Evolutionary trends in antifungal resistance: a meta-analysis

The present paper includes a meta-analysis of literature data on 318 species of fungi belonging to 34 orders in their response to 8 antifungal agents (amphotericin B, caspofungin, fluconazole, itraconazole, ketoconazole, posaconazole, terbinafine, and voriconazole). Main trends of MIC results at the ordinal level were visualized. European Committee on Antimicrobial Susceptibility Testing and Clinical & Laboratory Standards Institute (CLSI) clinical breakpoints were used as the staff gauge to evaluate MIC values ranging from resistance to susceptibility, which were subsequently compared with a phylogenetic tree of the fungal kingdom. Several orders (Hypocreales, Microascales, and Mucorales) invariably showed resistance. Also the basidiomycetous orders Agaricales, Polyporales, Sporidiales, Tremellales, and Trichosporonales showed relatively high degrees of azole multi-resistance, while elsewhere in the fungal kingdom, including orders with numerous pathogenic and opportunistic species, that is, Onygenales, Chaetothyiales, Sordariales, and Malasseziales, in general were susceptible to azoles. In most cases, resistance vs susceptibility was consistently associated with phylogenetic distance, members of the same order showing similar behavior.

IMPORTANCE

A kingdom-wide the largest set of published wild-type antifungal data comparison were analyzed. Trends in resistance in taxonomic groups (monophyletic clades) can be compared with the phylogeny of the fungal kingdom, eventual relationships between fungus-drug interaction and evolution can be described.

Declined terrestrial ecosystem resilience

Terrestrial ecosystem resilience is crucial for maintaining the structural and functional stability of ecosystems following disturbances. However, changes in resilience over the past few decades and the risk of future resilience loss under ongoing climate change are unclear. Here, we identified resilience trends using two remotely sensed vegetation indices, analyzed the relative importance of potential driving factors to resilience changes, and finally assessed the risk of future resilience loss based on the output data of eight models from CMIP6. The results revealed that more than 60% of the ecosystems experienced a conversion from an increased trend to a declined trend in resilience. Attribution analysis showed that the most important driving factors of declined resilience varied regionally. The declined trends in resilience were associated with increased precipitation variability in the tropics, decreased vegetation cover in arid region, increased temperature variability in temperate regions, and increased average temperature in cold regions. CMIP6 reveals that terrestrial ecosystems under SPP585 are expected to experience more intense declines in resilience than those under SSP126 and SSP245, particularly in cold regions. These results highlight the risk of continued degradation of ecosystem resilience in the future and the urgency of climate mitigation actions.

A comparative analysis of mathematical methods for detecting lactate thresholds using muscle oxygenation data during a graded cycling test

Objective. Threshold determination for improving training and sports performance is important for researchers and trainers, who currently use different methods for determining lactate, ventilatory or muscle oxygenation (SmO2) thresholds. Our study aimed to compare the identification of the intensity at the first and second thresholds using lactate and SmO2data by different mathematical methods in different muscles during a graded cycling test.Approach. Twenty-six cyclists (15 males and 11 females; 23 ±6 years, 1.71 ± 0.09 m, 64.3 ± 8.8 Kg and 12 ± 3 training hours per week) performed a graded test on the cycle ergometer. Power output and saturation of muscle oxygen in four muscles (vastus lateralis, biceps femoris, gastrocnemius and tibialis anterior) were measured, along with systemic lactate concentration.Main Results. Our results showed that any method was reliable for determining the first muscle oxygenation threshold (MOT1) when comparing the lactate threshold in any muscle. However, the best method for determining the second muscle oxygenation threshold (MOT2) was the Exp-Dmax (p< 0.01; ICC = 0.79-0.91) in all muscles. In particular, the vastus lateralis muscle showed the highest intraclass correlation coefficient (ICC = 0.91, CI95% [0.81, 0.96]). However, results varied per sex across all muscles analyzed.Significance. Although the first muscle oxygenation threshold could not be determined using mathematical methods in all the muscles analyzed, the Exp-Dmax method presented excellent results in detecting the second systemic threshold in the vastus lateralis.

Case report: Identification of a novel triplication of alpha-globin gene by the third-generation sequencing: pedigree analysis and genetic diagnosis

BACKGROUND

Thalassemia, a common autosomal hereditary blood disorder worldwide, mainly contains α- and β-thalassemia. The α-globin gene triplicates allele is harmless for carriers, but aggravates the phenotype of β-thalassemia. Therefore, it is particularly crucial to accurately detect the structural variants of α-globin gene clusters.

CASE REPORT

We reported a 28-year-old man, the proband, with microcytic hypochromic anemia. From pedigree analysis, his mother and sister had hypochromic microcytosis, and his father was normal. Genetic testing of thalassemia identified a novel α-globin gene triplicate named αααanti4.2del726bp (NC_000016.10:g.170769_174300dupinsAAAAAA) by third-generation sequencing (TGS) in the proband and his father, which was further validated by multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. The genotypes of the proband's mother and sister were both -α3.7/αα compounded with heterozygous HBB:c.126_129delCTTT. They were categorized as silent α-thalassemia with co-inheritance of β-thalassemia trait. The proband's genotype additionally had the α-globin gene triplicates compared with his mother and sister, which increased the imbalance between α/β-globin, so the proband had more severe hematological parameters. The proband's wife was diagnosed as HBA2:c.427T > C heterozygosis, and his daughter had the novel α-globin gene triplicates compounded with HBA2:c.427T > C, therefore the girl might be asymptomatic.

CONCLUSION

The identification of the novel α-globin gene triplicates provides more insight for the research of thalassemia variants and indicates that TGS has significant advantages on genetic testing of thalassemia for the reliability, accuracy and comprehensiveness.

Sex-related differences in profiles of muscle oxygen saturation of different muscles in trained cyclists during graded cycling exercise

Although in recent years near-infrared spectroscopy has been used in many sports to monitor muscle oxygen saturation (SmO2), there is a lack of knowledge about the sex differences in SmO2 during exercise in different muscles. Our study aimed to examine SmO2 differences in muscles between female and male cyclists, during a graded cycling test and at the first and second lactate thresholds. Twenty-five trained cyclists and triathletes (15 males: 23 ± 7 yr, 1.78 ± 0.05 m, 70.2 ± 5.3 kg, and 10 females: 22 ± 5 yr, 1.64 ± 0.06 m, 58 ± 8 kg) performed a graded cycling test on the cycle ergometer. Power output and SmO2 in five muscles (dominant vastus lateralis, tibialis anterior, gastrocnemius medial, biceps femoris, and triceps brachii) were measured. Our mixed regression models showed that the interaction between power output and sex was significant for all the muscles analyzed (P < 0.001), indicating a greater decrease in SmO2 for males as power output increased. Moreover, the statistical parametric mapping analyses showed for females higher SmO2 in the middle of the test in biceps femoris (P = 0.03), gastrocnemius medial (P = 0.02), and tibialis anterior (P = 0.04). Finally, the males presented a lower SmO2 in all muscles where the second lactate threshold occurred, with greater evidence than in the first lactate threshold. In conclusion, females have higher SmO2 in all muscles, and these differences are more noticeable during the graded cycling test, such that males seem to have a greater reliance on oxygen extraction than females for a given relative intensity of exercise.NEW & NOTEWORTHY This study investigated the profiles of muscle oxygen saturation (SmO2) during incremental exercise in females and males. Females presented higher overall SmO2 than males during moderate and heavy intensity domain exercise in all muscles including muscles that are not mainly involved in pedaling (triceps brachii), from those that are stabilizers (medial gastrocnemius, tibialis anterior, and biceps femoris), to those that are related to power output production (vastus lateralis).

Assessment of Intercostal Muscle Near-Infrared Spectroscopy for Estimating Respiratory Compensation Point in Trained Endurance Athletes

This study aimed to assess the reliability and validity of estimating the respiratory compensation point (RCP) in trained endurance athletes by analyzing intercostal muscles' NIRS-derived tissue oxygenation dynamics. Seventeen experienced trail runners underwent an incremental treadmill protocol on two separate occasions, with a 7-day gap between assessments. Gas exchange and muscle oxygenation data were collected, and the oxygen saturation breakpoint (SmO2BP) measured in the intercostal muscles was compared to the RCP, which was identified by the increase in the VE/V.CO2 slope and the point at which the PetCO2 started to decrease. No statistically significant differences were observed between the two methods for any of the variables analyzed. Bland-Altman analysis showed significant agreement between the NIRS and gas analyzer methods for speed (r = 0.96, p < 0.05), HR (r = 0.98, p < 0.05), V.O2 relative to body mass (r = 0.99, p < 0.05), and %SmO2 (r = 0.98, p < 0.05). The interclass correlation coefficient values showed moderate to good reliability (0.60 to 0.86), and test-retest analysis revealed mean differences within the confidence intervals for all variables. These findings suggest that the SmO2BP measured using a portable NIRS device in the intercostal muscles is a reliable and valid tool for estimating the RCP for experienced trail runners and might be useful for coaches and athletes to monitor endurance training.

