Short-Chain Acids of Pseudomonas Species Encountered in Clinical Specimens

The short-chain acids of 36 strains of Pseudomonas grown on Trypticase soy agar were determined by gas-liquid chromatography. Distinct acid profiles were observed for each of the eight species tested. Propionic, isobutyric, and isovaleric acids were the principal acids detected in media extracts of P. maltophilia, P. cepacia, P. pseudoalcaligenes, P. diminuta, and P. vesiculare. The presence and relative amounts of the isobutyric and isovaleric acids clearly distinguished P. maltophilia, P. pseudoalcaligenes, and P. cepacia from other species. P. diminuta could be distinguished from P. vesiculare by the production of glutaric acid; P. testosteroni was the only species tested which produced relatively large amounts of phenylacetic acid.     

Characterization of Pseudomonas Species Isolated from Clinical Specimens

More than 90 morphological and physiological characters of 227 strains of pseudomonads isolated from clinical specimens and 16 reference strains are described. The clinical isolates included P. aeruginosa (apyocyanogenic), P. fluorescens, P. putida, P. pseudomallei, P. cepacia, P. acidovorans, P. alcaligenes, P. pseudoalcaligenes, P. stutzeri, P. putrefaciens, P. maltophilia, and P. diminuta.     

Species Spectrum of Nontuberculous Mycobacteria Isolated from Clinical Specimens in Kuwait

Specific identification of mycobacteria is of clinical relevance since treatment varies according to the Mycobacterium species causing infection. All mycobacterial isolates are currently identified as M. tuberculosis (MTB) or nontuberculous mycobacteria (NTM) based on p-nitro-α-acetylamino-β-hydroxypropiophenone (NAP) test, and the species spectrum of NTM-causing infections in Kuwait remains unknown. This study identified all NTM strains isolated in Kuwait from 1 October 2003 to 31 March 2004 to the species level. The mycobacteria were cultured from various clinical specimens using the BACTEC 460 TB system and NAP test was performed to differentiate MTB from NTM strains. The INNO-LiPA MYCOBACTERIA v2 assay (LiPA) was used for species-specific identification of NTM strains and some randomly selected MTB strains. The LiPA results for selected isolates were confirmed by DNA sequencing of the 16S-23S internal transcribed spacer region. A total of 325 isolates of Mycobacterium species originating from 305 individual patients were recovered during the study period, with 307 and 18 isolates identified as MTB and NTM, respectively. The LiPA correctly identified all 18 MTB isolates analyzed. Seven different NTM species were identified among 18 NTM isolates originating from 14 patients, with M. fortuitum causing the majority of NTM infections in Kuwait. One patient was infected with two NTM species. Rapid species-specific identification of NTM may help with appropriate treatment regimens for proper patient management. The DNA sequencing data reported in this study are deposited in EMBL under accession numbers AM709724 to AM709731.     

Distribution of Streptococcal Groups in Clinical Specimens with Evaluation of Bacitracin Screening

During a 2-year period, 4,968 strains of beta-hemolytic streptococci were examined for the clinical source distribution and bacitracin sensitivity of each group. In the upper respiratory tract, groups A (51.7%) and C (20.4%) accounted for most of the isolates, and in wounds and exudates group A (79.1%) made up most of the isolates. Group B (71.2%) was the major component of isolates from the genitorinary tract and, while composing 29.3% of the lower respiratory tract isolates, competed with group A (18.8%) and the nongroupables (22.8%) for supremacy. Bacitracin screening showed that 0.5% of group A streptococci were resistant, and sensitive non-group A isolates were group B (2.6%), group C (6.0%), group G (8.0%), and the nongroupables (2.2%). It was found that those groups which were most predominant in wounds and the upper respiratory tract gave the highest rate of false positives with bacitracin, whereas the predominant group of the genitourinary tract gave the lowest rate of false positives.     

