First report of disseminated Mycobacterium skin infections in two liver transplant recipients and rapid diagnosis by hsp65 gene sequencing

Mycobacterium haemophilum infection with cutaneous involvement: two case reports and an updated literature review: Mycobacterium haemophilum skin infection

Mycobacterium haemophilum (MH) is a slow-growing, non-tuberculous Mycobacterium that most commonly causes infections in immunocompromised patients. The skin is the most prevalent site of infection and can be an isolated presentation or part of a disseminated disease. Herein, we reported a case of isolated MH infection of the hand and a case of disseminated MH infection with multiple skin lesions. In addition, other MH cases with cutaneous involvement over the last 10 years, from 2011-2022, were reviewed and analyzed. Among the 79 included cases, the common skin findings in MH infections included nodules, ulcers, abscesses, swelling, and pustules. Middle-aged patients with iatrogenic immunosuppression from glucocorticoids, mycophenolate mofetil, cyclosporine, and cyclophosphamide are the most susceptible to MH infection, with a higher risk of dissemination to internal organs. Disseminated MH infections commonly present as tenosynovitis, arthritis/arthralgia, or osteomyelitis. There is a lack of strong evidence for treatment; however, triple therapy of quinolone, macrolides, and rifampicin is most often used in clinical practice. The overall prognosis is good. The presence of iatrogenic immunocompromised diseases, lesions involving the proximal limbs, and dissemination of MH infections are associated with worse clinical outcomes.

Hautbeteiligung bei Infektionen mit Mycobacterium haemophilum: Zwei Fallberichte und eine aktualisierte Literaturübersicht: Mycobacterium haemophilum infection with cutaneous involvement: Two case reports and an updated literature review

Mycobacterium haemophilum (MH) ist ein langsam wachsendes, nicht‐tuberkulöses Mykobakterium. Infektionen treten am häufigsten bei Patienten mit beeinträchtigtem Immunsystem auf; sie manifestieren sich meist an der Haut und kommen isoliert oder bei disseminierten Infektionen vor. Wir berichten hier über einen Fall mit isolierter MH‐Infektion an der Hand sowie über einen weiteren Fall von disseminierter MH‐Infektion mit multiplen Hautläsionen. Zusätzlich haben wir weitere Fallberichte über MH‐Infektionen mit kutaner Beteiligung aus den letzten zehn Jahren (2011–2022) ausgewertet. Die am häufigsten beobachteten Hautmanifestationen der insgesamt 79 Fälle waren Knötchen, Ulzera, Abszesse, Schwellungen und Pusteln. Patienten mittleren Alters mit iatrogener Immunsuppression durch Glucocorticoide, Mycophenolat‐Mofetil, Ciclosporin und Cyclophosphamid scheinen besonders anfällig für MH‐Infektionen zu sein und haben auch ein höheres Risiko für eine Dissemination in die inneren Organe. Disseminierte MH‐Infektionen manifestieren sich gewöhnlich als Tenosynovitis, Arthritis/Arthralgie oder Osteomyelitis. Derzeit gibt es keine starke Evidenz für bestimmte Therapeutika; in der Praxis wird am häufigsten eine Dreifachkombination aus Chinolon, Makroliden und Rifampicin eingesetzt. Die Prognose ist allgemein gut. Iatrogene Immunsuppression, Läsionen im proximalen Bereich der Extremitäten sowie disseminierte Manifestation sind mit schlechteren klinischen Verläufen assoziiert.

