Routine Surveillance Research Articles

Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation.

Epidemiological surveillance of animal tuberculosis (TB) based on whole genome sequencing (WGS) of Mycobacterium bovis has recently gained track due to its high resolution to identify infection sources, characterize the pathogen population structure, and facilitate contact tracing. However, the workflow from bacterial isolation to sequence data analysis has several technical challenges that may severely impact the power to understand the epidemiological scenario and inform outbreak response. While trying to use archived DNA from cultured samples obtained during routine official surveillance of animal TB in Portugal, we struggled against three major challenges: the low amount of M. bovis DNA obtained from routinely processed animal samples; the lack of purity of M. bovis DNA, i.e., high levels of contamination with DNA from other organisms; and the co-occurrence of more than one M. bovis strain per sample (within-host mixed infection). The loss of isolated genomes generates missed links in transmission chain reconstruction, hampering the biological and epidemiological interpretation of data as a whole. Upon identification of these challenges, we implemented an integrated solution framework based on whole genome amplification and a dedicated computational pipeline to minimize their effects and recover as many genomes as possible. With the approaches described herein, we were able to recover 62 out of 100 samples that would have otherwise been lost. Based on these results, we discuss adjustments that should be made in official and research laboratories to facilitate the sequential implementation of bacteriological culture, PCR, downstream genomics, and computational-based methods. All of this in a time frame supporting data-driven intervention.

Criteria pollutant and greenhouse gas emissions from cargo handling equipment operating at the Ports of Los Angeles and Long Beach

This study reports in-use emissions from eight pieces of diesel or natural gas cargo handling equipment (CHE) moving containerized freight at the Ports of Los Angeles and Long Beach. Equipment had engines certified to the legacy on-road model year (MY) 2010 or the off-road Tier 3, Tier 4 Interim, or Tier 4 Final emission standards. Overall, load factors were about half of the values in the California Air Resources Board's (CARB) current CHE emissions inventory, oxides of nitrogen (NOx) emissions were 2.7 times higher than certification standards, and tailpipe-emitted fine particulate matter (PM2.5) emissions were 2.2 times higher than certification standards. This is yet another study, the first dedicated to in-use operations by CHE at a large commercial seaport, showing elevated in-use emissions from combustion-powered mobile sources compared to certification levels. These results underscore the need to perform routine surveillance emissions testing of any off-road mobile source fleet when developing emission inventories and air quality programs for any jurisdiction worldwide. The Energy Economy Ratio (EER) – or ratio of increased efficiency from converting combustion to zero-emission battery-electric equipment – ranged from 2.8 to 3.7, which highlights potential energy savings and therefore greenhouse gas benefits of transitioning CHE and other freight sectors to zero-emission technologies.

Sex-Specific Developmental Scales for Surveillance.

Developmental surveillance, conducted routinely worldwide, is fundamental for early detection of children at risk for developmental delay. We aimed to explore sex-related difference in attainment rates of developmental milestones and to evaluate the clinical need for separate sex-specific scales. This is a cross-sectional, natiowide retrospective study, utilizing data from a national child surveillance program of ∼1000 maternal child health clinics. The main cohort, used for constructing sex-specific developmental scales, included all children born between January 2014 to September 2020, who visited maternal child health clinics from birth to 6 years of age (n = 839 574). Children with abnormal developmental potential were excluded (n = 195 616). A validation cohort included all visits between 2020 and 2021 (n = 309 181). The sex-differences in normative attainment age of 59 developmental milestones from 4 domains were evaluated. The milestones with a significant gap between males and females were identified, and the projected error rates when conducting unified versus sex-specific surveillance were calculated. A new sex-specific developmental scale was constructed. In total, females preceded males in most milestones of all developmental domains, mainly at older ages. Conducting routine developmental surveillance using a unified scale, compared with sex-specific scales, resulted in potential missing of females at risk for developmental delay (19.3% of failed assessments) and over-diagnosis of males not requiring further evaluation (5.9% of failed assessments). There are sex-related differences in the normative attainment rates of developmental milestones, indicating possible distortion of the currently used unified scales. These findings suggest that using sex-specific scales may improve the accuracy of early childhood developmental surveillance.