Benefits and challenges of creating veterinary antibiograms for empiric antimicrobial selection in support of antimicrobial stewardship and advancement of one-health goals

Antibiograms are important tools for antimicrobial stewardship that are often underutilized in veterinary medicine. Antibiograms summarize cumulative antimicrobial susceptibility testing (AST) data for specific pathogens over a defined time period; in veterinary medicine, they are often stratified by host species and site of infection. They can aid practitioners with empiric therapy choices and assessment of antimicrobial resistance trends within a population in support of one-health goals for antimicrobial stewardship. For optimal application, consideration must be given to the number of isolates used, the timeframe of sample collection, laboratory analytical methodology, and the patient population contributing to the data (eg, treatment history, geographic region, and production type). There are several limitations to veterinary antibiograms, including a lack of breakpoint availability for bacterial species, a lack of standardization of laboratory methodology and technology for culture and AST, and a lack of funding to staff veterinary diagnostic laboratories at a level that supports antibiogram development and education. It is vital that veterinarians who use antibiograms understand how to apply them in practice and receive relevant information pertaining to the data to utilize the most appropriate antibiogram for their patients. This paper explores the benefits and challenges of developing and using veterinary antibiograms and proposes strategies to enhance their applicability and accuracy. Further detail regarding the application of veterinary antibiograms by privately practicing clinicians is addressed in the companion Currents in One Health article by Lorenz et al (JAVMA, September 2023).

Assessing the urinary concentration of nitrofurantoin and its antibacterial activity against Escherichia coli, Staphylococcus pseudintermedius, and Enterococcus faecium isolated from dogs with urinary tract infections

Nitrofurantoin, a broad-spectrum nitrofuran class antibiotic, is applied as a first-line antibiotic in treating human urinary tract infections (UTIs) due to its great efficacy and high achievable concentration. The interest in using this antibiotic in companion animals has increased due to the growing demand for effective antibiotics to treat UTIs caused by multidrug-resistant bacteria. Currently, the susceptibility interpretations for nitrofurantoin are based on the breakpoints set for humans, while the canine-specific breakpoints are still unavailable. In this study, we assessed the concentration of nitrofurantoin reaching the dog's urine using the recommended oral dosing regimen. In addition, we examined the efficacy of this breakpoint concentration against the common canine UTI pathogens, Escherichia coli, Staphylococcus pseudintermedius, and Enterococcus faecium. Eight experimental beagle dogs were treated with ~5 mg/kg of nitrofurantoin macrocrystal PO 8qh for 7 days. The urine samples were collected via cystocentesis at 2, 4, and 6 h after administration on day 2 and day 7 and used to quantify nitrofurantoin concentrations by ultra-high performance liquid chromatography. The results showed that 26.13-315.87 μg/mL nitrofurantoin was detected in the dogs' urine with a mean and median concentration of 104.82 and 92.75 μg/mL, respectively. Additionally, individual dogs presented with urinary nitrofurantoin concentrations greater than 64 μg/mL for at least 50% of the dosing intervals. This concentration efficiently killed E. coli, and S. pseudintermedius, but not E. faecium strains carrying an MIC₉₀ value equal to 16, 16, and 128 μg/mL, respectively. Taken together, these results suggest that the value of 64 μg/mL may be set as a breakpoint against UTI pathogens, and nitrofurantoin could be an effective therapeutic drug against E. coli and S. pseudintermedius for canine UTIs.

A Rat Model of the Brain-Derived Neurotrophic Factor Val66Met Polymorphism Shows Attenuated Motivation for Alcohol Self-Administration and Diminished Propensity for Cue-Induced Relapse in Females

Brain-derived neurotrophic factor (BDNF) has been implicated in alcohol use disorder. The Val66Met polymorphism is a common variant of the BDNF gene (rs6265) which reduces activity-dependent BDNF release, and has been suggested as a risk factor for psychiatric disorders and substance use. Using an operant self-administration paradigm, this study aimed to investigate ethanol preference and ethanol seeking in a novel rat model of the BDNF Val66Met polymorphism, Val68Met rats. Male and female BDNF Val68Met rats of three genotypes (Val/Val, Val/Met and Met/Met) were trained to lever press for a 10% ethanol solution. There was no effect of Val68Met genotype on acquisition of stable response to ethanol or its extinction. Met/Met rats of both sexes had a slight, but significantly lower breakpoint during progressive ratio sessions while female rats with the Met/Met genotype demonstrated a lower propensity for reinstatement of responding to cues. There were no effects of Val68Met genotype on anxiety-like behaviour or locomotor activity. In conclusion, Met/Met rats showed lower motivation to continue to press for a reward, and also a decreased propensity to relapse, suggesting a possible protective effect of the Met/Met genotype against alcohol use disorder, at least in females.

NMDA Receptor Glycine Binding Site Modulators for Prevention and Treatment of Ketamine Use Disorder

Ketamine offers a fast-acting approach to relieving treatment-resistant depression, but its abuse potential is an issue of concern. As ketamine is a noncompetitive N-methyl-D-aspartate receptor (NMDAR) ion channel blocker, modulation of NMDAR might be an effective strategy to counteract the abuse liability of ketamine and even to treat ketamine use disorder. This study evaluated whether NMDAR modulators that act on glycine binding sites can decrease motivation to obtain ketamine and reduce reinstatement to ketamine-seeking behavior. Two NMDAR modulators, D-serine and sarcosine were examined. Male Sprague-Dawley rats underwent training to acquire the ability to self-administer ketamine. The motivation to self-administer ketamine or sucrose pellets was examined under a progressive ratio (PR) schedule. The reinstatement of ketamine-seeking and sucrose pellet-seeking behaviors were assessed after extinction. The results showed that both D-serine and sarcosine significantly decreased the breakpoints for ketamine and prevented reinstatement of ketamine seeking. However, these modulators did not alter motivated behavior for sucrose pellets, the ability of the cue and sucrose pellets to reinstate sucrose-seeking behavior or spontaneous locomotor activity. These findings indicate that two NMDAR modulators can specifically reduce the measures of motivation and relapse for ketamine in rats, suggesting that targeting the glycine binding site of the NMDAR is a promising approach for preventing and treating ketamine use disorder.

Assessment of accredited veterinary diagnostic laboratory use of breakpoints for canine and feline Escherichia coli infections in the United States and Canada

The objective of this study was to assess the use of breakpoints in antibiotic susceptibility testing among veterinary diagnostic laboratories in the United States and Canada. An eight-question survey was conducted via phone and email to determine how often laboratories use breakpoints consistent with published guidelines in wounds, lower urinary tract infections and upper urinary tract infections (pyelonephritis) involving Escherichia coli, both in dogs and cats, for a total of 6 different hypothetical clinical scenarios. Nineteen veterinary diagnostic laboratories that perform antibiotic susceptibility testing on samples from dogs and cats in the United States or Canada and were accredited by the American Association of Veterinary Laboratory Diagnosticians (AAVLD) responded to the survey between January 15th and September 15th, 2022. The overall response rate of laboratories that were not excluded for known lack of dog and cat antibiotic susceptibility testing was 19 of 44 laboratories. Of the 17 respondent laboratories that reported using minimal inhibitory concentration breakpoints, only four laboratories used breakpoints consistent with published guidelines in all six clinical scenarios included in the survey. Our results suggest that there is clinically important variation in what breakpoints laboratories use to determine antibiotic susceptibility, which is of antibiotic stewardship and clinical relevance. Using breakpoints that are too high, too low, or inappropriately reporting "not interpreted" as the interpretive category may result in inappropriate use of antibiotics.

Precise definition of the breakpoints of an apparently balanced translocation between chromosome 3q26 and chromosome 7q36: Role of KMT2C disruption

When a de novo balanced reciprocal translocation is identified in the patient, the cause of phenotype of the patient can be explained by detecting the breakpoints of the genes. Here, we report a 3-year-old patient with developmental delay, autism spectrum disorder, and distinctive facial features who had an apparently balanced translocation between chromosome 3q26 and chromosome 7q36. Nanopore long-read sequencing revealed that balanced translocation disrupted the KMT2C gene, the haploinsufficiency of which leads to Kleefstra syndrome 2 characterized by delayed psychomotor development, variable intellectual disability and mild dysmorphism. Nanopore long read sequencing was shown to be useful in elucidating the exact genetic etiology of patients with nonspecific clinical findings.

