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.

Surfactant free rapid synthesis of hydroxyapatite nanorods by a microwave irradiation method for the treatment of bone infection

Mesoporous nanocrystalline hydroxyapatite (nHAp) rods of size 40-75 nm long and 25 nm wide (resembling bone mineral) were synthesized under microwave irradiation without using any surfactants or modifiers. The surface area and average pore size of the nHAp were found to be 32 m(2) g(-1) and 4 nm, respectively. Rifampicin (RIF) and ciprofloxacin (CPF) loaded nHAp displayed an initial burst followed by controlled release (zero order kinetics). Combination of CPF and RIF loaded nHAp showed enhanced bacterial growth inhibition against Staphylococcus aureus (S. aureus), Staphylococcus epidermidis (S. epidermidis) and Escherichia coli (E. coli) compared to individual agent loaded nHAp and pure nHAp. In addition, decreased bacterial adhesion (90%) was observed on the surface of CPF plus RIF loaded nHAp. The biocompatibility test toward MG63 cells infected with micro-organisms showed better cell viability and alkaline phosphatase activity (ALP) for the combination of CPF and RIF loaded nHAp. The influence on cell viability of infected MG63 cells was attributed to the simultaneous and controlled release of CPF and RIF from nHAp, which prevented the emergence of subpopulations that were resistant to each other. Hence, apart from the issue of the rapid synthesis of nHAp without surfactants or modifiers, the simultaneous and controlled release of dual drugs from nHAp would be a simple, non-toxic and cost-effective method to treat bone infections.

Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects

Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17(th) to the 19(th) century, we propose a methodology that includes the: 1) amplification of all 16S rDNA gene sequences present in each sample; 2) identification of all bacterial DNA sequences with a degree of identity ≥ 95%, according to quality criteria; 3) identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4) establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1) the correct identification of bacterial molecular sequence signatures by quality criteria; 2) the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3) the distribution of bacterial species for each subject and for each burial; and 4) the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17(th) century to the early 18(th) century.

Efficacy of the new cephalosporin ceftaroline in the treatment of experimental methicillin-resistant Staphylococcus aureus acute osteomyelitis

OBJECTIVES

To evaluate the activity of a new cephalosporin, ceftaroline, in comparison with other antistaphylococcal drugs (linezolid and vancomycin) at projected human therapeutic doses against methicillin-resistant Staphylococcus aureus (MRSA) and glycopeptide-intermediate S. aureus (GISA) strains.

METHODS

Using a rabbit experimental model of acute osteomyelitis, efficacy was assessed following 4 days of treatment by colony counts of infected bone tissues (joint fluid, femoral bone marrow and bone).

RESULTS

Although vancomycin remains the standard treatment for MRSA osteomyelitis, it was ineffective against the MRSA strain and poorly active against GISA infections in this model. Ceftaroline and linezolid demonstrated significant activity in bone marrow and bone, and were significantly better than vancomycin treatment. However, ceftaroline was the only drug to exhibit significant activity against MRSA in infected joint fluid.

CONCLUSIONS

The present study supports ceftaroline as a promising therapeutic option for the treatment of severe MRSA infections, including osteomyelitis.

Histopathologic findings in bone from edentulous alveolar ridges: a role in osteonecrosis of the jaws?

Bisphosphonate-related osteonecrosis of the jaws (BONJ) is characterized by a breach in the oral mucosa with exposure of necrotic bone. Although bisphosphonates impact multiple biologic processes, including bone turnover and vascularity, factors contributing to the pathogenesis of BONJ remain poorly understood. In this retrospective analysis, the histopathologic findings from 154 alveolar bone specimens obtained during osteotomy preparation for dental implant placement were reviewed from 147 consecutively treated patients [male (79); female (68); Caucasian (141); African-American (6)]. The alveolar ridge sites had been edentulous for 1 year or longer. None of the patients in this study had a history of bisphosphonate therapy or clinical evidence of BONJ. Two pathologists, masked, using predetermined criteria, reviewed and substantiated the pathology reports provided by the licensed pathology service. In selected cases, special stains had been conducted to help establish the presence of bacteria. The histopathologic findings for the core specimens were as follows: 76 viable bone (49.4%); 54 nonviable bone (35.0%); and 24 osteomyelitis (15.6%). These histopathologic findings indicate that the edentulous jaw can contain regions of nonviable bone and microbial biofilm formation for 1 year or more after tooth extraction and mucosal healing. Regions of necrotic bone and subclinical infection may contribute to the development of untoward clinical events, such BONJ and early implant failure.

