2018—2020年平顶山地区非结核分枝杆菌菌种鉴定及耐药性分析

本文旨在观察2018—2020年河南省平顶山地区非结核分枝杆菌(nontuberculous mycobacteria,NTM)的菌种分布及耐药情况。收集2018年1月—2020年12月平顶山市传染病医院分离到的326株NTM,采用DNA微阵列芯片鉴定菌种,改良罗氏培养基比例法进行药敏试验。结果显示,从61～80岁患者中分离的NTM菌株最多,其次是41～60岁患者。共鉴定出8个NTM菌种,分别为胞内分枝杆菌(35.28%)、龟/脓肿分枝杆菌(24.85%)、鸟分枝杆菌(18.40%)、偶然分枝杆菌(5.21%)、戈登分枝杆菌(1.23%)、堪萨斯分枝杆菌(12.58%)、浅黄分枝杆菌(1.53%)、瘰疬分枝杆菌(0.92%)。NTM对异烟肼的耐药率最高,为97.85%。除戈登分枝杆菌外,其他NTM菌种对异烟肼的耐药率均＞94%;胞内分枝杆菌对丙硫异烟胺的耐药率(8.70%)相对较低,鸟分枝杆菌对丙硫异烟胺的耐药率为10.00%;龟/脓肿分枝杆菌对异烟肼、利福平、链霉素、乙胺丁醇、阿米卡星的耐药率均＞95%;偶然分枝杆菌对左氧氟沙星的耐药率为35.29%,堪萨斯分枝杆菌对左氧氟沙星的耐药率最低(7.32%);戈登分枝杆菌对异烟肼、乙胺丁醇、链霉素、对氨基水杨酸的耐药率均≥50%;浅黄分枝杆菌对乙胺丁醇、左氧氟沙星、阿米卡星、卡那霉素的耐药率均＜50%;瘰疬分枝杆菌对阿米卡星和丙硫异烟胺的耐药率为0。结果提示,2018—2020年河南省平顶山地区鉴定出的8个NTM菌种中,胞内分枝杆菌占比最高,不同菌种对不同抗结核药物的耐药性差异较大,因此菌种鉴定对临床治疗有重要意义。     

Thermal inactivation of several Mycobacterium spp. in milk by pasteurization

I.R. GRANT, H.J. BALL AND M.T. ROWE. 1996. The thermal inactivation of Mycobacterium avium, Myco. bovis, Myco. fortuitum, Myco. intracellulare and Myco. kansaii in milk at 63.5°C was investigated. Survivors were enumerated after heating for 0, 5, 10, 15, 20 and 30 min and thermal death curves were constructed for each species. Mycobacterium bovis and Myco. fortuitum were found to exhibit linear thermal death curves and neither species demonstrated any survival after heating at 63.5°C for 30 min (equivalent to holder pasteurization). In contrast, Myco. avium, Myco. intracellulare and Myco. kansassi yielded thermal death curves which exhibited significant 'tailing' and all three strains survived holder pasteurization.     

Non-tuberculous mycobacteria I: one year clinical isolates identification in Tertiary Hospital Aids Reference Center,Rio de Janeiro,Brazil, in pre highly active antiretroviral therapy era

The aim of this study was to determine the prevalence of non-tuberculous mycobacteria (NTM) isolates at University Hospital, Reference Center for Aids in Rio de Janeiro, Brazil, during one year. We used standard biochemical tests for species identification and IS1245 PCR amplification was applied as a Mycobacterium avium specific identification marker. Four hundred and four specimens from 233 patients yielded acid-fast bacilli growth. M. tuberculosis was identified in 85% of the patients and NTM in 15%. NTM disseminated infection was a common event correlated with human immunodeficiency virus (HIV) infected patients and only in HIV negative patients the source of NTM was non sterile site. M. avium complex (MAC) was biochemically identified in 57.8% (49/83) of NTM isolates, most of them from sterile sites (75.5%), and in 94% (46/49) the IS 1245 marker specific for M. avium was present. Twenty NTM strains showed a MAC biochemical pattern with the exception of a urease-positive (99% of MAC are urease-negative), however IS1245 was detected in 96% of the strains leading to their identification as M. avium. In this group differences in NTM source was not significant. The second most frequently isolated NTM was identified as M. scrofulaceum (7.2%), followed by M. terrae (3.6%), M. gordonae (2.4%), M. chelonae (1.2%), M. fortuitum (1.2%) and one strain which could not be identified. All were IS1245 negative except for one strain identified as M. scrofulaceum. It is interesting to note that non-sterile sites were the major source of these isolates (92.8%). Our finding indicated that M. avium is still the major atypical species among in the MAC isolates recovered from Brazilian Aids patients without highty active antiretroviral therapy schema. Some discrepancies were seen between the identification methods and further investigations must be done to better characterize NTM isolates using other phenotypic and genotypic methods.     

