rapidly growing environmental mycobacteria that are responsible for a broad spectrum of illnesses, including surgical wound and catheter infections, and disseminated cutaneous and pulmonary diseases (1). To our knowledge, this is the first case of infection due to M neoaurum reported in the Canadian literature.     

Isolation and identification of multidrug-resistant Staphylococcus haemolyticus from a laboratory-breeding mouse

ObjectiveTo analysis and identify a bacterium strain isolated from laboratory breeding mouse far away from a hospital.MethodsPhenotype of the isolate was investigated by conventional microbiological methods, including Gram–staining, colony morphology, tests for haemolysis, catalase, coagulase, and antimicrobial susceptibility test. The mecA and 16S rRNA genes were amplified by the polymerase chain reaction (PCR) and sequenced. The base sequence of the PCR product was compared with known 16S rRNA gene sequences in the GenBank database by phylogenetic analysis and multiple sequence alignment.ResultsThe isolate in this study was a gram positive, coagulase negative, and catalase positive coccus. The isolate was resistant to oxacillin, methicillin, penicillin, ampicillin, cefazolin, ciprofloxacin erythromycin, et al. PCR results indicated that the isolate was mecA gene positive and its 16S rRNA was 1 465 bp. Phylogenetic analysis of the resultant 16S rRNA indicated the isolate belonged to genus Saphylococcus, and multiple sequence alignment showed that the isolate was Saphylococcus haemolyticus with only one base difference from the corresponding 16S rRNA deposited in the GenBank.Conclusions16S rRNA gene sequencing is a suitable technique for non–specialist researchers. Laboratory animals are possible sources of lethal pathogens, and researchers must adapt protective measures when they manipulate animals.     

hsp65 and rpoB PCR-RFLP用于龟/脓肿分枝杆菌复合群种的快速鉴定(英文)

目的探讨和评价hsp65and rpoB PCR-RFLP用于龟/脓肿分枝杆菌复合群种的快速鉴定。方法收集经PNB/TCH鉴别培养基表型鉴定和16s rRNA基因测序鉴定为龟/脓肿分枝杆菌复合群的临床分离菌株,用hsp65and rpoBPCR-RFLP进行种/亚种鉴定。结果经表型鉴定为非结核分枝杆菌的27株临床菌株,16s rRNA基因测序分析与龟/脓肿分枝杆菌的同源性达到99.7%。经hsp65PCR-RFLP and rpoBPCR-RFLP鉴定18株为脓肿分枝杆菌(M.abscessus),4株为溃疡分枝杆菌(M.absecces),另5株表现为独特的指纹特征,可能是一个新的亚种。结论能够快速进行龟/脓肿分枝杆菌复合群种/亚种的鉴定。     

产丙酮酸棒状杆菌的鉴定及微生物学性状研究

目的对临床分离于皮脂腺囊肿标本中的菌株进行表型和基因型鉴定,描述该菌株的生物学特性及致病性,为临床诊断提供准确地病原学依据。方法对分离菌株进行革兰氏染色等,并使用VITEK 2Compact全自动微生物分析仪进行鉴定。采用K-B法进行药敏试验。提取分离菌株DNA,采用通用引物对16S rRNA基因进行PCR扩增并测序,将测序结果与GenBank中收录的16S rRNA基因序列进行BLAST同源性对比。结果分离菌株经VITEK 2Compact鉴定为玫瑰色库克菌,后经16S rRNA序列测定方法鉴定,分离菌株为产丙酮酸棒状杆菌。药敏试验显示该菌株对四环素、万古霉素、利福平敏感,对青霉素、红霉素、克林霉素、环丙沙星、左氧氟沙星、复方新诺明、头孢吡肟、亚胺培南、庆大霉素等均耐药。结论对于表现型不易鉴定或鉴定不准确的细菌,采用16SrRNA序列测定的方法进行鉴定是最准确的。产丙酮酸棒状杆菌是引起患者疾病的致病菌。在完善产丙酮酸棒状杆菌生化反应信息的同时,探索出有效可行的生物学鉴定方法。     

Species identification of neglected nontuberculous mycobacteria in a developing country

