Performance characteristics of genus or species-specific Polymerase Chain Reaction (PCR) for the microbial diagnosis of joint infections: A systematic review and meta-analysis.

Joint infections cause significant morbidity and mortality. Rapid diagnosis enables prompt initiation of appropriate antimicrobial therapy and surgical treatment. We conducted a systematic review and meta-analysis to evaluate the accuracy of genus- or species-specific polymerase chain reaction (PCR) in diagnosing joint infections. The literature databases were searched for articles from January 2010 to December 2022. The meta-analysis using the split component synthesis (SCS) method, included 20 studies with 2,457 adult participants. The pooled sensitivity, specificity, diagnostic odds ratio, and AUC of PCR were 49 % (95 % CI [37.9-60.2]), 95.7 % (95 % CI [91.6-97.8]), 21.32, and 0.82 respectively. Sensitivity was highest for sonicate fluid and lowest for periprosthetic tissue. The mean turnaround time to results was 4.7 hours (SD 1.1). PCR is a favourable option for diagnosing joint infections due to its rapid results, but it has low sensitivity. To enhance diagnostic yield, the test should be used in conjunction with other methods.

Performance of the BioFire Blood Culture Identification 2 panel for the diagnosis of bloodstream infections.

Background: Conventional blood cultures methods are associated with long turnaround times, preventing early treatment optimization in bloodstream infections. The BioFire Blood Culture Identification 2 (BCID2) Panel is a new multiplex PCR applied on positive blood cultures, reducing time to pathogen identification and resistant markers detection. Methods: We conducted a prospective observational study including positive blood cultures from Intensive Care Units and Emergency Departments and performed BCID2 in addition to conventional testing. Concordance between the two methods was assessed and BCID2 performance characteristics were evaluated. Resistance markers detected by BCID2 were confirmed by in-house PCR. Whole genome sequencing was performed in discordant cases. Results: Among 60 monomicrobial blood cultures, BCID2 correctly identified 55/56 (91.7%) on-panel pathogens, showing an overall concordance of 98%. In 4/60 cases BCID2 did not detect any target and these all grew BCID2 off-panel bacteria. Only one discordant case was found. Sensitivity and specificity for Gram-positive bacteria on monomicrobial samples were 100% (95% CI 85.8-100%) and 100% (95% CI 90.3-100%) respectively, while for Gram-negatives 100% (95% CI 87.7-100) and 96.9% (95% CI 83.8-99.9%), respectively. Among two polymicrobial blood cultures, full concordance was observed in one case only. BCID2 identified antimicrobial resistance genes in 6/62 samples, all confirmed by in-house PCR (3 mecA/C S. epidermidis, 3 bla CTX-M E. coli). Estimated time to results gained using BCID2 as compared to conventional testing was 9.69 h (95% CI: 7.85-11.53). Conclusions: BCID2 showed good agreement with conventional methods. Studies to assess its clinical impact are warranted.

Unexpected benefit of COVID-19 hospital restrictions: Reduction in patients isolating with multidrug resistant organisms after restrictions were lifted.

BACKGROUND: During the COVID-19 pandemic, measures to prevent microorganism transmission were implemented across hospitals, including wearing compulsory surgical masks, minimising non-urgent procedures and restricting visitors. Previously, concerns have been raised that MRO-associated deaths could rise during a future pandemic through superimposed bacterial infections, inappropriate antibiotic use and reduced focus on preventing MRO infections. METHODS: In the state of Queensland, Australia with a population of 5 million, only a short first wave of coronavirus cases occurred and restrictions were quickly scaled back. This presented a natural experiment of pre-, during and post-COVID-19 restriction timings to evaluate the effectiveness of heightened prevention measures on multidrug resistant organism (MRO) infections. Patient isolation days and MRO types were collected weekly from routine infection control reports, at a large public hospital, from 28th January 2020 to 24th July 2020. In this interrupted time series design, we employed Poisson mixed effect regression modelling to evaluate the difference in incidence of patient isolation days between time periods. RESULTS: Compared to pre-COVID, patient isolation days reduced during COVID restrictions (incidence rate ratio 0.65, 95%CI: 0.59, 0.70; p < 0.001) and increased again post-COVID restrictions, but did not return to pre-COVID levels (0.87, 95%CI: 0.80, 0.95; p = 0.001). The efficiency of isolating patients improved after COVID-19 with fewer bed closures required. CONCLUSION: Heightened infection control awareness, hand sanitation and mask wearing after COVID-19 restrictions were lifted appear to effectively prevent common hospital-acquired MRO infections.

Clinical Burkholderia pseudomallei isolates from north Queensland carry diverse bimABm genes that are associated with central nervous system disease and are phylogenomically distinct from other Australian strains.

BACKGROUND: Burkholderia pseudomallei is an environmental gram-negative bacterium that causes the disease melioidosis and is endemic in many countries of the Asia-Pacific region. In Australia, the mortality rate remains high at approximately 10%, despite curative antibiotic treatment being available. The bacterium is almost exclusively found in the endemic region, which spans the tropical Northern Territory and North Queensland, with clusters occasionally present in more temperate climates. Despite being endemic to North Queensland, these infections remain understudied compared to those of the Northern Territory. METHODOLOGY/PRINCIPAL FINDINGS: This study aimed to assess the prevalence of central nervous system (CNS) disease associated variant bimABm, identify circulating antimicrobial resistance mutations and genetically distinct strains from Queensland, via comparative genomics. From 76 clinical isolates, we identified the bimABm variant in 20 (26.3%) isolates and in 9 (45%) of the isolates with documented CNS infection (n = 18). Explorative analysis suggests a significant association between isolates carrying the bimABm variant and CNS disease (OR 2.8, 95% CI 1.3-6.0, P = 0.009) compared with isolates carrying the wildtype bimABp. Furthermore, 50% of isolates were identified as novel multi-locus sequence types, while the bimABm variant was more commonly identified in isolates with novel sequence types, compared to those with previously described. Additionally, mutations associated with acquired antimicrobial resistance were only identified in 14.5% of all genomes. CONCLUSIONS/SIGNIFICANCE: The findings of this research have provided clinically relevant genomic data of B. pseudomallei in Queensland and suggest that the bimABm variant may enable risk stratification for the development CNS complications and be a potential therapeutic target.