Routine EWS Fusion Analysis in the Oncology Clinic to Identify Cancer-Specific Peptide Sequence Patterns That Span Breakpoints in Ewing Sarcoma and DSRCT

(1) Background: EWS fusion genes are associated with Ewing sarcoma and other Ewing family tumors including desmoplastic small round tumor, DSRCT. We utilize a clinical genomics workflow to reveal real-world frequencies of EWS fusion events, cataloging events that are similar, or divergent at the EWS breakpoint. (2) Methods: EWS fusion events from our next-generation sequencing panel (NGS) samples were first sorted by breakpoint or fusion junctions to map out the frequency of breakpoints. Fusion results were illustrated as in-frame fusion peptides involving EWS and a partner gene. (3) Results: From 2471 patient pool samples for fusion analysis at the Cleveland Clinic Molecular Pathology Laboratory, we identified 182 fusion samples evolved with the EWS gene. They are clustered in several breakpoints: chr22:29683123 (65.9%), and chr22:29688595 (2.7%). About 3/4 of Ewing sarcoma and DSRCT tumors have an identical EWS breakpoint motif at Exon 7 (SQQSSSYGQQ-) fused to a specific part of FLI1 (NPSYDSVRRG or-SSLLAYNTSS), ERG (NLPYEPPRRS), FEV (NPVGDGLFKD) or WT1 (SEKPYQCDFK). Our method also worked with Caris transcriptome data, too. Our primary clinical utility is to use this information to identify neoantigens for therapeutic purposes. (4) Conclusions and future perspectives: our method allows interpretation of what peptides result from the in-frame translation of EWS fusion junctions. These sequences, coupled with HLA-peptide binding data, are used to identify potential sequences of cancer-specific immunogenic peptides for Ewing sarcoma or DSRCT patients. This information may also be useful for immune monitoring (e.g., circulating T-cells with fusion-peptide specificity) to detect vaccine candidates, responses, or residual disease.

Antimicrobial susceptibility testing: An updated primer for clinicians in the era of antimicrobial resistance: Insights from the Society of Infectious Diseases Pharmacists

Antimicrobial susceptibility testing (AST) is a critical function of the clinical microbiology laboratory and is essential for optimizing care of patients with infectious diseases, monitoring antimicrobial resistance (AMR) trends, and informing public health initiatives. Several methods are available for performing AST including broth microdilution, agar dilution, and disk diffusion. Technological advances such as the development of commercial automated susceptibility testing platforms and the advent of rapid diagnostic tests have improved the rapidity, robustness, and clinical application of AST. Numerous accrediting and regulatory agencies are involved in the process of AST and setting and revising breakpoints, including the U.S. Food and Drug Administration and the Clinical and Laboratory Standards Institute. Challenges to optimizing AST include the emergence of new resistance mechanisms, the development of new antimicrobial agents, and generation of new data requiring updates and revisions to established methods and breakpoints. Together, the challenges in AST methods and their interpretation create important opportunities for well-informed clinicians to improve patient outcomes and provide value to antimicrobial stewardship programs, especially in the setting of rapidly changing and increasing AMR. Addressing AST challenges will involve continued development of new technologies along with collaboration between clinicians and the laboratory to facilitate optimal antimicrobial use, combat the increasing burden of AMR, and inform the development of novel antimicrobials. This updated primer serves to reinforce important principles of AST, and to provide guidance on their implementation and optimization.

Methods for detecting heat stress in hutch-housed dairy calves in a continental climate

Dairy calves exposed to solar radiation, elevated ambient temperature, and humidity are at risk of impaired welfare and productivity. Initial detection of thermal discomfort requires determination of optimal heat stress indicators and thresholds. Such values have recently been established in calves in chronic, subtropical, and acute continental environments but not in continuous, temperate conditions. Herein, the objectives were to determine associations between animal-based and environmental heat stress indicators and establish environmental breakpoints for hutch-raised dairy calves during a continental summer. From June to August, dairy calves (n = 63; 14 to 42 d of age) were individually hutch-housed and managed according to the dairy standard operating procedures in Arlington, Wisconsin. Calf respiration rates (RR), rectal temperatures (RT), shaved or unshaved skin temperatures (ST), and hutch internal and external air speed were measured thrice weekly at 0700 and 1400 h after a 15 min hutch restriction. Environmental indices including dry bulb temperature (T_db), black globe temperature, and relative humidity were measured every 15 min, averaged hourly, and used to calculate temperature-humidity index (THI) using 8 different equations (THI_1-8). Correlation and linear regression models were used to determine relationships within and between animal-based and environmental indicators. Environmental breakpoints were established using segmented regression models to estimate THI and T_db thresholds for abrupt changes in animal responses. There were strong, positive correlations between animal-based indicators and T_db or THI_1-8, with the strongest association observed between unshaved ST and T_db (r = 0.80). The linear regression of animal-based indicators with the best fit included T_db or T_db plus relative humidity and air speed. The threshold at which RR and RT began to rise was at a THI of 69 for both or at a T_db of 21.0 or 21.5°C, respectively. No threshold was established for ST. Together, these outcomes indicate that T_db is an appropriate measurement to detect thermal discomfort for calves in a temperate summer climate and individual hutch housing. Monitoring of calves is warranted before ambient temperature reaches 21.0°C, corresponding to RR of 40 breaths per minute and RT of 38.5°C, to promote calf comfort and reduce the risk of hyperthermia-related welfare and productivity consequences.

Pharmacokinetics/pharmacodynamics of polymyxin B in patients with bloodstream infection caused by carbapenem-resistant Klebsiella pneumoniae

Introduction: Polymyxin B is a last-line therapy for carbapenem-resistant microorganisms. However, a lack of clinical pharmacokinetic/pharmacodynamic (PK/PD) data has substantially hindered dose optimization and breakpoint setting. Methods: A prospective, multi-center clinical trial was undertaken with polymyxin B [2.5 mg/kg loading dose (3-h infusion), 1.25 mg/kg/12 h maintenance dose (2-h infusion)] for treatment of carbapenem-resistant K. pneumoniae (CRKP) bloodstream infections (BSI). Safety, clinical and microbiological efficacy were evaluated. A validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was applied to determine the concentrations of polymyxin B in blood samples. Population pharmacokinetic (PK) modeling and Monte Carlo simulations were conducted to examine the susceptibility breakpoint for polymyxin B against BSI caused by CRKP. Results: Nine patients were enrolled and evaluated for safety. Neurotoxicity (5/9), nephrotoxicity (5/9), and hyperpigmentation (1/9) were recorded. Blood cultures were negative within 3 days of commencing therapy in all 8 patients evaluated for microbiological efficacy, and clinical cure or improvement occurred in 6 of 8 patients. C_max and C_min following the loading dose were 5.53 ± 1.80 and 1.62 ± 0.41 mg/L, respectively. With maintenance dosing, AUC_ss,24 h was 79.6 ± 25.0 mg h/L and C_ss,avg 3.35 ± 1.06 mg/L. Monte Carlo simulations indicated that a 1 mg/kg/12-hourly maintenance dose could achieve >90% probability of target attainment (PTA) for isolates with minimum inhibitory concentration (MIC) ≤1 mg/L. PTA dropped substantially for MICs ≥2 mg/L, even with a maximally recommended daily dose of 1.5 mg/kg/12-hourly. Conclusion: This is the first clinical PK/PD study evaluating polymyxin B for BSI. These results will assist to optimize polymyxin B therapy and establish its breakpoints for CRKP BSI.

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

BACKGROUND

Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events.

METHODS

We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant.

FINDINGS

We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5' end of the viral genome was from the Delta genome and the 3' end from Omicron, including the majority of the spike protein gene, though the breakpoints were different.

CONCLUSIONS

Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages.

FUNDING

This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).

Fertility problems in men carrying a translocation involved in breakpoints on chromosome 17p13: A retrospective, observational study

Male infertility is a multifactorial reproductive disorder. The effect of genetic factors on male infertility has been the focus of research. Although a variety of genetic techniques are applied to male infertility in clinical practice, karyotype analysis remains a powerful and inexpensive technology. Reciprocal chromosomal translocation (RCT) is closely related to male infertility, but the clinical phenotypes of RCT carriers are varied, and the underlying pathological mechanism is unclear. Some studies suggest that RCT breakpoints disrupt the structure and function of important genes responsible for spermatogenesis. Several breakpoints of chromosome 17 are related to important genes, which can lead to spermatogenic failure. This study aimed to identify the clinical features of 3 men with translocation karyotypes involving breakpoints on chromosome 17p13. Semen analysis and cytogenetic analysis were performed with informed consent. Gene ontology analysis was performed for 60 pathogenic genes on chromosome band 17p13. Cytogenetic analysis showed that the karyotypes were 46, XY, t(6;17) (p21;p13), 46,XY,t(10;17)(q11.2;p13), and 46, XY, t(17;20) (p13;q13), respectively. Relevant studies and genes on breakpoints on chromosome 17p13 were searched for using PubMed. Fourteen reported cases of the same karyotype were reviewed. The results suggest that although chromosome 17 is closely related to spermatogenic failure, the clinical phenotypes of RCT carriers with involvement of 17p13 breakpoints are varied. The important genes involved in the breakpoint were analyzed. The results of molecular functions suggested that these targets genes on chromosome band 17p13 were mostly involved in microfilament motor activity, ATPase activity. These results suggested that the translocation chromosome and breakpoint analysis should be considered in the clinical assessment of the patients. Physicians should be aware of these in genetic counseling. These breakpoints and the function of related genes require further study.