Biochemical characteristics and fatty acid compositions of some armadillo-derived mycobacteria and their relation to Mycobacterium gordonae

The long-chain components of 75 strains of mycobacteria, cultivated from Mycobacterium leprae-infected or non-infected armadillos, and of eight clinical and 15 environmental isolates of M. gordonae, were compared. Four major groups could be distinguished based on the presence of 10-methyloctadecanoic (tuberculostearic) and 2-methyl 3-hydroxyeicosanoic acids and secondary alcohols (2-octadecanol and 2-eicosanol). Some heterogeneity was found in strains assigned to M. gordonae: the characteristic absence of tuberculostearic acid and secondary alcohols and the presence of the branched C14 and the hydroxylated C20 acids were seen in only 34 of the 49 strains studied. Three strains were identified as M. malmoense, one as M. kansasii, ten as belonging to the M. avium-M. intracellulare-M. scrofulaceum complex and eight as belonging to new groups of armadillo-derived mycobacteria (ADM 1, ADM 2 and ADM 3) by conventional bacteriological tests and fatty acid compositions, though M. malmoense was heterogeneous in its fatty acids composition. Four strains, identified as M. avium by conventional tests, differed from this species by their fatty acid compositions. Thirteen strains showed some similarity to M. simiae and ten strains differed from all other known mycobacteria.     

Yersinia spp. Identification Using Copy Diversity in the Chromosomal 16S rRNA Gene Sequence

API 20E strip test, the standard for Enterobacteriaceae identification, is not sufficient to discriminate some Yersinia species for some unstable biochemical reactions and the same biochemical profile presented in some species, e.g. Yersinia ferderiksenii and Yersinia intermedia, which need a variety of molecular biology methods as auxiliaries for identification. The 16S rRNA gene is considered a valuable tool for assigning bacterial strains to species. However, the resolution of the 16S rRNA gene may be insufficient for discrimination because of the high similarity of sequences between some species and heterogeneity within copies at the intra-genomic level. In this study, for each strain we randomly selected five 16S rRNA gene clones from 768 Yersinia strains, and collected 3,840 sequences of the 16S rRNA gene from 10 species, which were divided into 439 patterns. The similarity among the five clones of 16S rRNA gene is over 99% for most strains. Identical sequences were found in strains of different species. A phylogenetic tree was constructed using the five 16S rRNA gene sequences for each strain where the phylogenetic classifications are consistent with biochemical tests; and species that are difficult to identify by biochemical phenotype can be differentiated. Most Yersinia strains form distinct groups within each species. However Yersinia kristensenii, a heterogeneous species, clusters with some Yersinia enterocolitica and Yersinia ferderiksenii/intermedia strains, while not affecting the overall efficiency of this species classification. In conclusion, through analysis derived from integrated information from multiple 16S rRNA gene sequences, the discrimination ability of Yersinia species is improved using our method.     