Fatal disseminated Mycobacterium haemophilum infection involving the central nervous system in a renal transplant recipient

Mycobacterium haemophilum is a slow growing nontuberculous mycobacterium which prefers cooler temperatures and requires iron for growth. It usually causes skin and soft tissue infections in immunocompromised hosts and cervical lymphadenitis in healthy children. We present the case of fatal disseminated M. haemophilum in an immunocompromised host with central nervous system (CNS) involvement. Our case is a 65-year-old Hispanic male with history of end-stage renal disease status post renal transplantation six years prior (on maintenance immunosuppression with mycophenolate, tacrolimus and prednisone), diabetes mellitus type 2, coronary artery disease, ventricular arrhythmias with implantable cardioverter defibrillator, prior stroke and cochlear implant. In the four months preceding admission to our institution he had frequent hospitalizations for altered mental status (AMS), sepsis syndromes and failure to thrive. Two months prior to presentation he developed progressive swelling and redness of the wrists, right third and left fifth digits. Computed tomography (CT) showed extensive cellulitis in distal right forearm and hand with chronic osteomyelitis. Serial incision and drainage (I&D) of right wrist yielded positive AFB stain and growth on AFB culture. PCR was negative for Mycobacterium tuberculosis. Patient was started on rifampin, clarithromycin and ethambutol. Two days later patient developed AMS and severe septic shock requiring transfer to our facility. CT head revealed indeterminate lesion in the left frontal lobe along with nonspecific hypodensities in the pons and thalamus. Repeat CT upper extremities showed osteomyelitis of distal radius and small hand bones with adjacent abscesses. I&D also revealed bilateral tenosynovitis. Cultures were resent. With suspicion for rapidly growing mycobacterial infection, the regimen was changed to linezolid, imipenem and azithromycin. Several changes in antimicrobials were necessary throughout hospitalization due to complicated hospital course. Unfortunately, despite aggressive measures, patient developed multiorgan failure culminating in death 10 days after starting anti-mycobacterial drugs. On the day of death, the organism was identified as M. haemophilum. Susceptibilities were not done as patient had died. On autopsy the brain was noted to have multiple abscesses containing AFB. The organism also grew from the wrists and right finger cultures. M. haemophilum of the CNS is extremely rare and has been reported in HIV or AIDS patients. To our knowledge this is the first reported case of M. haemophilum brain abscesses in a patient without HIV/AIDS. Because of its fastidious growth requirements, M. haemophilum usually shows on acid fast stains but does not grow on routine AFB cultures. Although it prefers lower temperatures for growth and is usually limited to skin and soft tissues, disseminated disease occurs in immunocompromised patients and has high mortality. It is usually treated with a multi drug regimen including clarithromycin, rifampin, ciprofloxacin and amikacin.

Antiretroviral therapy-induced paradoxical worsening of previously healed Mycobacterium haemophilum cutaneous lesions in advanced HIV infection

Mycobacterium haemophilum is a nontuberculous mycobacterium that causes localized or disseminated disease, mainly in immunocompromised hosts. We report the case of a 35-year-old HIV-infected woman who presented with several enlarging cutaneous lesions over the arms and legs. Histopathological examination revealed the diagnosis of a cutaneous mycobacterial disease. Mycobacterial analyses unveiled M. haemophilum infection. Six months after completion of a successful antimycobacterial treatment, she developed an immune reconstitution inflammatory syndrome (IRIS). This paradoxical relapse presented as tenderness, redness and swelling at the precise sites of the healed lesions and took place in the setting of significant recovery of the CD4 cell count (from 05 to 318 cells/mm 3 ). Microbiological analyses of these worsening lesions were negative, and they spontaneously remitted without the initiation of a novel antimycobacterial treatment cycle. M. haemophilum infection should always be considered as a cause of skin lesions in immunocompromised subjects. Physicians should be aware of the possibility of IRIS as a complication of successful antiretroviral therapy in HIV-infected patients with M. haemophilum infection.

Clinical, Dermatoscopical and Laboratory Essentials of Fish Tank Granuloma

In immunocompetent individuals Mycobacterium marinum (M. marinum) infection usually presents with localized skin lesions, better known as “swimming pool granuloma” or “fish tank granuloma” (FTG). When establishing the diagnosis of FTG, doctors encounter several problems in the clinical practice: granulomas are detected in less than two thirds of biopsies and acid-fast bacilli are identified only in a minority of cases. Majority of disseminated and aggressive FTG forms are unrecognized at the beginning, and occur in immunosuppressed patients, including organ transplant patients. Functional impairment or even amputation of the extremity, visceral involvement and lethal outcome have been reported. Although more than one thousand cases of FTG have been reported worldwide, dermatoscopy of FTG, as a diagnostic aid, has not been reported yet. Presenting the case of FTG of recent onset where, guided by dermatoscopy, microorganisms were isolated and identified from the biopsy material, we summarize the essentials of clinical and laboratory diagnostics of M. marinum infection.

