Identification of Mycobacterium spp. of veterinary importance using rpoB gene sequencing

Coinfection by Mycobacterium marinum and Mycolicibacterium fortuitum in a captive adult diamondback water snake causing disseminated mycobacteriosis with acute cutaneous ulceration

An adult male captive diamondback water snake (Nerodia rhombifer) was found dead after a 1-d history of lethargy and cutaneous ulcers. The snake had eaten 2 sunfish (Mola spp.) 5 d before death. Gross examination revealed white-to-tan nodules in the lung and liver and segmental intestinal impactions with digested fish. Histopathology confirmed disseminated granulomas with numerous intrahistiocytic acid-fast bacteria in the skin, skeletal muscle, lung, liver, and intestines. Mycobacterium marinum and Mycolicibacterium fortuitum were identified by culture of the hepatic granuloma, followed by PCR and rpoB gene sequencing. To our knowledge, this is the first description of M. marinum and M. fortuitum coinfection in this species. Although M. fortuitum has been isolated from reptiles, lesions associated with its presence in tissues have not been described previously. Interestingly, the mineralization within granulomas that we observed in our case is not reported in mycobacterial infection in reptiles, whereas this finding is common in mammals.

A Rare Case of Osteomyelitis of an Ankle Caused by Mycobacterium chelonae

Mycobacterium chelonae, a rapidly growing nontuberculous mycobacterium, is usually described as a causative agent of soft tissue infections (postsurgical, posttraumatic, posttransplantation, postinjection, catheter infection, etc.), but only rarely as a cause of osteomyelitis. The authors describe a case report of a 72-year-old man with osteomyelitis of the talus. Initially, the infection was assessed as a soft tissue infection, without any osteolytic changes on the X-ray. After cultivation with subsequent targeted molecular typing of the rpoB gene, M. chelonae was identified from the affected tissue. The bone involvement was subsequently detected on MRI and confirmed histologically with findings of the granulomatous tissue and acid-fast bacilli. The patient was initially treated intravenously with a combination of tigecycline, amikacin, and moxifloxacin for 4 weeks, after which the oral combination of doxycycline and moxifloxacin continued. Identification of the infecting pathogen using molecular typing thus helped to establish the correct diagnosis and represents a rarely described case of osteomyelitis caused by M. chelonae.

Short Signature rpoB Gene Sequence to Differentiate Species in Mycobacterium abscessus Group

Mycobacterium abscessus group (MAG) are rapidly growing acid-fast bacteria that consist of three closely related species: M. abscessus (Ma), M. bolletii (Mb), and M. massiliense (Mm). Differentiation of these species can be difficult but is increasingly requested owing to recent infectious outbreaks and their differential drug resistance. We developed a novel and rapid pyrosequencing method using short signature sequences (35 to 45 bp) at a hypervariable site in the rpoB gene to differentiate the three MAG species, along with M. chelonae (Mc), and M. immunogenum (Mi). This method was evaluated using 111 M. chelonae-abscessus complex (MCAC) isolates, including six reference strains. All isolates were successfully differentiated to the species level (69 Ma, four Mb, six Mm, 23 Mc, and nine Mi). The species identifications by this method had 100% agreement with Sanger sequencing as well as an in-silico rpoB typing method. This short signature sequencing (SSS) method is rapid (6 to 7 h), accurately differentiates MAG species, and is useful for informing antimicrobial therapy decision.

IMPORTANCEMycobacterium abscessus group (MAG) are rapidly growing acid-fast bacteria that include three species: M. abscessus, M. massiliense, and M. bolletii. These species are among the leading causes of nontuberculosis mycobacteria infections in humans but difficult to differentiate using commonly used methods. The differences of drug resistance among the species shape the treatment regimens and make it significant for them to be differentiated accurately and quickly. We developed and evaluated a novel short signature sequencing (SSS) method utilizing a gene called rpoB to differentiate the three MAG species, as well as other two species (M. chelonae and M. immunogenum). The identification results had 100% agreement with both the reference method of Sanger sequencing and rpoB typing method via a computer-simulated analysis. This SSS method was accurate and quick (6 to 7 h) for species differentiation, which will benefit patient care. The technology used for this method is affordable and easy to operate.