Nisin A depletes intracellular ATP and acts in bactericidal manner against Mycobacterium smegmatis

Nisin is a bacteriocin produced by many strains of Lactococcus lactis. This study examined the effect of nisin on Mycobacterium smegmatis, a non-pathogenic species of Mycobacterium. Nisin had a minimum inhibitory concentration of 8.0 micrograms ml-1 and a minimum inhibitory dose of 7.5 micrograms ml-1 against Myco. smegmatis. Treatment with 25.0 micrograms ml-1 nisin caused partial inhibition of Myco smegmatis; the survivors were nisin-sensitive when tested in a separate experiment. Mycobacterium smegmatis cells exposed to 50.0 micrograms ml-1 of nisin, lost their viability. the effect of nisin on the growth of Myco. smegmatis was both time- and concentration-dependent. Nisin (10.0 micrograms ml-1) caused 97.7 +/- 2.0% reduction in internal ATP and leakage of intracellular ATP out of Myco. smegmatis cells after several hours of treatment. These data suggest that nisin inhibits Myco. smegmatis by the same mechanism by which it inhibits other bacteria and warrants further investigation as a possible antitubercular agent.     

Characterisation of Bacteroides from sheep periodontal disease by SDS-PAGE of outer membrane proteins

Isolates of Bacteroides species obtained from a longitudinal study of developing periodontal disease in sheep were analysed by SDS-PAGE. Protein profiles of Sarkosyl-insoluble outer membrane extracts were compared within groups of isolates which had already been defined by conventional biochemical techniques. Heterogeneity was exhibited within most groups. Isolates of B. gingivalis and B. asaccharolyticus shown to be similar to human isolates by conventional biochemical tests, gave different protein profiles from the respective type cultures. The sheep B. gingivalis-like isolates were however homogeneous, while the B. asaccharolyticus-like organisms could be divided into 3 subgroups. SDS-PAGE appears to be a useful tool for the examination of bacterial flora and recognition of subgroups of subspecies.     

DNA-DNA hybridization studies and phenotypic characteristics of strains within the 'Streptococcus milleri group'

Twenty-five strains resembling 'Streptococcus milleri' were compared by DNA-DNA hybridization, by whole-cell-derived polypeptide patterns on SDS-PAGE, and by biochemical tests. Four homology groups were revealed by DNA-DNA hybridization. DNA homology groups 1, 2 and 3 were closely related and contained the type strains NCDO 2226 (Streptococcus constellatus), NCDO 2227 (Streptococcus intermedius) and NCTC 10713 (Streptococcus anginosus), respectively. DNA homology group 4 consisted of four strains received as variants of Streptococcus intermedius which were found not to be closely related to strains in groups 1-3. The data from SDS-PAGE polypeptide patterns and biochemical tests supported the recognition of three centres of variation within the 'Streptococcus milleri group' corresponding to DNA homology groups 1-3 and indicated that strains of DNA homology group 4 are members of an as yet undescribed species within the viridans streptococci.     

Variation within Pseudomonas syringae pv. philadelphi, the cause of a leaf spot of Philadelphus spp.

R oberts , S.J. 1985. Variation within Pseudomonas syringae pv. philadelphi , the cause of a leaf spot of Philadelphius spp. Journal of Applied Bacteriology 59 , 283–290
In pathogenicity tests on Philadelphus and other plant species, belonging to ten genera in seven families, isolates of Pseudomonas syringae from leaf spots on Philadelphus spp. in England did not produce symptoms on any plants other than Philadelphus . It is therefore proposed that these isolates should be designated a distinct pathovar of Ps. syringae with the name Pseudomonas syringae pv. philadelphi . Isolates of this new pathovar varied in their reactions to 6 of 57 biochemical tests. In phage typing tests isolates also varied in their sensitivity to five of seven bacteriophage strains. Four of the six biochemical tests (aesculin hydrolysis, utilization of DL-homoserine L-leucine and sorbitol) and all five of the phages (P11, Pls, P2, A15, and A26) were used to separate the isolates into seven groups. These groups had some relation to their geographical origin, species of Philadelphus from which they were originally isolated, and relative virulence on P. coronarius and P. x purpureo-maculatus . They may represent ecotypes of this new pathovar.     

The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria.