Cutaneous Mycobacterium Marinum Infection (Fish Tank Granuloma) in a Renal Transplant Recipient: Case Report and Literature Review

Atypical mycobacterioses are unusual infections of the skin and other organs caused by non-tuberculous mycobacteria. Fish tank granuloma and swimming pool granuloma are two forms of atypical mycobacterioses caused by Mycobacterium marinum. So far, only a few cases of these infections have been reported in organ transplant patients, and these usually are more severe when compared with atypical mycobacterioses in immunocompetent hosts. We report a kidney transplant patient with a rather mild form of atypical mycobacteriosis (fish tank granuloma) who responded well to treatment with doxycycline and will provide a review of all similar cases reported in the literature.

Management of Mycobacterium Other than Tuberculosis in Solid Organ Transplantation

Mycobacteria other than tuberculosis are important pathogens to consider in solid organ transplant recipients. Delay in recognition and treatment may incur significant morbidity and mortality. Management of mycobacteria other than tuberculosis requires a knowledge of treatment specific for each species and drug-drug interactions between antimicrobial and immunosuppressive drugs. Therapy in solid organ transplant can be prolonged and may require a reduction in immunosuppression to improve outcomes.

Case of Mycobacterium haemophilum misdiagnosed as Mycobacterium intracellulare due to one base insertion in the bacterial genome

Mycobacterium haemophilum is a slow-growing, non-tuberculous mycobacteria that causes cutaneous infection. We describe a case of cutaneous infection in a 68-year-old Japanese man with polymyositis. This was caused by M. haemophilum harboring one base insertion in gene sequence. At first, the causal microorganism was misidentified as M. intracellulare by COBAS^® TaqMan^® MAI test. However, poor growth on Ogawa media and growth enhancement on 7H11C agar around a hemin-containing disk prompted us to reinvestigate the causal microorganisms, which were revealed to be M. haemophilum. Amplified polymerase chain reaction products were sequenced, and the 16S rRNA gene, rpoB, hsp65 and internal transcribed spacer region sequences showed a 100%, 100%, 99.66% and 99.7% match, respectively, with the corresponding regions of M. haemophilum, but it harbored a novel gene sequence in hsp65. The sequences determined by gene analysis of the M. haemophilum strain were deposited into the International Nucleotide Sequence Database. Although numerous cases of M. haemophilum infection have been reported in other countries, only six cases have been reported in Japan to date. It could be possible that this novel mutation lead to misdiagnosis. As M. haemophilum prefers a lower growth temperature (30-32°C) and it requires iron in the culture medium, M. haemophilum could be misidentified or overlooked. Accordingly, a M. haemophilum infection should be considered in cases of cutaneous infection of the body sites, of which surface temperature is low.

Disseminated Mycobacterium haemophilum infection in a renal transplant recipient

Opportunistic infections are a major concern in renal and transplant medicine. We present the case of a renal transplant recipient with a generalised Mycobacterium haemophilum infection after an increase in immunosuppressive therapy and treatment with a tumour necrosis factor-α (TNF-α) inhibitor. Infection involved skin and soft tissue, joints and bones, as well as the renal transplant with an interstitial nephritis. Rapid diagnosis using PCR and DNA sequencing allowed early appropriate treatment. Triple antibiotic therapy and reduction in immunosuppression resulted in a slow but sustained recovery. Immunosuppression causes severe opportunistic infections. TNF-α inhibitors are very effective and well tolerated but have an increased susceptibility to infections with mycobacteria. Mycobacterial infections represent a significant clinical risk to transplant recipients because of their aggressive clinical course and the need for complex toxic antibiotic treatments. In these patients, M. haemophilum is a cause of skin infections.