Pathology and Prevalence of Antibiotic-Resistant Bacteria: A Study of 398 Pet Reptiles

Reptiles are potential reservoirs of bacteria that could be transmitted, thus becoming a zoonotic hazard. (1) Background: This three-year investigation surveyed the pathological status of 398 pet reptiles: chelonians, snakes (venomous/non-venomous), and lizards. The main pathological entities found were related to the skin, the sensory organs, the digestive system, the respiratory system, the cardiovascular system, the urinary system, the genitalia, the osteo−muscular tract, surgical issues, tumors, and intoxications. (2) Methods: In 25 individuals treated with antibiotics, no clinical healing was recorded, for this reason, an antimicrobial resistance profile analysis of the 43 samples gathered was processed. An antibiogram was performed using the VITEK®2 ID-GP (bio-Mérieux, Marcy l’Etoile, France) automated platform, with 22 bacterial strains being isolated. (3) Results: The statistics (ANOVA) revealed that the most common disease category was diseases of the digestive system, followed by diseases of the skin, respiratory system, nervous system, and reproductive system. A significant correlation (p < 0.01) between disease incidence and reptile species was reported, with correlations found between all species and diseases diagnosed. The most common bacteria isolated were Enterococcus faecalis, Pseudomonas aeruginosa, Stenotrophomas (Xanthomonas) maltophilia, Escherichia coli, Klebsiella oxytoca, and Salmonella spp., but Beta-hemolytic Streptococcus, Staphylococcus aureus, Citrobacter spp., and Proteus spp. were also identified. (4) Conclusions: These microorganisms revealed degrees of resistance against penicillins, cephalosporins, macrolides, lincosamides, aminoglycosides, and tetracyclines. The animals can be categorized according to their sensitivity to diseases in the following order (most sensitive to least sensitive): chelonians, venomous snakes, non-venomous snakes, and lizards.

High female mortality caused by an atypical Mycobacterium species closely related to the Mycobacterium ulcerans-marinum complex in a colony of bearded dragons (Pogona vitticeps)

A commercial breeding colony of bearded dragons (Pogona vitticeps) experienced an increase in mortality that affected females only. Before death, the animals had lost appetite and weight, were dehydrated, and some had labored breathing. Necropsy revealed granulomas in many organs (ovaries, lungs, liver, kidneys, heart, bone marrow) in which numerous acid-fast bacteria were identified. Bacterial isolation confirmed Mycobacterium spp., which was identified by whole genome sequencing as closely related to the Mycobacterium ulcerans-marinum complex. Due to the zoonotic potential of this bacterium and the poor prognosis for the remaining sick animals, the entire colony was culled and 7 animals were evaluated. The possible routes for introduction of this bacterium, the female predisposition to the disease, as well as the zoonotic potential of this microorganism are discussed. Key clinical message: An atypical Mycobacterium species closely related to Mycobacterium ulcerans-marinum complex can cause high female morality in captive bearded dragons.