Comparative 16S rRNA sequencing was used to infer the phylogenetic relationships among selected species of mycobacteria and related organisms. The phylogeny inferred reflects the traditional classification, with major branches of the phylogenetic tree in general correspondence to the four Runyon groups and with numerical classification analyses. All the mycobacterial species compared, with the exception of M. chitae, are closely related (average similarity values greater than 95%). The slow growers form a coherent line of descent, distinct from the rapid growers, within which the overt pathogens are clustered. The distant relationship between M. chitae and the remaining mycobacteria suggests that this organism is incorrectly classified with the mycobacteria. M. paratuberculosis 18 was indistinguishable from M. avium-M. intracellulare-M. scrofulaceum serovar 1 by this analysis.     

Biochemical Characterization and Phylogenetic Analysis Based on 16S rRNA Sequences for V-Factor Dependent Members of <Emphasis Type="Italic">Pasteurellaceae</Emphasis> Derived from Laboratory Rats

Phylogenetic analysis based on 16S rRNA sequences with sequence data of some bacterial species of Pasteurellaceae related to rodents deposited in GenBank was performed along with biochemical characterization for the 20 strains of V-factor dependent members of Pasteurellaceae derived from laboratory rats to obtain basic information and to investigate the taxonomic positions. The results of biochemical tests for all strains were identical except for three tests, the ornithine decarboxylase test, and fermentation tests of D(+) mannose and D(+) xylose. The biochemical properties of 8 of 20 strains that showed negative results for the fermentation test of D(+) xylose agreed with those of Haemophilus parainfluenzae complex. By phylogenetic analysis, the strains were divided into two clusters that agreed with the results of the fermentation test of xylose (group I: negative reaction for xylose, group II: positive reaction for xylose). The clusters were independent of other bacterial species of Pasteurellaceae tested. The sequences of the strains in group I showed 99.7–99.8% similarity and the strains in group II showed 99.3–99.7% similarity. None of the strains in group I had a close relation with Haemophilus parainfluenzae by phylogenetic analysis, although they showed the same biochemical properties. In conclusion, the strains had characteristic biochemical properties and formed two independent groups within the “rodent cluster” of Pasteurellaceae that differed in the results of the fermentation test of xylose. Therefore, they seemed to be hitherto undescribed taxa in Pasteurellaceae.     

Discriminant analysis of volatile fatty acids produced in culture medium: a novel approach to the identification of Pseudomonas species

The volatile fatty acids produced in culture medium by 357 Pseudomonas strains belonging to eight species were determined quantitatively by GLC. The resultant chromatograms were submitted to discriminant analysis. Stable discriminant functions were computed and included in a computerized identification system which also involved some distinctive volatile fatty acids regarded as two-state qualitative characters (presence or absence characters). Using a test group of 249 strains belonging to the studied species, more than 89% of the identifications made by this system agreed with those made by conventional biochemical methods despite the relatively poor differentiation between P. putida and P. fluorescens. When the individual species within the matrices were weighted with prior probabilities reflecting results given by two simple biochemical tests, 96% of the 249 strains were correctly identified.     

Naturally occurring Mycobacterium scrofulaceum infection in a laboratory mouse colony.

A contamination with Mycobacterium scrofulaceum was experienced in a colony of BALB/c-nu/nu mice. The contamination was noticed after introduction of C57BL/6 and C57BL/6. Lyt l. 1 strains into facilities that kept the colony. M. scrofulaceum seemed to be spread by oral infestation and cross-contamination of fecal excretions during handling of the mice. The organisms were shed continually or intermittently into feces of weaned nu/+ and nu/nu mice of BALB/c background, and were isolated from the mesenteric lymph nodes and spleen of some of the mice. Some of the bacillus-carrying mice developed serum antibody to M. scrofulaceum of IgG and IgA classes and gave a low degree of hypersensitivity to PPD from M. tuberculosis.     

