Clinical and laboratory features of Mycobacterium porcinum

Mycobacterium porcinum Disseminated Infection in Non-severely Immunocompromised Host

Mycobacterium porcinum is a nontuberculous mycobacteria (NTM) recently identified to cause human infection. Correct speciation of NTMs can be difficult and result in misdiagnosis and delayed treatment. Because of the paucity of the literature, there is a lack of awareness of the possibility of serious infections caused by M. porcinum. Although severe infections tend to occur in individuals with certain risk factors, the primary being an immunocompromised state, our case illustrates that it can also be possible in non-severely immunocompromised individuals. A 65-year-old male with a medical history of diabetes mellitus (DM), end-stage renal disease (ESRD) on hemodialysis (HD), congestive heart failure (CHF), and chronic obstructive pulmonary disease (COPD) was admitted to the emergency room due to a laceration on his right lower leg following a fall. He reported shortness of breath but denied other respiratory symptoms. On examination, he showed signs of infection and increased oxygen requirement compared to baseline. Blood culture was positive for acid-fast bacilli (AFB), initially reported as M. avium complex (MAC) and later confirmed as M. porcinum through gene sequencing and morphology analysis. Interval blood cultures taken a week later confirmed true M. porcinum bacteremia. Treatment initially involved intravenous antibiotics- imipenem and ciprofloxacin before transitioning to oral linezolid and ciprofloxacin based on sensitivities. Following 10 days of antibiotic therapy, subsequent blood cultures returned negative, and treatment with oral antibiotics was advised, with continued outpatient follow-up with infectious disease in two weeks. M. porcinum, typically considered a contaminant in healthy individuals, was identified as the causative agent of a disseminated infection in a non-severely immunocompromised patient. This case underscores the importance of accurately identifying the specific mycobacterial species, confirming true infection, and conducting antibiotic susceptibility testing due to the distinct antibiotic susceptibility profile of M. porcinum compared to other NTM like MAC.

Mycobacterium porcinum Infection of Hilar and Mediastinal Lymph Nodes: A Case Report and Literature Review

In the available reports on clinical medicine, the infection sites of Mycobacterium porcinum include wounds, bone marrow, respiratory tract, and catheters. A 61-year-old woman was admitted to our hospital; her hilar and mediastinal lymph nodes were found to be enlarged during health examination, but there was no specific discomfort. Initially, she had undergone a mediastinal lymph node biopsy and pathology, but the diagnosis was not confirmed. However, 16S rRNA gene sequencing revealed M. porcinum infection of hilar and mediastinal lymph nodes. Subsequently, she was treated with clarithromycin, amikacin, imipenem, and tigecycline. After 2 months, chest computed tomography showed a significant reduction in lymph nodes. M. porcinum infection was considered to be the cause of disease.

Antimicrobial Resistance in Rapidly Growing Nontuberculous Mycobacteria among Domestic and Wild Animals Emphasizing the Zoonotic Potential

Non-tuberculous mycobacteria (NTM) are opportunistic pathogens capable of causing infections in humans and animals. The aim of this study was to demonstrate the potential role of domestic and wild animals as a reservoir of multiple resistant, rapidly growing NTM strains representing a potential zoonotic threat to humans. A total of 87 animal isolates belonging to 11 rapidly growing species (visible colonies appear within three to seven days) were genotyped and tested for susceptibility to the 15 most commonly used antibiotics in the treatment of such infections in a human clinic. By determining the antimicrobial susceptibility, the most prevalent resistance was found to cephalosporins (>50%), followed by amoxicillin-clavulanate (31.0%), clarithromycin (23.0%), tobramycin (14.9%) and doxycycline (10.3%). Resistance to imipenem, ciprofloxacin, minocycline and linezolid was notably lower (<7.0%). All tested isolates were susceptible to amikacin and moxifloxacin. The most frequent resistance was proved in the most pathogenic species: M. fortuitum, M. neoaurum, M. vaccae and M. porcinum. Meanwhile, other species displayed a higher sensitivity rate. No significant resistance differences between domestic and wild animals were found. The established significant frequency of resistance highlights the significant zoonotic potential posed by circulating rapidly growing NTM strains, which could lead to challenges in the treatment of these infections.