Unusual Fermentative, Gram-Negative Bacilli Isolated from Clinical Specimens: II. Characterization of Aeromonas Species

Morphological and physiological characterization of 12 Aeromonas strains isolated from clinical specimens demonstrated several important diagnostic features. These included polar arrangement of the flagella; production of oxidase, deoxyribonuclease, amylase, gelatinase, and lipase; lack of ornithine decarboxylase; and sensitivity to polymyxin. Awareness of these features should result in more frequent differentiation of aeromonads from the physiologically similar members of the genus Plesiomonas and the late- or non-lactose-fermenting species of Enterobacteriaceae.     

Direct Species Identification of Common Pathogenic Dermatophyte Fungi in Clinical Specimens by Semi-nested PCR and Restriction Fragment Length Polymorphism

OBJECTIVE: To seek a rapid and reliable molecular biology method to identify the common pathogenic dermatophyte fungi from clinical samples. METHOD: The genome DNA was extracted from cultured strains of seven common dermatophyte fungi species and part of each positive clinical specimen by microscopy. Intergenic spacer regions of ribosomal DNA (ITS) were amplified by semi-nested PCR (snPCR) with three universal primers (NS5, ITS1, and ITS4) for fungi. The amplified products were digested with two restriction endonucleases (BciT130 I, Dde I), the Restriction Fragment Length Polymorphism(RFLP). The rest of each clinical specimen was cultured in Sabouraud's Agar medium. Then the results of RFLP were compared with the traditional culture results. RESULTS: The digestion of seven common dermatophyte fungi produced seven different restriction profiles. Restriction profiles of 17 clinical specimens matched, respectively, to that of the cultured strains, and 14 profiles of the 17 ones matched the culture result completely. The coincidence was 100.0%. CONCLUSIONS: snPCR-RFLP analysis of intergenic spacer regions of ribosomal DNA is a valuable method of exactness and clarity for species identification of common dermatophyte fungi from clinical specimens.     

Species Distribution of Clinical Acinetobacter Isolates Revealed by Different Identification Techniques

A total of 2582 non-duplicate clinical Acinetobacter spp. isolates were collected to evaluate the performance of four identification methods because it is important to identify Acinetobacter spp. accurately and survey the species distribution to determine the appropriate antimicrobial treatment. Phenotyping (VITEK 2 and VITEK MS) and genotyping (16S rRNA and rpoB gene sequencing) methods were applied for species identification, and antimicrobial susceptibility test of imipenem and meropenem was performed with a disk diffusion assay. Generally, the phenotypic identification results were quite different from the genotyping results, and their discrimination ability was unsatisfactory, whereas 16S rRNA and rpoB gene sequencing showed consistent typing results, with different resolution. Additionally, A. pittii, A. calcoaceticus and A. nosocomialis, which were phylogenetically close to A. baumannii, accounted for 85.5% of the non-A. baumannii isolates. One group, which could not be clustered with any reference strains, consisted of 11 isolates and constituted a novel Acinetobacter species that was entitled genomic species 33YU. None of the non-A. baumannii isolates harbored a bla _OXA-51-like gene, and this gene was disrupted by ISAba19 in only one isolate; it continues to be appropriate as a genetic marker for A. baumannii identification. The resistance rate of non-A. baumannii isolates to imipenem and/or meropenem was only 2.6%, which was significantly lower than that of A. baumannii. Overall, rpoB gene sequencing was the most accurate identification method for Acinetobacter species. Except for A. baumannii, the most frequently isolated species from the nosocomial setting were A. pittii, A. calcoaceticus and A. nosocomialis.     