Biochemical tests for identification of mycelial cultures of basidiomycetes

Twenty-four biochemical tests have been developed to identify basidiomycetes from mycelial cultures. Eleven are designated ‘instant tests’ because results are obtained within 24 h; ten of these test for specific enzymes, the other is based on a reaction between vanillin and unknown fungal metabolites. The remaining thirteen tests require incubation periods ranging from 1 to 4 days and are thus designated ‘incubated tests’. Sixteen of these tests were applied first to identified isolates of Peniophora sacrata, Sclerotium rolfsii, Stereum purpureum and Trametes versicolor. They distinguished these species satisfactorily, so these sixteen tests, and eight others devised subsequently, were applied to unidentified basidiomycetes isolated from diseased roots of fruit crops. The results of these tests enabled the isolates to be placed in seven groups. All isolates in a particular group were morphologically similar which further suggested that each group might correspond to a species and that isolates could be defined on the basis of biochemical tests.     

Identification of a novel protein with a role in lipoarabinomannan biosynthesis in mycobacteria

All species of Mycobacteria synthesize distinctive cell walls that are rich in phosphatidylinositol mannosides (PIMs), lipomannan (LM), and lipoarabinomannan (LAM). PIM glycolipids, having 2-4 mannose residues, can either be channeled into polar PIM species (with 6 Man residues) or hypermannosylated to form LM and LAM. In this study, we have identified a Mycobacterium smegmatis gene, termed lpqW, that is required for the conversion of PIMs to LAM and is highly conserved in all mycobacteria. A transposon mutant, Myco481, containing an insertion near the 3' end of lpqW exhibited altered colony morphology on complex agar medium. This mutant was unstable and was consistently overgrown by a second mutant, represented by Myco481.1, that had normal growth and colony characteristics. Biochemical analysis and metabolic labeling studies showed that Myco481 synthesized the complete spectrum of apolar and polar PIMs but was unable to make LAM. LAM biosynthesis was restored to near wild type levels in Myco481.1. However, this mutant was unable to synthesize the major polar PIM (AcPIM6) and accumulated a smaller intermediate, AcPIM4. Targeted disruption of the lpqW gene and complementation of the initial Myco481 mutant with the wild type gene confirmed that the phenotype of this mutant was due to loss of LpqW. These studies suggest that LpqW has a role in regulating the flux of early PIM intermediates into polar PIM or LAM biosynthesis. They also suggest that AcPIM4 is the likely branch point intermediate in polar PIM and LAM biosynthesis.     

Fluorescent acid-fast microscopy for measuring phagocytosis of Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum by Tetrahymena pyriformis and their intracellular growth

Fluorescent acid-fast microscopy (FAM) was used to enumerate intracellular Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum in the ciliated phagocytic protozoan Tetrahymena pyriformis. There was a linear relationship between FAM and colony counts of M. avium cells both from cultures and within protozoa. The Ziehl-Neelsen acid-fast stain could not be used to enumerate intracellular mycobacteria because uninfected protozoa contained acid-fast, bacterium-like particles. Starved, 7-day-old cultures of T. pyriformis transferred into fresh medium readily phagocytized M. avium, M. intracellulare, and M. scrofulaceum. Phagocytosis was rapid and reached a maximum in 30 min. M. avium, M. intracellulare, and M. scrofulaceum grew within T. pyriformis, increasing by factors of 4- to 40-fold after 5 days at 30 degrees C. Intracellular M. avium numbers remained constant over a 25-day period of growth (by transfer) of T. pyriformis. Intracellular M. avium cells also survived protozoan encystment and germination. The growth and viability of T. pyriformis were not affected by mycobacterial infection. The results suggest that free-living phagocytic protozoa may be natural hosts and reservoirs for M. avium, M. intracellulare, and M. scrofulaceum.     