New RAPMYCOI SensititreTM Antimicrobial Susceptibility Test for Atypical Rapidly Growing Mycobacteria (RGM)

Rapidly growing mycobacteria (RGM) cause an increasing international concern, mainly due to their natural resistance to many antibiotics. The aim of this study was to conduct species identification and determine the antimicrobial susceptibility profiles of RGM isolated in Poland. Antimicrobial susceptibility was tested using broth microdilution and the RAPMYCOI panel. A total of 60 strains were analysed, including the following species: M. fortuitum complex (30), M. abscessus subsp. abscessus (16), M. abscessus subsp. massiliense (7), M. chelonae (5), and M. mucogenicum (2). For 12 M. abscessus subsp. abscessus strains, the presence of the erm 41T28 genotype associated with inducible macrolide resistance and a functional erm gene was confirmed. A MUT2 mutation in the rrl gene (constitutive resistance) was identified for two strains from the subtype M. abscessus subsp. massiliense. Among the 15 tested antibiotics, amikacin and linezolid had the strongest antimycobacterial activity. Most of the tested strains were resistant to doxycycline and trimethoprim/sulfamethoxazole. Tigecycline MICs were low for all tested strains. Findings from our study highlight the importance of correct identification of clinical isolates and antimicrobial susceptibility testing.

General characteristics, features of cultivation and antibiotic resistance representatives of mycobacterium fortuitum group representatives (review of literature)

Recently, more and more scientific works have been devoted to non-tuberculous mycobacteria, both by domestic and foreign researchers. One of the main reasons for this is the increase in patients with immunosuppression of various origins, improvement of the quality of laboratory and instrumental diagnostics of mycobacteriosis. This article focuses on the representatives of the M. fortuitum group, as the main pathogens among the group of fast-growing mycobacteria. The data on the modern classification based on the use of molecular genetic studies are indicated. The M. fortuitum group includes: Mycobacterium fortuitum, M. peregrinum, M. senegalense, M. porcinum, M. houstonense, M. neworleansense, M. boenickei, M. conceptionense, M. septicum, M. alvei. According to the new data, mycobacteria were divided into 5 clades (Abscessus-Chelonae, Fortuitum-Vaccae, Terrae, Triviale, Tuberculosis-Simiae), and based on molecular genetic studies, new genera in the Mycobacteriaceae family were isolated: Mycolicibacter spp., Mycolicibacillus spp., Mycolicibacillus spp., Mycobacteroides spp., Mycolicibacterium spp. In accordance with the new classification, representatives of the Mycobacterium fortuitum group belong to the genus Mycolicibacterium. The main epidemiological features of the main sources of the spread of mycobacteria, factors and ways of their transmission are indicated. Due to their wide distribution in the environment, representatives of the M. fortuitum group are capable of causing diseases of the pulmonary and extrapulmonary localization. The distinctive features of pathogenicity factors, due to which the course of the disease is determined, are noted. The article also indicates the main difficulties and features of determining the sensitivity to antimicrobial chemotherapy drugs, provides data on the main features of antibiotic resistance of M.fortuitum group. In preparing the review, literature sources obtained from international and domestic databases were used: Scopus, Web of Science, Springer, RSCI.

Nontuberculous Mycobacteria Show Differential Infectivity and Use Phospholipids to Antagonize LL-37

Comparisons of infectivity among the clinically important nontuberculous mycobacteria (NTM) species have not been explored in great depth. Rapid-growing mycobacteria, including Mycobacterium abscessus and M. porcinum, can cause indolent but progressive lung disease. Slow-growing members of the M. avium complex are the most common group of NTM to cause lung disease, and molecular approaches can now distinguish between several distinct species of M. avium complex including M. intracellulare, M. avium, M. marseillense, and M. chimaera. Differential infectivity among these NTM species may, in part, account for differences in clinical outcomes and response to treatment; thus, knowing the relative infectivity of particular isolates could increase prognostication accuracy and enhance personalized treatment. Using human macrophages, we investigated the infectivity and virulence of nine NTM species, as well as multiple isolates of the same species. We also assessed their capacity to evade killing by the antibacterial peptide cathelicidin (LL-37). We discovered that the ability of different NTM species to infect macrophages varied among the species and among isolates of the same species. Our biochemical assays implicate modified phospholipids, which may include a phosphatidylinositol or cardiolipin backbone, as candidate antagonists of LL-37 antibacterial activity. The high variation in infectivity and virulence of NTM strains suggests that more detailed microbiological and biochemical characterizations are necessary to increase our knowledge of NTM pathogenesis.

Identification of Mycobacterium porcinum in patients with cystic Fibrosis: Pathogen or contaminant?

BACKGROUND

Mycobacterium porcinum is a non-tuberculous mycobacterium (NTM) identified in potable water. The identification and clinical impact of M. porcinum in patients with cystic fibrosis (CF) has not been described. In our institution, M. porcinum was isolated exclusively during hospitalization in a cluster of patients with CF.

METHODS

Patients with CF who were hospitalized between September 2016 and September 2018 and could expectorate sputum were included, and samples were processed per institutional guidelines. Post-hospitalization and one-year clinical outcomes on those who isolated M. porcinum in respiratory cultures were reviewed. Whole genome sequencing was performed on M. porcinum isolates obtained from patients and environmental sources to identify source of acquisition.