Non-tuberculous mycobacterial infections in solid organ transplant recipients: An update

Non-tuberculous mycobacteria are ubiquitous environmental organisms that are now increasingly recognized as important causes of clinical disease in solid organ transplant recipients. Risk factors of non-tuberculous mycobacteria infection are severe immunologic defects and structural abnormalities. Lung transplant recipients are at higher risk for non-tuberculous mycobacterial disease compared to recipients of other solid organs. The clinical presentation could be skin and soft tissue infection, osteoarticular disease, pleuropulmonary infection, bloodstream (including catheter-associated) infection, lymphadenitis, and disseminated or multi-organ disease. Management of non-tuberculous mycobacteria infection is complex due to the prolonged treatment course with multi-drug regimens that are anticipated to interact with immunosuppressive medications. This review article provides an update on infections due to non-tuberculous mycobacteria after solid organ transplantation, and discusses the epidemiology, risk factors, clinical presentation, and management.

Septic arthritis caused by Mycobacterium marinum

The incidence of infection by Mycobacterium marinum is rising, mainly due to the increasing popularity of home aquariums. The infection typically manifests as skin lesions, with septic arthritis being a rare presentation form. The disease is difficult to diagnose even when there is a high clinical suspicion, as culture in specific media may not yield positive findings. Thus, establishment of appropriate treatment is often delayed. Synovectomy, capsular thinning, and joint drainage together with prolonged, combined antibiotic therapy may be needed to cure the infection.

A Challenging Case of Multifocal Mycobacterium marinum Osteoarticular Infection in a Patient with Anorexia Nervosa

Disseminated infection due to Mycobacterium marinum is rare but has been described in immunosuppressed and transplant recipients. We describe a case of multifocal osteoarticular involvement by this pathogen in a patient with anorexia nervosa. Serial surgical debridements and a prolonged course of antimicrobial therapy including intravenous amikacin, imipenem, and oral ethambutol and azithromycin were needed to treat the infection. Cell mediated immune deficits related to the patient's anorexia nervosa predisposed her to a severe infection with M. marinum. Aggressive surgical intervention in conjunction with multiple antimicrobial agents helped cure the infection.

Identification of specific metabolites in culture supernatant of Mycobacterium tuberculosis using metabolomics: exploration of potential biomarkers

Although previous studies have reported the use of metabolomics for Mycobacterium species differentiation, little is known about the potential of extracellular metabolites of Mycobacterium tuberculosis (MTB) as specific biomarkers. Using an optimized ultrahigh performance liquid chromatography-electrospray ionization-quadruple time of flight-mass spectrometry (UHPLC-ESI-Q-TOF-MS) platform, we characterized the extracellular metabolomes of culture supernatant of nine MTB strains and nine non-tuberculous Mycobacterium (NTM) strains (four M. avium complex, one M. bovis Bacillus Calmette-Guérin (BCG), one M. chelonae, one M. fortuitum and two M. kansasii). Principal component analysis readily distinguished the metabolomes between MTB and NTM. Using multivariate and univariate analysis, 24 metabolites with significantly higher levels in MTB were identified. While seven metabolites were identified by tandem mass spectrometry (MS/MS), the other 17 metabolites were unidentified by MS/MS against database matching, suggesting that they may be potentially novel compounds. One metabolite was identified as dexpanthenol, the alcohol analog of pantothenic acid (vitamin B5), which was not known to be produced by bacteria previously. Four metabolites were identified as 1-tuberculosinyladenosine (1-TbAd), a product of the virulence-associated enzyme Rv3378c, and three previously undescribed derivatives of 1-TbAd. Two derivatives differ from 1-TbAd by the ribose group of the nucleoside while the other likely differs by the base. The remaining two metabolites were identified as a tetrapeptide, Val-His-Glu-His, and a monoacylglycerophosphoglycerol, phosphatidylglycerol (PG) (16∶0/0∶0), respectively. Further studies on the chemical structure and biosynthetic pathway of these MTB-specific metabolites would help understand their biological functions. Studies on clinical samples from tuberculosis patients are required to explore for their potential role as diagnostic biomarkers.

