TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.

MOTIVATION: Whole-genome sequencing (WGS) is increasingly used to aid the understanding of Mycobacterium tuberculosis (MTB) transmission. The epidemiological analysis of tuberculosis based on the WGS technique requires a diverse collection of bioinformatics tools. Effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. RESULTS: Here, we present TransFlow (Transmission Workflow), a user-friendly, fast, efficient and comprehensive WGS-based transmission analysis pipeline. TransFlow combines some state-of-the-art tools to take transmission analysis from raw sequencing data, through quality control, sequence alignment and variant calling, into downstream transmission clustering, transmission network reconstruction and transmission risk factor inference, together with summary statistics and data visualization in a summary report. TransFlow relies on Snakemake and Conda to resolve dependencies among consecutive processing steps and can be easily adapted to any computation environment. AVAILABILITY AND IMPLEMENTATION: TransFlow is free available at https://github.com/cvn001/transflow. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Emergence and evolution of drug-resistant Mycobacterium tuberculosis in eastern China: A six-year prospective study.

Understanding the emergence and evolution of drug resistance can inform public health intervention to combat tuberculosis (TB). In this prospective molecular epidemiological surveillance study from 2015 to 2021 in eastern China, we prospectively collected whole-genome sequencing and epidemiological data on TB patients. We dissect the ordering of drug resistance mutation acquisition for nine commonly used anti-TB drugs, and we found that the katG S315T mutation first appeared around 1959, followed by rpoB S450L (1969), rpsL L43A (1972), embB M306V (1978), rrs 1401 (1981), fabG1 (1982), pncA (1985) and folC (1988) mutations. GyrA gene mutations appeared after the year of 2000. We observed that the first expansion of Mycobacterium tuberculosis (M.tb) resistance population among eastern China appeared after the introduction of isoniazid, streptomycin and para-amino salicylic acid, and the second expansion after the ethambutol, rifampicin, pyrazinamide, ethionamide and aminoglycosides. We speculate these two expansions are linked with population shift historically. By geospatial analysis, we found drug-resistant isolates migrated within eastern China. With epidemiological data of clonal strains, we observed some strains can evolve continuously in individuals and transmit readily in a population. In conclusion, this study mirrored the emergence and evolution of drug-resistant M.tb in eastern China were linked to the sequence and timing of introduction of anti-TB drugs, and multiple factors may contribute to the resistant population enlarged. To resolve the epidemic of drug-resistant TB, it requires applying anti-TB drugs carefully and/or identifying resistant patients timely to prevent them from developing high-level resistance and transmitting to others.

Long-Term Increases in Mental Disorder Diagnoses After Invasive Mechanical Ventilation for Severe Childhood Respiratory Disease: A Propensity Matched Observational Cohort Study.