Xanthomonas rydalmerensis sp. nov., a non-pathogenic member of Group 1 Xanthomonas.

Five bacterial isolates were isolated from Fragaria × ananassa in 1976 in Rydalmere, Australia, during routine biosecurity surveillance. Initially, the results of biochemical characterisation indicated that these isolates represented members of the genus Xanthomonas. To determine their species, further analysis was conducted using both phenotypic and genotypic approaches. Phenotypic analysis involved using MALDI-TOF MS and BIOLOG GEN III microplates, which confirmed that the isolates represented members of the genus Xanthomonas but did not allow them to be classified with respect to species. Genome relatedness indices and the results of extensive phylogenetic analysis confirmed that the isolates were members of the genus Xanthomonas and represented a novel species. On the basis the minimal presence of virulence-associated factors typically found in genomes of members of the genus Xanthomonas, we suggest that these isolates are non-pathogenic. This conclusion was supported by the results of a pathogenicity assay. On the basis of these findings, we propose the name Xanthomonas rydalmerensis, with DAR 34855T = ICMP 24941 as the type strain.

Occurrence and genomic characterization of antimicrobial-resistant and potential pathogenic <i>Escherichia coli</i> from Italian artisanal food productions of animal origin

Escherichia coli can harbor a broad repertoire of virulence and antimicrobial resistance (AMR) genes, which can be exchanged across the human gastrointestinal microflora, thus posing a public health risk. In this study, six batches of artisanal soft cheese and a 6-month ripened fermented dried sausage were investigated to assess the occurrence, phylogeny, and genomic traits (AMR, virulence, and mobilome) of E. coli. Thirty and three strains isolated from salami and cheese food chains, respectively, were confirmed as E. coli by whole genome sequencing. The accumulation of single nucleotide polymorphism differences within small clusters of strains encompassing batches or processing stages, combined with high serotype and phylogroup diversity, suggested the occurrence of different contamination phenomena among the facilities. A total of eight isolates harbored plasmid-mediated resistance genes, including one cheese strain that carried an IncQ1 plasmid carrying AMR determinants to macrolides [mph(B)], sulfonamides (sul1, sul2), trimethoprim (dfrA1), and aminoglycosides [aph(3'')-Ib and aph(6)-Id]. A pool of virulence-associated genes in the class of adhesion, colonization, iron uptake, and toxins, putative ColV-positive iron uptake systems sit, iro, or iuc (eight salami and two cheese), plasmid-encoded hemolysin operon hlyABCD (one salami), and potential atypical enteropathogenic E. coli (three salami environment) were reported. Overall, our findings underscore the importance of routine surveillance of E. coli in the artisanal food chain to prevent the dissemination of AMR and virulence.

Epidemiology of Escherichia coli bloodstream infection antimicrobial resistance trends across South West England during the first 2 years of the coronavirus disease 2019 pandemic response

