Identification of bacterial determinants of tuberculosis infection and treatment outcomes: a phenogenomic analysis of clinical strains.

BACKGROUND: Bacterial diversity could contribute to the diversity of tuberculosis infection and treatment outcomes observed clinically, but the biological basis of this association is poorly understood. The aim of this study was to identify associations between phenogenomic variation in Mycobacterium tuberculosis and tuberculosis clinical features. METHODS: We developed a high-throughput platform to define phenotype-genotype relationships in M tuberculosis clinical isolates, which we tested on a set of 158 drug-sensitive M tuberculosis strains sampled from a large tuberculosis clinical study in Ho Chi Minh City, Viet Nam. We tagged the strains with unique genetic barcodes in multiplicate, allowing us to pool the strains for in-vitro competitive fitness assays across 16 host-relevant antibiotic and metabolic conditions. Relative fitness was quantified by deep sequencing, enumerating output barcode read counts relative to input normalised values. We performed a genome-wide association study to identify phylogenetically linked and monogenic mutations associated with the in-vitro fitness phenotypes. These genetic determinants were further associated with relevant clinical outcomes (cavitary disease and treatment failure) by calculating odds ratios (ORs) with binomial logistic regressions. We also assessed the population-level transmission of strains associated with cavitary disease and treatment failure using terminal branch length analysis of the phylogenetic data. FINDINGS: M tuberculosis clinical strains had diverse growth characteristics in host-like metabolic and drug conditions. These fitness phenotypes were highly heritable, and we identified monogenic and phylogenetically linked variants associated with the fitness phenotypes. These data enabled us to define two genetic features that were associated with clinical outcomes. First, mutations in Rv1339, a phosphodiesterase, which were associated with slow growth in glycerol, were further associated with treatment failure (OR 5·34, 95% CI 1·21-23·58, p=0·027). Second, we identified a phenotypically distinct slow-growing subclade of lineage 1 strains (L1.1.1.1) that was associated with cavitary disease (OR 2·49, 1·11-5·59, p=0·027) and treatment failure (OR 4·76, 1·53-14·78, p=0·0069), and which had shorter terminal branch lengths on the phylogenetic tree, suggesting increased transmission. INTERPRETATION: Slow growth under various antibiotic and metabolic conditions served as in-vitro intermediate phenotypes underlying the association between M tuberculosis monogenic and phylogenetically linked mutations and outcomes such as cavitary disease, treatment failure, and transmission potential. These data suggest that M tuberculosis growth regulation is an adaptive advantage for bacterial success in human populations, at least in some circumstances. These data further suggest markers for the underlying bacterial processes that contribute to these clinical outcomes. FUNDING: National Health and Medical Research Council/A∗STAR, National Institutes of Allergy and Infectious Diseases, National Institute of Child Health and Human Development, and the Wellcome Trust Fellowship in Public Health and Tropical Medicine.

Performance of 4Kscore as a Reflex Test to Prostate-specific Antigen in the GÖTEBORG-2 Prostate Cancer Screening Trial.

BACKGROUND AND OBJECTIVE: We investigated whether adding 4Kscore as a reflex test to prostate-specific antigen (PSA) could improve the screening algorithm for prostate cancer (PC). METHODS: In the GÖTEBORG-2 PC screening trial, 38 000men (50-60 yr) were invited to PSA testing and, if elevated, followed by magnetic resonance imaging (MRI). For 571 men with PSA ≥3.0 ng/ml and evaluable outcomes, 4Kscore was calculated. The performance using a prespecified 4Kscore cutoff of 7.5% was evaluated. KEY FINDINGS AND LIMITATIONS: The area under the curve for 4Kscore to identify intermediate- and high-risk PC was 0.84 (95% confidence interval 0.79-0.89), and the positive predictive value, and negative predictive value were 15% (0.12-0.20) and 99% (97-100%), respectively. Of the 54 men diagnosed with intermediate- or high-grade PC, two had a 4Kscore cutoff below 7.5%, both with organ-confined intermediate-risk PC. Per 1000 men with elevated PSA, adding 4Kscore would have resulted in avoidance of MRI for 408 (41%) men, biopsies for 95 (28% reduction) men, and diagnosis of 23 low-grade cancers (23% reduction) while delaying the diagnosis of four men with intermediate-grade cancers (4%). CONCLUSIONS AND CLINICAL IMPLICATIONS: Including 4Kscore as a reflex test for men with elevated PSA reduces the need for MRI and biopsy markedly, and results in less overdiagnosis of low-grade PC at the cost of delaying the diagnosis of intermediate-grade PC in a few men. These results add further evidence for including new blood-based biomarkers in addition to PSA to improve the harm and benefit ratio of PC screening and reduce the need for resource-demanding MRI and biopsies. PATIENT SUMMARY: In this study, 4Kscore, a blood-based biomarker, as a reflex test for men with elevated prostate-specific antigen (PSA), reduces the need for magnetic resonance imaging and biopsy. These results support the inclusion of new blood-based biomarkers in addition to PSA.