OBJECTIVES: To evaluate neurodevelopmental and mental disorders after PICU hospitalization in children requiring invasive mechanical ventilation for severe respiratory illness. DESIGN: Retrospective longitudinal observational cohort. SETTING: Texas Medicaid Analytic eXtract data from 1999 to 2012. PATIENTS: Texas Medicaid-enrolled children greater than or equal to 28 days old to less than 18 years old hospitalized for a primary respiratory illness, without major chronic conditions predictive of abnormal neurodevelopment. INTERVENTIONS: We examined rates of International Classification of Diseases, 9th revision-coded mental disorder diagnoses and psychotropic medication use following discharge among children requiring invasive mechanical ventilation for severe respiratory illness, compared with general hospital patients propensity score matched on sociodemographic and clinical characteristics prior to admission. Children admitted to the PICU for respiratory illness not necessitating invasive mechanical ventilation were also compared with matched general hospital patients as a negative control exposure. MEASUREMENTS AND MAIN RESULTS: Of 115,335 eligible children, 1,351 required invasive mechanical ventilation and were matched to 6,755 general hospital patients. Compared with general hospital patients, children requiring invasive mechanical ventilation had increased mental disorder diagnoses (hazard ratio, 1.43 [95% CI, 1.26-1.64]; p < 0.0001) and psychotropic medication use (hazard ratio, 1.67 [1.34-2.08]; p < 0.0001) following discharge. Seven-thousand seven-hundred eighty children admitted to the PICU without invasive mechanical ventilation were matched to 38,900 general hospital patients and had increased mental disorder diagnoses (hazard ratio, 1.08 [1.02-1.15]; p = 0.01) and psychotropic medication use (hazard ratio, 1.11 [1.00-1.22]; p = 0.049). CONCLUSIONS: Children without major comorbidity requiring invasive mechanical ventilation for severe respiratory illness had a 43% higher incidence of subsequent mental disorder diagnoses and a 67% higher incidence of psychotropic medication use. Both increases were substantially higher than in PICU patients with respiratory illness not necessitating invasive mechanical ventilation. Invasive mechanical ventilation is a life-saving therapy, and its application is interwoven with underlying health, illness severity, and PICU management decisions. Further research is required to determine which factors related to invasive mechanical ventilation and severe respiratory illness are associated with abnormal neurodevelopment. Given the increased risk in these children, identification of strategies for prevention, neurodevelopmental surveillance, and intervention after discharge may be warranted.

Long-term Healthcare Utilization by Medicaid Enrolled Children with Neonatal Abstinence Syndrome.

OBJECTIVE: To evaluate healthcare utilization in Medicaid enrolled children with neonatal abstinence syndrome (NAS) in the first 2 years of life. STUDY DESIGN: A retrospective, longitudinal cohort study evaluating Medicaid enrolled children born in New York (1999-2011) and Texas (1999-2010) was performed. Healthcare utilization, including inpatient days, emergency department and outpatient visits, and filled prescriptions in children after birth hospitalization was assessed. A tapered propensity-matching methodology was used, matching each child with NAS with 5 children without NAS, first on demographics, then on both demographics and clinical covariates (clinical diagnoses and congenital anomalies at birth). Poisson and negative binomial regression were used to calculate healthcare utilization ratios (HUR). RESULTS: In the first 2 years of life, children with NAS (n = 3799) had increased healthcare utilization with more inpatient days and emergency department visits than demographically similar children without NAS. This increased utilization however did not persist after matching on clinical covariates and performing multiple comparisons adjustment (inpatient days [HUR, 1.01; 95% CI, 0.88-1.16; P = .89], total emergency department visits [HUR, 1.06; 95% CI, 1.01-1.11; P = .02]). Children with NAS conversely had 9% fewer outpatient office visits (HUR, 0.91; 95% CI, 0.87-0.95; P < .0001). CONCLUSIONS: A diagnosis of NAS does not appear to be an independent predictor of increased healthcare utilization in the first 2 years of life. These results differ from some other published studies, but may suggest that the increased healthcare utilization observed in children with NAS is due to higher incidences of perinatal complications and congenital anomalies in children with prenatal drug exposures.

Exposure to Surgery and Anesthesia in Early Childhood and Subsequent Use of Attention Deficit Hyperactivity Disorder Medications.