ISOLATION AND ANTIMICROBIAL SUSCEPTIBILITIES OF NONTUBERCULOUS MYCOBACTERIA FROM WILDLIFE IN JAPAN

Nontuberculous mycobacteria (NTM) are opportunistic pathogens of humans and animals and are transmitted among the environment, wildlife, livestock, and humans. The aim of this study was to investigate the rate of isolation and antimicrobial susceptibility of NTM in wildlife. In total, 178 samples of feces (n=131) and tissues (n=47) were collected from 11 wildlife species in Gifu Prefecture and Mie Prefecture, Japan, between June 2016 and October 2018. We isolated NTM from 15.3% (20/ 131) of fecal samples using Ogawa medium, and isolates were identified by sequencing the rpoB and hsp65 genes. The rpoB sequences were compared with those from other strains of human and environmental origin. The NTM isolates were obtained from sika deer (Cervus nippon), wild boar (Sus scrofa), Japanese monkey (Macaca fuscata), raccoon dog (Nyctereutes procyonoides), masked palm civet (Paguma larvata), and Japanese weasel (Mustela itatsi) and were classified as rapidly growing mycobacteria (RGM) and slowly growing mycobacteria (SGM). The 12 RGM identified were Mycolicibacterium peregrinum (n=5), Mycolicibacterium fortuitum (n=3), Mycolicibacterium septicum (n=3), and Mycolicibacterium thermoresistibile (n=1), and the eight SGM were Mycobacterium paraense (n=4), Mycolicibacter arupensis (n=2), Mycolicibacter virginiensis (n=1), and Mycobacterium nebraskense (n=1). The NTM from wildlife showed ≥99% similarity with strains from different sources including humans. The RGM were susceptible to the antimicrobial agents tested except for M. fortuitum, which was resistant to azithromycin and clarithromycin. The SGM showed multiple drug resistance qualities but were susceptible to amikacin, clarithromycin, and rifabutin. These results indicate that wildlife may be reservoir hosts of NTM in Japan. The presence of antimicrobial-resistant NTM in wildlife suggests that the trends of NTM antimicrobial susceptibility in wildlife should be monitored.

Seasonal Variability in the Microbial Community and Pathogens in Wastewater Final Effluents

Numerous bacteria, especially pathogens, exist in wastewater final effluents, which can lead to possible human health and ecological security risks when effluents are reused or discharged. However, the diversity, composition, and spatiotemporal dynamics of bacteria in wastewater final effluents remain poorly understood. In this study, a comprehensive analysis of the microbial community and pathogens in wastewater final effluents was performed using high-throughput sequencing. The results revealed that wastewater final effluents in autumn exhibited the highest bacterial community richness and diversity, while those in winter exhibited the lowest. Bacteria in wastewater final effluents predominantly belonged to five phyla, in the order of Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and Firmicutes. At the species level, there were 8~15 dominant species in the wastewater final effluent in each season, and Dokdonella immobilis, Rhizobium gallicum, Candidatus Flaviluna lacus, and Planctomyces limnophilus were the most dominant species in spring, summer, autumn, and winter, respectively. The seasonal variability in bacteria suggested that the microbial diversity and community in wastewater final effluents were mainly influenced by temperature, salinity, disinfection methods, and flocculants. Notably, pathogenic bacteria in wastewater effluents had both the highest relative abundance and species abundance in summer. Arcobacter spp., Legionella spp., and Mycobacterium spp. were the dominant pathogenic bacteria, and all pathogenic bacteria were mainly associated with dermatosis, enteropathies, septicemia, and pneumonia.

Fate of internalized Campylobacter jejuni and Mycobacterium avium from encysted and excysted Acanthamoeba polyphaga

Association of the water- and foodborne pathogen Campylobacter jejuni with free-living Acanthamoeba spp. trophozoites enhances C. jejuni survival and resistance to biocides and starvation. When facing less than optimal environmental conditions, however, the Acanthamoeba spp. host can temporarily transform from trophozoite to cyst and back to trophozoite, calling the survival of the internalized symbiont and resulting public health risk into question. Studies investigating internalized C. jejuni survival after A. castellanii trophozoite transformation have neither been able to detect its presence inside the Acanthamoeba cyst after encystation nor to confirm its presence upon excystation of trophozoites through culture-based techniques. The purpose of this study was to detect C. jejuni and Mycobacterium avium recovered from A. polyphaga trophozoites after co-culture and induction of trophozoite encystation using three different encystation methods (Neff's medium, McMillen's medium and refrigeration), as well as after cyst excystation. Internalized M. avium was used as a positive control, since studies have consistently detected the organism after co-culture and after host excystation. Concentrations of C. jejuni in A. polyphaga trophozoites were 4.5 × 10⁵ CFU/ml, but it was not detected by PCR or culture post-encystation. This supports the hypothesis that C. jejuni may be digested during encystation of the amoebae. M. avium was recovered at a mean concentration of 1.9 × 10⁴ from co-cultured trophozoites and 4.4 × 10¹ CFU/ml after excystation. The results also suggest that M. avium recovery post-excystation was statistically significantly different based on which encystation method was used, ranging from 1.3 × 10¹ for Neff's medium to 5.4 × 10¹ CFU/ml for refrigeration. No M. avium was recovered from A. polyphaga cysts when trophozoites were encysted by McMillen's medium. Since C. jejuni internalized in cysts would be more likely to survive harsh environmental conditions and disinfection, a better understanding of potential symbioses between free-living amoebae and campylobacters in drinking water distribution systems and food processing environments is needed to protect public health. Future co-culture experiments examining survival of internalized C. jejuni should carefully consider the encystation media used, and include molecular detection tools to falsify the hypothesis that C. jejuni may be present in a viable but not culturable state.