Scenario of extrapulmonary tuberculosis in a tertiary care center

BACKGROUND

Tuberculosis is a worldwide disease and one of the major health problems of Nepal. Extrapulmonary tuberculosis is increasing all over the world. The main aim of this study was to assess the frequency of extrapulmonary tuberculosis in various organ systems of the body and to assess the pattern of disease in different age groups and gender.

METHODS

This observational retrospective study was carried out from December 2003 to October 2009 at the Department of Pathology, Kathmandu University Hospital, Kavre, Nepal. A total of 259 extrapulmonary tuberculosis cases diagnosed by fine needle aspiration cytology and biopsy were included. Frequency of extrapulmonary tuberculosis in the lymph nodes in relation to age and sex were studied.

RESULTS

Lymph nodes tuberculosis was present in 179 (69.11%) cases. Among all extrapulmonary tuberculosis, 132 (50.56%) cases were in males and 127 (49.04%) were in females. Out of total 179 tuberculosis of lymph nodes, 116 (74.35%) were seen in age group of 25 years and above (p=0.018) and 86 (48.04%) in males and 93 (51.95%) in females (p=0.18).

CONCLUSIONS

Extrapulmonary tuberculosis is common in lymph nodes, equally in both sexes and more in age group of 25 and above. Therefore, this age group should be focused upon more for investigation and management of extrapulmonary tuberculosis.

[Screening of collagenase-producing strain and purification of Bacillus cereus collagenase]

We isolated the strain MBL13 with high collagenase productivity from the soil of piled up animal bones. It was identified as Bacillus cereus. We purified and characterized Bacillus cereus collagenase (BCC). The molecular weight of BCC was 38.0 kDa and the optimum temperature and pH for the enzyme activity were 40 degrees C and 8.0 respectively. The enzyme was stable when the temperature was below 50 degrees C, but only retained 10% activity when kept at 60 degrees C for 1 h. The enzyme activity was stable between pH 7.0-8.5. Some metal ions such as Ca2+, Zn2+, Mg2+ enhanced the enzyme activity, and Cu2+ brought the obvious inhibition. In addition, EDTA and EGTA could inhibit the enzyme activity. We suggested that the purified enzyme was a member of the metalloproteases. Based on the experiment of substrate specificity, we found that the purified enzyme was bone collagenolytic protease, and had a much stronger capacity of hydrolysis for type I collagen than that for type II collagen and type III collagen. By BCC hydrolyzing bone collagen, we obtained polypeptides with different chain lengths. The comparative test indicated that the hydrolysis capacity of BBC was higher than that of standard type I collagenase. The results introduced a new strain and a novel collagenolytic protease for industrial enzyme.

Two consecutive deep sinus tract cultures predict the pathogen of osteomyelitis

OBJECTIVES

The value of non-bone microbiological cultures in the diagnosis of osteomyelitis with sinus tract is not clear. We aimed to establish the concordance between deep sinus tract cultures and bone cultures in cases of osteomyelitis with a cutaneous fistula.

METHODS

This was a non-randomized, prospective diagnostic trial at the Orthopedic Service of the University Hospital of Geneva. Each patient with osteomyelitis with a cutaneous sinus tract had four microbiological samples taken: two consecutive sinus tract cultures with bone contact at different times (samples A-1 and A-2), surgical bone biopsy performed through the sinus tract (sample B), and a surgical bone biopsy performed through an uninfected area outside the sinus tract (sample C), the latter considered as the 'gold standard'.