RESULTS

Review of 14 CF patients with 16 M. porcinum isolates revealed rapid time to culture positivity within 0.8 (0.04-8.0) days after admission. M. porcinum was isolated in teenagers and adults irrespective of baseline pulmonary function, body mass index, or CF genotype. Whole genome sequencing suggested all isolates belong to the same M. porcinum strain and confirmed the source of acquisition to the ice machine. Review of patients' clinical course, including three patients who underwent lung transplantation, suggested a pseudo-outbreak with minimal clinical impact.

CONCLUSIONS

NTM, including M. porcinum, are ubiquitous in potable water and institutional water reservoirs. Our findings suggest M. porcinum is a transient colonizer rather than a pathogen. Challenges exist in discerning the role of NTM as a contributor of pulmonary morbidity in patients with CF, and adherence to established guidelines regarding NTM related pulmonary disease remains important.

Mycobacterium porcinum causing panniculitis in the cat

A 4-year-old domestic shorthair cat was presented with a 7-month history of nodules and draining fistulous tracts of the ventral abdomen. Histopathological examination of affected tissue revealed acid-fast bacilli stained by the Ziehl-Neelsen procedure. Deep tissue culture confirmed infection with a rapidly growing mycobacterium, and gene sequencing characterized the organism as Mycobacterium porcinum. Treatment with pradofloxacin and doxycycline resulted in clinical resolution of the lesions. On continued antibiotic therapy 7 months later, there was no local recurrence nor were there clinical signs associated with distant spread of the infection. This is the first clinical description of a feline infection with this organism. Key clinical message: This is the first clinical description of mycobacterial panniculitis in a cat due to genetically characterized Mycobacterium porcinum. This case report highlights a disease entity that can present a diagnostic and therapeutic challenge to clinicians.

An improved simple method for the identification of Mycobacteria by MALDI-TOF MS (Matrix-Assisted Laser Desorption- Ionization mass spectrometry)

The aim of this study was to establish a simple method for the rapid identification of Mycobacteria species by MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass spectrometry) using the Bruker MALDI-TOF Biotyper system (Bruker Daltonik, Bremen, Germany). A multicentre, prospective, and single blind study was performed in three European Hospitals, two Spanish and one UK hospital from May to August 2018. The BD BACTEC MGIT (Becton Dickinson, Berks, UK) liquid culture system was used in all three centres for the growth of Mycobacteria. When signal positive, tubes were removed from the analyser and in addition to standard laboratory procedures were subcultured on blood agar plates for MALDI-TOF analysis. Plates were incubated aerobically for 1 to 7 days at 37 °C and inspected every day. Once any growth was visible, it was transferred to the steel target plate, overlaid with 1 μl of neat formic acid and 1 μl HCCA matrix (alpha hydroxyl 4 cinnamic acid), and analysed in a Bruker Biotyper MALDI-TOF. Results given by MALDI-TOF were compared with the reference methods used for identification in the different centres. At two Spanish hospitals, identification by MALDI-TOF was only attempted on presumptive non-tuberculosis mycobacteria (NTM) and the results were initially compared with the results obtained by a commercial reverse hybridisation assay, GenoType CM/AS (Hain Lifescience, Tübingen, Germany). At the UK Hospital, identification of any presumptive mycobacteria was attempted and compared with the results obtained by whole genome sequencing (WGS). Overall in 142/167 (85%) of cases the identifications obtained were concordant; all Mycobacterium tuberculosis (MTB) isolates 43/43 (100%), 57/76 (75%) of the rapid growing nontuberculous mycobacteria (NTM), and 42/48 (85%) slow growing NTM tested were identified correctly. We report a new, easy, cheap and quick method for isolation and identification of Mycobacterium spp. without the need for additional steps or equipment and this method is in routine used in all three centres.

Global Environmental Nontuberculous Mycobacteria and Their Contemporaneous Man-Made and Natural Niches

Seminal microbiological work of environmental nontuberculous mycobacteria (NTM) includes the discovery that NTM inhabit water distribution systems and soil, and that the species of NTM found are geographically diverse. It is likely that patients acquire their infections from repeated exposures to their environments, based on the well-accepted paradigm that water and soil bioaerosols - enriched for NTM - can be inhaled into the lungs. Support comes from reports demonstrating NTM isolated from the lungs of patients are genetically identical to NTM found in their environment. Well documented sources of NTM include peat-rich soils, natural waters, drinking water, hot water heaters, refrigerator taps, catheters, and environmental amoeba. However, NTM have also been recovered in biofilms from ice machines, heated nebulizers, and heater-cooler units, as well as seat dust from theaters, vacuum cleaners, and cobwebs. New studies on the horizon aim to significantly expand the current knowledge of environmental NTM niches in order to improve our current understanding of the specific ecological factors driving the emergence of NTM lung disease. Specifically, the Hawaiian Island environment is currently being studied as a model to identify other point sources of exposure as it is the U.S. state with the highest number of NTM lung disease cases. Because of its geographic isolation and unique ecosystem, the Hawaiian environment is being probed for correlative factors that may promote environmental NTM colonization.

