Mycobacterium florentinum sp. nov., isolated from humans

Detection of Free-Living Amoebae and Their Intracellular Bacteria in Borehole Water before and after a Ceramic Pot Filter Point-of-Use Intervention in Rural Communities in South Africa

Free-living amoebae (FLA) are ubiquitous in nature, whereas amoeba-resistant bacteria (ARB) have evolved virulent mechanisms that allow them to resist FLA digestion mechanisms and survive inside the amoeba during hostile environmental conditions. This study assessed the prevalence of FLA and ARB species in borehole water before and after a ceramic point-of-use intervention in rural households. A total of 529 water samples were collected over a five-month period from 82 households. All water samples were subjected to amoebal enrichment, bacterial isolation on selective media, and molecular identification using 16S PCR/sequencing to determine ARB species and 18S rRNA PCR/sequencing to determine FLA species present in the water samples before and after the ceramic pot intervention. Several FLA species including Acanthamoeba spp. and Mycobacterium spp. were isolated. The ceramic pot filter removed many of these microorganisms from the borehole water. However, design flaws could have been responsible for some FLA and ARB detected in the filtered water. FLA and their associated ARB are ubiquitous in borehole water, and some of these species might be potentially harmful and a health risk to vulnerable individuals. There is a need to do more investigations into the health risk of these organisms after point-of-use treatment.

Mycobacterial infections in wild boars (Sus scrofa) from Southern Switzerland: Diagnostic improvements, epidemiological situation and zoonotic potential

The occurrence of mycobacterial infections in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. In addition to the well-known pathogenic members of the Mycobacterium tuberculosis - complex (MTBC), over 180 non-tuberculous mycobacteria (NTM) species have been described. Although the large majority of the NTM is assumed to be non-pathogenic to most individuals, an increasing trend in NTM infections has been observed over the last decades. The reasons of such augmentation are probably more than one: improved laboratory diagnostics, an increasing number of immunocompromised patients and individuals with lung damage are some of the possible aspects. Mandibular lymph nodes of 176 hunted wild boars from the pre-Alpine region of Canton Ticino, Switzerland, were collected. Following gross inspection, each lymph node was subjected to culture and to an IS6110 based real-time PCR specific for MTBC members. Histology was performed of a selection of lymph nodes (n = 14) presenting gross visible lesions. Moreover, accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) species identification was compared with sequence analysis of a combination of housekeeping genes. Mycobacteria of the MTBC were detected in 2.8% of the wild boars (n = 5; CI_95% 1.2-6.5) and were all confirmed to be Mycobacterium microti by molecular methods. In addition, based on the examined lymph nodes, NTM were detected in 57.4% (n = 101; CI_95% 50.0-64.5) of the wild boars originating from the study area. The 111 isolates belonged to 24 known species and three potentially undescribed Mycobacterium species. M. avium subsp. hominissuis thereby predominated (22.5%) and was found in lymph nodes with and without macroscopic changes. Overall, the present findings show that, with the exception of undescribed Mycobacterium species where identification was not possible (3.6%; 4/111), MALDI-TOF MS had a high concordance rate (90.1%; 100/111 isolates) to the sequence-based reference method.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Mycobacterium ahvazicum sp. nov., the nineteenth species of the Mycobacterium simiae complex

Four slowly growing mycobacteria isolates were isolated from the respiratory tract and soft tissue biopsies collected in four unrelated patients in Iran. Conventional phenotypic tests indicated that these four isolates were identical to Mycobacterium lentiflavum while 16S rRNA gene sequencing yielded a unique sequence separated from that of M. lentiflavum. One representative strain AFP-003^T was characterized as comprising a 6,121,237-bp chromosome (66.24% guanosine-cytosine content) encoding for 5,758 protein-coding genes, 50 tRNA and one complete rRNA operon. A total of 2,876 proteins were found to be associated with the mobilome, including 195 phage proteins. A total of 1,235 proteins were found to be associated with virulence and 96 with toxin/antitoxin systems. The genome of AFP-003^T has the genetic potential to produce secondary metabolites, with 39 genes found to be associated with polyketide synthases and non-ribosomal peptide syntases and 11 genes encoding for bacteriocins. Two regions encoding putative prophages and three OriC regions separated by the dnaA gene were predicted. Strain AFP-003^T genome exhibits 86% average nucleotide identity with Mycobacterium genavense genome. Genetic and genomic data indicate that strain AFP-003^T is representative of a novel Mycobacterium species that we named Mycobacterium ahvazicum, the nineteenth species of the expanding Mycobacterium simiae complex.