Provider Perceptions of an Electronic Health Record Prostate Cancer Screening Tool.

OBJECTIVES: We conducted a focus group to assess the attitudes of primary care physicians (PCPs) toward prostate-specific antigen (PSA)-screening algorithms, perceptions of using decision support tools, and features that would make such tools feasible to implement. METHODS: A multidisciplinary team (primary care, urology, behavioral sciences, bioinformatics) developed the decision support tool that was presented to a focus group of 10 PCPs who also filled out a survey. Notes and audio-recorded transcripts were analyzed using Thematic Content Analysis. RESULTS: The survey showed that PCPs followed different guidelines. In total, 7/10 PCPs agreed that engaging in shared decision-making about PSA screening was burdensome. The majority (9/10) had never used a decision aid for PSA screening. Although 70% of PCPs felt confident about their ability to discuss PSA screening, 90% still felt a need for a provider-facing platform to assist in these discussions. Three major themes emerged: (1) confirmatory reactions regarding the importance, innovation, and unmet need for a decision support tool embedded in the electronic health record; (2) issues around implementation and application of the tool in clinic workflow and PCPs' own clinical bias; and (3) attitudes/reflections regarding discrepant recommendations from various guideline groups that cause confusion. CONCLUSION: There was overwhelmingly positive support for the need for a provider-facing decision support tool to assist with PSA-screening decisions in the primary care setting. PCPs appreciated that the tool would allow flexibility for clinical judgment and documentation of shared decision-making. Incorporation of suggestions from this focus group into a second version of the tool will be used in subsequent pilot testing.

A Provider-Facing Decision Support Tool for Prostate Cancer Screening in Primary Care: A Pilot Study.

OBJECTIVES: Our objective was to pilot test an electronic health record-embedded decision support tool to facilitate prostate-specific antigen (PSA) screening discussions in the primary care setting. METHODS: We pilot-tested a novel decision support tool that was used by 10 primary care physicians (PCPs) for 6 months, followed by a survey. The tool comprised (1) a risk-stratified algorithm, (2) a tool for facilitating shared decision-making (Simple Schema), (3) three best practice advisories (BPAs: <45, 45-75, and >75 years), and (4) a health maintenance module for scheduling automated reminders about PSA rescreening. RESULTS: All PCPs found the tool feasible, acceptable, and clear to use. Eight out of ten PCPs reported that the tool made PSA screening conversations somewhat or much easier. Before using the tool, 70% of PCPs felt confident in their ability to discuss PSA screening with their patient, and this improved to 100% after the tool was used by PCPs for 6 months. PCPs found the BPAs for eligible (45-75 years) and older men (>75 years) more useful than the BPA for younger men (<45 years). Among the 10 PCPs, 60% found the Simple Schema to be very useful, and 50% found the health maintenance module to be extremely or very useful. Most PCPs reported the components of the tool to be at least somewhat useful, with 10% finding them to be very burdensome. CONCLUSION: We demonstrated the feasibility and acceptability of the tool, which is notable given the marked low acceptance of existing tools. All PCPs reported that they would consider continuing to use the tool in their clinic and were likely or very likely to recommend the tool to a colleague.

Transfers and anesthesia-related postoperative outcomes after 3361 same-day cancer surgeries at a freestanding surgery center: An observational retrospective study.