Infections caused by non-tuberculous mycobacteria in recipients of hematopoietic stem cell transplantation

Non-tuberculous mycobacteria (NTM) are acid-fast bacteria that are ubiquitous in the environment and can colonize soil, dust particles, water sources, and food supplies. They are divided into rapidly growing mycobacteria such as Mycobacterium fortuitum, Mycobacterium chelonae, and Mycobacterium abscessus as well as slowly growing species such as Mycobacterium avium, Mycobacterium kansasii, and Mycobacterium marinum. About 160 different species, which can cause community acquired and health care-associated infections, have been identified. NTM are becoming increasingly recognized in recipients of hematopoietic stem cell transplantation (HSCT) with incidence rates ranging between 0.4 and 10%. These infections are 50–600 times commoner in transplant recipients than in the general population and the time of onset ranges from day 31 to day 1055 post-transplant. They have been reported following various forms of HSCT. Several risk factors predispose to NTM infections in recipients of stem cell transplantation and these are related to the underlying medical condition and its treatment, the pre-transplant conditioning therapies as well as the transplant procedure and its complications. Clinically, NTM may present with: unexplained fever, lymphadenopathy, osteomyelitis, soft tissue and skin infections, central venous catheter infections, bacteremia, lung, and gastrointestinal tract involvement. However, disseminated infections are commonly encountered in severely immunocompromised individuals and bloodstream infections are almost always associated with catheter-related infections. It is usually difficult to differentiate colonization from true infection, thus, the threshold for starting therapy remains undetermined. Respiratory specimens such as sputum, pleural fluid, and bronchoalveolar lavage in addition to cultures of blood, bone, skin, and soft tissues are essential diagnostically. Susceptibility testing of mycobacterial isolates is a basic component of optimal care. Currently, there are no guidelines for the treatment of NTM infections in recipients of stem cell transplantation, but such infections have been successfully treated with surgical debridement, removal of infected or colonized indwelling intravascular devices, and administration of various combinations of antimicrobials. Monotherapy can be associated with development of drug resistance due to new genetic mutation. The accepted duration of treatment is 9 months in allogeneic stem cell transplantation and 6 months in autologous setting. Unfortunately, eradication of NTM infections may be impossible and their treatment is often complicated by adverse effects and interactions with other transplant-related medication.

Romance of the three domains: how cladistics transformed the classification of cellular organisms

Cladistics is a biological philosophy that uses genealogical relationship among species and an inferred sequence of divergence as the basis of classification. This review critically surveys the chronological development of biological classification from Aristotle through our postgenomic era with a central focus on cladistics. In 1957, Julian Huxley coined cladogenesis to denote splitting from subspeciation. In 1960, the English translation of Willi Hennig’s 1950 work, Systematic Phylogenetics, was published, which received strong opposition from pheneticists, such as numerical taxonomists Peter Sneath and Robert Sokal, and evolutionary taxonomist, Ernst Mayr, and sparked acrimonious debates in 1960–1980. In 1977–1990, Carl Woese pioneered in using small subunit rRNA gene sequences to delimitate the three domains of cellular life and established major prokaryotic phyla. Cladistics has since dominated taxonomy. Despite being compatible with modern microbiological observations, i.e. organisms with unusual phenotypes, restricted expression of characteristics and occasionally being uncultivable, increasing recognition of pervasiveness and abundance of horizontal gene transfer has challenged relevance and validity of cladistics. The mosaic nature of eukaryotic and prokaryotic genomes was also gradually discovered. In the mid-2000s, high-throughput and whole-genome sequencing became routine and complex geneologies of organisms have led to the proposal of a reticulated web of life. While genomics only indirectly leads to understanding of functional adaptations to ecological niches, computational modeling of entire organisms is underway and the gap between genomics and phenetics may soon be bridged. Controversies are not expected to settle as taxonomic classifications shall remain subjective to serve the human scientist, not the classified.

