Journal of Clinical Microbiology最新文献

Non-tuberculous mycobacterial (NTM) skin infections present diagnostic and therapeutic challenges in resource-limited primary care settings. This retrospective study evaluated the diagnosis and treatment of NTM skin infections at a primary care hospital in Shouguang City, a coastal region of China with high-risk occupational exposure to aquatic environments, from 2021 to 2022. We analyzed 144 patients, using real-time PCR on formalin-fixed paraffin-embedded (FFPE) tissue samples to validate empirical diagnoses based on clinical symptoms, exposure history, and histopathology. Our results demonstrated a high concordance (79.17%) between empirical and molecular diagnoses, confirming the reliability of the primary care hospital's diagnostic approach. Real-time PCR successfully identified specific NTM species in a subset of cases, with Mycobacterium marinum and Mycobacteroides abscessus being the most prevalent. Empirical treatment with combination antibiotics (primarily clarithromycin and rifampicin) was highly effective, achieving a cure rate of 90.97%. This study highlights the effectiveness of integrated clinical-histopathological assessment for managing NTM infections in resource-limited settings and underscores the value of molecular techniques such as PCR in enhancing diagnostic precision and facilitating retrospective research using archived FFPE samples.

Importance: This study addresses a critical gap in managing non-tuberculous mycobacterial (NTM) skin infections in resource-limited primary care settings, with particular relevance to coastal regions like Shouguang, where occupational exposure to marine environments elevates infection risk. By validating empirical diagnosis through molecular testing, we demonstrate that integrated clinical-histopathological assessment is a reliable method for identifying NTM infections where advanced diagnostics are unavailable. Our adaptation of real-time PCR to archived FFPE tissues provides a feasible model for retrospective species identification and research, overcoming key resource constraints. The high documented cure rate with clarithromycin-rifampicin regimens provides practical treatment benchmarks for regions with similar epidemiological profiles. These findings offer immediate clinical value by: (i) reinforcing the reliability of empirical diagnosis in resource-limited contexts, (ii) establishing a practical pathway for molecular confirmation using stored samples, and (iii) validating effective treatment protocols for high-risk occupational groups. As NTM incidence increases globally, this work equips primary care systems with evidence-based strategies to improve diagnostic accuracy and patient outcomes in settings with high marine exposure while simultaneously enabling future research through the utilization of existing biospecimen repositories.

Population-based HIV Impact Assessment surveys were conducted in 14 countries to measure HIV prevalence, incidence, and viral load suppression in children aged 0-14 years and adults aged ≥15 years. We examined the performance of rapid HIV testing algorithms in multiple countries. Survey participants received an HIV diagnosis based on two serial tests in Cameroon, Côte d'Ivoire, Eswatini, Haiti, Kenya, Lesotho, Malawi, Mozambique, Tanzania, and Zambia. Whereas in Ethiopia, Kenya, Namibia, Uganda, and Zimbabwe, diagnosis was based on a tie-breaker algorithm. Testers received intensive training on specimen collection, testing, and results reporting. HIV-positive and indeterminate results were confirmed by Geenius HIV-1/2 test (Bio-Rad). Pooled test 1 and 2 positive concordance, test 2 and 3 negative concordance, and the positive predictive value (PPV) of the algorithm were calculated. A total of 312,069 participants aged ≥18 months (except for Eswatini, Mozambique, and Uganda, where only adults aged 15+ years were included) were tested by either the two-test (n = 243,311) or tie-breaker (n = 98,757) algorithm for diagnosis. The combined test 1 and 2 positive concordance and PPV were 93.8% and 99.4%, respectively, for countries with a two-test algorithm. Similarly, test 1 and 2 positive concordance, test 2 and 3 negative concordance, and PPV were 87.5%, 84.4%, and 98.8%, respectively, for the tie-breaker algorithm. The PPV ranged from 94.2% to 99.9%, with higher PPV in high burden countries. The HIV testing algorithms performed with high accuracy, with PPV reaching 99% or higher. Adoption of continuous quality improvement is essential to ensure accuracy of HIV diagnosis in service delivery settings.

Importance: HIV diagnostic testing in most African countries follows national algorithms that typically use two tests, with or without a tie-breaker. We assessed the accuracy of these algorithms using data from population-based surveys in 14 sub-Saharan African countries, where all HIV-positive results were further confirmed with the Geenius HIV-1/2 supplemental assay. Our findings show that inter-test concordance and positive predictive values (PPVs) varied by HIV prevalence, with higher PPVs observed in higher-prevalence settings. Overall, the PPV of HIV diagnosis was close to 99%, indicating that two-test algorithms can provide highly accurate results when testing is performed with strict adherence to quality standards and tester competency. These results underscore the importance of quality assurance (QA) and suggest that countries with lower HIV prevalence may benefit from adopting a three-test algorithm. However, such changes should be accompanied by careful attention to logistics, procurement, training, record keeping, and other QA measures.