BACKGROUND: Some recent clinical studies have found that early childhood exposure to anesthesia is associated with increased risks of behavioral deficits and clinical diagnoses of attention deficit hyperactivity disorder (ADHD). While diagnoses in claims data may be subject to inaccuracies, pharmacy claims are highly accurate in reflecting medication use. This study examines the association between exposure to surgery and anesthesia and subsequent ADHD medication use. METHODS: Longitudinal data for children enrolled in Texas and New York Medicaid from 1999 to 2010 were used. We assessed the association between a single exposure to anesthesia before age 5 years for 1 of 4 common pediatric surgical procedures (pyloromyotomy, inguinal hernia repair, circumcisions outside the perinatal period, and tonsillectomy and/or adenoidectomy) and persistent ADHD medication use (event defined as the initial ADHD medication prescription, and persistent use defined as filling 2 or more ≥30-day prescriptions between 6 months following surgery until censoring). Exposed children (n = 42,687) were matched on propensity score (ie, the probability of receiving surgery) estimated in logistic regression including sociodemographic and clinical covariates, to children without anesthesia exposure before age 5 years (n = 213,435). Cox proportional hazards models were used to evaluate the hazard ratio (HR) of ADHD medication use following exposure. Nonpsychotropic medications served as negative controls to determine if exposed children simply had higher overall medication use. RESULTS: Children with a single exposure to surgery and anesthesia were 37% more likely than unexposed children to persistently use ADHD medication (HR, 1.37; 95% confidence interval [CI], 1.30-1.44). The estimated HRs for common nonpsychotropic medication use following a single anesthetic exposure were 1.06 (95% CI, 1.04-1.07) for amoxicillin, 1.10 (95% CI, 1.08-1.12) for azithromycin, and 1.08 (95% CI, 1.05-1.11) for diphenhydramine. In comparison, the risk of using other psychotropic medication to treat conditions besides ADHD was also significantly higher, with HRs of 1.37 (95% CI, 1.24-1.51) for sedative/anxiolytics, 1.40 (95% CI, 1.25-1.58) for antidepressants, 1.31 (95% CI, 1.20-1.44) for antipsychotics, and 1.24 (95% CI, 1.10-1.40) for mood stabilizers. CONCLUSIONS: Medicaid-enrolled children receiving anesthesia for a single common pediatric surgical procedure under age 5 years were 37% more likely to require subsequent persistent use of ADHD medications than unexposed children. Because the increased use of ADHD medication is disproportionately higher than that of nonpsychotropic medications, unmeasured confounding may not account for all of the increase in ADHD medication use. By evaluating Medicaid data, this study assesses children who may be particularly vulnerable to neurotoxic exposures.

Transmission dynamics of drug-resistant tuberculosis in Ningbo, China: an epidemiological and genomic analysis.

Background: Tuberculosis (TB), particularly drug-resistant TB (DR-TB), remains a significant public health concern in Ningbo, China. Understanding its molecular epidemiology and spatial distribution is paramount for effective control. Methods: From December 24, 2020, to March 12, 2023, we collected clinical Mycobacterium tuberculosis (MTB) strains in Ningbo, with whole-genome sequencing performed on 130 MTB strains. We analyzed DR-related gene mutations, conducted phylogenetic and phylodynamic analyses, identified recent transmission clusters, and assessed spatial distribution. Results: Among 130 DR-TB cases, 41% were MDR-TB, 36% pre-XDR-TB, 19% RR-TB, and 3% HR-TB. The phylogenetic tree showed that 90% of strains were Lineage 2 (Beijing genotype), while remaining 10% were Lineage 4 (Euro-American genotype). The spatial analysis identified hotspots of DR-TB in Ningbo's northern region, particularly in traditional urban centers. 31 (24%) of the DR-TB cases were grouped into 7 recent transmission clusters with a large outbreak cluster containing 15 pre-XDR-TB patients. Epidemiological analyses suggested a higher risk of recent DR-TB transmission among young adult patients who frequently visited Internet cafes, game rooms, and factories. Conclusion: Our study provides comprehensive insights into the epidemiology and genetics of DR-TB in Ningbo. The presence of genomic clusters highlights recent transmission events, indicating the need for targeted interventions. These findings are vital for informing TB control strategies in Ningbo and similar settings.

Genomic and spatial analysis reveal the transmission dynamics of tuberculosis in areas with high incidence of Zhejiang, China: A prospective cohort study.