Detection of Mycobacterium tuberculosis from the stool of HIV sero-positive individuals suspected of pulmonary tuberculosis

BACKGROUND

The impact of tuberculosis (TB) is exacerbated in Africa because of the human immunodeficiency virus (HIV) pandemic. Pulmonary tuberculosis (PTB) diagnosis is difficult in HIV-infected patients and negative sputum results are more common which leads to diagnostic delay and increases morbidity and mortality. Extra-pulmonary samples such as stool may be easier to obtain and our approach may therefore significantly improve PTB detection in people living with HIV.

OBJECTIVE

To detect Mycobacterium tuberculosis from the stool of HIV sero-positive individuals suspected of pulmonary TB.

METHOD

A total of 117 HIV-infected individuals from three public health facilities in Addis Ababa, Ethiopia were enrolled consecutively in the study. Paired morning sputum and stool samples were simultaneously collected from anti-retroviral therapy (ART) naïve individuals living with HIV and suspected for PTB. The diagnostic accuracy of the smear microscopy, culture and region of difference (RD)9-based polymerase chain reaction (PCR) in stool was compared with the accuracy of sputum testing. Chi-square test and kappa value were used to compare different method used.

RESULTS

Sputum culture positivity for mycobacteria was confirmed in 33(28.2%) of the study subjects. Of 33 individuals positive for sputa culture, 10 individuals were observed to be stools culture positive. Of the 84 individuals negative for mycobacteria by sputum culture, three (3.6%) were stool culture positive and thus, the sensitivity and agreement between stool culture as compare to sputum culture were 30.3% and 0.33, respectively. Of 117 individuals, 11(9.4%) were sputum smear positive and of 11 sputum smear positive three were also stool smear positive. While of the 106 sputum smear negative individuals', only one was stool smear positive resulting in 12.1% sensitivity and 0.18 agreements against sputum culture. On the other hand, the sensitivity of RD9-based PCR directly on stool was 69.7% by considering sputum culture as a reference standard. Moreover, RD9-based PCR directly on sputum detected 7(6.0%) individuals who were sputum culture negative for M. tuberculosis.

CONCLUSION

M. tuberculosis was detected in stool of individuals living with HIV who were negative for sputum smear microscopy and culture. Hence, examination of stool samples alongside with sputum samples increases the detection of PTB in individuals living with HIV.

Draft genome sequence of Mycobacterium rufum JS14(T), a polycyclic-aromatic-hydrocarbon-degrading bacterium from petroleum-contaminated soil in Hawaii

Mycobacterium rufum JS14^T (=ATCC BAA-1377^T, CIP 109273^T, JCM 16372^T, DSM 45406^T), a type strain of the species Mycobacterium rufum sp. . belonging to the family Mycobacteriaceae, was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil in Hilo (HI, USA) because it harbors the capability of degrading PAH. Here, we describe the first genome sequence of strain JS14^T, with brief phenotypic characteristics. The genome is composed of 6,176,413 bp with 69.25 % G + C content and contains 5810 protein-coding genes with 54 RNA genes. The genome information on M. rufum JS14^T will provide a better understanding of the complexity of bacterial catabolic pathways for degradation of specific chemicals.

Molecular Identification of Nontuberculous Mycobacteria in Humans in Zimbabwe Using 16S Ribosequencing

Background:

Several nontuberculous mycobacteria (NTM) were previously isolated from diverse environments such as water, soil, sewage, food and animals. Some of these NTM are now known to be opportunistic pathogens of humans.

Objective:

The main purpose of the study was to identify NTM isolates stored at the National Microbiology Reference Laboratory (NMRL) and were previously isolated from humans during a national tuberculosis (TB) survey.

Methods:

Pure NTM cultures already isolated from human sputum samples during the national TB survey were retrieved from the NMRL and used for this study. DNA was extracted from the samples and 16S ribosomal RNA gene amplified by polymerase chain reaction. The amplicons were sequenced and bioinformatics tools were used to identify the NTM species.