ObjectivesBetween 2016 and 2019, the proportion of Escherichia coli bloodstream infection (BSI) with resistance to at least one antibiotic increased nationally. Public health interventions implemented in response to the COVID-19 pandemic changed population contact patterns and healthcare systems, with consequent effects on epidemiological trends of numerous pathogens. We investigated the impact of COVID-19 restrictions on epidemiological trends of E. coli BSI antimicrobial resistance (AMR) across South West England. MethodsWe undertook a retrospective ecological analysis utilizing routine surveillance data of E. coli BSI cases reported to the UK Health Security Agency between 2016 and 2021. We analysed AMR trends for antimicrobial agents including amoxicillin–clavulanate, ciprofloxacin, piperacillin–tazobactam, gentamicin, third-generation cephalosporins and carbapenems before and after the implementation of COVID-19 restrictions (23 March 2020) using Bayesian segmented regression. ResultsWe identified 19 055 cases. A total of 50.2% were male. Median age was 76 (interquartile range, 65–85 years). Piperacillin–tazobactam (–2.90% [95% highest density interval {HDI} –4.51%, –0.48%]) and ciprofloxacin (–2.40% [95% HDI –4.35%, 0.48%]) resistance demonstrated immediate step changes at the implementation of COVID-19 restrictions. Gentamicin (odds ratio [OR] 0.92 [95% HDI 0.76, 1.12]) and third-generation cephalosporins (OR 0.95 [95% HDI 0.80, 1.14]) exhibited decreasing annual resistance trends after the implementation of COVID-19 restrictions, with moderate evidence for a lower OR after restrictions as compared to the period before (gentamicin Bayes Factor = 5.10, third-generation cephalosporins Bayes Factor = 6.67). DiscussionCOVID-19 restrictions led to abrupt and longer term changes to E.coli BSI AMR. The immediate effects suggest altered transmission, whereas changes to resistant E. coli reservoirs may explain trend effects.

Comparison of bacteriological culture method and multiplex real-time PCR for detection of mastitis

This study includes the evaluation of multiplex real-time PCR (rPCR) kit, which was developed to provide rapid diagnosis of mastitis infections, by working with milk samples of 2 different sources of mastitis and comparing the results with the classical bacteriological culture method (BC). A total of 273 bacteria were isolated in 226 samples (47.88%) out of 472 samples by BC. These were 139 (50.91%) Staphylococcus spp., 61 (22.34%) Streptococcus spp., 15 (5.49%) E. coli, 8 (2.93%) Enterococcus spp., 50 (18.31%) other bacteria. When we look at the multiplex rPCR results; 1052 positive were obtained for the gene regions of 14 different bacteria, 1 yeast, and 1 β-lactamase gene examined in 472 samples. While no searched gene region was found by rPCR in 78 (16.5%) of the 472 samples studied, at least 1 gene was detected in 394 (83.5%) samples. These 1052 positive samples by rPCR were; 263 (28.43%) Staphylococcus spp., 51 (5.51%) S. aureus, 57 (6.16%) Enterococcus spp., 49 (5.29%) C. bovis, 16 (1.73%) S. dysgalactiae, 84 (9.08%) S. agalactiae, 71 (7.67%) S. uberis, 73 (7.89%) E. coli, 14 (1.51%) Prototheca spp., 39 (4.21%) T. pyogenes/P. indolicus, 5 (0.54%) S. marcescens, 15 (1.62%) K. oxytoca/pneumonia, 117 (12.64%) Mycoplasma spp., 31 (3.35%) M. bovis, 40 (4.32%) yeast, and 127 samples (26.90%) were β-lactamase positive. When the antibiotic resistance of the isolates was evaluated, 78 (31.96%) tetracycline, 72 (29.5%) penicillin, and 60 (24.59%) clindamycin resistance were observed predominantly in Gram-positive isolates, while 6 (23.07%) tigecycline, 6 (23.07%) netilmicin, 6 (23.07%) pipercillin resistance was found in gram-negative isolates.While a bacteria and/or yeast gene was found by rPCR in 187 of 246 (76.01%) samples with no bacterial growth, a bacterium was isolated with BC in only 20 (8.84%) samples whose gene region was not found by rPCR. As a result, the multiplex rPCR system used in the diagnosis of mastitis has been found to be quite reliable as it can detect a large number of bacteria in a very short time compared to classical methods. Therefore, we advise the use of rPCR and/or culture for confirmation of clinical signs in mastitis and at routine mastitis surveillance.

Characteristic SNPs defining the major multidrug-resistant Mycobacterium tuberculosis clusters identified by EuSeqMyTB to support routine surveillance, EU/EEA, 2017 to 2019.