Do efficient commodity markets co-move: evidence from Indian base metals market

The present study is an attempt to investigate in Indian context two important issues with respect to base metals (these are primarily non-ferrous metals), first to test whether the market for base metals is efficient like other financial markets and second to explore a possibility of any co-integration in prices amongst these base metals. To this end, we collect daily closing prices of five base metals, viz. aluminum, copper, zinc, lead and nickel for the study period Jan 1, 2016, to Dec 31, 2020. The methodology involves three different co-integration tests and two different ‘Day of the Week’ (market efficiency) tests. The results of the study showed that co-integration existed only when aluminium was taken as dependent variable with other metals as forcing variables. Also, no co-integration existed for other four base metals and these results were confirmed by both Engle-Granger and Gregory-Hansen tests; however, Johansen test failed to reveal any co-integration amongst any of these metals. Furthermore, test of market efficiency using ‘Day of the Week’ methodology, with Dummy OLS and GARCH(p,q) approaches, revealed that market for all the metals was efficient except copper. The study also tested model building pre-requisites of stationarity and serial correlation of variables and found these to be satisfactory. The results of the study thus revealed that copper’s prices showed market inefficiency which if exploited could provide a big opportunity for investors, traders and speculators to make profits. Market for remaining four metals was found to be efficient thus making profits difficult; however, these metals can be considered in combination with other financial assets to explore the unexplored opportunities in these markets.

Analysis of 2 men with t(8;22)(q13;q13) and t(8;14)(q13;q22) chromosomal translocation karyotypes

Male infertility is a multifactorial condition that is closely associated with chromosomal abnormalities. Reciprocal chromosomal translocation (RCT) is a significant structural genetic abnormality. The specific mechanisms of forms of RCT affecting male infertility include the product of chromosomally unbalanced gametes, thereby disrupting the structure and function of important genes responsible for spermatogenesis. RCT breakpoints have been found to disrupt gene structure and function in many medical fields However, the relationship between RCT breakpoints and male infertility remains to be determined. The purpose of this study is to describe 2 male carriers of RCTs 46,XY,t(8;22)(q13;q13) and 46,XY,t(8;14)(q13;q22). Both patients were collected from the second hospital of Jilin University. Semen parameters were detected using the computer-aided semen analysis system. Cytogenetic analysis was performed using standard operating procedure. Related genes on chromosomal breakpoints were searched using Online Mendelian Inheritance in Man. One man had semen parameters within the normal range, but the couple was infertile after 5 years of marriage. The other man showed normal semen parameters, and his wife had experienced 2 spontaneous miscarriages. Using a literature search, the association between chromosome 22q13 breakpoint and fertility were investigated. The results suggest that physicians should focus on the clinical phenotype of the patients and the breakpoints of RCT in genetic counseling. An important gene related to human male infertility is clearly located in chromosome region 22q13, and its function is worthy of further study.

The nonlinear association between grandiose and vulnerable narcissism: An individual data meta-analysis

OBJECTIVE

Narcissism can manifest in grandiose and vulnerable patterns of experience and behavior. While largely unrelated in the general population, individuals with clinically relevant narcissism are thought to display both. Our previous studies showed that trait measures of grandiosity and vulnerability were unrelated at low-to-moderate levels of grandiose narcissism, but related at high levels.

METHOD

We replicate and extend these findings in a preregistered individual data meta-analysis ("mega-analysis") using data from the Narcissistic Personality Inventory (NPI)/Hypersensitive Narcissism Scale (HSNS; N = 10,519, k = 28) and the Five-Factor Narcissism Inventory (FFNI; N = 7,738, k = 17).

RESULTS

There was strong evidence for the hypothesis in the FFNI (β_{Grandiose < 1 SD}  = .08, β_{Grandiose > 1 SD}  = .36, β_{Grandiose > 2 SD}  = .53), and weaker evidence in the NPI/HSNS (β_{Grandiose < 1 SD}  = .00, β_{Grandiose > 1 SD}  = .12, β_{Grandiose > 2 SD}  = .32). Nonlinearity increased with age but was invariant across other moderators. Higher vulnerability was predicted by elevated antagonistic and low agentic narcissism at subfactor level.

CONCLUSION

Narcissistic vulnerability increases at high levels of grandiosity. Interpreted along Whole Trait Theory, the effects are thought to reflect state changes echoing in trait measures and can help to link personality and clinical models.

Location of Tandem Repeats on Wheat Chromosome 5B and the Breakpoint on the 5BS Arm in Wheat Translocation T7BS.7BL-5BS Using Single-Copy FISH Analysis

Wheat (Triticum aestivum L.) is rich in tandem repeats, and this is helpful in studying its karyotypic evolution. Some tandem repeats have not been assembled into the wheat genome sequence. Alignment using the blastn tool in the B2DSC web server indicated that the genomic sequence of 5B chromosome (IWGSC RefSeq v2.1) does not contain the tandem repeat pTa-275, and the tandem repeat (GA)₂₆ distributed throughout the whole 5B chromosome. The nondenaturing fluorescence in situ hybridization (ND-FISH) using the oligonucleotide (oligo) probes derived from pTa-275 and (GA)₂₆ indicated that one signal band of pTa-275 and two signal bands of (GA)₂₆ appeared on the 5B chromosome of Chinese Spring wheat, indicating the aggregative distribution patterns of the two kinds of tandem repeats. Single-copy FISH indicated that the clustering region of pTa-275 and the two clustering regions of (GA)₂₆ were located in ~160-201 Mb, ~153-157 Mb, and ~201-234 Mb intervals, respectively. Using ND-FISH and single-copy FISH technologies, the translocation breakpoint on the 5BS portion of the translocation T7BS.7BL-5BS, which exists widely in north-western European wheat cultivars, was located in the region from 157,749,421 bp to 158,555,080 bp (~0.8 Mb), and this region mainly contains retrotransposons, and no gene was found. The clustering regions of two kinds of tandem repeats on wheat chromosome 5B were determined and this will be helpful to improve the future sequence assembly of this chromosome. The sequence characteristics of the translocation breakpoint on the translocation T7BS.7BL-5BS obtained in this study are helpful to understand the mechanism of wheat chromosome translocation.

Comparison of Three Different Commercial Methods for Fosfomycin Susceptibility Testing in Pseudomonas aeruginosa

The lack of internationally approved breakpoint and a handy susceptibility testing reduces fosfomycin usefulness against Pseudomonas aeruginosa. Previous works defined low or moderate agreement between commercial methods and the reference method (agar dilution [AD]). In particular, data lack about testing against P. aeruginosa. We compared disk diffusion (DD), E-test (ET), and automated broth microdilution (BMD) to AD by testing 150 P. aeruginosa isolates. We obtained better categorical agreement (CA) for DD and ET for minimal inhibitory concentration >128 mg/L (84.7% and 92.7%, respectively), but with high very major error (VME). BMD had the lowest VME rate (2/42), but with 64% CA and 52/108 major errors. We cannot define a method comparable to AD. Larger studies, as well as the definition of a breakpoint value are needed for fosfomycin against P. aeruginosa.

Molecular characterization of a novel recombinant lumpy skin disease virus isolated during an outbreak in Tyumen, Russia, in 2019

Lumpy skin disease virus causes a debilitating pox disease of domesticated cattle and water buffalos. In the last decade, LSDV has spread from Africa into the Middle East, Europe and most recently Asia. As of 2017 atypical outbreaks caused by novel LSDV strains were reported in Russia, followed by China and Vietnam between 2018 and 2020. In this work we describe another unique recombinant LSDV strain recovered from Tyumen, Russia in 2019. Typing of the virus using currently available qPCR protocols produced inconclusive results and subsequently the complete genome of the isolate was determined. The consensus genome contained statistically significant signals of possible recombination events between parental strains KSGPO-240/Kenya/1958 and the live attenuated vaccine LW/1958. The novel strain carries 25 unique breakpoints different from the known recombinant strains. Additionally, the findings reiterate the importance of complete genome sequencing when analysing outbreak samples caused in particular by mosaic LSDV, in contrast to only performing specified qPCRs. This article is protected by copyright. All rights reserved.

Comparing the Respiratory Compensation Point With Muscle Oxygen Saturation in Locomotor and Non-locomotor Muscles Using Wearable NIRS Spectroscopy During Whole-Body Exercise

The relationship between the muscle deoxygenation breakpoint (Deoxy-BP) measured with near-infrared spectroscopy (NIRS), and the respiratory compensation point (RCP) has been well established. This relationship has also been reported using wearable NIRS, however not in locomotor and non-locomotor muscles simultaneously during whole-body cycling exercise. Our aim was to measure muscle oxygen saturation (SmO₂) using wearable NIRS sensors, and to compare the Deoxy-BPs at each muscle with RCP during a ramp cycling exercise test. Twenty-two trained female and male cyclists completed a ramp exercise test to task intolerance on a cycling ergometer, at a ramp rate of 1 W every 2 s (30 W/min). SmO₂ was recorded at the subjects' right vastus lateralis (VL) and right lateral deltoid. SmO₂ and the Deoxy-BPs were assessed using a piecewise double-linear regression model. Ventilation (V̇_E) and gas exchange were recorded, and RCP was determined from V̇_E and gas exchange using a V-slope method and confirmed by two physiologists. The SmO₂ profiles of both muscles and gas exchange responses are reported as V̇O₂, power output (W), and time of occurrence (TO). SmO₂ profiles at both muscles displayed a near-plateau or breakpoint response near the RCP. No differences were detected between the mean RCP and mean Deoxy-BP from either the locomotor or non-locomotor muscles; however, a high degree of individual variability was observed in the timing and order of occurrence of the specific breakpoints. These findings add insight into the relationships between ventilatory, locomotor, and non-locomotor muscle physiological breakpoints. While identifying a similar relationship between these breakpoints, individual variability was high; hence, caution is advised when using wearable NIRS to estimate RCP in an incremental ramp test.