Draft Genome Sequence of Mycobacterium porcinum CSURP1564

Mycobacterium porcinum is a rapidly growing environmental mycobacterium responsible for opportunistic infections. The 7,025,616-bp draft genome of M. porcinum strain CSURP1564 exhibits a 66.71% G+C content, 6,687 protein-coding genes, and 65 predicted RNA genes. In silico DNA-DNA hybridization confirms its assignment to the Mycobacterium fortuitum complex.

Rapidly Growing Mycobacteria

Rapidly growing mycobacteria (RGM) compose approximately one-half of the currently validated mycobacterial species and are divided into six major groups, including the Mycobacterium fortuitum group, M. chelonae/M. abscessus complex, M. smegmatis group, M. mucogenicum group, M. mageritense / M. wolinskyi , and the pigmented RGM. This review discusses each group and highlights the major types of infections associated with each group. Additionally, phenotypic and molecular laboratory identification methods, including gene sequencing, mass spectrometry, and the newly emerging whole-genome sequencing, are detailed, along with a discussion of the current antimicrobial susceptibility methods and patterns of the most common pathogenic species.

Environmental Nontuberculous Mycobacteria in the Hawaiian Islands

Lung disease caused by nontuberculous mycobacteria (NTM) is an emerging infectious disease of global significance. Epidemiologic studies have shown the Hawaiian Islands have the highest prevalence of NTM lung infections in the United States. However, potential environmental reservoirs and species diversity have not been characterized. In this cross-sectional study, we describe molecular and phylogenetic comparisons of NTM isolated from 172 household plumbing biofilms and soil samples from 62 non-patient households and 15 respiratory specimens. Although non-uniform geographic sampling and availability of patient information were limitations, Mycobacterium chimaera was found to be the dominant species in both environmental and respiratory specimens. In contrast to previous studies from the continental U.S., no Mycobacterium avium was identified. Mycobacterium intracellulare was found only in respiratory specimens and a soil sample. We conclude that Hawai’i’s household water sources contain a unique composition of Mycobacterium avium complex (MAC), increasing our appreciation of NTM organisms of pulmonary importance in tropical environments.

In the U.S., the Hawaiian Islands have the highest number of nontuberculous mycobacterial (NTM) lung disease cases per capita. The tropical climate, geographical isolation of the islands, and aquifer water sources may have influence such prevalence. Previous studies suggest that NTM thrive in water biofilms and soil. To broaden our understanding of potential environmental reservoirs and species composition of NTM in the Hawaiian Islands, we sampled environmental sites and examined patient isolates. Our recovery and identification of Mycobacterium chimaera and several other clinically relevant NTM species and the absence of Mycobacterium avium in both the indigenous environment and clinical specimens underscore the need for further studies to define the environmental factors that drive NTM lung disease and species composition in high prevalence locations such as the Hawaiian Islands.

Epidemiology of Nontuberculous Mycobacteria in French Polynesia

As few data are available in the Pacific countries and territories of the Oceania region regarding nontuberculous mycobacteria,we retrospectively identified 87 such isolates from French Polynesia from 2008 to 2013 by hybridization using DNA-strip, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and partial rpoB gene sequencing. Partial rpoB gene sequencing classified 42/87 (48.3%) isolates in the Mycobacterium fortuitum complex, 28 (32.2%) in the Mycobacterium abscessus complex, 8 (9.2%) in the Mycobacterium mucogenicum complex, and 5 (5.7%) in the Mycobacterium avium complex. Two isolates were identified as Mycobacterium acapulcensis and Mycobacterium cosmeticum by partial 16S rRNA gene sequencing. One isolate, unidentified by MALDI-TOF MS and yielding less than 92% and 96% sequence similarity with rpoB and hsp65 reference sequences, respectively, was regarded as a potentially new species. Samples from three patients exhibiting>2 Mycobacterium porcinum isolates and from one patient with emphysema and a lung abscess exhibiting 2 Mycobacterium senegalense isolates fulfilled the American Thoracic Society microbiological criteria for nontuberculous mycobacterial lung infection.Remote geographic areas, such as French Polynesia, are potential sources for the discovery of new mycobacterial species.