Use of slide scrape lysates for polymerase chain reaction confirmation of disseminated Mycobacterium avium infection in a cat

Disseminated mycobacteriosis in a 3-year-old domestic medium-haired cat was diagnosed on lymph node cytology. Slide scrape lysates from the cytology submission were used to confirm Mycobacterium avium by polymerase chain reaction (PCR) and sequencing and proved a simple technique that could be a valuable tool in veterinary diagnostics and research.

Use of whole-genome sequencing and evaluation of the apparent sensitivity and specificity of antemortem tuberculosis tests in the investigation of an unusual outbreak of Mycobacterium bovis infection in a Michigan dairy herd

OBJECTIVE To describe use of whole-genome sequencing (WGS) and evaluate the apparent sensitivity and specificity of antemortem tuberculosis tests during investigation of an unusual outbreak of Mycobacterium bovis infection in a Michigan dairy herd. DESIGN Bovine tuberculosis (bTB) outbreak investigation. ANIMALS Cattle, cats, dog, and wildlife. PROCEDURES All cattle in the index dairy herd were screened for bTB with the caudal fold test (CFT), and cattle ≥ 6 months old were also screened with a γ-interferon (γIFN) assay. The index herd was depopulated along with all barn cats and a dog that were fed unpasteurized milk from the herd. Select isolates from M bovis-infected animals from the index herd and other bTB-affected herds underwent WGS. Wildlife around all affected premises was examined for bTB. RESULTS No evidence of bTB was found in any wildlife examined. Within the index herd, 53 of 451 (11.8%) cattle and 12 of 21 (57%) cats were confirmed to be infected with M bovis. Prevalence of M bovis-infected cattle was greatest among 4- to 7-month-old calves (16/49 [33%]) followed by adult cows (36/203 [18%]). The apparent sensitivity and specificity were 86.8% and 92.7% for the CFT and 80.4% and 96.5% for the γIFN assay when results for those tests were interpreted separately and 96.1% and 91.7% when results were interpreted in parallel. Results of WGS revealed that M bovis-infected barn cats and cattle from the index herd and 6 beef operations were infected with the same strain of M bovis. Of the 6 bTB-affected beef operations identified during the investigation, 3 were linked to the index herd only by WGS results; there was no record of movement of livestock or waste milk from the index herd to those operations. CONCLUSIONS AND CLINICAL RELEVANCE Whole-genome sequencing enhanced the epidemiological investigation and should be used in all disease investigations. Performing the CFT and γIFN assay in parallel improved the antemortem ability to detect M bovis-infected animals. Contact with M bovis-infected cattle and contaminated milk were major risk factors for transmission of bTB within and between herds of this outbreak.

MYCOBACTERIOSIS IN CAPTIVE PSITTACINES: A BRIEF REVIEW AND CASE SERIES IN COMMON COMPANION SPECIES (ECLECTUS RORATUS, AMAZONA ORATRIX, AND PIONITES MELANOCEPHALA)