Detecting mechanical breakpoints during treadmill-based graded exercise test: Relationships to ventilatory thresholds

BACKGROUND

While changes in cardiorespiratory variables during graded exercise tests (GXTs) are well described, less is known about running mechanical alterations.

PURPOSE

We determined mechanical breakpoints during GXT and compared their temporal location with thresholds in ventilation.

METHODS

Thirty-one recreational male runners completed continuous GXT on an instrumented treadmill, starting at 2.5 m.s^-1 with velocity increases of + 0.14 m.s^-1 every 30 s. Subsequently, the first and second ventilatory thresholds (VT1 and VT2) were determined from expired gases. Spatio-temporal and antero-posterior force variables, and spring-mass model characteristics were averaged for each stage. Mechanical breakpoints were detected using a linear fit process that partitioned the timeseries into two regions and minimised the error sum of squares. All measurements were normalised to % GXT duration for subsequent comparisons.

RESULTS

Fifteen out of 16 mechanical variables (all except leg stiffness) displayed breakpoints occurring between 61.9% and 82.3% of GXT duration; these occurred significantly later than VT1 (46.9 ± 6.4% of GXT duration, p < 0.05). Mechanical breakpoints for eight variables (step frequency, aerial time, step length, peak push-off force, braking impulse, peak vertical force, maximal downward vertical displacement and leg compression) occurred at a time point not different to VT2 (75.3 ± 6.2% of GXT duration; all p > 0.05). Relationships between mechanical breakpoints and either VT1 or VT2 were weak (all r < 0.25).

CONCLUSION

During treadmill GXT, breakpoints can be detected for the vast majority of mechanical variables (except leg stiffness), yet these are not related with ventilatory thresholds.

Clinical Outcomes of Drug-resistant Shigellosis Treated With Azithromycin in Bangladesh

BACKGROUND

Azithromycin is frequently used to treat shigellosis; however, clinical outcomes are uncertain.

METHODS

We performed an observational cohort study in Bangladesh of patients with invasive diarrhea treated empirically with azithromycin. Susceptibility testing was performed by broth microdilution and disk diffusion post hoc on all Shigella isolates and clinical response was correlated with in vitro susceptibility.

RESULTS

There were 149 Shigella culture-positive patients in the primary analysis. Infection with Shigella with decreased susceptibility to azithromycin was significantly associated with persistence of diarrhea at day 5 (31% vs 12%; relative risk [RR], 2.66; 95% confidence interval [CI], 1.34-5.28), culture positivity at day 5 or 6 (35% vs 5%; RR, 5.26; 95% CI, 1.84-14.85), and a higher rate of overnight hospitalization (58% vs 39%; RR, 1.49; 95% CI, 1.06-2.09). Shigella flexneri was more common than Shigella sonnei (58% vs 36%); however, S. sonnei constituted most of the isolates with decreased susceptibility to azithromycin (67%) and most of the multidrug-resistant strains (54%); thus, poor clinical outcomes were associated with S. sonnei. The current epidemiological cutoff for S. flexneri of ≥16 µg/mL to define decreased susceptibility to azithromycin was clinically predictive of poor outcome. Patients with S. sonnei and a low MIC (4 µg/mL) still had elevated rates of persistent diarrhea and culture positivity.

CONCLUSIONS

This study documents worse clinical outcomes for S. flexneri with decreased susceptibility to azithromycin, as well as S. sonnei, and supports the utility of susceptibility testing and clinical breakpoints for azithromycin. S. sonnei is an emerging drug-resistant threat.

CLINICAL TRIALS REGISTRATION

NCT03778125.

Clinical Impact of the Revised 2019 CLSI Levofloxacin Breakpoints in Patients with Enterobacterales Bacteremia

The Clinical and Laboratory Standards Institute (CLSI) revised the fluoroquinolone MIC breakpoints for Enterobacterales in 2019, based on pharmacokinetic/pharmacodynamic analyses. However, clinical evidence supporting these breakpoint revisions is limited. A retrospective study was conducted at 3 hospitals in Taiwan between January 2017 and March 2019. Patients treated with levofloxacin for bacteremia caused by members of the Enterobacterales with high MICs (1 or 2 μg/ml; levofloxacin susceptible by pre-2019 CLSI breakpoints) were compared with those with low-MIC bacteremia (≤0.5 μg/ml; levofloxacin susceptible by 2019 CLSI breakpoints) to assess therapeutic effectiveness by multivariable logistic regression. The primary outcome was 30-day mortality, and the secondary outcome was the emergence of levofloxacin-resistant isolates within 90 days after levofloxacin initiation. A total of 308 patients were eligible for the study. Kaplan-Meier analysis showed that patients infected with high-MIC isolates (n = 63) had a significantly lower survival rate than those infected with low-MIC isolates (n = 245) (P = 0.001). Multivariable logistic regression revealed that high levofloxacin MIC was a predictor of 30-day mortality (odds ratio [OR], 6.05; 95% confidence interval [CI], 1.51 to 24.18; P = 0.011). We consistently found similar results in a propensity score-matched cohort (OR, 5.38; 95% CI, 1.06 to 27.39; P = 0.043). The emergence of levofloxacin-resistant isolates was more common in the high-MIC group than the low-MIC group (25.0% versus 7.5%; P = 0.065). An estimated area under the concentration-time curve/MIC ratio of ≥87 was significantly associated with better survival (P = 0.002). In conclusion, patients infected with isolates with levofloxacin MICs within the pre-2019 CLSI susceptible range of 1 or 2 μg/ml exhibited higher mortality than those infected with isolates with MICs of ≤0.5 μg/ml.

Discrepancy between colistin and polymyxin B susceptibility results among Escherichia coli and Klebsiella pneumoniae clinical isolates

The selection of therapeutic agent to be used for the treatment of multidrug-resistant bacteria is a major concern. Polymyxin B use has been commenced in Turkey, although its clinical breakpoint is not listed in the EUCAST. This study aimed to determine the correlation between the MIC values of polymyxin B and colistin. A total of 505 isolates, including 122 isolates of Escherichia coli and 383 isolates of Klebsiella pneumoniae were included in the present study. All the isolates were assessed for colistin and polymyxin B using the broth microdilution method. The categorical agreement in the E. coli isolates was 98.4%, and the rate of very major error was 33.3%. The categorical agreement in the K. pneumoniae isolates was 99.5%, the rate of major error was 0.36%, and the rate of very major error was 0.98%. In the evaluation of the essential agreement, 1.6% error in E. coli and 2.3% error in K. pneumoniae were observed. It was concluded that polymyxin B should never be used in the treatment of the isolates reported as colistin-resistant, and if the MIC values are above 4 mg/L in E. coli and K. pneumoniae. Our results indicate importance of reporting both polymyxin B and colistin susceptibility results of clinical isolates.

Pharmacokinetics and Pharmacodynamics of Nemonoxacin in a Neutropenic Murine Lung Infection Model Against Streptococcus Pneumoniae

Nemonoxacin, a novel nonfluorinated quinolone for the treatment of community-acquired pneumonia. We reported the pharmacokinetic/pharmacodynamic (PK/PD) targets and PK/PD breakpoints of nemonoxacin against Streptococcus pneumoniae using a neutropenic murine lung infection model. Single-dose PK analysis after subcutaneous administration of nemonoxacin at doses from 2.5 to 80 mg/kg showed maximum plasma concentration (C_max) 0.56-7.32 mg/L, area under the concentration-time curve from 0 to 24 h (AUC_0-24) 0.67-26.10 mg·h/L, and elimination half-life (T_1/2) 0.8-1.4 h. The epithelial lining fluid (ELF) penetration ratio of total drug was 1.40. Dose fractionation (1.25-80 mg/kg/day, every 24, 12, 8, and 6 h) and dose escalation studies (1.25-160 mg/kg, every 24 h) were conducted. The sigmoid E_max Hill equation was used to describe the dose-response data. The free-drug plasma fAUC_0-24/MIC ratio was considered the PK/PD index most closely associated with efficacy (R² 0.9268). Median fAUC_0-24/MIC associated with static, 1-log₁₀ and 2-log₁₀ CFU reduction from baseline were 8.6, 23.2 and 44.4, respectively. Monte Carlo simulation showed 500 mg qd and 750 mg qd oral doses of nemonoxacin were able to achieve 90% probability of target attainment (PTA) against bacteria with MIC of 0.5 mg/L and 1 mg/L. We recommended susceptibility (S) ≤ 0.5 mg/L, intermediate (I) = 1 mg/L and resistant (R) ≥ 2 mg/L as the PK/PD breakpoints for nemonoxacin against S. pneumoniae.