Mycobacterium abscessus bacteremia after receipt of intravenous infusate of cytokine-induced killer cell therapy for body beautification and health boosting

BACKGROUND

We report the first series of Mycobacterium abscessus bacteremia after cytokine-induced killer cell therapy for body beautification and health boosting.

METHODS

The clinical manifestations, laboratory and radiological investigations, cytokine/chemokine profiles, and outcomes were described and analyzed.

RESULTS

Four patients were admitted, and 3 patients had septic shock. Chest radiographs showed pulmonary infiltrates in all patients. Three patients developed peripheral gangrene, and 1 patient required lower limb and finger amputations. Patient 1 also developed disseminated infection including meningitis and urinary tract infection. Postmortem examination of patient 1 showed focal areas of pulmonary hemorrhage and diffuse alveolar damage, splenic infarct, adrenal necrosis, and hemorrhage, and acid-fast bacilli (AFB) were seen in the lung, liver, kidney, and adrenal gland. Patient 2 developed inguinal granulomatous lymphadenitis about 40 days after onset of lower limb gangrene. Wedge-shaped pulmonary infarcts were found in patient 3, and retinitis and subcutaneous lesions developed in patient 4. Patients in septic shock had dysregulated cytokine/chemokine profiles. Patient 4 with relatively milder presentation had increasing levels of interleukin 17 and cytokines in the interferon-γ/interleukin 12 pathway. All survivors required prolonged intravenous antibiotics. Blood cultures grew M. abscessus for all patients, and admission peripheral blood smear revealed AFB for 3 patients. Mycobacterium abscessus was also isolated from respiratory specimens (2 patients), urine (1 patient), and cerebrospinal fluid (1 patient). Time to initial blood culture positivity (patients 1, 2, and 3: ≤52 hours; patient 4: 83 hours) appeared to correlate with disease severity.

CONCLUSIONS

Empirical coverage for rapidly growing mycobacteria should be considered in patients with sepsis following cosmetic procedures.

Streptococcus hongkongensis sp. nov., isolated from a patient with an infected puncture wound and from a marine flatfish

A bacterium, HKU30T, was isolated from the infected tissue of a patient with wound infection after puncture by a fish fin. Cells are facultative anaerobic, non-spore-forming, non-motile, Gram-positive cocci arranged in chains. Colonies were non-haemolytic. The strain was catalase, oxidase, urease and Voges–Proskauer test negative. It reacted with Lancefield’s group G antisera and was resistant to optochin. It grew on bile aesculin agar and in 5 % NaCl. It was unidentified by three commercial identification systems. 16S rRNA gene sequence analysis indicated that the bacterium shared 98.2, 97.7, 97.4 and 97.1 % nucleotide identities with Streptococcus iniae , Streptococcus pseudoporcinus , Streptococcus parauberis and Streptococcus uberis , respectively. The DNA G+C content was 35.6±0.9 mol% (mean±sd). In view of the occupational exposure of the patient, an epidemiological study was performed to isolate the bacterium from marine fish. Two strains, with similar phenotypic and genotypic characteristics to those of HKU30T, were isolated from a three-lined tongue sole (Cynoglossus abbreviatus) and an olive flounder (Paralichthys olivaceus) respectively. Phylogenetic analysis of four additional housekeeping genes, groEL, gyrB, sodA and rpoB, showed that the three isolates formed a distinct branch among known species of the genus Streptococcus , being most closely related to S. parauberis (CCUG 39954T). DNA–DNA hybridization demonstrated ≤53.8 % DNA relatedness between the three isolates and related species of the genus Streptococcus . A novel species, Streptococcus hongkongensis sp. nov., is proposed. The type strain is HKU30T ( = DSM 26014T = CECT 8154T).