RESULTS

One hundred and forty-one patients with 154 episodes of osteomyelitis were included in the study. When both sinus tract cultures yielded the same microorganism (86.4%), the concordance between both samples A and sample C was 96%. In the case of identical sinus tract culture infections, sensitivity was 91%, specificity 86%, and accuracy 90%. The accuracy in monomicrobial infections (50%) was higher than in polymicrobial infections (94.3% vs. 78.9%, respectively; p=0.02).

CONCLUSIONS

In cases of monomicrobial osteomyelitis with sinus tract, two concordant tract cultures with bone contact accurately predict the pathogen.

Secondary syphilis presenting as SAPHO syndrome features

The SAPHO syndrome may evolve following low virulent infections. This report describes a patient who developed a clinical syndrome that complied with the formal diagnostic criteria of the SAPHO following an infection with syphilis. His clinical manifestations gradually resolved following antibiotic therapy. This interesting association underlines the pathogenic circumstances linking infections and various rheumatic conditions. It is less evident whether resolution of the symptoms was ascribed to the eradication of the bacteria or perhaps due to cessation of the auto-inflammatory reaction to the infection induced. In our description we suggest a correlation between infection with Treponema pallidum and the induction of SAPHO syndrome.

High hydrostatic pressure, a novel approach in orthopedic surgical oncology to disinfect bone, tendons and cartilage

High hydrostatic pressure (HHP) is widely used in the food processing industry, for example to inactivate vegetative microorganisms in meat products, milk and juice, thereby avoiding the addition of any chemical preservatives. Besides this, HHP is also an attractive novel approach to effectively kill vegetative microorganisms or tumor cells in bone, cartilage and tendon ex vivo while leaving the tissues' mechanical properties unimpaired, thus allowing reimplantation of the resected tissue explants. In contrast, sterilization by gamma irradiation and thermal or chemical inactivation of potentially infected autografts, allografts and other biomaterials considered for tissue regeneration and reconstruction is often associated with deterioration of the mechanical, physical and biological properties of the implant. HHP technology is now in preclinical testing with the aim of disinfecting/devitalizing grafts in order to inactivate both vegetative microorganisms and tumor cells in resected bone tissue segments, eventually allowing reimplantation of resected bone segments initially afflicted with osteomyelitis or tumors. The technical advantages, state-of-the-art, and potential application of HHP in orthopedic surgery are reviewed.

Detection and molecular characterization of 9,000-year-old Mycobacterium tuberculosis from a Neolithic settlement in the Eastern Mediterranean

Background

Mycobacterium tuberculosis is the principal etiologic agent of human tuberculosis. It has no environmental reservoir and is believed to have co-evolved with its host over millennia. This is supported by skeletal evidence of the disease in early humans, and inferred from M. tuberculosis genomic analysis. Direct examination of ancient human remains for M. tuberculosis biomarkers should aid our understanding of the nature of prehistoric tuberculosis and the host/pathogen relationship.

Methodology/Principal Findings

We used conventional PCR to examine bone samples with typical tuberculosis lesions from a woman and infant, who were buried together in the now submerged site of Atlit-Yam in the Eastern Mediterranean, dating from 9250-8160 years ago. Rigorous precautions were taken to prevent contamination, and independent centers were used to confirm authenticity of findings. DNA from five M tuberculosis genetic loci was detected and had characteristics consistent with extant genetic lineages. High performance liquid chromatography was used as an independent method of verification and it directly detected mycolic acid lipid biomarkers, specific for the M. tuberculosis complex.

Conclusions/Significance

Human tuberculosis was confirmed by morphological and molecular methods in a population living in one of the first villages with evidence of agriculture and animal domestication. The widespread use of animals was not a source of infection but may have supported a denser human population that facilitated transmission of the tubercle bacillus. The similarity of the M. tuberculosis genetic signature with those of today gives support to the theory of a long-term co-existence of host and pathogen.