Probability distributions of helminth parasite burdens within the human host population following repeated rounds of mass drug administration and their impact on the transmission breakpoint

The existence of multiple stable equilibria in models of parasitic helminth transmission was a ground-breaking discovery over 30 years ago. An implication of this discovery, that there is a level of infection below which transmission cannot self-sustain called the transmission breakpoint, has in part motivated the push towards the elimination of many human diseases caused by the multiple species of helminth worldwide. In the absence of vaccines, the predominant method in this push towards elimination is to repeatedly administer endemic populations with anthelmintic drugs, over several treatment rounds, in what has become to be known as mass drug administration (MDA). MDA will inevitably alter the distribution of parasite burdens among hosts from the baseline distribution, and significantly, the location of the transmission breakpoint is known to be dependent on the level of aggregation of this distribution-for a given mean worm burden, more highly aggregated distributions where fewer individuals harbour most of the burden, will have a lower transmission breakpoint. In this paper, we employ a probabilistic analysis of the changes to the distribution of burdens in a population undergoing MDA, and simple approximations, to determine how key aspects of the programmes (including compliance, drug efficacy and treatment coverage) affect the location of the transmission breakpoint. We find that individual compliance to treatment, which determines the number of times an individual participates in mass drug administration programmes, is key to the location of the breakpoint, indicating the vital importance to ensure that people are not routinely missed in these programmes.

Evaluation of Surrogate Tests for the Presence of mecA-Mediated Methicillin Resistance in Staphylococcus capitis, Staphylococcus haemolyticus, Staphylococcus hominis, and Staphylococcus warneri

Testing of staphylococci other than Staphylococcus aureus (SOSA) for mecA-mediated resistance is challenging. Isolates of Staphylococcus capitis, Staphylococcus haemolyticus, Staphylococcus hominis, and Staphylococcus warneri were evaluated by cefoxitin and oxacillin broth microdilution (BMD), disk diffusion (DD), and PBP2a immunoassay, and the results were compared to mecA PCR results. No phenotypic susceptibility test correlated well with PCR results across all species, although the PBP2a immunoassay yielded 100% correlation. Oxacillin BMD testing by current Clinical and Laboratory Standards Institute (CLSI) SOSA breakpoints led to 2.1% very major errors (VMEs) and 7.1% major errors (ME). Adjusting this breakpoint up by a dilution (susceptible, ≤0.5 μg/ml; resistant, ≥1.0 μg/ml) led to 2.8% VMEs and 0.3% MEs. Among species evaluated, S. haemolyticus had unacceptable VMEs with this new breakpoint (6.4%), as did S. hominis (4.0%). MEs were acceptable by this new breakpoint, ranging from 0 to 1.2%. Oxacillin DD yielded high ME rates (20.7 to 21.7%) using CLSI or European Committee on Antimicrobial Susceptibility Testing breakpoints. VMEs ranged from 0 to 5.3%. Cefoxitin BMD led to 4.9% VMEs and 1.6% MEs. Cefoxitin DD performed best when interpreted with the CLSI SOSA breakpoint, with 1.0% VMEs and 2.9% MEs. This study led CLSI to adjust the oxacillin MIC breakpoints for SOSA. Laboratories should be aware that no individual phenotypic test correlates well across all species of SOSA with mecA PCR results. Molecular testing for mecA or evaluation for PBP2a is the preferred approach.

Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies

Gene order can be used as an informative character to reconstruct phylogenetic relationships between species independently from the local information present in gene/protein sequences. PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively, supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances. PhyChro estimates branch lengths based on the number of synteny breakpoints and provides confidence scores for the branches. PhyChro performance is evaluated on two data sets of 13 vertebrates and 21 yeast genomes by using up to 130,000 and 179,000 breakpoints, respectively, a scale of genomic markers that has been out of reach until now. PhyChro reconstructs very accurate tree topologies even at known problematic branching positions. Its robustness has been benchmarked for different synteny block reconstruction methods. On simulated data PhyChro reconstructs phylogenies perfectly in almost all cases, and shows the highest accuracy compared with other existing tools. PhyChro is very fast, reconstructing the vertebrate and yeast phylogenies in <15 min.

Chromosome 1q21 translocation and spermatogenesis failure: Two case reports and review of the literature

RATIONALE

For the carriers of chromosome reciprocal translocation, the reason why some are fertile and others are infertile remains unclear. Here, we describe 2 patients who are carriers of chromosome 1q21 translocation with azoospermia.

PATIENT CONCERNS

A 29-year-old male and a 33-year-old male presented at the clinic with a diagnosis of infertility.

DIAGNOSIS

Both patients with azoospermia were diagnosed with Routine semen analysis, cytogenetic diagnosis and detection of serum reproductive hormones. The karyotype results of 2 patients were 46,XY,t(1;17)(q21;q23) and 46,XY,t(1;10)(q21;p12), respectively.

INTERVENTIONS

After genetic counseling and informed consent, 1 patient (Case 2) chose microsopic testicular sperm extraction (micro-TESE).

OUTCOMES

After micro-TESE, no sperm was found for the patient. Finally, both patients chose clinical treatment through artificial insemination with donor sperm.

LESSONS

These outcomes suggest that breakpoint at 1q21 should be paid attention by physician in genetic counseling, may harbor some genes associated with spermatogenesis, and deserves further be studied on the function of related genes.

Don't Get Wound Up: Revised Fluoroquinolone Breakpoints for Enterobacteriaceae and Pseudomonas aeruginosa

Fluoroquinolones remain some of the more commonly prescribed antimicrobial agents in the United States, despite the wide array of reported side effects that are associated with their use. In 2019, the Clinical and Laboratory Standards Institute revised the fluoroquinolone antimicrobial susceptibility testing breakpoints for both Enterobacteriaceae and Pseudomonas aeruginosa This breakpoint revision was deemed necessary on the basis of pharmacokinetic and pharmacodynamic analyses suggesting that the previous breakpoints were too high, in addition to the inability of the previous breakpoints to detect low-level resistance to this antibiotic class. In this minireview, we review the published data in support of this revision, as well as the potential challenges that these breakpoint revisions are likely to pose for clinical laboratories.

The New, New Daptomycin Breakpoint for Enterococcus spp

In 2019, the Clinical and Laboratory Standards Institute revised the daptomycin breakpoints for Enterococcus spp. twice in rapid succession. Analyses leading to these revisions included review of testing issues, murine and human in vivo pharmacodynamics, safety of off-label doses, and treatment outcomes. The data review brought up a dilemma that is encountered with increasing frequency: a breakpoint supported by pharmacokinetic/pharmacodynamic modeling that bisected the wild-type Enterococcus faecium MIC distribution. In such instances, not only does the probability of pharmacokinetic/pharmacodynamic targets need to be taken into account but also the probability that the laboratory can generate an accurate MIC that is reproducible within one interpretive category.

Parasite Removal for Malaria Elimination in Costa Rica

In Costa Rica, malaria parasite removal via treatment shift and focalized mass drug administration (MDA) largely decreased malaria transmission between 2006 and 2009, and led to malaria elimination from 2013 to 2015. These results can help to shape a regional strategy for malaria elimination in Mesoamerica and México.

Non-Robertsonian translocations involving chromosomes 13, 14, or 15 in male infertility: 28 cases and a review of the literature

For genetic counseling of male carriers of chromosomal translocations, the specific chromosomes and breakpoints involved in the translocation are relevant to know. The structural chromosomal abnormalities may lead to abnormal sperm counts, infertility, and miscarriage. These are related to the specific chromosomes and breakpoints involved in the translocation. To date, over 200 cases of non-Robertsonian translocation in male carriers have been described that involve chromosomes 13, 14, or 15.This study reports of 28 male carriers from our clinic with balanced reciprocal translocations of chromosome 13, 14, or 15, and a literature review of 201 cases. The 28 male carriers from our clinic were diagnosed by cytogenetic analyses: 19 subjects suffered from pregestational infertility and 9 from gestational infertility. The most common translocations were t(7;13), t(10;14), and t(3;15), observed respectively in 13 (46%), 8 (29%), and 8 (29%) of our subjects. The literature cases (n = 201) involved chromosome 13 (n = 83, 41%), chromosome 14 (n = 56, 28%) or 15 (n = 62, 31%) in which 75 breakpoints were identified, the most common breakpoint, 13q22, was observed in 12 subjects (6%), followed by 14q32 (n = 11), 15q15 (n = 9), and 15q22 (n = 9). Most breakpoints were related to gestational infertility, while breakpoints at 13p13, 13p12, 13p11.2, 13p11, 13q11, 13q15, 14p12, 14p10, 15p13, 15p10, and 15q22.2 were associated with pregestational infertility.Carriers of non-Robertsonian translocations involving chromosome 13, 14, or 15 and experiencing infertility should receive counseling with regard to chromosomal breakpoints as there seem to be consequences for treatment. Intracytoplasmic sperm injection with preimplantation genetic diagnosis (PGD) for the carriers with oligozoospermia, microscopic testicular sperm extraction or sperm from the sperm bank for the carriers with azoospermia should be considered for pregestational infertility. The carriers with gestational infertility can choose PGD or prenatal diagnosis.