In developing countries where tuberculosis is still a health challenge, the prevalence of nontuberculous mycobacterial diseases is expected to rise as medical conditions that compromise the immune system become more widespread. In the current study, we aimed to determine the presence and diversity of nontuberculous mycobacteria (NTM) causing infections in Iranian patients. Sixty-seven clinical NTM isolates were identified using conventional and molecular methods, including PCR-restriction fragment length polymorphism analysis (PRA) and 16S rRNA sequencing. Out of 67 patients with confirmed mycobacterial infection, 29 had an associated immunosuppressive syndrome, including 9 who were HIV-infected. Forty-nine NTM isolates were identified using PRA, and the remaining 18 isolates were identified using 16S rRNA sequencing. We obtained the following results: Mycobacterium fortuitum, 30 isolates; M. kansasii, 12 isolates; M. gordonae, 8 isolates; M. porcinum, 3 isolates; M. conceptionense, 3 isolates; M. phlei, 2 isolates; and M. austroafricanum, M. avium, M. elephantis, M. intracellulare, M. lentiflavum, M. monacense, M. parascrofulaceum, and M. thermoresistibile, 1 isolate each; and 1 potentially novel mycobacterial species. With regard to the complexity of identification, it is recommended that laboratory diagnosis of NTM diseases be centralized by strengthening or setting up quality national and regional infrastructure.     

Antimycobacterial susceptibility against nontuberculous mycobacteria using brothmic NTM

PURPOSE: Recently the incidence of pulmonary nontuberculous mycobacteria infection has increased among patients not only implicated with AIDS, but also without predisposing conditions. However, an effective antimicrobial therapy for the disease has not been established yet, because of the absence of highly active therapeutic drugs. We compared the in vitro antimicrobial activities of five antituberculous drugs, clarithromycin and fluoroquinolones against 92 clinical isolates belonging to three species of slowly growing nontuberculous mycobacteria. MATERIAL AND METHODS: M. avium (31 strains), M. intracellulare (44 strains), and M. kansasii (17 strains), all of which were isolated from sputum specimens of previously untreated patients with pulmonary nontuberculous mycobacteria infection, were used. The eight agents tested were streptomycin, ethambutol, kanamycin, isoniazid, rifampicin, clarithromycin, levofloxacin and gatifloxacin. The drug susceptibility of these strains in terms of MIC (minimum inhibitory concentration) was determined by BrothMIC NTM. RESULTS: The MICs of rifampicin, clarithromycin, levofloxacin and gatifloxacin for all three species were low and gatifloxacin was more active than levofloxacin between two fluoroquinolones. Regarding clarithromycin, 100% of the strains were susceptible to 2 micrograms/ml or less and none of the strains were resistant on this level. In contrast, the MICs of ethambutol and isoniazid for M. avium and M. intracellulare were high and less active in vitro than the other antimicrobial agents. CONCLUSION: These MIC studies suggest that rifampicin, clarithromycin, levofloxacin, and gatifloxacin have excellent in vitro antimicrobial activities against M. avium, M. intracellulare and M. kansasii and especially clarithromycin may be very useful as a drug therapy for previously untreated patients. In the treatment of pulmonary nontuberculous mycobacterium infection, further studies are needed to evaluate the clinical effects of these drugs and to observe the drug resistance, on the basis of the results of the drug susceptibility test by BrothMIC NTM.     

Regional differences of nontuberculous mycobacteria species in Ulsan,Korea

Background

In Korea recently, nontuberculous mycobacteria (NTM) have been more frequently isolated in respiratory specimens, while Mycobacterium tuberculosis (MTB) isolations have decreased. The major NTM lung disease species in Korea are M. intracellulare, M. avium, and M. abscessus, whereas M. kansasii is a rare species. This retrospective study was performed to determine if there are region-specific characteristics of lung disease-causing NTM species in Ulsan, a highly industrialized city in Korea.

Methods

Between January 2010 and July 2013, the results of all acid-fast bacilli (AFB) cultures of respiratory specimens performed at Ulsan University Hospital (Ulsan, Korea) were collected. NTM were identified and regional differences of NTM species were compared.

Results

AFB cultures were performed on 33,567 respiratory specimens, obtained from 10,208 patients, during the study period. Further, 10% of the specimens (3,287/33,567) were AFB culture-positive [MTB, 2,288/3,287 (70%); NTM 999/3,287 (30%)]. The proportion of NTM isolations gradually increased between 2010 and 2013, at 25% and 38%, respectively. The most common NTM species was M. intracellulare (356/999, 36%), followed by M. kansasii (295/999, 30%), M. avium (161/999, 16%), M. abscessus (117/999, 12%) and M. fortuitum (39/999, 4%). This trend was maintained throughout the study period.