Results:

Out of total of 963 NTM isolates stored at the NMRL, 81 were retrieved for speciation. Forty isolates (49.4%) were found to belong to Mycobacterium avium-intracellulare complex (MAC) species. The other 41 isolates (50.6%) were identified as M. lentiflavum (6.2%), M. terrae complex (4.9%), M. paraense (4.9%), M. kansasii (3.7%), M. moriokaense (3.7%), M. asiaticum (2.5%), M. novocastrense (2.5%), M. brasiliensis (2.5%), M. elephantis (2.5%), M. paraffinicum (1.2%), M. bohemicum (1.2%), M. manitobense (1.2%), M. intermedium (1.2%), M. tuberculosis complex (1.2%), M. parakoreense (1.2%), M. florentinum (1.2%), M. litorale (1.2%), M. fluoranthenivorans (1.2%), M. sherrisii (1.2%), M. fortuitum (1.2%) and M septicum (1.2%). Two isolates (2.5%) could not be identified, but were closely related to M. montefiorense and M. phlei respectively. Interestingly, the MAC species were the commonest NTM during the survey.

Conclusion:

The study emphasizes the importance of identifying species of NTM in Zimbabwe. Future studies need to ascertain their true diversity and clinical relevance.

Synovitis of the wrist caused by Mycobacterium florentinum

Mycobacterium florentinum is a newly identified, rare, slow-growing species of nontuberculous mycobacteria (NTM). Here, we report a case of M. florentinum-induced synovitis of the wrist in an immunocompromised Japanese patient. M. florentinum was identified by sequence analysis of the rpoB, hsp65, and 16S rRNA genes. The M. florentinum strain in this study could not be differentiated from certain M. triplex strains by the hsp65 or 16S rRNA sequences alone, because they occasionally shared more than 99 % sequence identity. The isolated M. florentinum strain was only susceptible to clarithromycin and amikacin. Initially, the patient was treated with clarithromycin, levofloxacin, and ethambutol, and then with clarithromycin, levofloxacin, and rifampicin. To our knowledge, M. florentinum-induced synovitis has not been previously reported. Our results suggest that, in addition to other well-known pathogenic NTM, the recently identified M. florentinum strain should be considered as a possible cause of synovitis. Moreover, we should be cautious when identifying M. florentinum because this strain closely resembles M. triplex in genotype.

Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165(T.)

Mycobacterium simiae is a non-tuberculosis mycobacterium causing pulmonary infections in both immunocompetent and imunocompromized patients. We announce the draft genome sequence of M. simiae DSM 44165^T. The 5,782,968-bp long genome with 65.15% GC content (one chromosome, no plasmid) contains 5,727 open reading frames (33% with unknown function and 11 ORFs sizing more than 5000 -bp), three rRNA operons, 52 tRNA, one 66-bp tmRNA matching with tmRNA tags from Mycobacterium avium, Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium microti, Mycobacterium marinum, and Mycobacterium africanum and 389 DNA repetitive sequences. Comparing ORFs and size distribution between M. simiae and five other Mycobacterium species M. simiae clustered with M. abscessus and M. smegmatis. A 40-kb prophage was predicted in addition to two prophage-like elements, 7-kb and 18-kb in size, but no mycobacteriophage was seen after the observation of 10⁶M. simiae cells. Fifteen putative CRISPRs were found. Three genes were predicted to encode resistance to aminoglycosides, betalactams and macrolide-lincosamide-streptogramin B. A total of 163 CAZYmes were annotated. M. simiae contains ESX-1 to ESX-5 genes encoding for a type-VII secretion system. Availability of the genome sequence may help depict the unique properties of this environmental, opportunistic pathogen.

Epidemiology of cervico-facial pediatric lymphadenitis as a result of nontuberculous mycobacteria

Cervical lymphadenitis as a result of nontuberculous mycobacteria, otherwise known as scrofula, is a disease occurring almost exclusively in immunocompetent young children. The most frequent mycobacterial species responsible is Mycobacterium avium, but a large number of other species may also be involved. The epidemiology of such disease is revised here, and the impact of different species as causative agents of adenitis is also discussed.

Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex

Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228(T) ( = DSM 45397(T)  = CCUG 58464(T)) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the 'Mycobacterium simiae complex' for this group.

Detection of Mycobacterium tuberculosis complex organisms in the stools of patients with pulmonary tuberculosis