The incidence of syphilis has risen dramatically in many regions despite the availability of affordable facility-based testing and curative treatment. The recent approval of over-the-counter syphilis self-tests (SSTs) represents an important advance for expanding diagnostic access and disease control and prevention. Evidence demonstrates that SSTs are accurate, usable, and acceptable. However, as with HIV and COVID-19 self-testing, implementation challenges remain, including ensuring equitable access, supporting vulnerable groups, securing linkage to care, and maintaining quality assurance.

Knowledge of novel and revised bacterial taxonomy facilitates routine operations in the medical microbiology laboratory and communication with important stakeholders. Notable new gram-positive taxa accepted in 2024 include the clinically significant Staphylococcus brunensis sp. nov., as well as Streptococcus suis subsp. hashimotonensis subsp. nov., which can be delineated from other Streptococcus suis subsp. by possession of the Lancefield group A antigen. Four novel Enterobacterales species are discussed, plus a novel eighth family Gallaecimonadaceae. One of these, Providencia huashanensis sp. nov. is clinically significant and harbors multiple genetic determinants that encode antimicrobial resistance mechanisms. Stenotrophomonas forensis sp. nov., derived from specimen transport medium, was determined to be a distinct component within the Stenotrophomonas maltophilia complex. Bartonella tamiae sp. nov. has become officially recognized as the agent of the first culture-confirmed bartonelloses in Thailand. Significant taxonomic revisions include the return of Chlamydophila caviae to the Chlamydia genus, creation of the novel Metaclostridioides genus for Clostridioides mangenotii, and reclassification of two Kocuria spp. into two subspecies of Kocuria rosea. Clinical updates are provided for 13 past Journal of Clinical Microbiology taxonomic compendium entries for which extensive clinical data were not previously available. These include potential clinical significance for non-vaginalis species of the Gardnerella genus and for Pandoraea commovens in a non-cystic fibrosis setting.

Bronchoalveolar lavage fluid (BAL) is commonly obtained for diagnosing invasive mold disease (IMD) in immunocompromised patients. This study investigated the accuracy, turnaround time, and clinical actionability of mold polymerase chain reaction (PCR) on BAL. All BAL tested with mold PCR and fungal culture during the study period were included in this study. The mold PCR detected Aspergillus species, Mucorales agents, Fusarium species, and Scedosporium spp./Lomentospora prolificans. Cases were classified per the EORTC/MSGERC definitions. The sensitivity, specificity, turnaround time, and actionability of the mold PCR were measured. Out of 1,958 BAL samples tested, mold PCR was positive in 160 (8.2%) and culture in 75 (3.8%). Mold PCR was most commonly positive for Aspergillus species (77.5%), followed by Scedosporium spp./L. prolificans (20.0%), Mucorales agents (8.3%), and Fusarium species (1.2%). The sensitivity and specificity of the mold PCR using culture as the reference standard were 92.0% (69/75, 95% CI 83.4-97.1) and 95.2% (1794/1883, 95% CI 94.2-96.2), respectively. In 32 proven IMD cases, the sensitivity of mold PCR panel and culture was 90.6% (29/32, 95% CI 74.9-98.1) and 56.3% (18/32, 95% CI 37.7-73.7) (P < 0.001), respectively. The median time to positivity for mold PCR and culture was 1 day (interquartile range [IQR] 1-2) and 3 days (IQR 2-4) (P < 0.001), respectively. Among positive mold PCR results that provided a new finding (n = 91), 65.9% were clinically actionable. Mold PCR performed on BAL was more sensitive and rapid compared with fungal culture, and positive results were highly actionable.IMPORTANCEInvasive mold disease (IMD) in immunocompromised patients is associated with high morbidity and mortality. Bronchoalveolar lavage fluid (BAL) is commonly obtained for diagnosing pulmonary IMD, but rapid and accurate diagnosis of IMD is challenging with conventional diagnostics. The aim of this study was to investigate the accuracy, turnaround time, and clinical actionability of a BAL mold PCR assay detecting the five most common genera causing IMD. The BAL mold PCR was highly sensitive and specific compared to BAL fungal culture used as the reference method. In patients with proven pulmonary IMD, the BAL mold PCR was highly sensitive and significantly more sensitive compared with fungal culture. The BAL mold PCR was significantly more rapid than fungal culture, and the results were highly actionable. Overall, findings indicate the BAL mold PCR is highly accurate, rapid, and actionable for diagnosis of pulmonary IMD.