In the mountainous, rural regions of eastern China, tuberculosis (TB) remains a formidable challenge; however, the long-term molecular epidemiological surveillance in these regions is limited. This study aimed to investigate molecular and spatial epidemiology of TB in two mountainous, rural counties of Zhejiang Province, China, from 2015 to 2021, to elucidate the recent transmission and drug-resistance profiles. The predominant Lineage 2 (L2) Beijing family accounted for 80.1% of total 532 sequenced Mycobacterium tuberculosis (Mtb) strains, showing consistent prevalence over seven years. Gene mutations associated with drug resistance were identified in 19.4% (103/532) of strains, including 47 rifampicin or isoniazid-resistant strains, eight multi-drug-resistant (MDR) strains, and five pre-extensively drug-resistant (pre-XDR) strains. Genomic clustering revealed 53 distinct clusters with an overall transmission clustering rate of 23.9% (127/532). Patients with a history of retreatment and those infected with L2 strains had a higher risk of recent transmission. Spatial and epidemiological analysis unveiled significant transmission hotspots, especially in densely populated urban areas, involving various public places such as medical institutions, farmlands, markets, and cardrooms. The study emphasizes the pivotal role of Beijing strains and urban-based TB transmission in the western mountainous regions in Zhejiang, highlighting the urgent requirement for specific interventions to mitigate the impact of TB in these unique communities.

Outbreak of OXA-232-producing carbapenem-resistant Klebsiella pneumoniae ST15 in a Chinese teaching hospital: a molecular epidemiological study.

Background and Aims: The incidence of OXA-232-producing carbapenem-resistant Klebsiella pneumoniae (CRKP) has been on the rise in China over the past five years, potentially leading to nosocomial epidemics. This study investigates the first outbreak of CRKP in the Second Affiliated Hospital of Jiaxing University. Methods: Between February 2021 and March 2022, 21 clinical isolates of OXA-232-producing CRKP were recovered from 16 patients in the Second Affiliated Hospital of Jiaxing University. We conducted antimicrobial susceptibility tests, whole genome sequencing, and bioinformatics to determine the drug resistance profile of these clinical isolates. Results: Whole-genome sequencing revealed that all 21 OXA-232-producing CRKP strains belonged to the sequence type 15 (ST15) and shared similar resistance, virulence genes, and plasmid types, suggesting clonal transmission between the environment and patients. Integrated genomic and epidemiological analysis traced the outbreak to two clonal transmission clusters, cluster 1 and cluster 2, including 14 and 2 patients. It was speculated that the CRKP transmission mainly occurred in the ICU, followed by brain surgery, neurosurgery, and rehabilitation department. Phylogenetic analysis indicated that the earliest outbreak might have started at least a year before the admission of the index patient, and these strains were closely related to those previously isolated from two major adjacent cities, Shanghai and Hangzhou. Comparative genomics showed that the IncFII-type and IncHI1B-type plasmids of cluster 2 had homologous recombination at the insertion sequence sites compared with the same type of plasmids in cluster 1, resulting in the insertion of 4 new drug resistance genes, including TEM-1, APH(6)-Id, APH(3'')-Ib and sul2. Conclusions: Our study observed the clonal spread of ST15 OXA-232-producing between patients and the hospital environment. The integration of genomic and epidemiological data offers valuable insights and facilitate the control of nosocomial transmission.

Whole-Genome Sequencing to Predict Mycobacterium tuberculosis Drug Resistance: A Retrospective Observational Study in Eastern China.