In 2015, three psittacines were presented within 30 days, each with differing clinical signs and patient histories. A 13-yr-old male eclectus parrot (Eclectus roratus) was presented for weakness, depression, and acute anorexia. On presentation it was determined to have a heart murmur, severely elevated white blood cell count (93.9 10³/μl) with a left shift (2.8 10³/μl bands), and anemia (30%). Severe hepatomegaly was noted on radiographs, ultrasonography, and computed tomography. A cytological sample of the liver obtained through a fine needle aspirate revealed intracellular acid-fast bacilli identified as Mycobacterium avium. A 20-yr-old female double yellow-headed Amazon parrot (Amazona oratrix) was presented for a 1-mo history of lethargy and weight loss despite a good appetite. The parrot's total white blood cell count was 16.8 10³/μl and the PCV was 35%. Following its death, a necropsy revealed a generalized granulomatous condition that involved the small intestines, lungs, liver, spleen, and medullary cavities of the long bones, with intracellular acid-fast bacilli identified as Mycobacterium genavense. The third case, an 18-mo-old female black-headed caique (Pionites melanocephala), was presented with a 1-day history of lethargy and depression. On presentation, the caique had a heart murmur, distended coelom, palpable thickening of the coelomic organs, and increased lung sounds. Following the caique's death, a complete necropsy revealed mycobacteriosis of the liver, spleen, small intestines, pericardial fat, and bone marrow. The infection was identified as Mycobacterium genavense. The importance of advances in Mycobacterium spp. identification, continued presence of this organism in captive avian populations, difficulty in obtaining a definitive antemortem diagnosis, and conflicting recommendations regarding treatment are thought-provoking areas of focus in this case series.

Mycobacteria in aquarium fish: results of a 3-year survey indicate caution required in handling pet-shop fish

Fish are commonly infected with non-tuberculous mycobacteria (NTM), which should be regarded as potential pathogens when handling aquarium fish and equipment. This study examined 107 aquarium fish from pet shops. Cultivation of the fish samples using different selective media was conducted for identification of NTM. Isolates were identified using the GenoType Mycobacterium common mycobacteria and additional species assays, sequencing of the 16S rRNA and rpoB genes, and real-time PCR assay for identification of Mycobacterium (M.) marinum. Among the investigated fish, 79.4% (85/107) were positive for mycobacteria, with 8.2% (7 of 85) having two mycobacterial species present. Among the positive fish, the common pathogens M. marinum, Mycobacterium fortuitum (M. fortuitum group) and Mycobacterium chelonae were identified in approx. 90% of fish and other NTM species in 10%, including Mycobacterium peregrinum/septicum, Mycobacterium gordonae, Mycobacterium arupense, Mycobacterium kansasii, Mycobacterium ulcerans and Mycobacterium setense. The well-known human pathogen M. marinum was present in 10.6% of the positive fish (9 of 85). The species of mycobacteria identified in the study are not only recognized as aquarium fish pathogens, but can also cause pathology in humans. Microbiological and clinical communities should therefore be sensitized to the role of NTM in infections associated with exposure to aquarium fish.

Genotyping and strain distribution of Mycobacterium avium subspecies hominissuis isolated from humans and pigs in Belgium, 2011-2013

Mycobacterium avium represents a health concern for both humans and pigs. The characterisation of its subspecies is an important step improving the understanding of the epidemiology and the control of this pathogen. Ninety-two human M. avium strains were selected for a retrospective study. Subspecies determination by rpoB sequencing and IS1245/IS901 analysis showed that 98.9% of Belgian human M. avium strains belong to the subspecies hominissuis (MAH). Some of these MAH strains present particular IS1245/IS901 profiles (absence of IS1245 and false IS901 detection provoked by the presence of ISMav6). In addition, 54 MAH strains isolated from submandibular lymph nodes of Belgian pigs with lymphadenitis were included in this study. Genotyping of human and porcine isolates was performed using multispacer sequence typing (MST). In total, 49 different MST types were identified among pig (n = 11) and human (n = 43) MA isolates, with only five shared by both hosts. Among these MST types, 34 were newly identified. Our findings demonstrate the extensive genetic diversity among MAH isolates. Some genotypes were more prevalent in human or pigs but no correlation was observed between MST type and place of residence or the farm of origin for human and porcine isolates respectively, suggesting an environmental source of infection.