BACKGROUND AND OBJECTIVES: Expanding outpatient surgery to the increasing number of procedures and patient populations warrants continuous evaluation of postoperative outcomes to ensure the best care and safety. We describe adverse postoperative outcomes and transfer rates related to anesthesia in a large sample of patients who underwent same-day cancer surgery at a freestanding ambulatory surgery center. METHODS: Between January 2017 and June 2021, 3361 cancer surgeries, including breast and plastic, head and neck, gynecology, and urology, were performed. The surgeries were indicated for diagnosis, staging, and/or treatment. We report the incidence of transfers and adverse postoperative outcomes related to anesthesia. RESULTS: Breast and plastic surgeries were the most common (1771, 53%), followed by urology (1052, 31%), gynecology (410, 12%), and head and neck surgeries (128, 4%). Based on patients' first procedure, comorbidity levels were highest for urology (75% American Society of Anesthesiologists physical status score 3, 1.7% score 4) and lowest for breast surgeries (31% score 3, 0.2% score 4). Most gynecology surgeries used general anesthesia (97.6%), whereas breast surgeries used the least (38%). A total of seven patients (0.2%; 95% CI: 0.08%-0.4%) were immediately transferred to an outside hospital; four due to anesthesia-related reasons. Only 7 (0.2%) patients needed additional postoperative care related to anesthesia-related adverse events, specifically cardiac events (4), difficult intubations (2), desaturation (1), and agitation, nausea, and headache (1). CONCLUSIONS: The incidence of anesthesia-related adverse postoperative outcomes is low in cancer patients undergoing outpatient surgeries at our freestanding ambulatory surgery center. This suggests that carefully selected cancer patients, including patients with metastatic cancer, can undergo anesthesia for same-day surgery, making cancer care accessible locally and reducing stress associated with travel for treatment. More research investigating complication rates related to surgery and to cancer disease trajectory are needed to establish a complete evaluation of safety for outpatient cancer surgery.

Electronic Patient-Reported Symptoms After Ambulatory Cancer Surgery.

Importance: Complex cancer procedures are now performed in the ambulatory surgery setting. Remote symptom monitoring (RSM) with electronic patient-reported outcomes (ePROs) can identify patients at risk for acute hospital encounters. Defining normal recovery is needed to set patient expectations and optimize clinical team responses to manage evolving problems in real time. Objective: To describe the patterns of postoperative recovery among patients undergoing ambulatory cancer surgery with RSM using an ePRO platform-the Recovery Tracker. Design, Setting, and Participants: In this retrospective cohort study, patients who underwent 1 of 5 of the most common procedures (prostatectomy, nephrectomy, mastectomy, hysterectomy, or thyroidectomy) at the Josie Robertson Surgery Center at Memorial Sloan Kettering Cancer Center from September 2016 to June 2022. Patients completed the Recovery Tracker, a brief ePRO platform assessing symptoms for 10 days after surgery. Data were analyzed from September 2022 to May 2023. Main Outcomes and Measures: Symptom severity and interference were estimated by postoperative day and procedure. Results: A total of 12 433 patients were assigned 110 936 surveys. Of these patients, 7874 (63%) were female, and the median (IQR) age at surgery was 57 (47-65) years. The survey response rate was 87% (10 814 patients responding to at least 1 of 10 daily surveys). Among patients who submitted at least 1 survey, the median (IQR) number of surveys submitted was 7 (4-8), and each assessment took a median (IQR) of 1.7 (1.2-2.5) minutes to complete. Symptom burden was modest in this population, with the highest severity on postoperative days 1 to 3. Pain was moderate initially and steadily improved. Fatigue was reported by 6120 patients (57%) but was rarely severe. Maximum pain and fatigue responses (very severe) were reported by 324 of 10 814 patients (3%) and 106 of 10 814 patients (1%), respectively. The maximum pain severity (severe or very severe) was highest after nephrectomy (92 of 332 [28%]), followed by mastectomy with reconstruction (817 of 3322 [25%]) and prostatectomy (744 of 3543 [21%]). Nausea (occasionally, frequently, or almost constantly) was common and experienced on multiple days by 1485 of 9300 patients (16%), but vomiting was less common (139 of 10 812 [1%]). Temperature higher than 38 °C was reported by 740 of 10 812 (7%). Severe or very severe shortness of breath was reported by 125 of 10 813 (1%). Conclusions and Relevance: Defining detailed postoperative symptom burden through this analysis provides valuable data to inform further implementation and maintenance of RSM programs in surgical oncology patients. These data can enhance patient education, set expectations, and support research to allow iterative improvement of clinical care based on the patient-reported experience after discharge.

