Mycobacterium tuberculosis genetic features associated with pulmonary tuberculosis severity.

OBJECTIVES: Mycobacterium tuberculosis (Mtb) infections result in a wide spectrum of clinical presentations but without proven Mtb genetic determinants. Herein, we hypothesized that the genetic features of Mtb clinical isolates, such as specific polymorphisms or microdiversity, may be linked to tuberculosis (TB) severity. METHODS: A total of 234 patients with pulmonary TB (including 193 drug-susceptible and 14 monoresistant cases diagnosed between 2017 and 2020 and 27 multidrug-resistant cases diagnosed between 2010 and 2020) were stratified according to TB disease severity, and Mtb genetic features were explored using whole genome sequencing, including heterologous single-nucleotide polymorphism (SNP), calling to explore microdiversity. Finally, we performed a structural equation modeling analysis to relate TB severity to Mtb genetic features. RESULTS: The clinical isolates from patients with mild TB carried mutations in genes associated with host-pathogen interaction, whereas those from patients with moderate/severe TB carried mutations associated with regulatory mechanisms. Genome-wide association study identified an SNP in the promoter of the gene coding for the virulence regulator espR, statistically associated with moderate/severe disease. Structural equation modeling and model comparisons indicated that TB severity was associated with the detection of Mtb microdiversity within clinical isolates and to the espR SNP. CONCLUSION: Taken together, these results provide a new insight to better understand TB pathophysiology and could provide a new prognosis tool for pulmonary TB severity.

Accuracy of 6 commercial systems for identifying clinical Aeromonas isolates.

We compared the accuracy of 6 commercial systems for Aeromonas identification by testing 87 clinical isolates in routine conditions, using partial rpoB gene sequencing as the reference standard. The systems were API-20E, API-32GN, the ID-GN card with the Vitek2 system (bioMérieux, Marcy l'Etoile, France), the identification portion of the NFC47 panel (MicroScan Walk/Away system; Siemens Healthcare, Sacramento, CA), ID69 (Phoenix system; BD Diagnostic Systems, Sparks, MD), and GN2 microplates (Omnilog system; Biolog, Hayward, CA), for which 67 (77.1%), 80 (91.9%), 72 (82.7%), 70 (80.5%), 64 (73.5%), and 59 (67.8%) isolates, respectively, were correctly identified at the genus and species level. Confusion with Vibrio affected 6.9% and 16.1% of results obtained with NFC47 and API-20E, respectively. Overall, the accuracy of identification for aeromonads was hampered by outdated databases and taxonomy, weak algorithms, and impractical additional tests. Commercial identification systems should be redesigned to make Aeromonas identification algorithms more robust and to cover infrequent clinical species of this genus.

Identification of the capsular polysaccharides in Staphylococcus aureus clinical isolates by PCR and agglutination tests.

Staphylococcus aureus is a major cause of nosocomial and community-acquired infections. The predominance of two capsular polysaccharides, types 5 and 8, on the surface of clinical isolates led to the development of a conjugate vaccine (StaphVAX) based on capsular polysaccharides types 5 and 8 conjugated to a carrier protein. We have studied the capsular phenotypes and genotypes of 195 isolates representative of all clinical syndromes that encompassed both hospital and community-acquired infections. These isolates were mainly detected in France between January 2001 and December 2004. In this population, most of clinical isolates (87%) expressed either capsular polysaccharide type 5 (42%) or 8 (45%), whereas 13% were nontypeable by the serotyping method with antibodies specific to capsular polysaccharide type 5 or 8. These 26 nontypeable strains were further serotyped and were demonstrated to express the cell wall surface antigen 336, a polyribitol phosphate N-acetylglucosamine, which resembles cell wall teichoic acid. Among methicillin-resistant Staphylococcus aureus (MRSA) strains, we found a predominance of serotype 5 for 64% of strains, whereas MSSA isolates were predominantly capsular serotype 8 (60%). All S. aureus clinical isolates included in the present study have been investigated by PCR method, demonstrating that all isolates carried either the cap5 or the cap8 locus.

Contribution of a broad range polymerase chain reaction to the diagnosis of osteoarticular infections caused by Kingella kingae: description of twenty-four recent pediatric diagnoses.

BACKGROUND: Microbiologic diagnosis of septic arthritis and osteomyelitis in children is hindered by the less than optimal yield of blood and osteoarticular fluid cultures. PATIENTS AND METHODS: All patients admitted to a pediatric unit for osteoarticular infections (OAI) between January 2001 and February 2004 were enrolled in this prospective study. Osteoarticular fluid and biopsy samples that were negative by conventional culture were tested by polymerase chain reaction (PCR) with universal 16S ribosomal DNA primers. RESULTS: We enrolled 171 children. Culture was positive in 64 cases (37.4%), yielding Kingella kingae in 9 cases. The 107 culture-negative specimens were tested by 16S ribosomal DNA PCR. Fifteen samples (14%) were positive, all for Kingella DNA sequences. K. kingae was the second cause of OAI in this population (30.4%), after Staphylococcus aureus (38%). Patients with Kingella infection diagnosed by culture (9 cases) did not differ from those diagnosed by PCR (15 cases) in terms of their clinical characteristics (including prior antibiotic therapy). The characteristics of the 24 children with arthritis (n = 17) or osteomyelitis (n = 7) were similar to those reported elsewhere. Fever (>38 degrees C) and symptom onset shortly before hospitalization (median, 4.5 days) were significantly associated with arthritis. CONCLUSION: Use of molecular diagnostic methods increases the identification of K. kingae in osteoarticular infections.

Specific identification of Staphylococcus aureus by Staphychrom II, a rapid chromogenic staphylocoagulase test.

We compared the performance of Staphychrom II (International Microbio, Signes, France), a rapid (2-h) chromogenic staphylocoagulase test that uses human prothrombin and protease inhibitors, with those of the reference tube coagulase test (TCT) and the latex agglutination test (LAT) Slidex Staph Plus for the rapid identification of S. aureus. Prospective evaluation with 293 fresh clinical isolates yielded sensitivities, specificities, and predictive and negative predictive values of 98.1, 100, 100, and 95.1%, respectively, for the Staphychrom II test; 98.6, 98.7, 99.6, and 96.3%, respectively, for LAT; and 97.6, 98.7, 99.5, and 93.9%, respectively, for TCT. The perfect specificity of the Staphychrom II test was confirmed by testing 193 collection strains selected because of their potential testing pitfalls. The Staphychrom II test was positive for 90% of the 215 S. aureus strains tested after only 1 h of incubation. The Staphychrom II test was as sensitive as the reference TCT and was 100% specific.

Staphylococcus aureus isolates with reduced susceptibility to glycopeptides belong to accessory gene regulator group I or II.

We used multiplex PCR to determine the agr group membership of 18 European glycopeptide heterointermediate and intermediate-resistant Staphylococcus aureus strains. Of the 15 agr group I strains, 13 were resistant and 2 were susceptible to methicillin. The remaining three strains, like the United States and Japanese control strains, belonged to agr group II.