Use of MALDI-TOF MS for Identification of Nontuberculous Mycobacterium Species Isolated from Clinical Specimens

The aim of this study was to compare the results obtained for identification by MALDI-TOF of nontuberculous mycobacteria (NTM) isolated in clinical samples with those obtained by GenoType Mycobacterium CM/AS (common mycobacteria/additional species). A total of 66 Mycobacterium isolates from various clinical specimens (mainly respiratory) were tested in this study. They were identified using MALDI-TOF Bruker from strains isolated in Lowenstein, following the recommended protocol of heat inactivation and extraction, and were simultaneously analyzed through hybridization by GenoType Mycobacterium from liquid culture MGIT. Our results showed that identification by MALDI-TOF was correct in 98.4% (65/66) of NTM isolated in our clinical practice (M. avium, M. intracellulare, M. abscessus, M. chelonae, M. fortuitum, M. mucogenicum, M. kansasii, and M. scrofulaceum). MALDI-TOF was found to be an accurate, rapid, and cost-effective system for identification of mycobacteria species.

Amoebae as potential environmental hosts for Mycobacterium ulcerans and other mycobacteria, but doubtful actors in Buruli ulcer epidemiology

BACKGROUND

The reservoir and mode of transmission of Mycobacterium ulcerans, the causative agent of Buruli ulcer, remain unknown. Ecological, genetic and epidemiological information nonetheless suggests that M. ulcerans may reside in aquatic protozoa.

METHODOLOGY/PRINCIPAL FINDINGS

We experimentally infected Acanthamoeba polyphaga with M. ulcerans and found that the bacilli were phagocytised, not digested and remained viable for the duration of the experiment. Furthermore, we collected 13 water, 90 biofilm and 45 detritus samples in both Buruli ulcer endemic and non-endemic communities in Ghana, from which we cultivated amoeboid protozoa and mycobacteria. M. ulcerans was not isolated, but other mycobacteria were as frequently isolated from intracellular as from extracellular sources, suggesting that they commonly infect amoebae in nature. We screened the samples as well as the amoeba cultures for the M. ulcerans markers IS2404, IS2606 and KR-B. IS2404 was detected in 2% of the environmental samples and in 4% of the amoeba cultures. The IS2404 positive amoeba cultures included up to 5 different protozoan species, and originated both from Buruli ulcer endemic and non-endemic communities.

CONCLUSIONS/SIGNIFICANCE

This is the first report of experimental infection of amoebae with M. ulcerans and of the detection of the marker IS2404 in amoeba cultures isolated from the environment. We conclude that amoeba are potential natural hosts for M. ulcerans, yet remain sceptical about their implication in the transmission of M. ulcerans to humans and their importance in the epidemiology of Buruli ulcer.

Antimicrobial susceptibility testing, drug resistance mechanisms, and therapy of infections with nontuberculous mycobacteria

Within the past 10 years, treatment and diagnostic guidelines for nontuberculous mycobacteria have been recommended by the American Thoracic Society (ATS) and the Infectious Diseases Society of America (IDSA). Moreover, the Clinical and Laboratory Standards Institute (CLSI) has published and recently (in 2011) updated recommendations including suggested antimicrobial and susceptibility breakpoints. The CLSI has also recommended the broth microdilution method as the gold standard for laboratories performing antimicrobial susceptibility testing of nontuberculous mycobacteria. This article reviews the laboratory, diagnostic, and treatment guidelines together with established and probable drug resistance mechanisms of the nontuberculous mycobacteria.

Laboratory aspects of clinically significant rapidly growing mycobacteria

The pathogenic potential of the rapidly growing mycobacteria (RGM) has started being recognized. This is due to more sensitive and specific techniques in the laboratory. The RGM are generally defined as nontuberculous species of mycobacteria that show visible growth on agar media within 7 days. RGM are widely distributed in nature and have been isolated from natural water, tap water, and soil. Several biochemical tests, high performance liquid chromatography, and molecular techniques have been developed for rapid identification of these species. The American Thoracic Society and the Infectious Disease Society of America recommend that RGM should be identified to the species level using a recognized acceptable methodology such as polymerase chain reaction restriction enzyme analysis or biochemical testing and routine susceptibility testing of RGM should include amikacin, imipenem, doxycycline, the fluorinated quinolones, a sulphonamide or trimethoprim-sulphamethoxazole, cefoxitin, clarithromycin, linezolid, and tobramycin. The diseases caused by these organisms have varied manifestations. They have been responsible for a number of healthcare-associated outbreaks and pseudo-outbreaks. For recognition of outbreaks, it is important to be familiar with the causative organisms like RGM which are most frequently involved in healthcare-associated outbreaks and pseudo outbreaks. It is essential to intervene as soon as possible to interrupt this transmission. Large gaps still exist in our knowledge of RGM. Unquestionably more studies are required. Through this review, we wish to emphasize that reporting of RGM from clinical settings along with their sensitivity patterns is an absolute need of the hour.