Recovery of Bilophila wadsworthiafrom Clinical Specimens in Italy

This report is the first survey in Italy to evaluate the incidence of recovery of Bilophila wadsworthia in clinical situations. The survey was carried out at the departments of Microbiology in two Northern Italian hospitals over a one-year period. Tests for B. wadsworthia were carried out on a range of specimens from different body sites, when etiology by anaerobes was suspected. Out of a total of 350 samples examined, 67% were positive in bacteriological tests. Mixed anaerobic infections were detected in 53 specimens, corresponding to 23% of all cases. Strains of B. wadsworthia were isolated from 12 samples, equivalent to 5% and 22% of total and mixed/anaerobic infections, respectively. Bilophila wadsworthia was always isolated in mixed infections, mainly from the large intestine (67% of cases). The infectious process of B. wadsworthia was often complicated by abscess formation, regardless of body site. Interestingly, a strain was isolated from one case of bacteremia. The microorganisms most frequently isolated with B. wadsworthia were Escherichia coli for facultative species (38%), and Bacteroides fragilis, from anaerobic isolates (25%). Production of beta-lactamases by B. wadsworthia isolates was found in ten strains (83%), which appeared to be penicillin G resistant at concentration equal to or greater than the break-point (4 microg/mL). Epidemiological and clinical data from this and previous studies point to the involvement of B. wadsworthia in mixed infections. To assess the specific contribution of the species to the disease, studies of pathogenetic factors are to be considered in parallel. Nonetheless, production of beta-lactamases by most B. wadsworthia isolates could easily interfere with the therapeutical approach to infections involving the new species. The addition of a selective medium to culture specimens from the abdominal cavity should be considered in order to detect the presence of B. wadsworthia.     

Pseudomonas putrefaciens Isolates from Clinical Specimens

A total of 109 cultures of Pseudomonas putrefaciens isolated from clinical specimens were studied. The cultures were separated into two groups. The majority of the group 1 isolates, comprising 31 cultures, were characterized by (i) growth in plain nutrient broth, but no growth in broth supplemented with NaCl at concentrations of 7% and above, (ii) no growth on Salmonella-Shigella (SS) agar, and (iii) production of acid from the carbohydrates, sucrose, maltose, arabinose, and dextrin. Most group 2 isolates, comprising 78 cultures, were (i) unable to grow in plain nutrient broth, but grew well in broth supplemented with NaCl at a concentration of 7 to 10%, (ii) able to grow on SS agar, and (iii) unable to produce detectable amounts of acid from any of the carbohydrates tested except for variable results with glucose and fructose.     

Individualism, Type Specimens, and the Scrutability of Species Membership

The view that species are individuals, as developed by Ghiselinand Hull, has been touted as explaining the role of type specimens intaxonomy. The kinship of this explanation with the Kripke-Putnam theoryof names has long been recognized. In light of this kinship, however,Hull's account of type specimens can be seen to entail two relatedinscrutability problems – unreasonable limits placed on the natureand extent of biological knowledge. An appreciation for these problemsinvites us to consider the proper relation between metaphysical andepistemological inquires in the philosophy of science.     

Distribution and Clinical Manifestations of Cryptosporidium Species and Subtypes in HIV/AIDS Patients in Ethiopia

Background

Cryptosporidiosis is an important cause for chronic diarrhea and death in HIV/AIDS patients. Among common Cryptosporidium species in humans, C. parvum is responsible for most zoonotic infections in industrialized nations. Nevertheless, the clinical significance of C. parvum and role of zoonotic transmission in cryptosporidiosis epidemiology in developing countries remain unclear.

Methodology/Principal Findings

In this cross-sectional study, 520 HIV/AIDS patients were examined for Cryptosporidium presence in stool samples using genotyping and subtyping techniques. Altogether, 140 (26.9%) patients were positive for Cryptosporidium spp. by PCR-RFLP analysis of the small subunit rRNA gene, belonging to C. parvum (92 patients), C. hominis (25 patients), C. viatorum (10 patients), C. felis (5 patients), C. meleagridis (3 patients), C. canis (2 patients), C. xiaoi (2 patients), and mixture of C. parvum and C. hominis (1 patient). Sequence analyses of the 60 kDa glycoprotein gene revealed a high genetic diversity within the 82 C. parvum and 19 C. hominis specimens subtyped, including C. parvum zoonotic subtype families IIa (71) and IId (5) and anthroponotic subtype families IIc (2), IIb (1), IIe (1) and If-like (2), and C. hominis subtype families Id (13), Ie (5), and Ib (1). Overall, Cryptosporidium infection was associated with the occurrence of diarrhea and vomiting. Diarrhea was attributable mostly to C. parvum subtype family IIa and C. hominis, whereas vomiting was largely attributable to C. hominis and rare Cryptosporidium species. Calf contact was identified as a significant risk factor for infection with Cryptosporidium spp., especially C. parvum subtype family IIa.