Studies on the Bacteriophagy of Pseudomonas mors-prunorum, Ps. syringae and Related Organisms

S ummary : A group of 23 phages, mainly isolated with Pseudomonas mors-prunorum and Ps. syringae as the propagating strains, was tested against more than 200 pseudomonads including named plant pathogens and a variety of saprophytes. The majority of the phages had a wide host range, and did not distinguish between plant pathogens and saprophytes, thus confirming the close relationship between these two groups. The most reactive bacteria were 60 English isolates of Ps. mors-prunorum , 48 from cherry and 12 from plum, and 28 isolates of Ps. syringae from pear. Patterns of reaction within these 3 groups were relatively homogeneous and each group was distinct and differed from all other isolates tested. Ps. syringae isolates from other hosts were less uniform and occasionally shared reaction patterns with other species, e.g. Ps. cannabina and Ps. glycinea. Similar relationships were observed with phages at both high titre and at routine test dilution including the difference in phage sensitivity between the cherry and plum strains of Ps. mors-prunorum. On the basis of 7 biochemical tests the plum and cherry strains were indistinguishable but they differed from all Ps. syringae isolates tested by giving white growth in 5% sucrose broth and in failing to liquefy gelatin. Furthermore, unlike most Ps. syringae isolates they were also unable to hydrolyze aesculin and were tyrosinase positive. There was no clear evidence in this investigation of correlation between phage sensitivity and biochemical activity. Eleven isolates from various European countries, designated Ps. mors-prunorum , differed widely both in phage sensitivity and biochemical activity and some of them may be more appropriately called Ps. syringae. Others may be intermediate forms between these species. The relationship between Ps. mors-prunorum and Ps. syringae and the nomenclature of these organisms are discussed and a concept of ecotypes suggested as a substitute for species.     

Biochemical characterization of some additional mycelial cultures of basidiomycetes

Twenty-six biochemical tests were used to study cultures of basidiomycetes isolated from roots of fruit-trees and other plants. The results enabled isolates to be placed into one of sixteen groups. Three of these groups were identified as Collybia drucei, Corticium utriculicum and Heteroporus biennis by matching their biochemical reactions with those of isolates from fruiting bodies of these fungi. This suggests that the other groups might also correspond to species. The three named fungi are indigenous, the first two not having been recorded elsewhere. Thus, root infections by these fungi may have originated from the indigenous fungal flora. Isolates of C. utriculicum and Stereum purpureum which were indistinguishable in culture were also separated using biochemical tests.     

Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium

16S rRNA sequences from Mycobacterium tuberculosis, M. avium, M. gastri, M. kansasii, M. marinum, M. chelonae, M. smegmatis, M. terrae, M. gordonae, M. scrofulaceum, M. szulgai, M. intracellulare, M. nonchromogenicum, M. xenopi, M. malmoense, M. simiae, M. flavescens, M. fortuitum, and M. paratuberculosis were determined and compared. The sequence data were used to infer a phylogenetic tree, which provided the basis for a systematic phylogenetic analysis of the genus Mycobacterium. The groups of slow- and fast-growing mycobacteria could be differentiated as distinct entities. We found that M. simiae occupies phylogenetically an intermediate position between these two groups. The phylogenetic relatedness within the slow-growing species did not reflect the Runyon classification of photochromogenic, scotchromogenic, and nonchromogenic mycobacteria. In general, the phylogenetic units identified by using rRNA sequences confirmed the validity of phenotypically defined species; an exception was M. gastri, which was indistinguishable from M. kansasii when this kind of analysis was used.     

The cytologic diagnosis of Mycobacterium kansasi tuberculosis by fluorescence microscopy of Papanicolaou-stained specimens

The cytologic diagnosis of Mycobacterium kansasi tuberculosis by fluorescence microscopy of Papanicolaou-stained specimens
The sensitivities of (i) Papanicolaou fluorescence, (ii) auramine rhodamine fluorescence, and (iii) Ziehl-Neelsen staining were compared for their ability to detect the atypical mycobacterium Myco. kansasi in cytological samples. Ninety-two cases were investigated, and the sensitivities of the three methods of detection were found to be 36.9%, 12.0%, and 20.7%, respectively. The control groups consisted of 30 specimens from cases of bronchial carcinoma and 30 of pneumonia. All cases were proved by microbiology. No false-positive results were recorded using Papanicolaou fluorescence. An important but coincidental finding arising from this study was that infection by the atypical mycobacterium Myco. kansasi causes cytological patterns corresponding to those normally associated with acute pneumonia and not to tuberculosis.