Anatomical distribution of Mycobacterium bovis genotypes in experimentally infected white-tailed deer

Mycobacterium bovis (M. bovis) causes tuberculosis in white-tailed deer (WTD). Natural infection of WTD with M. bovis is most closely mimicked by instilling inoculum into palatine tonsillar crypts. One hundred fifty days after intratonsillar inoculation, M. bovis was cultured from 30 tissues originating from 14 deer. Whole-genome sequencing (WGS) was performed on the original inoculum, single colonies subcultured from the original inoculum, and M. bovis isolated from each culture positive tissue. Single nucleotide polymorphisms (SNP) were identified by comparing the derived sequences to the reference strain AF2122/97. Results indicate that the majority of the SNPs that were identified were homogeneous between the inoculum and the isolates from the tissues. The majority of individual tissues had different WGS genotypes from each other, suggesting that dissemination of M. bovis beyond the initial site of infection may require few mycobacteria representing a bottleneck.

Multifocal respiratory and vertebral mycobacteriosis in a red-tailed hawk (Buteo jamaicensis)

An adult, female, free-ranging red-tailed hawk (Buteo jamaicensis) was presented to a rehabilitation facility for an inability to stand. On examination, it displayed bilateral exaggeration of the pelvic limb reflexes with extensor muscle rigidity, intact superficial pain response, and positive withdrawal reflexes. A complete blood count identified moderate leukocytosis characterized by moderate heterophilia. No abnormalities were appreciable on radiographic evaluation. After initial improvement, it regressed and was euthanized 27 days after presentation. Necropsy and histologic investigation identified reduction in the diameter of the vertebral canal and spinal cord at cervical segments 8-9 with coalescing granulomas and intralesional acid-fast bacilli within the intertrabecular space, left side of the clavicular air sac, and cranial left lung. Bacterial culture and genetic sequencing from respiratory lesions identified Mycobacterium avium avium. Real time-polymerase chain reaction of paraffin-fixed spinal tissue tested positive for M. avium complex. Mycobacteriosis should be considered when peripheral neurologic deficits are present in raptors.

Molecular identification of Mycobacterium avium subsp. silvaticum by duplex high-resolution melt analysis and subspecies-specific real-time PCR

Accurate identification of mycobacterial species and subspecies is essential to evaluate their significance and to perform epidemiological studies. The subspecies of Mycobacterium avium have different attributes but coincide in their zoonotic potential. Our knowledge about M. avium subsp. silvaticum is limited, since its identification is uncertain. Mycobacterium avium subsp. avium and M. avium subsp. silvaticum can be discriminated from each other based only on phenotypic characteristics, as they have almost identical genome sequences. Here we describe the development of a diagnostic method which enables the molecular identification of M. avium subsp. silvaticum and discrimination from M. avium subsp. avium based on genomic differences in a duplex high-resolution melt and M. avium subsp. silvaticum-specific mismatch real-time PCR. The developed assay was tested on reference strains and 199 field isolates, which were analyzed by phenotypic methods previously. This assay not only identified all 63 M. avium subsp. silvaticum and 138 M. avium subsp. avium strains correctly but also enabled the detection of mixed M. avium subsp. avium-M. avium subsp. silvaticum cultures. This is the first time that such a large panel of strains has been analyzed, and we also report the first isolation of M. avium subsp. silvaticum from red fox, red deer, wild boar, cattle, and badger. This assay is reliable, rapid, simple, inexpensive, and robust. It eliminates the long-existing problem of ambiguous phenotypic identification and opens up the possibility for detailed and comprehensive strain studies.

Non-tuberculous mycobacterial infections of veterinary relevance

Mycobacteria play an important role in human and animal health fields. We here examine the place of non tuberculous mycobacteria (NTM) infections in the veterinary context. Relevant aspects of a reference laboratory experience and a literature review are presented in this article. Importance is given both to productivity and to economic losses due to misdiagnosis with bovine tuberculosis and paratuberculosis. The impact NTM may have is relative to geographical location, ecology, husbandry, extent of surveillance programs and bovine tuberculosis and paratuberculosis prevalence. The role of the most relevant NTM in animal disease is summarized with a special focus on Mycobacterium avium subsp. paratuberculosis, given its role as causative agent of paratuberculosis, a disease with huge economic consequences for ruminant livestock.