Effect of hydroxyapatite coating and polymethylmethacrylate on stainless steel implant-site infection with Staphylococcus epidermidis in a sheep model

We aimed to study the influence of hydroxyapatite (HA) coating and polymethylmethacrylate (PMMA) cement on the risk of development of stainless steel implant-site infection with Staphylococcus epidermidis in a sheep model. Uncoated, HA-coated, and PMMA-cemented stainless steel implants were inserted in the left femur of 30 sheep. For each type of implant, sheep were inoculated with S. epidermidis in the intramedullary canal and one non-inoculated group was used as control. After 6 weeks, infection was evaluated using clinical, radiological, bacteriological, and histological criteria. Radiological and clinical results were normal. Cultures were negative in the control sheep. In the inoculated sheep, interposition tissue and bone cultures were positive in 2 of 6 uncoated, 6 of 6 HA, and 6 of 6 PMMA implants with a mean bacteria count of 5.2 +/- 1.17, 3.5 +/- 0.7, and 3.9 +/- 0.9 log10 cfu/g, respectively (NS), for interposition tissue, and 4 +/- 0.01, 2.9 +/- 0.6, and 2.5 +/- 1.3 log10 cfu/g, respectively (NS) for bone. The polymorphonuclear leukocyte (PMN) score (mean number of PMN per 10 different microscopic high-power fields >or=5) in interposition tissue was >or=3 in 6 of 6 HA, significantly different from uncoated (3 of 6) and PMMA (2 of 6) groups (p = 0.04). The HA and PMMA inoculated groups had a higher infection rate than the uncoated inoculated group (p = 0.06). In this experimental sheep model of S. epidermidis infection at the bone-biomaterial interface, HA seems to be at higher risk of infection compared with uncoated or PMMA-cemented stainless steel, when inoculation is intramedullary and contemporary with implantation.

[Diagnostic algorithm of a lesion of jaws bone tissues in purulent inflammatory diseases of maxillofacial region]

The writer detects changes of density of strontium, calcium, zinc and ratio Ca/Sr, Zn/Sr in oral liquid at examination 162 patients with acute odontogenic inflammatory diseases and 85 ill with a fracture of a mandible and at it inflammatory complication. By her is established the increase density of calcium in a stomatic liquid at all purulent-inflammatory diseases of maxillofacial area. The strontium is reduced only at an acute odontogenic osteomyelitis and odontogenic lymphadenitis complicated by a phlegmon. The ratio Ca/Sr, Zn/Sr is-augmented also only at the data diseases.

Imaging of musculoskeletal bacterial infections by [124I]FIAU-PET/CT

Background

Traditional imaging techniques for the localization and monitoring of bacterial infections, although reasonably sensitive, suffer from a lack of specificity. This is particularly true for musculoskeletal infections. Bacteria possess a thymidine kinase (TK) whose substrate specificity is distinct from that of the major human TK. The substrate specificity difference has been exploited to develop a new imaging technique that can detect the presence of viable bacteria.

Methodology/Principal Findings

Eight subjects with suspected musculoskeletal infections and one healthy control were studied by a combination of [¹²⁴I]FIAU-positron emission tomography and CT ([¹²⁴I]FIAU-PET/CT). All patients with proven musculoskeletal infections demonstrated positive [¹²⁴I]FIAU-PET/CT signals in the sites of concern at two hours after radiopharmaceutical administration. No adverse reactions with FIAU were observed.

Conclusions/Significance

[¹²⁴I]FIAU-PET/CT is a promising new method for imaging bacterial infections.

[A rapid diagnostic test for plague detects Yersinia pestis F1 antigen in ancient human remains]

A rapid diagnostic dipstick test (RDT) that detects Yersinia pestis F1 antigen has been recently applied on 18 putative plague victims exhumed from four archaeological burial sites in southeastern France dating back to the 16(th), 17(th) and 18(th) centuries. The Y. pestis antigen F1 was detected in 12 ancient samples out of 18 (67%). Negative controls confirmed their negativity (100%). Our results emphasize that the detection threshold of the RDT for plague (0.5 ng/ml) is sufficient for a first retrospective diagnosis of Y. pestis infection in ancient remains, and confirm the high specificity and sensitivity of the assay. Double-blind analyses performed by using two different techniques (RDT and 'suicide PCR') led us to the identification of the Y. pestis F1 antigen and the Y. pestis pla and gplD genes. These data provide clear evidence of the presence of Y. pestis in the examined specimens.