Conclusions/Significance

Results of the study indicate that C. parvum is a major cause of cryptosporidiosis in HIV-positive patients and zoonotic transmission is important in cryptosporidiosis epidemiology in Ethiopia. In addition, they confirm that different Cryptosporidium species and subtypes are linked to different clinical manifestations.     

Distribution of Zearalenone-Producing Fusarium Species in Japan

One hundred sixty-six isolates of Fusarium spp. from domestic cereal grains, feed, and other sources were examined for their ability to produce zearalenone on autoclaved moist rice grains. They belonged to the following species (number of producers/number tested): F. roseum (9/28), F. roseum (Culmorum) (3/4), F. roseum (Gibbosum) (2/5), F. roseum (Avenaceum) (1/2), F. roseum (Scirpi) (0/1), F. tricinctum (1/4), F. tricinctum (Sporotrichiella) (0/7), F. lateritium (1/1), F. episphaeria (0/2), F. moniliforme (0/3), F. oxysporum (0/12), F. rigidiusculum (0/4), F. solani (0/4), F. splendens (0/1), F. nivale (0/2), and Fusarium spp. (15/86). Zearalenone was isolated from molded rice by ethanol extraction and purified by column chromatography. Selected isolates of F. roseum M-3-2 and F. roseum (Gibbosum) A-O-2 produced 50 to 100 mg of zearalenone per kg of rice. Increased yields (250 to 407 mg/kg of rice) were obtained by F. roseum M-3-2 when the substrate was supplemented with 1% peptone.     

Specific Distribution of R Factors in Serratia marcescens Strains Isolated from Hospital Infections

Serratia marcescens strains from three hospitals in the city of New York were tested for antibiotic susceptibility patterns and the presence of transmissible antibiotic resistance factors. There appears to be a pattern characteristic for each hospital with regard to the sensitivity to nalidixic acid, tetracycline, chloramphenicol, and sulfonamides, whereas the resistance to ampicillin, cephalothin, and streptomycin is similar in the strains isolated from all three hospitals. In one hospital, a single type of R factor was found which transfers resistance to streptomycin, kanamycin, ampicillin, and sulfonamides, whereas strains isolated from a second hospital transfer only ampicillin resistance. No R factors could be detected in multiply resistant Serratia strains isolated in a third hospital. The presence of a single type of R factor probably reflects the relative ecological isolation of S. marcescens and could be useful for epidemiological studies of hospital infections with Serratia.     

Clinical relevance and virulence factors of pigmented Serratia marcescens

Pigmented Serratia marcescens isolated in a Brazilian hospital were studied with respect to frequency of isolation, serotyping, antibiotic resistance and virulence factors. The serotype most frequent was O6:K14 (53%) and all isolates were resistant to ampicillin, cephalothin and tetracycline. The majority of the isolates (92%) were resistant to the action of human serum and all produced cytotoxins on Vero, CHO, HEp-2 and HeLa cells. These isolates were virulent for mice (LD(50)=10(7) bacteria ml(-1)) and showed virulence factors, but were isolated with low frequency (3. 4%) and caused infection in only 31% of cases. Analysis of serotyping, phage typing and chromosomal DNA revealed at least 13 unrelated strains among pigmented S. marcescens. In conclusion, this work describes a low frequency of isolation of pigmented S. marcescens from clinical specimens, indicating that non-pigmented strains are clinically more significant.     

克隆化探针中载体与临床样品同源性的研究

当前,克隆化探针(由病毒核酸片段和细菌质粒一载体组成)在临床样品的实验诊断和研究中得到了应用。它具有简便、快速、灵敏等优点,并有助于检测那些难于或不能培养的病毒。但是克隆化探针中载体与临床样品的同源性问题应引起重视。我们用常见的克隆载体pBR322作探针,用核酸点杂交和Southern吸印方法,检测了来自173人的213例样品。结果表明,在常用的临床样品:人宫颈脱落细胞、宫颈活检组织、血液中都含有pBR322 DNA的同源序列,这就意味着如果用克隆化探针检测这些临床样品时,可能出现样品与载体发生非特异性反应,而不是与病毒基因片段的特异性反应。实验还表明,经一次电泳纯化的病毒基因片段与pBR322探针杂交,阳性信号明显减弱,但没有完全消失,说明仍有少量pBR322污染。因此,在运用克隆化探针检测临床各类样品时,各系统要按常规设载体探针对照,或者用多次纯化的分离病毒基因片段作探针,以排除载体与临床样品的同源性问题。     