Pulmonary tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (MTB). Whole-genome sequencing (WGS) holds great promise as an advanced technology for accurately predicting anti-TB drug resistance. The development of a reliable method for detecting drug resistance is crucial in order to standardize anti-TB treatments, enhance patient prognosis, and effectively reduce the risk of transmission. In this study, our primary objective was to explore and determine the potential of WGS for assessing drug resistance based on genetic variants recommended by the World Health Organization (WHO). A total of 1105 MTB strains were selected from samples collected from 2014-2018 in Zhejiang Province, China. Phenotypic drug sensitivity tests (DST) of the anti-TB drugs were conducted for isoniazid (INH), rifampicin (RFP), streptomycin, ethambutol, fluoroquinolones (levofloxacin and moxifloxacin), amikacin, kanamycin, and capreomycin, and the drug-resistance rates were calculated. The clean WGS data of the 1105 strains were acquired and analyzed. The predictive performance of WGS was evaluated by the comparison between genotypic and phenotypic DST results. For all anti-TB drugs, WGS achieved good specificity values (>90%). The sensitivity values for INH and RFP were 91.78% and 82.26%, respectively; however, they were ≤60% for other drugs. The positive predictive values for anti-TB drugs were >80%, except for ethambutol and moxifloxacin, and the negative predictive values were >90% for all drugs. In light of the findings from our study, we draw the conclusion that WGS is a valuable tool for identifying genome-wide variants. Leveraging the genetic variants recommended by the WHO, WGS proves to be effective in detecting resistance to RFP and INH, enabling the identification of multi-drug resistant TB patients. However, it is evident that the genetic variants recommended for predicting resistance to other anti-TB drugs require further optimization and improvement.

[Association between myocardial connexin 40 and 45 expression and myocardial fibrosis in the rapid atrial pacing canine model].

OBJECTIVE: Electrical and structural remodeling are of importance for the occurrence and maintenance of atrial fibrillation. We observed association between atrial connexin protein expression and fibrosis in a canine model of prolonged rapid atrial pacing. METHODS: "J"-type electrodes were placed in the right atrial appendage under the guidance of X-ray in 16 dogs, Animals in model group (n = 8) received fast pacing (400 beats/min) for 10 weeks while animals in control group (n = 8) maintained at sinus rhythm. Limb-lead ECGs were recorded at 2, 4, 6, 8 weeks respectively. Burst stimulation was applied to induce atrial fibrillation in all animals after 10 weeks, animals were sacrificed thereafter and the left atrial tissues were taken for myocardial collagen measurement (Masson staining) and myocardial ultrastructure examination and detection of protein expression of connexin (Cx) 40 and 45 (immune staining). Procollagen type III N-terminal peptide and type IV collagen in serum were also detected by radioimmunoassay. RESULTS: Two dogs died in model group due to atrial rupture induced cardiac tamponade or lung emboli. Spontaneously atrial fibrillation was not observed in all animals, but two dogs developed atrial flutter and atrial premature beats. Atrial fibrillation was induced by burst stimulation in 4 out of 6 dogs in model group and in none of the dogs in control group. Atrial myocardial collagen volume fraction was significantly increased in model group compared with the control group (P < 0.05). Ultrastructure examination in atrial tissue evidenced disorder, fracture, collagen fiber proliferation, mitochondrial swelling, blurred cristae, and intercalated disc distortion, expansion, part of gap junction disappears in model group. The serum levels of procollagen type III N-terminal peptide and type IV collagen in model group were significantly higher than in the control group (P < 0.05). The protein expression of Cx 40 in atrial myocardium in model group was significantly higher than in control group (P < 0.05), while Cx 45 protein expression was similar between two groups (P > 0.05). The left atrial CVF was positively correlated with Cx 40 (r = 0.671, P < 0.01). CONCLUSION: Increased myocardial fibrosis is positively correlated with upregulation of myocardial Cx 40 protein expression in left atrium in rapid atrial paced canine.

Implementation of Specialist Palliative Care and Outcomes for Hospitalized Patients with Dementia.