Remote Symptom Monitoring with Clinical Alerts Following Mastectomy: Do Early Symptoms Predict 30-Day Surgical Complications.

BACKGROUND: Electronic patient-reported outcome measures (ePROMs) for real-time remote symptom monitoring facilitate early recognition of postoperative complications. We sought to determine whether remote, electronic, patient-reported symptom-monitoring with Recovery Tracker predicts 30-day readmission or reoperation in outpatient mastectomy patients. METHODS: We conducted a retrospective review of breast cancer patients who underwent outpatient (< 24-h stay) mastectomy with or without reconstruction from April 2017 to January 2022 and who received the Recovery Tracker on Days 1-10 postoperatively. Of 5,130 patients, 3,888 met the inclusion criteria (2,880 mastectomy with immediate reconstruction and 1,008 mastectomy only). We focused on symptoms concerning for surgical complications and assessed if symptoms reaching prespecified alert levels-prompting a nursing call-predicted risk of 30-day readmission or reoperation. RESULTS: Daily Recovery Tracker response rates ranged from 45% to 70%. Overall, 1,461 of 3,888 patients (38%) triggered at least one alert. Most red (urgent) alerts were triggered by pain and fever; most yellow (less urgent) alerts were triggered by wound redness and pain severity. The 30-day readmission and reoperation rates were low at 3.8% and 2.4%, respectively. There was no statistically significant association between symptom alerts and 30-day reoperation or readmission, and a clinically relevant increase in risk can be excluded (odds ratio 1.08; 95% confidence interval 0.8-1.46; p = 0.6). CONCLUSIONS: Breast cancer patients undergoing mastectomy with or without reconstruction in the ambulatory setting have a low burden of concerning symptoms, even in the first few days after surgery. Patients can be reassured that symptoms that do present resolve quickly thereafter.

Paravertebral and erector spinae plane blocks decrease length of stay compared with local infiltration analgesia in autologous breast reconstruction.

BACKGROUND: Autologous breast reconstruction is associated with significant pain impeding early recovery. Our objective was to evaluate the impact of replacing surgeon-administered local infiltration with preoperative paravertebral (PVB) and erector spinae plane (ESP) blocks for latissimus dorsi myocutaneous flap reconstruction. METHODS: Patients who underwent mastectomy with latissimus flap reconstruction from 2018 to 2022 were included in three groups: local infiltration, PVB, and ESP blocks. Block effect on postoperative length of stay (LOS) and the association between block status and pain, opioid consumption, time to first analgesic, and postoperative antiemetic administration were assessed. RESULTS: 122 patients met the inclusion criteria for this retrospective cohort study: no block (n=72), PVB (n=26), and ESP (n=24). On adjusted analysis, those who received a PVB block had a 20-hour shorter postoperative stay (95% CI 11 to 30; p<0.001); those who received ESP had a 24-hour (95% CI 15 to 34; p<0.001) shorter postoperative stay compared with the no block group, respectively. Using either block was associated with a reduction in intraoperative opioids (23 morphine milligram equivalents (MME)), 95% CI 14 to 31, p<0.001; ESP versus no block: 23 MME, 95% CI 14 to 32, p<0.001). CONCLUSIONS: Replacing surgical infiltration with PVB and ESP blocks for autologous breast reconstruction reduces LOS. The comparable reduction in LOS suggests that ESP may be a viable alternative to PVB in patients undergoing latissimus flap breast reconstruction following mastectomy. Further research should investigate whether ESP or PVB have better patient outcomes in complex breast reconstruction.

Ongoing evolution of the Mycobacterium tuberculosis lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressure.