Clinical Significance of Mycobacterium kansasii Isolates from Respiratory Specimens

The clinical significance of Mycobacterium kansasii respiratory isolates is uncertain. The aims of this study were to determine the clinical relevance of M. kansasii isolates and to identify the clinical features and outcomes of M. kansasii lung disease. We reviewed the medical records of 104 patients from whom at least one respiratory M. kansasii isolate was obtained from January 2003 to July 2014 at Samsung Medical Center, South Korea. Of these 104 patients, 54 (52%) met the diagnostic criteria for nontuberculous mycobacterial lung disease; among them, 41 (76%) patients received antibiotic treatment for a median time of 15.0 months (interquartile range [IQR], 7.0–18.0 months). The remaining 13 (24%) without overt disease progression were observed for a median period of 24.0 months (IQR, 5.0–34.5 months). Patients with M. kansasii lung disease exhibited various radiographic findings of lung disease, including the fibrocavitary form (n = 24, 44%), the nodular bronchiectatic form (n = 17, 32%), and an unclassifiable form (n = 13, 24%). The fibrocavitary form was more common in patients who received treatment (n = 23, 56%), while the nodular bronchiectatic form was more common in patients with M. kansasii lung disease who did not receive treatment (n = 9, 70%). None of the patients with a single sputum isolate (n = 18) developed M. kansasii disease over a median follow-up period of 12.0 months (IQR, 4.0–26.5 months). In total, 52% of all patients with M. kansasii respiratory isolates exhibited clinically significant disease. Moreover, patients with M. kansasii lung disease displayed diverse radiographic findings in addition to the fibrocavitary form. The nodular bronchiectatic form was more common in patients with M. kansasii lung disease with an indolent clinical course. Thus, since the clinical significance of a single M. kansasii respiratory isolate is not definite, strict adherence to recommended diagnostic criteria is advised.     

Distribution of Plasmids in Distinct Leptospira Pathogenic Species

Leptospirosis, caused by pathogenic Leptospira, is a worldwide zoonotic infection. The genus Leptospira includes at least 21 species clustered into three groups—pathogens, non-pathogens, and intermediates—based on 16S rRNA phylogeny. Research on Leptospira is difficult due to slow growth and poor transformability of the pathogens. Recent identification of extrachromosomal elements besides the two chromosomes in L. interrogans has provided new insight into genome complexity of the genus Leptospira. The large size, low copy number, and high similarity of the sequence of these extrachromosomal elements with the chromosomes present challenges in isolating and detecting them without careful genome assembly. In this study, two extrachromosomal elements were identified in L. borgpetersenii serovar Ballum strain 56604 through whole genome assembly combined with S1 nuclease digestion following pulsed-field gel electrophoresis (S1-PFGE) analysis. Further, extrachromosomal elements in additional 15 Chinese epidemic strains of Leptospira, comprising L. borgpetersenii, L. weilii, and L. interrogans, were successfully separated and identified, independent of genome sequence data. Southern blot hybridization with extrachromosomal element-specific probes, designated as lcp1, lcp2 and lcp3-rep, further confirmed their occurrences as extrachromosomal elements. In total, 24 plasmids were detected in 13 out of 15 tested strains, among which 11 can hybridize with the lcp1-rep probe and 11 with the lcp2-rep probe, whereas two can hybridize with the lcp3-rep probe. None of them are likely to be species-specific. Blastp search of the lcp1, lcp2, and lcp3-rep genes with a nonredundant protein database of Leptospira species genomes showed that their homologous sequences are widely distributed among clades of pathogens but not non-pathogens or intermediates. These results suggest that the plasmids are widely distributed in Leptospira species, and further elucidation of their biological significance might contribute to our understanding of biology and infectivity of pathogenic spirochetes.