Relation between flomoxef minimum inhibitory concentrations and clinical outcomes of patients treated with flomoxef for Enterobacteriaceae bacteremia

Background

Flomoxef is potentially effective against β-lactamase-producing Enterobacteriaceae because limited clinical data demonstrate its effectiveness against Enterobacteriaceae bloodstream infections (BSIs) based on its minimum inhibitory concentrations (MICs). This study was conducted to determine the optimal breakpoints based on the survival of patients with Enterobacteriaceae BSIs treated with flomoxef.

Methods

The 30-day crude mortality rate was analyzed among 224 adults who initiated flomoxef monotherapy for Enterobacteriaceae BSIs at a medical center over a 3-year period, according to the flomoxef MICs of the initial isolates. The outcome was evaluated by classification and regression tree modeling and by logistic regression analysis.

Results

The 30-day crude mortality was approximately two fold greater in patients whose isolates had flomoxef MICs of ≥2 mg/L (54.9% [62/113]) than in those with isolates with MICs of ≤1 mg/L (26.1% [29/111]); the differences were significant in bivariate analysis (P<0.01) and in survival analysis (log-rank test; P<0.001). The classification and regression tree analysis revealed a split between MICs of 1 and 2 mg/L and predicted the same difference in mortality, with a P-value of <0.001. Flomoxef for Enterobacteriaceae BSIs caused by isolates with flomoxef MICs of ≥2 mg/L was an independent predictor of 30-day crude mortality (adjusted OR 3.76, 95% CI 1.94–7.29).

Conclusion

Patients with Enterobacteriaceae bacteremia who received flomoxef had a lower 30-day crude mortality when the flomoxef MICs of the isolates were ≤1 mg/L than those with MICs ≥2 mg/L.

Antimicrobial Susceptibility Testing and Tentative Epidemiological Cutoff Values for Five Bacillus Species Relevant for Use as Animal Feed Additives or for Plant Protection

Bacillus megaterium (n = 29), Bacillus velezensis (n = 26), Bacillus amyloliquefaciens (n = 6), Bacillus paralicheniformis (n = 28), and Bacillus licheniformis (n = 35) strains from different sources, origins, and time periods were tested for the MICs for nine antimicrobial agents by the CLSI-recommended method (Mueller-Hinton broth, 35°C, for 18 to 20 h), as well as with a modified CLSI method (Iso-Sensitest [IST] broth, 37°C [35°C for B. megaterium], 24 h). This allows a proposal of species-specific epidemiological cutoff values (ECOFFs) for the interpretation of antimicrobial resistance in these species. MICs determined by the modified CLSI method were 2- to 16-fold higher than with the CLSI-recommended method for several antimicrobials. The MIC distributions differed between species for five of the nine antimicrobials. Consequently, use of the modified CLSI method and interpretation of resistance by use of species-specific ECOFFs is recommended. The genome sequences of all strains were determined and used for screening for resistance genes against the ResFinder database and for multilocus sequence typing. A putative chloramphenicol acetyltransferase (cat) gene was found in one B. megaterium strain with an elevated chloramphenicol MIC compared to the other B. megaterium strains. In B. velezensis and B. amyloliquefaciens, a putative tetracycline efflux gene, tet(L), was found in all strains (n = 27) with reduced tetracycline susceptibility but was absent in susceptible strains. All B. paralicheniformis and 23% of B. licheniformis strains had elevated MICs for erythromycin and harbored ermD The presence of these resistance genes follows taxonomy suggesting they may be intrinsic rather than horizontally acquired. Reduced susceptibility to chloramphenicol, streptomycin, and clindamycin could not be explained in all species.IMPORTANCE When commercializing bacterial strains, like Bacillus spp., for feed applications or plant bioprotection, it is required that the strains are free of acquired antimicrobial resistance genes that could potentially spread to pathogenic bacteria, thereby adding to the pool of resistance genes that may cause treatment failures in humans or animals. Conversely, if antimicrobial resistance is intrinsic to a bacterial species, the risk of spreading horizontally to other bacteria is considered very low. Reliable susceptibility test methods and interpretation criteria at the species level are needed to accurately assess antimicrobial resistance levels. In the present study, tentative ECOFFs for five Bacillus species were determined, and the results showed that the variation in MICs followed the respective species. Moreover, putative resistance genes, which were detected by whole-genome sequencing and suggested to be intrinsic rather that acquired, could explain the resistance phenotypes in most cases.

Variation and diversity of the breakpoint sequences on 4AL for the 4AL/5AL translocation in Triticum

The translocation of 4AL/5AL in Triticum, which occurred before the differentiation of T. urartu and einkorn, is an important chromosomal rearrangement. Recently, the first identification of breakpoint sequence on 4AL for this translocation provides the opportunity to analyze the variation and diversity of breakpoints in Triticum. In this study, the breakpoint regions of 52 accessions from 21 species were isolated and further characterized. The sequences were divided into 12 types based on their lengths, which ranged from 2009 to 2552 bp. Cluster analysis showed that they were further divided into three groups. Interesting evolutionary relationships among a few of the species were observed and discussed. Multiple sequence alignment of the 52 sequences made it possible to detect 13 insertion and deletion length polymorphisms (InDels) and 101 single nucleotide polymorphisms (SNPs). Furthermore, several species- or accession-specific SNPs or InDels were also identified. Based on BLAST analysis of the conserved sequences, the breakpoint was narrowed down to a 125 bp fragment. Taken together, the results obtained in this study enrich our understanding of chromosomal breakpoints and will be useful for the identification of other breakpoints in wheat.

Pharmacokinetic/Pharmacodynamic Analysis for Doripenem Regimens in Intensive Care Unit Patient

Doripenem (DRPM) is a broad-spectrum antibacterial agent often used as empirical therapy for critically ill patients, although there is a lack of studies validating the recommended dosage regimen for patients admitted to intensive care unit (ICU), based on pharmacokinetic (PK)/pharmacodynamic (PD) index. In this study, we estimated the free time above minimum inhibitory concentration (fT>MIC (%)) of DRPM using population PK analysis of 12 patients in ICU, and evaluated the validity of the dosage regimen stratified by creatinine clearance. Using a 2-compartment population PK model reported previously, the mean total clearance or distribution volume of DRPM estimated by Bayesian estimation was significantly lower or higher than that of based on population PK model. The estimated fT>MIC (%) of the recommended standard (normal renal function: 0.5 g every 8 h, moderate: 0.25 g every 8 h, severe renal impairment: 0.25 g every 12 h) and higher doses (normal: 1.0 g every 8 h, moderate: 0.5 g every 8 h, severe: 0.25 g every 8 h) against MICs of 0.5, 1 and 2 µg/mL exceeded 40% in all patients. When stratified by creatinine clearance, the PK/PD breakpoints estimated by Monte Carlo simulation in three grades of renal function tended to be higher than the previously reported PK/PD breakpoints for patients with urinary tract infection, an infection of lesser severity than ICU patients. These results suggest that the dosage regimen stratified by renal function derived from Japanese package insert may be sufficient to achieve effective treatment in ICU patients.

Human papillomavirus genome integration in squamous carcinogenesis: what have next-generation sequencing studies taught us?

Human papillomavirus (HPV) infection is associated with ∼5% of all human cancers, including a range of squamous cell carcinomas. Persistent infection by high-risk HPVs (HRHPVs) is associated with the integration of virus genomes (which are usually stably maintained as extrachromosomal episomes) into host chromosomes. Although HRHPV integration rates differ across human sites of infection, this process appears to be an important event in HPV-associated neoplastic progression, leading to deregulation of virus oncogene expression, host gene expression modulation, and further genomic instability. However, the mechanisms by which HRHPV integration occur and by which the subsequent gene expression changes take place are incompletely understood. The advent of next-generation sequencing (NGS) of both RNA and DNA has allowed powerful interrogation of the association of HRHPVs with human disease, including precise determination of the sites of integration and the genomic rearrangements at integration loci. In turn, these data have indicated that integration occurs through two main mechanisms: looping integration and direct insertion. Improved understanding of integration sites is allowing further investigation of the factors that provide a competitive advantage to some integrants during disease progression. Furthermore, advanced approaches to the generation of genome-wide samples have given novel insights into the three-dimensional interactions within the nucleus, which could act as another layer of epigenetic control of both virus and host transcription. It is hoped that further advances in NGS techniques and analysis will not only allow the examination of further unanswered questions regarding HPV infection, but also direct new approaches to treating HPV-associated human disease. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Translocation breakpoints of chromosome 3 in male carriers: a report of twelve cases and a review of the literature

Background/aim: This study aimed to explore the breakpoints in chromosome 3 translocation and the clinical features present in male carriers to enable informed genetic counseling of these patients. Materials and methods: A total of 5235 men who were infertile or receiving counseling for infertility were recruited. Cytogenetic analyses were performed using G-banding. A search for translocations on chromosome 3 involved in male infertility was performed using PubMed, Google Scholar, and CNKI. The relationships of translocation breakpoints with male infertility and recurrent pregnancy loss were also analyzed. Results: Among the 82 patients with balanced reciprocal translocations among 5235 male patients, 12 patients were carriers of chromosome 3 translocation: two presented with pregestational infertility, while 10 presented with gestational infertility. The breakpoint at 3p13 was related to pregestational infertility, whereas those at 3p23, 3q10, 3q12, 3q21, 3q25, and 3q29 were related to gestational infertility. By an analysis combining data from the literature, 63 carriers of chromosome 3 translocation were reviewed and all breakpoints at chromosome 3 were correlated with gestational infertility. Conclusion: All breakpoints at chromosome 3 were correlated with gestational infertility. The breakpoints at 3q12 and 3q29 were the most common. Carriers of chromosome 3 translocation should thus be counseled on the need for other chromosomal breakpoints and preimplantation genetic diagnosis or prenatal testing.