Identification of nontuberculous mycobacteria isolated from Hanwoo (Bos taurus coreanae) in South Korea by sequencing analysis targeting hsp65, rpoB and 16S rRNA genes

Combinatorial molecular taxonomic approaches targeting 3 genes, 16S rRNA (1.2-1.3kbp), hsp65 (603-bp), and rpoB genes (711-bp) were applied to 43 non-tuberculous mycobacteria (NTM) strains isolated from a Korean native cattle from bronchial lymph nodes and lung, Hanwoo (Bos taurus coreanae) in South Korea. Of 43 NTM isolates, Mycobacterium avium complex strains (MAC) were isolated with the highest frequency (31 strains, 72.1%). Contrary to other reports, M. intracellulare strains (23 strains, 53.5%) of MACs were more prevalent than M. avium strains (8 strains, 18.6%). Further separation of isolated M. intracellulare into genotype level by hsp65 analysis showed that isolates of the HG-1 genotype (60.9%, 14/23 isolates), known to be specific to Korean patients, was more prevalent than the HG-2 type (17.4%, 4/23 strains), which include the type strain, M. intracellulare ATCC 13950(T). Compared to NTM infections of Korean human patients, the pronounced difference found in this study is that no M. abscessus infections in Hanwoo were found. In conclusion, our data showed that the isolated species frequency of NTMs, particularly MACs from Hanwoo, was very comparable to that obtained from Korean human infection, suggesting that humans and Korean native cattle may share common environmental sources for NTM infections.

Utility of rpoB gene sequencing for identification of nontuberculous mycobacteria in the Netherlands

In the Netherlands, clinical isolation of nontuberculous mycobacteria (NTM) has increased over the past decade. Proper identification of isolates is important, as NTM species differ strongly in clinical relevance. Most of the currently applied identification methods cannot distinguish between all different Mycobacterium species and complexes within species. rpoB gene sequencing exhibits a promising level of discrimination among rapidly and slowly growing mycobacteria, including the Mycobacterium avium complex. In this study, we prospectively compared rpoB gene sequencing with our routine algorithm of reverse line blot identification combined with partial 16S rRNA gene sequencing of 455 NTM isolates. rpoB gene sequencing identified 403 isolates to species level as 45 different known species and identified 44 isolates to complex level, and eight isolates remained unidentifiable to species level. In contrast, our reference reverse line blot assay with adjunctive 16S rRNA gene sequencing identified 390 isolates to species level (30 distinct species) and identified 56 isolates to complex level, and nine isolates remained unidentified. The higher discriminatory power of rpoB gene sequencing results largely from the distinction of separate species within complexes and subspecies. Also, Mycobacterium gordonae, Mycobacterium kansasii, and Mycobacterium interjectum were separated into multiple groupings with relatively low sequence similarity (98 to 94%), suggesting that these are complexes of closely related species. We conclude that rpoB gene sequencing is a more discriminative identification technique than the combination of reverse line blot and 16S rRNA gene sequencing and could introduce a major improvement in clinical care of NTM disease and the research on the epidemiology and clinical relevance of NTM.

Optimized nested polymerase chain reaction for antemortem detection of Mycobacteria in Amazon parrots (Amazona aestiva) and orange-winged Amazons (Amazona amazonica)

The objectives of this study were to optimize nested polymerase chain reaction (PCR) for Mycobacterium avium complex and Mycobacterium tuberculosis complex and apply them on samples from parrots. Results were negative for the presence of these Mycobacterium in the samples, and nested PCR was specific, faster, and more sensitive than other tests, thereby justifying its use in antemortem diagnosis.

Draft Genome Sequence of a Mycobacterium avium Complex Isolate from a Broadbill Bird

We report the draft genome sequence of a Mycobacterium avium complex isolate. This isolate has an estimated genome size of 5.1 Mb with an average GC content of 68.9% and is predicted to carry 4,497 protein-encoding genes and 317 pseudogenes.

Isolation of mycobacteria from clinical samples collected in the United States from 2004 to 2011

BACKGROUND

Mycobacteria other than M. bovis may interfere with current bovine tuberculosis diagnostic tests resulting in false positive test results. As the prevalence of M. bovis decreases in the United States, interference from other mycobacteria play an increasingly important role in preventing the eradication of M. bovis. To identify mycobacteria other than M. bovis that may be interfering with current diagnostic tests, a retrospective study was performed to identify mycobacteria isolated from clinical tissues at the National Veterinary Services Laboratories between 1 January 2004 and 9 October 2011.