Conclusions

In Ulsan, NTM isolation from respiratory specimens is increasing, consistent with previous studies performed in Korea. The distribution of respiratory NTM species, however, differed from previous studies that were performed in other regions of Korea: M. kansasii was the second most common NTM species in Ulsan. In Ulsan, there is a regional difference in the NTM species isolated.     

Identification and Characteristics of Co-isolation of Multiple Nontuberculous Mycobacteria

Objective Although multiple nontuberculous mycobacteria (NTM) species can be isolated from the same patient, little has been reported on co-isolation. We clarified the trends and characteristics of the co-isolation of multiple NTM species. Methods To collect data on multiple NTM isolation, we first extracted all patients who visited our hospital from 2006 through 2015 with a diagnosis of NTM lung diseases other than Mycobacterium avium complex (MAC) and then reviewed their medical records to evaluate the co-isolation of multiple NTM species. Results Of 213 patients with non-MAC lung disease, the most common NTM species was M. gordonae (32%), followed by M. kansasii (20%) and M. abscessus (14%). Non-MAC NTM lung disease tended to be associated with middle age with a low body mass index and male predominance. Multiple NTM species were isolated from 55 (26%) of the 213 patients. The clinical characteristics associated with multiple NTM species isolation included female predominance, never smokers and the absence of cavity lesions in the lungs. The highest co-isolation rate was observed in patients with M. gordonae isolation (30%), followed by M. furtuitum isolation (26%) and M. abscessus isolation (20%). Only MAC was isolated when co-isolated with M. abscessus. Among M. szulgai, M. peregrinum and M. terrae isolation, no other NTM species were detected. Conclusion Co-isolation of multiple NTM species was not uncommon, with 26% of patients with non-MAC NTM lung diseases showing co-isolation with multiple NTM species. Each NTM species had distinct characteristics in terms of co-isolation.     

First case of Nocardia nova spinal abscess in an immunocompetent patient

Nocardia are a group of aerobic actinomycetes that are filamentous gram-positive, weakly acid-fast, and cause opportunistic infection in immunocompromised patients. Primary Nocardia infection mostly involves lung, skin and less commonly, the central nervous system (CNS). Among Nocardia CNS infections, spinal infection is extremely rare. We describe the first case of a spinal abscess caused by Nocardia nova in an immunocompetent patient who experienced a penetrating facial injury six months earlier. Nocardia species were isolated from intradural spinal abscesses and identified by 16S rRNA, hsp65 and secA1 sequence analyses. Surgical excision and treatment with amikacin, cefotaxime, and oral erythromycin was successful.     

Mutational robustness of 16S ribosomal RNA, shown by experimental horizontal gene transfer in Escherichia coli

The bacterial ribosome consists of three rRNA molecules and 57 proteins and plays a crucial role in translating mRNA-encoded information into proteins. Because of the ribosome’s structural and mechanistic complexity, it is believed that each ribosomal component coevolves to maintain its function. Unlike 5S rRNA, 16S and 23S rRNAs appear to lack mutational robustness, because they form the structural core of the ribosome. However, using Escherichia coli Δ7 (null mutant of operons) as a host, we have recently shown that an active hybrid ribosome whose 16S rRNA has been specifically substituted with that from non–E. coli bacteria can be reconstituted in vivo. To investigate the mutational robustness of 16S rRNA and the structural basis for its functionality, we used a metagenomic approach to screen for 16S rRNA genes that complement the growth of E. coli Δ7. Various functional genes were obtained from the Gammaproteobacteria and Betaproteobacteria lineages. Despite the large sequence diversity (80.9–99.0% identity with E. coli 16S rRNA) of the functional 16S rRNA molecules, the doubling times (DTs) of each mutant increased only modestly with decreasing sequence identity (average increase in DT, 4.6 s per mutation). The three-dimensional structure of the 30S ribosome showed that at least 40.7% (628/1,542) of the nucleotides were variable, even at ribosomal protein-binding sites, provided that the secondary structures were properly conserved. Our results clearly demonstrate that 16S rRNA functionality largely depends on the secondary structure but not on the sequence itself.