The laboratory diagnosis of pulmonary tuberculosis mainly relies on the detection of Mycobacterium tuberculosis complex (MTC) organisms in the sputum. In patients who do not give sputum, alternative respiratory tract specimens can be obtained only by invasive procedures. Based on the known survival of MTC organisms in the gastric fluid, we hypothesized that swallowed MTC organisms would be detectable in stool samples. We compared the presence of MTC organisms in respiratory tract specimens and stool specimens collected in parallel from the same patients. MTC was detected in cultures grown on egg-based medium after appropriate decontamination, by microscopic examination after Ziehl–Neelsen staining and by real-time PCR detection of IS6110 using internal controls. A case of pulmonary tuberculosis was defined by the presence of (i) clinical and radiological signs and symptoms suggestive of pulmonary tuberculosis, and (ii) culture of MTC organisms from at least one respiratory tract specimen or (iii) the presence of acid-fast bacilli in the sputum that were subsequently identified as MTC organisms by real-time PCR. The observation of 134 patients suspected to be suffering pulmonary tuberculosis led to the identification of 24 cases and 110 non-infected control patients. Cases and controls did not significantly differ with respect to sex but cases were significantly younger than controls. The sensitivity/specificity was 37.5 %/100 % for the microscopic examination of stools, 54.2 %/100 % for culturing and 100 %/97.3 % for real-time PCR. The positive predicted value was 100 %, 100 % and 88.9 %, respectively, and the negative predicted value was 88 %, 90.9 % and 100 %, respectively. In four patients, a stool specimen initially yielded the correct diagnosis of pulmonary tuberculosis before evaluation of the respiratory tract specimen confirmed the diagnosis. These data indicate that stools could be used in conjunction with sputum testing or as an alternative specimen upon which to base the diagnosis of pulmonary tuberculosis by molecular identification of acid-fast bacilli and culture. This non-invasive alternative procedure is of particular interest for patients who cannot expectorate.

Mycobacterium stomatepiae sp. nov., a slowly growing, non-chromogenic species isolated from fish

Slowly growing, non-chromogenic mycobacteria were isolated from striped barombi mbo cichlids (Stomatepia mariae) maintained at the London Zoo Aquarium, UK. The isolates could be differentiated from other slowly growing, non-pigmented mycobacteria by a combination of phenotypic features including their inability to grow at 37 degrees C, positive tests for heat-stable catalase, tellurite reduction and arylsulfatase activity, and the absence of urease activity, Tween 80 hydrolysis, nitrate reductase, iron uptake and semiquantitative catalase. The almost full-length 16S rRNA gene sequence, together with partial sequences from the 65 kDa heat-shock protein (hsp65) and the beta-subunit of the bacterial RNA polymerase (rpoB) genes and the 16S-23S internal transcribed spacer 1 (ITS 1) region were identical for all three novel strains, but distinct from those of all known mycobacterial species. Phylogenetic analysis based on 16S rRNA gene sequences placed the novel isolates within the slowly growing mycobacteria group in close proximity to Mycobacterium florentinum. Based on genotypic and phenotypic findings, it is proposed that these isolates represent a novel species of the genus Mycobacterium, for which the name Mycobacterium stomatepiae sp. nov. is proposed with strain T11(T) (=DSM 45059(T)=CIP 109275(T)=NCIMB 14252(T)) as the type strain.

The new mycobacteria: an update

The continuous evolution of mycobacterial taxonomy may represent a source of confusion for laboratories and clinicians. Apart from the obvious pathogenic strains of the Mycobacterium tuberculosis complex, Mycobacterium leprae and Mycobacterium ulcerans, the role of other mycobacteria may be associated with varying conditions ranging from contamination to specific disease processes. Of the more than 120 mycobacterial species recognized currently, very few have not been reported as pathogenic in humans or animals. Although the attempt to keep pace with the steadily increasing number of mycobacterial species seems hopeless, a careful review of the recent literature relevant to the newly described species may be advantageous. The aim of this present update is to provide epidemiological and clinical information along with major phenotypic and genotypic characteristics of the species described in the last 3 years.

Uncommon respiratory pathogens

PURPOSE OF REVIEW

In many cases, the specific pathogen responsible for a respiratory infection is not identified and can lead to improper medical treatment, increased duration of illness, and possibly contributes to the development of antibiotic resistance. Molecular-based diagnostic methodologies have significantly improved our ability to identify common respiratory pathogens; these techniques are not useful, however, when a novel pathogen is responsible for the infection and clinicians must rely on differential diagnosis for the treatment of patients.

RECENT FINDINGS

New pathogens previously not associated with human infections have been identified in the past few years. In addition, new strains of bacteria and viruses have emerged as the causative agents of pneumonia and acute respiratory distress. Protozoans and saprophytic fungi, which are not normally associated with respiratory infection, have also emerged as respiratory pathogens particularly in individuals with AIDS or in those who are otherwise immunocompromised.

SUMMARY

This review discusses the recent literature on newly described respiratory pathogens as well as opportunistic pathogens that can infect the respiratory system of immunocompromised individuals. The studies referenced here reveal the need for expanded laboratory tests and highly trained microbiologists in clinical laboratories worldwide.