Successful treatment with allogeneic stem cell transplantation followed by DLI and TKIs for e6a2 BCR-ABL-positive acute myeloid leukaemia: A case report and literature review

RATIONALE

Patients with the e6a2 BCR-ABL transcript, 1 of the atypical transcripts, have been reported to have a poor prognosis, and allogeneic stem cell transplantation (ASCT) can be considered as additional therapy. However, long-term survival after ASCT for this disease is rare.

PATIENT CONCERNS

This report concerns a 55-year-old female patient with e6a2 BCR-ABL-positive acute myeloid leukemia including the outcome of ASCT followed by donor lymphocyte infusion (DLI).

DIAGNOSES

The breakpoint was confirmed by direct sequencing. Her minimal residual disease could be detected by nested reverse-transcription polymerase chain reaction using primers for the minor BCR-ABL (e1a2) transcript.

INTERVENTIONS

Treatment with tyrosine kinase inhibitors (TKIs) and ASCT followed by DLI.

OUTCOMES

Despite multiple cytogenetic and molecular relapses after ASCT, she remains in molecular remission at 46 months after ASCT.

LESSONS

This case indicates the efficacy of the combination of the graft-versus-leukemia effect and TKIs for e6a2 BCR-ABL-positive acute leukemia. When the Philadelphia chromosome with an unusual chromosomal breakpoint is suggested, we should clarify the breakpoint because that information can aid molecular assessments and decisions to provide an additional or alternative therapy.

Investigation of the Efficacy of an Administration Plan for Tazobactam/Piperacillin (TAZ/PIPC) and the Incidence of Kidney and Hepatic Disorders

Tazobactam/piperacillin (TAZ/PIPC) is widely used in the treatment of infectious disease. In this study, three hundred and sixty-three patients who were treated with the recommended dose of TAZ/PIPC were investigated for the proportion of time above the minimum inhibitory concentration (%TAM) and the frequency of renal and liver dysfunction. Of the whole patient population, 5.23%, exhibited increased creatinine levels, 9.37% and 8.82% exhibited increased aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels, respectively. The patients who exhibited high serum creatinine (SCr) levels before administration, exhibited significant increases of AST (p=0.0121). The patients who exhibited low albumin levels before administration, exhibited significant decreases in renal function (p=0.0041). In the case of a breakpoint (BP) of 64 μg/mL, the arrival probabilities of %TAM of 30% and 50% were 99.4% and 76.9%, respectively. We suggested that the dose of TAZ/PIPC should be adjusted according to the interview form finding and a %TAM>50% (maximal bactericidal action).

Blockade of dopamine D1-family receptors attenuates the mania-like hyperactive, risk-preferring, and high motivation behavioral profile of mice with low dopamine transporter levels

BACKGROUND

Patients with bipolar disorder mania exhibit poor cognition, impulsivity, risk-taking, and goal-directed activity that negatively impact their quality of life. To date, existing treatments for bipolar disorder do not adequately remediate cognitive dysfunction. Reducing dopamine transporter expression recreates many bipolar disorder mania-relevant behaviors (i.e. hyperactivity and risk-taking). The current study investigated whether dopamine D1-family receptor blockade would attenuate the risk-taking, hypermotivation, and hyperactivity of dopamine transporter knockdown mice.

METHODS

Dopamine transporter knockdown and wild-type littermate mice were tested in mouse versions of the Iowa Gambling Task (risk-taking), Progressive Ratio Breakpoint Test (effortful motivation), and Behavioral Pattern Monitor (activity). Prior to testing, the mice were treated with the dopamine D1-family receptor antagonist SCH 23390 hydrochloride (0.03, 0.1, or 0.3 mg/kg), or vehicle.

RESULTS

Dopamine transporter knockdown mice exhibited hyperactivity and hyperexploration, hypermotivation, and risk-taking preference compared with wild-type littermates. SCH 23390 hydrochloride treatment decreased premature responding in dopamine transporter knockdown mice and attenuated their hypermotivation. SCH 23390 hydrochloride flattened the safe/risk preference, while reducing activity and exploratory levels of both genotypes similarly.

CONCLUSIONS

Dopamine transporter knockdown mice exhibited mania-relevant behavior compared to wild-type mice. Systemic dopamine D1-family receptor antagonism attenuated these behaviors in dopamine transporter knockdown, but not all effects were specific to only the knockdown mice. The normalization of behavior via blockade of dopamine D1-family receptors supports the hypothesis that D1 and/or D5 receptors could contribute to the mania-relevant behaviors of dopamine transporter knockdown mice.

Decomposing Multifractal Crossovers

Physiological processes-such as, the brain's resting-state electrical activity or hemodynamic fluctuations-exhibit scale-free temporal structuring. However, impacts common in biological systems such as, noise, multiple signal generators, or filtering by transport function, result in multimodal scaling that cannot be reliably assessed by standard analytical tools that assume unimodal scaling. Here, we present two methods to identify breakpoints or crossovers in multimodal multifractal scaling functions. These methods incorporate the robust iterative fitting approach of the focus-based multifractal formalism (FMF). The first approach (moment-wise scaling range adaptivity) allows for a breakpoint-based adaptive treatment that analyzes segregated scale-invariant ranges. The second method (scaling function decomposition method, SFD) is a crossover-based design aimed at decomposing signal constituents from multimodal scaling functions resulting from signal addition or co-sampling, such as, contamination by uncorrelated fractals. We demonstrated that these methods could handle multimodal, mono- or multifractal, and exact or empirical signals alike. Their precision was numerically characterized on ideal signals, and a robust performance was demonstrated on exemplary empirical signals capturing resting-state brain dynamics by near infrared spectroscopy (NIRS), electroencephalography (EEG), and blood oxygen level-dependent functional magnetic resonance imaging (fMRI-BOLD). The NIRS and fMRI-BOLD low-frequency fluctuations were dominated by a multifractal component over an underlying biologically relevant random noise, thus forming a bimodal signal. The crossover between the EEG signal components was found at the boundary between the δ and θ bands, suggesting an independent generator for the multifractal δ rhythm. The robust implementation of the SFD method should be regarded as essential in the seamless processing of large volumes of bimodal fMRI-BOLD imaging data for the topology of multifractal metrics free of the masking effect of the underlying random noise.

Molecular Genetic Characterization of a Chinese Family with Severe Split Hand/Foot Malformation

AIMS

Split hand/foot malformation (SHFM) is a congenital limb malformation characterized by underdeveloped or absent central digital rays, clefts of the hands and feet, and variable syndactyly of the remaining digits. SHFM is a genetically heterogeneous disease; the aim of this study was to identify pathogenic variations in a Chinese family with SHFM.

MATERIALS AND METHODS

Haplotype analyses with microsatellite markers covering the five SHFM loci were performed to localize the causative locus. Real-time quantitative polymerase chain reaction (qPCR) assays and inverse PCR were performed to determine the copy number variations and to amplify junction breakpoints in affected individuals. Candidate genes were further screened for mutations through Sanger sequencing.

RESULTS

A potential haplotype in the SHFM3 locus was shared by all affected individuals. qPCR and inverse PCR showed a microduplication at chromosome 10q24 spanning 488,859 bp and encompassing five entire genes, LBX1, BTRC, POLL, DPCD, and FBXW4, that co-segregated with the SHFM phenotype. No coding or splice-site mutations of these genes were found.

CONCLUSION

We determined the molecular basis of SHFM in a Chinese family by haplotype analysis, qPCR, inverse PCR, and Sanger sequencing. Our work extends the clinical spectrum of SHFM3; provides a fine-scale delineation of the chromosomal breakpoints helping to narrow the critical region of SHFM3; and facilitates an understanding of the mechanisms underlying abnormal limb development and extraskeletal anomalies.

Establishment and Use of Epidemiological Cutoff Values for Molds and Yeasts by Use of the Clinical and Laboratory Standards Institute M57 Standard

Breakpoints are used to predict whether an antifungal agent will be clinically effective against a particular fungal isolate. They are based on a combination of MIC values, pharmacokinetic/pharmacodynamic values, and clinical outcome data. For many fungus-antifungal combinations, these data might never be available. For these combinations, epidemiological cutoff values (ECVs) provide a methodology for categorizing isolates as either wild type (WT) or non-WT. In this review, we define ECVs, explain how they are generated using the CLSI methodology in standard M57, and describe how they can be used in clinical practice.