RESULTS

During the study period, 2,366 mycobacteria other than M. bovis were isolated from samples submitted for clinical diagnosis of M. bovis. Fifty-five mycobacterial species were isolated during this time period. In cattle, M. avium complex, M. fortuitum/fortuitum complex, M. smegmatis, M. kansasii, and M. terrae complex were the predominate species other than M. bovis isolated from tissues submitted for culture. Mycobacteria other than M. bovis isolated from deer were predominantly M. avium complex, M. terrae/terrae complex, and M. fortuitum/fortuitum complex.

CONCLUSIONS

These data provide information characterizing the species and relative prevalence of mycobacteria other than M. bovis that may interfere with current diagnostic tests.

First case of pulmonary disease caused by a Mycobacterium avium complex strain of presumed veterinary origin in an adult human patient

We report the first case of pulmonary disease caused by a strain of Mycobacterium avium complex of presumed veterinary origin in an elderly patient. All serial isolates were identified by multilocus sequence analysis based on rpoB, hsp65, and 16S rRNA fragments. Disease persisted despite macrolide-based combination antibiotic therapy.

A gene expression study of the activities of aromatic ring-cleavage dioxygenases in Mycobacterium gilvum PYR-GCK to changes in salinity and pH during pyrene degradation

Polycyclic aromatic hydrocarbons (PAHs) are toxic pollutants found in the environment which can be removed through the use of physical and biological agents. The rate of PAH biodegradation is affected by environmental conditions of pH, salinity and temperature. Adaptation of the pyrene degrading bacteria, Mycobacterium gilvum PYR-GCK, to fluctuating environmental conditions during pyrene biodegrading activity was studied using the quantitative real time – Polymerase Chain Reaction (qRT-PCR) technique. Four aromatic ring-cleavage dioxygenase genes: phdF, phdI, pcaG and pcaH; critical to pyrene biodegradation, were studied in pH states of 5.5, 6.5, 7.5 and NaCl concentrations 0 M, 0.17 M, 0.5 M, 0.6 M, 1 M. First, we conducted a residual pyrene study using gas chromatography and flame ionization technologies. Central to a gene expression study is the use of a valid endogenous reference gene, making its determination our next approach, using the geNorm/NormFinder algorithms. Armed with a valid control gene, rpoB, we applied it to a gene expression study, using the comparative critical threshold (2^ΔΔCT) quantification method. The pyrene degrading activity of the strain was strongly functional in all the NaCl concentration states, with the least activity found at 1M (∼70% degraded after 48 hours of cultivation). The transcripts quantification of three genes backed this observation with high expression levels. The gene expression levels also revealed pH 6.5 as optimal for pyrene degradation and weak degradation activity at pH of 5.5, corroborating the residual pyrene analysis. The expression of these genes as proteins has already been studied in our laboratory using proteomics techniques and this validates our current study.

Field application of serodiagnostics to identify elephants with tuberculosis prior to case confirmation by culture

Three serologic methods for antibody detection in elephant tuberculosis (TB), the multiantigen print immunoassay (MAPIA), ElephantTB STAT-PAK kit, and DPP VetTB test, were evaluated using serial serum samples from 14 captive elephants infected with Mycobacterium tuberculosis in 5 countries. In all cases, serological testing was performed prior to the diagnosis of TB by mycobacterial culture of trunk wash or tissue samples collected at necropsy. All elephants produced antibody responses to M. tuberculosis antigens, with 13/14 recognizing ESAT-6 and/or CFP10 proteins. The findings supported the high serodiagnostic test accuracy in detecting infections months to years before M. tuberculosis could be isolated from elephants. The MAPIA and/or DPP VetTB assay demonstrated the potential for monitoring antimycobacterial therapy and predicting TB relapse in treated elephants when continuously used in the posttreatment period. History of exposure to TB and past treatment information should be taken into consideration for proper interpretation of the antibody test results. Data suggest that the more frequent trunk wash culture testing of seropositive elephants may enhance the efficiency of the TB diagnostic algorithm, leading to earlier treatment with improved outcomes.