The bacterial determinants that facilitate Mycobacterium tuberculosis (Mtb) adaptation to the human host environment are poorly characterized. We have sought to decipher the pressures facing the bacterium in vivo by assessing Mtb genes that are under positive selection in clinical isolates. One of the strongest targets of selection in the Mtb genome is lldD2, which encodes a quinone-dependent L-lactate dehydrogenase (LldD2) that catalyzes the oxidation of lactate to pyruvate. Lactate accumulation is a salient feature of the intracellular environment during infection and lldD2 is essential for Mtb growth in macrophages. We determined the extent of lldD2 variation across a set of global clinical isolates and defined how prevalent mutations modulate Mtb fitness. We show the stepwise nature of lldD2 evolution that occurs as a result of ongoing lldD2 selection in the background of ancestral lineage-defining mutations and demonstrate that the genetic evolution of lldD2 additively augments Mtb growth in lactate. Using quinone-dependent antibiotic susceptibility as a functional reporter, we also find that the evolved lldD2 mutations functionally increase the quinone-dependent activity of LldD2. Using 13C-lactate metabolic flux tracing, we find that lldD2 is necessary for robust incorporation of lactate into central carbon metabolism. In the absence of lldD2, label preferentially accumulates in dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P) and is associated with a discernible growth defect, providing experimental evidence for accrued lactate toxicity via the deleterious buildup of sugar phosphates. The evolved lldD2 variants increase lactate incorporation to pyruvate while altering triose phosphate flux, suggesting both an anaplerotic and detoxification benefit to lldD2 evolution. We further show that the mycobacterial cell is transcriptionally sensitive to the changes associated with altered lldD2 activity which affect the expression of genes involved in cell wall lipid metabolism and the ESX- 1 virulence system. Together, these data illustrate a multifunctional role of LldD2 that provides context for the selective advantage of lldD2 mutations in adapting to host stress.

Amount of Gleason Pattern 3 Is Not Predictive of Risk in Grade Group 2-4 Prostate Cancer.

We investigated whether total Gleason pattern 3 or the proportion of Gleason pattern 4 on biopsy is a significant predictor of adverse pathology. Our findings suggest that quantifying the amount rather than the proportion of Gleason pattern 4 would improve grade group assignment for decision-making in localized prostate cancer.

MRI-Targeted Prostate Biopsy Introduces Grade Inflation and Overtreatment.

Purpose: The use of MRI-targeted biopsies has led to lower detection of Gleason Grade Group 1 (GG1) prostate cancer and increased detection of GG2 disease. Although this finding is generally attributed to improved sensitivity and specificity of MRI for aggressive cancers, it might also be explained by grade inflation. Our objective was to determine the likelihood of definitive treatment and risk of post-treatment recurrence for patients with GG2 cancer diagnosed using targeted biopsies relative to men with GG1 cancer diagnosed using systematic biopsies. Methods: We performed a retrospective study on a large tertiary centre registry (HUS Acamedic Datalake) to retrieve data on prostate cancer diagnosis, treatment, and cancer recurrence. We included patients with either GG1 with systematic biopsies (3317 men) or GG2 with targeted biopsies (554 men) from 1993 to 2019. We assessed the risk of curative treatment and recurrence after treatment. Kaplan-Meier survival curves were computed to assess treatment- and recurrence-free survival. Cox proportional hazards regression analysis was performed to assess the risk of posttreatment recurrence. Results: Patients with systematic biopsy detected GG1 cancer had a significantly longer median time-to-treatment (31 months) than those with targeted biopsy detected GG2 cancer (4 months, p<0.0001). The risk of recurrence after curative treatment was similar between groups with the upper bound of 95% CI, excluding an important difference (HR: 0.94, 95% CI [0.71-1.25], p=0.7). Conclusion: GG2 cancers detected by MRI-targeted biopsy are treated more aggressively than GG1 cancers detected by systematic biopsy, despite having similar oncologic risk. To prevent further overtreatment related to the MRI pathway, treatment guidelines from the pre-MRI era need to be updated to consider changes in the diagnostic pathway.

Do Phosphodiesterase Type 5 Inhibitors Increase the Risk of Biochemical Recurrence After Radical Prostatectomy?