A systematic review of the effectiveness of bone collectors

PURPOSE

Bone collectors are used to harvest bone debris for grafting procedures during implant surgery. The particulate bone debris gathered through filtration has been frequently used in minor regenerative surgical procedures. Nevertheless, the biological potency of such grafts is still unclear. The objective of this study was to systematically review the use of bone collectors in implant dentistry, focusing on the quantity, quality, and bacterial contamination of the bone collected.

MATERIALS AND METHODS

Following the production of a detailed protocol, screening and quality assessment of the literature were conducted in duplicate and independently. The outcome measures that were assessed were: (1) quantity of collected debris, (2) quality of the collected bone debris, and (3) bacterial contamination.

RESULTS

There is a limited amount of information on the nature of bone obtained through collectors. Eleven studies satisfied the inclusion criteria. Bone collectors are able to retain a small amount of bone for minor surgical procedures. The presence of vital bone cells has not been demonstrated routinely, while consistent bacterial contamination has been observed.

DISCUSSION

Bone collected through bone filters appears to be sufficient for small regenerative procedures. Clinicians should bear in mind that presence of bacterial pathogens is always shown with the use of bone collectors. Presurgical chlorhexidine oral rinsing and a strict aspiration protocol must be used to minimize the bacterial contamination of the debris collected.

CONCLUSIONS

Although bone collectors are capable of amassing small amounts of bone, the vitality of this bone could not be consistently demonstrated and the collected debris was always contaminated by bacteria. Therefore, the bone debris amassed in bone collectors is not an ideal grafting material and should be utilized with caution.

Role of hypermutability on bacterial fitness and emergence of resistance in experimental osteomyelitis due to Staphylococcus aureus

This study was designed to investigate the role of hypermutability of Staphylococcus aureus on bacterial fitness and antibiotic resistance in a model of chronic bone infection. An isogenic pair of strains, S. aureus RN4220 and its mutator counterpart inactivated in the mutL gene were used in a rat model of osteomyelitis of the tibia. The effect of the mutator phenotype in the emergence of antibiotic resistance was assessed in rats infected by each strain separately and treated with rifampicin for 5 days. No difference between the two strains was found in bacterial growth in vitro and in bacterial survival in the animal model, indicating no fitness defect in the mutator strain. In competition studies performed in rats coinfected with the two strains at a same ratio and sacrificed at different times from day 3 to day 42 postinoculation, the mutator strain was clearly disadvantaged because it was found in all rats and at all study times at lower counts (P<0.05 from day 14 to day 42). Two of the 16 rats infected by the mutator strain and none of the 14 rats infected by the wild-type strain had acquired rifampicin-resistant mutants (P=0.4). Data suggest that the S. aureus mutator phenotype was associated with a decreased bacterial fitness in vivo and did not confer significant advantage in the acquisition of antibiotic resistance in a model of chronic bone infection.

Survival of Mycobacterium ulcerans at 37 degrees C

Bone infection and metastatic spread in cases of Buruli ulcer imply that Mycobacterium ulcerans is able to survive and multiply at 37 degrees C. This study investigated the survival at 37 degrees C of M. ulcerans isolates from diverse geographical and clinical sources. Although the viability of all isolates decreased after a few days at 37 degrees C, viable bacilli remained after 13 days at 37 degrees C in most instances. African isolates of M. ulcerans were more thermotolerant than isolates from temperate regions. Isolates from skin and bone lesions of the same patients showed no difference in thermotolerance.

Microbiologic and Histologic Assessment of Intentional Bacterial Contamination of Bone Grafts

PURPOSE

The purpose of this study was to investigate methods of removing pathogenic micro-organisms from bone grafts that have been contaminated during surgery.

MATERIALS AND METHODS

Femora were removed from Sprague-Dawley rats and were divided into sections and contaminated in solutions of the bacteria Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. Contaminated bone specimens in each group were immersed in various solutions for specified periods so their antibacterial effects could be evaluated. After these procedures were performed, bone specimens were cultured in nutrient media. Bone structure was evaluated, and the appropriate decontamination method was selected.