Reactive and infective dermatoses associated with adult-onset immunodeficiency due to anti-interferon-gamma autoantibody: Sweet's syndrome and beyond

Immunodeficiency due to anti-interferon-gamma autoantibody (anti-IFN-γ autoAb) is an emerging adult-onset immunodeficiency syndrome predominantly found in Southeast Asians. It is associated with severe or disseminated infections caused by non-tuberculous mycobacteria (NTM) and other opportunistic pathogens. We describe 3 patients with anti-IFN-γ autoAb who developed reactive and infective dermatoses, and thoroughly review the existing literature on dermatoses associated with the immunodeficiency syndrome. Case 1 developed Sweet's syndrome associated with Mycobacterium chelonae lymphadenitis and penicilliosis. Case 2 suffered from multiple episodes of lobular panniculitis during recurrent infections by NTM, Penicillium marneffei and Burkholderia pseudomallei. Both cases responded to immunomodulating agents including corticosteroid and non-steroidal anti-inflammatory drugs. Case 3 had direct skin invasion by M. chelonae and responded to prolonged anti-mycobacterial therapy. A novel working algorithm is proposed for the diagnosis and treatment of these patients who may be encountered by the dermatologist and histopathologist in clinical practice.

Detection of microorganisms in granulomas that have been formalin-fixed: review of the literature regarding use of molecular methods

Granuloma is an organized aggregate of immune cells that under the microscope appear as epithelioid macrophages. A granuloma can only be diagnosed when a pathologist observes this type of inflammation under the microscope. If a foreign body or a parasite is not observed inside the granuloma, stains for acid-fast bacilli and fungi are ordered since mycobacteria and fungi are frequently the cause of this type of inflammation. It is calculated that 12 to 36% of granulomas do not have a specific etiology and many have wondered if with new molecular methods we could reduce this number. This paper will summarize the frequently known causes of granulomas and will present the recent literature regarding the use of molecular techniques on tissue specimens and how these have helped in defining causative agents. We will also briefly describe new research regarding formation and function of granulomas and how this impacts our ability to find an etiologic agent.

Automated pangenomic analysis in target selection for PCR detection and identification of bacteria by use of ssGeneFinder Webserver and its application to Salmonella enterica serovar Typhi

With the advent of high-throughput DNA sequencing, more than 4,000 bacterial genomes have been sequenced and are publicly available. We report a user-friendly web platform, ssGeneFinder Webserver (http://147.8.74.24/ssGeneFinder/), which is updated weekly for the automated pangenomic selection of specific targets for direct PCR detection and the identification of clinically important bacteria without the need of gene sequencing. To apply the ssGeneFinder Webserver for identifying specific targets for Salmonella enterica serovar Typhi, we analyzed 11 S. Typhi genomes, generated two specific targets, and validated them using 40 S. Typhi, 110 non-Typhi Salmonella serovars (serovar Paratyphi A, n = 4; Paratyphi B, n = 1; Typhimurium, n = 5; Enteritidis, n = 12; non-Paratyphi group A, n = 6; non-Paratyphi group B, n = 29; non-Paratyphi group C, n = 12; non-Typhi group D, n = 35; group E and others, n = 6), 115 Enterobacteriaceae isolates (Escherichia, n = 78; Shigella, n = 2; Klebsiella, n = 13; Enterobacter, n = 9; others, n = 13), and 66 human stool samples that were culture negative for S. Typhi. Both targets successfully detected all typical and atypical S. Typhi isolates, including an H1-j flagellin gene mutant, an aflagellated mutant which reacted with 2O Salmonella antiserum, and the Vi-negative attenuated vaccine strain Ty21a. No false positive was detected from any of the bacterial isolates and stool samples. DNA sequencing confirmed the identity of all positive amplicons. The PCR assays have detection limits as low as 100 CFU per reaction and were tested using spiked stool samples. Using a pangenomic approach, ssGeneFinder Webserver generated targets specific to S. Typhi. These and other validated targets should be applicable to the identification and direct PCR detection of bacterial pathogens from uncultured, mixed, and environmental samples.