PURPOSE: There have been conflicting studies on the association between phosphodiesterase type 5 inhibitor (PDE5i) use and biochemical recurrence (BCR) following radical prostatectomy (RP). Our aim was to determine whether PDE5i drug exposure after RP increases the risk of BCR in patients undergoing RP. MATERIALS AND METHODS: An institutional database of prostate cancer patients treated between January 2009 and December 2020 was reviewed. BCR was defined as 2 PSA measurements greater than 0.1 ng/mL. PDE5i exposure was defined using a 0 to 3 scale, with 0 representing never use, 1 sometimes use, 2 regularly use, and 3 routinely use. The risk of BCR with any PDE5i exposure, the quantity of exposure, and the duration of PDE5i exposure were assessed by multivariable Cox proportional hazards models. RESULTS: The sample size included 4630 patients to be analyzed, with 776 patients having BCR. The median follow-up for patients without BCR was 27 (IQR 12, 49) months. Eighty-nine percent reported taking a PDE5i at any time during the first 12 months after RP, and 60% reported doing so for 6 or more months during the year after RP. There was no evidence of an increase in the risk of BCR associated with any PDE5i use (HR 1.05, 95% CI 0.84, 1.31, P = .7) or duration of PDE5i use in the first year (HR 0.98 per 1 month duration, 95% CI 0.96, 1.00, P = .055). Baseline oncologic risk was lower in patients using PDE5i, but differences between groups were small, suggesting that residual confounding is unlikely to obscure any causal association with BCR. CONCLUSIONS: Prescription of PDE5i to men after RP can be based exclusively on quality of life considerations. Patients receiving PDE5is can be reassured that their use does not increase the risk of BCR.

Transperineal Versus Transrectal Magnetic Resonance Imaging-targeted and Systematic Prostate Biopsy to Prevent Infectious Complications: The PREVENT Randomized Trial.

BACKGROUND AND OBJECTIVE: The transrectal biopsy approach is traditionally used to detect prostate cancer. An alternative transperineal approach is historically performed under general anesthesia, but recent advances enable transperineal biopsy to be performed under local anesthesia. We sought to compare infectious complications of transperineal biopsy without antibiotic prophylaxis versus transrectal biopsy with targeted prophylaxis. METHODS: We assigned biopsy-naïve participants to undergo transperineal biopsy without antibiotic prophylaxis versus transrectal biopsy with targeted prophylaxis (rectal culture screening for fluoroquinolone-resistant bacteria and antibiotic targeting to culture and sensitivity results) through a multicenter, randomized trial. The primary outcome was post-biopsy infection captured by a prospective medical review and patient report on a 7-d survey. The secondary outcomes included cancer detection, noninfectious complications, and a numerical rating scale (0-10) for biopsy-related pain and discomfort during and 7-d after biopsy. KEY FINDINGS AND LIMITATIONS: A total of 658 participants were randomized, with zero transperineal versus four (1.4%) transrectal biopsy infections (difference -1.4%; 95% confidence interval [CI] -3.2%, 0.3%; p = 0.059). The rates of other complications were very low and similar. Importantly, detection of clinically significant cancer was similar (53% transperineal vs 50% transrectal, adjusted difference 2.0%; 95% CI -6.0, 10). Participants in the transperineal arm experienced worse periprocedural pain (0.6 adjusted difference [0-10 scale], 95% CI 0.2, 0.9), but the effect was small and resolved by 7-d. CONCLUSIONS AND CLINICAL IMPLICATIONS: Office-based transperineal biopsy is tolerable, does not compromise cancer detection, and did not result in infectious complications. Transrectal biopsy with targeted prophylaxis achieved similar infection rates, but requires rectal cultures and careful attention to antibiotic selection and administration. Consideration of these factors and antibiotic stewardship should guide clinical decision-making. PATIENT SUMMARY: In this multicenter randomized trial, we compare prostate biopsy infectious complications for the transperineal versus transrectal approach. The absence of infectious complications with transperineal biopsy without the use of preventative antibiotics is noteworthy, but not significantly different from transrectal biopsy with targeted antibiotic prophylaxis.