BACKGROUND: In patients with serious illness, use of specialist palliative care may result in improved quality of life, patient and caregiver satisfaction and advance care planning, as well as lower health care utilization. However, evidence of efficacy is limited for patients with dementia, particularly in the setting of an acute hospitalization. OBJECTIVE: To determine whether implementation of hospital-based specialist palliative care was associated with differences in treatment intensity outcomes for hospitalized patients with dementia. DESIGN: Retrospective cohort study. SETTING: Fifty-one hospitals in New York State that either did or did not implement a palliative care program between 2008 and 2014. Hospitals that consistently had a palliative care program during the study period were excluded. PARTICIPANTS: Hospitalized patients with dementia. MEASUREMENTS: The primary outcome of this study was discharge to hospice from an acute hospitalization. Secondary outcomes included hospital length of stay, use of mechanical ventilation and dialysis, and days in intensive care. Difference-in-difference analyses were performed using multilevel regression to assess the association between implementing a palliative care program and outcomes, while adjusting for patient and hospital characteristics and time trends. RESULTS: During the study period, 82,118 patients with dementia (mean (SD) age, 83.04 (10.04), 51,170 (62.21%) female) underwent an acute hospitalization, of which 41,227 (50.27%) received care in hospitals that implemented a palliative care program. In comparison to patients who received care in hospitals without palliative care, patients with dementia who received care in hospitals after the implementation of palliative care were more 35% likely to be discharged to hospice (adjusted odds ratio (aOR) = 1.35 (1.19-1.51), P < .001). No meaningful differences in secondary outcomes were observed. CONCLUSION: Implementation of a specialist palliative care program was associated with an increase in discharge to hospice following acute hospitalization in patients with dementia.

Association Between the Implementation of Hospital-Based Palliative Care and Use of Intensive Care During Terminal Hospitalizations.

Importance: The use of intensive care at the end of life continues to be common. Although the provision of palliative care has been advocated as a way to mitigate the use of high-intensity care, it is unknown whether implementation of hospital-based palliative care services is associated with reduced use of intensive care at the end of life. Objective: To determine whether implementation of hospital-based palliative care services is associated with decreased intensive care unit (ICU) use during terminal hospitalizations. Design, Setting, and Participants: This cohort study included 51 hospitals in New York State that either did or did not implement a palliative care program between 2008 and 2014. Hospitals that consistently had a palliative care program during the study period were excluded. Participants were adult patients who died during hospitalization. Data analysis was performed between January 2018 and July 2019. Exposure: Implementation of a palliative care program. Main Outcomes and Measures: The primary outcome was ICU use. A difference-in-differences analysis was performed using multilevel regression to assess the association between implementing a palliative care program and ICU use during terminal hospitalizations while adjusting for patient and hospital characteristics and time trends. Results: During the study period, 73 370 patients (mean [SD] age, 76.5 [14.1] years; 38 467 [52.4%] women) died during hospitalization, of whom 37 628 (51.3%) received care in hospitals that implemented palliative care services and 35 742 (48.7%) received care in a hospital without palliative care implementation. Patients who received care in hospitals after implementation of palliative care services were less likely to receive intensive care than patients admitted to the same hospitals before implementation (49.3% vs 52.8%; difference 3.5%; 95% CI, 2.5%-4.5%; P < .001). Compared with hospitals that never had a palliative care program, the implementation of palliative care was associated with a 10% reduction in ICU use during terminal hospitalizations (adjusted relative risk, 0.90; 95% CI, 0.85-0.95; P < .001). Conclusions and Relevance: The implementation of hospital-based palliative care services in New York State was associated with a modest reduction in ICU use during terminal hospitalizations.

Tetracaine combined with propofol for painless oocyte retrieval: from a single center study.

BACKGROUND: In vitro fertilization-embryo transfer is a main assisted reproductive technique that can improve the success rate of conception. At present, the ultrasound-guided oocyte retrieval is often employed in clinics, but this process will cause pain and fear in outpatients. This study explored the safety and satisfaction of patients who received egg retrieval under vaginal topical tetracaine anesthesia combined with intravenous propofol anesthesia. METHODS: Patients who underwent elective egg retrieval in the Reproductive Center of Shanghai Tenth People's Hospital were recruited from January 2017 to August 2018 [tetracaine + propofol group (n=53); propofol group (n=48)]. RESULTS: Results showed that tetracaine combined with propofol anesthesia could effectively reduce the dose of propofol during surgery, ensure the quality of follicles, effectively reduce the postoperative pain and improve the operational satisfaction without affecting the prognosis. CONCLUSIONS: Our findings provide evidence for further clinical applications of this technique.