Five-year outbreak of community- and hospital-acquired Mycobacterium porcinum infections related to public water supplies

Mycobacterium porcinum is a rarely encountered rapidly growing Mycobacterium (RGM). We identified M. porcinum from 24 patients at a Galveston university hospital (University of Texas Medical Branch) over a 5-year period. M. porcinum was considered a pathogen in 11 (46%) of 24 infected patients, including 4 patients with community-acquired disease. Retrospective patient data were collected, and water samples were cultured. Molecular analysis of water isolates, clustered clinical isolates, and 15 unrelated control strains of M. porcinum was performed. Among samples of hospital ice and tap water, 63% were positive for RGM, 50% of which were M. porcinum. Among samples of water from the city of Galveston, four of five households (80%) were positive for M. porcinum. By pulsed-field gel electrophoresis (PFGE), 8 of 10 environmental M. porcinum were determined to belong to two closely related clones. A total of 26 of 29 clinical isolates subjected to PFGE (including isolates from all positive patients) were clonal with the water patterns, including patients with community-acquired disease. Fifteen control strains of M. porcinum had unique profiles. Sequencing of hsp65, recA, and rpoB revealed the PFGE outbreak clones to have identical sequences, while unrelated strains exhibited multiple sequence variants. M. porcinum from 22 (92%) of 24 patients were clonal, matched hospital- and household water-acquired isolates, and differed from epidemiologically unrelated strains. M. porcinum can be a drinking water contaminant, serve as a long-term reservoir (years) for patient contamination (especially sputum), and be a source of clinical disease. This study expands concern about public health issues regarding nontuberculous mycobacteria. Multilocus gene sequencing helped define clonal populations.

[Use of different PCR-based techniques integrated into a non-tuberculous identification algorithm]

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.

Web-accessible database of hsp65 sequences from Mycobacterium reference strains

Mycobacteria include a large number of pathogens. Identification to species level is important for diagnoses and treatments. Here, we report the development of a Web-accessible database of the hsp65 locus sequences (http://msis.mycobacteria.info) from 149 out of 150 Mycobacterium species/subspecies. This database can serve as a reference for identifying Mycobacterium species.

Mycobacterium porcinum peritonitis in a patient on continuous ambulatory peritoneal dialysis

Mycobacterium porcinum has been reported to cause a variety of illnesses including wound infections, respiratory tract infections, osteomyelitis and catheter-related bacteremias. We report the first case of M. porcinum peritonitis in a patient on continuous ambulatory peritoneal dialysis (CAPD). A 67-year-old woman on CAPD presented with three weeks of constitutional symptoms and abdominal pain. Peritoneal fluid cultures on day three grew acid-fast rods. Nocardiosis was suspected and the patient was empirically treated with amikacin and trimethoprim-sulfamethoxazole. The dialysis catheter was removed. Two weeks later final culture results revealed M. porcinum. Ciprofloxacin and trimethoprim-sulfamethoxazole were initiated with good clinical response.

Comparison of culture methods for isolation of nontuberculous mycobacteria from surface waters

The environment is the likely source of most nontuberculous mycobacteria (NTM) involved in human infections, especially pulmonary, skin, and soft tissue infections. In order to measure the prevalence of NTM in different aquatic ecosystems, we tried to standardize the culture methods used for surface water testing since many procedures have been described previously. Cultivation of mycobacteria requires long-term incubation in rich media and inactivation of rapidly growing microorganisms whose growth impedes observation of mycobacterial colonies. Consequently, the two criteria used for evaluation of the methods examined were (i) the rate of inhibition of nontarget microorganisms and (ii) the efficiency of recovery of mycobacteria. We compared the competitive growth of Mycobacterium chelonae and M. avium with nontarget microorganisms on rich Middlebrook 7H11-mycobactin medium after treatment by several chemical decontamination methods that included acids, bases, detergent, or cetylpyridinium chloride (CPC) with and without an antibiotic cocktail, either PANTA (40 U/ml polymyxin, 4 microg/ml amphotericin B, 16 microg/ml nalidixic acid, 4 microg/ml trimethoprim, and 4 microg/ml azlocillin) or PANTAV (PANTA plus 10 microg/ml vancomycin). Our results showed that treatment for 30 min with CPC (final concentration, 0.05%) of water concentrated by centrifugation, followed by culture on a rich medium supplemented with PANTA, significantly decreased the growth of nontarget microorganisms (the concentrations were 6.2 +/- 0.4 log(10) CFU/liter on Middlebrook 7H11j medium and 4.2 +/- 0.2 log(10) CFU/liter on Middlebrook 7H11j medium containing PANTA [P < 0.001]), while the effect of this procedure on NTM was not as great (the concentrations of M. chelonae on the two media were 7.0 +/- 0.0 log(10) CFU/liter and 6.9 +/- 0.0 log(10) CFU/liter, respectively, and the concentrations of M. avium were 9.1 +/- 0.0 log(10) CFU/liter and 8.9 +/- 0.0 log(10) CFU/liter, respectively). We propose that this standardized culture procedure could be used for detection of NTM in aquatic samples.