RESULTS

Solutions such as povidone-iodine, neomycin, cephazolin sodium, and rifamycin were found to be effective decontaminants. These solutions did not damage the bone structure. Among these solutions, only rifamycin was effective against all bacteria used in this study to contaminate bone grafts.

CONCLUSIONS

Rifamycin seems to be the most suitable agent for the elimination of contamination introduced into bone grafts during surgery.

Osseous Coagulum Collected in Bone Traps: Potential for Bacterial Contamination and Methods for Decontamination

Because of its excellent osteogenic potential, autogenous bone is the preferred grafting material for dental procedures; however, bone collected in osseous coagulum traps is subject to contamination by oral bacteria. This study assessed bacterial contamination of osseous coagulum and tested treatments for reducing contamination. Fifty bone samples from patients undergoing implant osteotomy procedures were collected in osseous coagulum traps, divided into groups of 10, and rinsed with normal saline, 0.12% chlorhexidine, or 50 mg/mL tetracycline. Twenty control samples received no treatment. The bone samples were plated in triplicate on selective and differential media to assay aerobic and anaerobic bacteria and potential bacterial pathogens, including staphylococci, streptococci, enterics, and black-pigmented bacteria (BPB). Inoculations were performed with an Autoplate 4000, and plates were incubated at 37 degrees C either aerobically or in a Coy anaerobic chamber. Bacteria were isolated from all samples. In control samples, the mean colony-forming units (cfu) per milliliter of suspended osseous coagulum was 6.5 x 10(4) +/- 9.6 x 10(4) in aerobic cultures and 4.8 x 10(4) +/- 6.9 x 10(4) in anaerobic cultures. Viridans streptococci were isolated from 46 samples, with a mean of 2.9 x 10(4) +/- 4.1 x 10(4) cfu/mL. Enterics were in 16 samples with cfu ranging from 200 cfu/mL to 3.4 x 10(4) cfu/mL. Mannitol nonfermenting staphylococci were found in one sample at 106 cfu/mL. BPB were not isolated. A Mann-Whitney U test with significance set at P = .05 determined that the only statistically significant reductions in bacterial numbers occurred in tetracycline-treated samples of anaerobic bacteria (5-fold decrease, P = .02) and aerobic bacteria (6-fold decrease, P = .01). Tetracycline treatments effected a 7-fold decrease in streptococci, but the difference was not significant (P = .07). These data indicate significant bacterial contamination of bone collected in osseous coagulum traps and justify further research into methods for eliminating that contamination.

State-of-the-Art Treatment of Coccidioidomycosis Skeletal Infections

Coccidioidomycosis is a fungal infection endemic to the southwestern United States. Typically a respiratory illness, coccidioidomycosis can rarely present as extrapulmonary infection. Skeletal coccidioidomycosis occurs in 20% to 50% of disseminated infections. Skeletal coccidioidomycosis is a chronic and progressive infection that eventually results in bone destruction and loss of function and often involves adjacent structures, such as joints, muscles, and tendons and other soft tissues. Sinus tract formation may occur. This infection may be multifocal. Although radiographs, white blood cell count scans, and other imaging methods identify and define relevant abnormalities, histopathologic examination with culture of the involved bone is the only means to confirm the diagnosis. Serologic testing is adjunctive, and complement fixation titers can be evaluated serially to assess response to treatment. A number of studies addressing the efficacy of various antifungal agents have been performed, and the results of these studies as they pertain to skeletal coccidioidomycosis are summarized herein. Among the various studies, response rates ranged from 23% to 100%, but relapse was common. A combination of medical therapy-often, itraconazole or fluconazole-and surgical débridement is often needed to control skeletal coccidioidomycosis. Early diagnosis and treatment are critical to avoid long-term problems with chronically infected bones and joints. Anatomical issues, diagnostic studies, and data related to treatment of this form of extrapulmonary coccidioidomycosis are reviewed in this article.

Quantitative phylogenetic assessment of microbial communities in diverse environments

The taxonomic composition of environmental communities is an important indicator of their ecology and function. We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA-based approaches depending on the polymerase chain reaction. Mapping marker genes from four diverse environmental data sets onto a reference species phylogeny shows that certain communities evolve faster than others. The method also enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time.