Identification of heterotrophic plate count bacteria isolated from drinking water in Japan by DNA sequencing analysis

Heterotrophic plate count (HPC) test has been employed to indicate the effectiveness of water treatment processes and the microbiological condition of the distribution system. In Japan, because the majority of HPC bacteria are supposed to be harmless and all tap water should maintain residual chlorine, there are few studies of the virulence of HPC bacteria. In this study, we examined HPC bacteria isolated from finished and tap water for hemolytic activity to determine their virulence potential. 34 of 39 colonies expressing hemolytic activity were identified by partial 16S rDNA sequencing, but some of their percent identity were relatively low. This may have been due to the mismatching of the primer pair with some strains, or these strains may be unidentified new species. A total of 30 of 34 isolates identified have been reported to be opportunistic pathogens or food poisoning bacteria. To control the growth of these opportunistic pathogens among HPC bacteria, appropriate water quality control must always be done and residual chlorine must be maintained in every tap for a safe water supply.

Evaluation of the INNO-LiPA mycobacteria v2 assay for identification of aquatic mycobacteria

Fifty-seven isolates of mycobacteria comprising 10 reference strains, 47 field isolates and one non-Mycobacterium isolate were screened using commercial INNO-LiPA v2 assay kits. All mycobacteria isolates tested hybridized with the Mycobacterium genus probe on the LiPA strip. All M. marinum, M. fortuitum and M. chelonae reference and field strains and three out of the four M. gordonae isolates hybridized to their corresponding species- or complex-specific probes. Two cultures (a type strain and a field isolate) yielded mixed growth of two mycobacterial species, i.e. M. chelonae and M. fortuitum. A Mycobacterium isolate from one of these cultures was subsequently purified and correctly identified with the kit. However, sequence analysis of the 16S-23S rRNA internal transcribed spacer (ITS) region of various mycobacteria isolates revealed a misidentification of M. shottsii and M. pseudoshottsii with the kit because these isolates reacted with the M. marinum/M. ulcerans probe. Moreover, nine of the 13 field isolates presumed to be M. fortuitum from the results of the kit had closer ITS sequence homology with M. conceptionense, a species which, to our knowledge, has never been reported in fish. These findings highlight the need to redesign the M. fortuitum-M. peregrinum probe included in the INNO-LiPA assay and to introduce additional complex-specific probes into the kit. Nevertheless, the kit proved to be a rapid and reliable method for identifying mycobacteria in the aquatic environment and would be particularly useful in laboratories without sequencing facilities.

Application of polymerase chain reaction-based restriction fragment length polymorphism in typing ocular rapid-growing nontuberculous mycobacterial isolates from three patients with postoperative endophthalmitis

PURPOSE

We describe postoperative endophthalmitis caused by rapid-growing nontuberculous mycobacteria (RGNTM) in 3 patients after small-incision cataract surgery with intraocular lens (IOL) implantation performed elsewhere and referred to us for management. Subsequent identification and confirmation was carried out with biochemical tests and polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP).

MATERIALS AND METHODS

The corneal scraping and eviscerated material of the first patient, the corneal button and the IOL of the second patient, and the corneal scraping of the third patient were processed for routine bacteriologic studies including acid-fast bacilli (AFB) by smear (excepting the IOL) and culture. Subsequent identification of the RGNTM was carried out by using biochemical tests and PCR-RFLP by using primers targeting the heat shock protein 65 region of mycobacteria.

RESULTS

AFB smear was positive in all 3 patients. The corneal scraping of the first patient, the corneal button and IOL of the second patient, and the corneal scraping of the third patient were culture positive for RGNTM and were identified as Mycobacterium abscessus in the first and second patients and M. fortuitum sorbitol-positive third biovariant in the third patient.

CONCLUSIONS

A clinical suspicion of infection by RGNTM in delayed-onset postoperative endophthalmitis should be considered when resistance to standard therapy is encountered.

Mycobacterium avium in the postgenomic era

The past several years have witnessed an upsurge of genomic data pertaining to the Mycobacterium avium complex (MAC). Despite clear advances, problems with the detection of MAC persist, spanning the tests that can be used, samples required for their validation, and the use of appropriate nomenclature. Additionally, the amount of genomic variability documented to date greatly outstrips the functional understanding of epidemiologically different subsets of the organism. In this review, we discuss how postgenomic insights into the MAC have helped to clarify the relationships between MAC organisms, highlighting the distinction between environmental and pathogenic subsets of M. avium. We discuss the availability of various genetic targets for accurate classification of organisms and how these results provide a framework for future studies of MAC variability. The results of postgenomic M. avium study provide optimism that a functional understanding of these organisms will soon emerge, with genomically defined subsets that are epidemiologically distinct and possess different survival mechanisms for their various niches. Although the status quo has largely been to study different M. avium subsets in isolation, it is expected that attention to the similarities and differences between M. avium organisms will provide greater insight into their fundamental differences, including their propensity to cause disease.

Mycobacterium monacense sp. nov

Four bacterial strains were isolated from independent clinical specimens in different countries and their genotypic and phenotypic characters support their classification in a novel species within the genus Mycobacterium. One strain was clearly responsible for a severe, post-traumatic wound infection in a healthy boy. The novel species, for which the name Mycobacterium monacense sp. nov. is proposed, is yellow-pigmented, non-photochromogenic and grows in less than a week on solid medium. Based on phenotypic investigations alone, distinction of these four strains from known scotochromogenic rapidly growing strains is problematic. However, the novel strains differ from any other mycobacterium in each of the molecular species markers investigated: the 16S rRNA gene, the 16S-23S rRNA gene internal transcribed spacer and the hsp65 gene. Of the strains investigated, two different sequevars were detected for the hsp65 region. Phylogenetic analysis revealed that these four strains were most closely related to Mycobacterium doricum. The type strain of Mycobacterium monacense sp. nov. is B9-21-178T (=DSM 44395T=CIP 109237T).

Description of Mycobacterium conceptionense sp. nov., a Mycobacterium fortuitum group organism isolated from a posttraumatic osteitis inflammation

A nonpigmented rapidly growing mycobacterium was isolated from wound liquid outflow, bone tissue biopsy, and excised skin tissue from a 31-year-old woman who suffered an accidental open right tibia fracture and prolonged stay in a river. The three isolates grew in 3 days at 24 to 37 degrees C. 16S rRNA sequence analyses over 1,483 bp showed that they were identical and shared 99.7% (4-bp difference) sequence similarity with that of Mycobacterium porcinum, the most closely related species. Partial rpoB (723 bp) sequence analyses showed that the isolates shared 97.0% sequence similarity with that of M. porcinum. Further polyphasic approaches, including biochemical tests, antimicrobial susceptibility analyses, and hsp65, sodA, and recA gene sequence analysis, as well as % G+C determination and cell wall fatty acid composition analysis supported the evidence that these isolates were representative of a new species. Phylogenetic analyses showed the close relationship with M. porcinum in the Mycobacterium fortuitum group. The isolates were susceptible to most antibiotics and exhibited evidence for penicillinase activity, in contrast to M. porcinum. We propose the name Mycobacterium conceptionense sp. nov. for this new species associated with posttraumatic osteitis. The type strain is D16(T) (equivalent to CIP 108544(T) and CCUG 50187(T)).

Polyphasic characterization reveals that the human pathogen Mycobacterium peregrinum type II belongs to the bovine pathogen species Mycobacterium senegalense

Mycobacterium peregrinum consists of two taxa: types I and II. We evaluated 43 clinical type II strains from throughout the United States. They were responsible for soft-tissue and bone infections, catheter-related infections, and possible pneumonitis. By carbohydrate utilization, they were indistinguishable from type I strains, being D-mannitol and trehalose positive. However, they had a distinct susceptibility pattern that included intermediate ciprofloxacin MICs but low clarithromycin and doxycycline MICs of < or =1 microg/ml. These features were also shared by reference isolates of Mycobacterium senegalense from African bovine cases of "farcy." By 16S rRNA gene sequencing, the type II isolates shared 100% sequence identity with M. senegalense. Partial sequencing of the type II hsp65 gene (441 bp) revealed four sequevars showing > or =98.4% identity with each other and > or =98.6% identity with the sequence of five bovine strains of M. senegalense. There was < or =97.1% identity with M. peregrinum type I isolates and other Mycobacterium fortuitum group species. Sequencing of additional gene targets including the 16S-23S rDNA internal transcribed spacer region and the rpoB gene (partial sequence) revealed a similar phylogenetic grouping. DNA-DNA hybridization showed 76 to 99% relatedness between the bovine and human strains. These studies demonstrate that type II isolates are not isolates of M. peregrinum but represent human strains of M. senegalense. This study is the first to demonstrate this species as a human pathogen. Representative human M. senegalense strains include ATCC 35755 and newly submitted strains ATCC BAA-849, ATCC BAA-850, and ATCC BAA-851.