BackgroundThe EUSeqMyTB project, conducted in 2020, used whole genome sequencing (WGS) for surveillance of drug-resistant Mycobacterium tuberculosis in the European Union/European Economic Area (EU/EEA) and identified 56 internationally clustered multidrug-resistant (MDR) tuberculosis (TB) clones.AimWe aimed to define and establish a rapid and computationally simple screening method to identify probable members of the main cross-border MDR-TB clusters in WGS data to facilitate their identification and track their future spread.MethodsWe screened 34 of the larger cross-border clusters identified in the EuSeqMyTB pilot study (2017-19) for characteristic single nucleotide polymorphism (SNP) signatures that could identify and define members of each cluster. We also linked this analysis with published clusters identified in previous studies and identified more distant genetic relationships between some of the current clusters.ResultsA panel of 30 characteristic SNPs is presented that can be used as an initial (routine) screen for members of each cluster. For four of the clusters, no unique defining SNP could be identified; three of these are closely related (within approximately 20 SNPs) to one or more other clusters and likely represent a single established MDR-TB clade composed of multiple recent subclusters derived from the previously described ECDC0002 cluster.ConclusionThe identified SNP signatures can be integrated into routine pipelines and contribute to the more effective monitoring, rapid and widespread screening for TB. This SNP panel will also support accurate communication between laboratories about previously identified internationally transmitted MDR-TB genotypes.

Risk factors and genetic characteristics of the carriage of hypervirulent and carbapenem-resistant Acinetobacter baumannii among pregnant women.

Carbapenem-resistant Acinetobacter baumannii (CRAB) and its emerging evolutionary branch toward hypervirulence have been neglected in pregnancy. From September 2020 to August 2021, an active surveillance culture program encompassed 138 randomly selected pregnant women, with five subjected to sample collection at two different time points. The clinical characterization was explored through statistical analysis. Whole-genome sequencing, a Galleria mellonella infection model, and a global database were used to investigate the genetic characterization, pathogenicity, evolutionary history, and phylogenetic relationships of the isolates. Of the 41 CRAB isolates obtained, they were divided into four ClustersRS and an orphan pattern. ClusterRS 1 (n = 31), with eight complex types in pregnancy, was also the dominant ClusterRS globally, followed by ClusterRS 13 (n = 5), identified as hypervirulent KL49 CRAB, exhibiting phylogeographical specificity to Guangdong. A maternal carriage CRAB rate of 26.09% (36/138) was revealed, with half of the isolates representing novel complex types, prominently including CT3071, as the first KL7 isolates identified in Shenzhen. Both KL49 and KL7 isolates were most commonly found in the same participant, suggesting potential intraspecific competition as a possible reason for CRAB infection without carriers during pregnancy. The independent risk factors for carriers were revealed for the first time, including advanced maternal age, gestational diabetes mellitus, and Group B Streptococcus infection. The significant carriage rate and enhanced virulence of CRAB during pregnancy emphasize the imperative for routine surveillance to forestall dissemination within this high-risk group, especially in Guangdong for ClusterRS 13 isolates.

Validation of a Method for Surveillance of Nanoparticles in Mussels Using Single-Particle Inductively Coupled Plasma-Mass Spectrometry.

Determining the concentration of nanoparticles (NPs) in marine organisms is important for evaluating their environmental impact and to assess potential food safety risks to human health. The current work aimed at developing an in-house method based on single-particle inductively coupled plasma-mass spectrometry (SP-ICP-MS) suitable for surveillance of NPs in mussels. A new low-cost and simple protease mixture was utilized for sample digestion, and novel open-source data processing was used, establishing detection limits on a statistical basis using false-positive and false-negative probabilities. The method was validated for 30 and 60 nm gold NPs spiked to mussels as a proxy for seafood. Recoveries were 76-77% for particle mass concentration and 94-101% for particle number concentration. Intermediate precision was 8-9% for particle mass concentration and 7-8% for particle number concentration. The detection limit for size was 18 nm, for concentration 1.7 ng/g, and 4.2 × 105 particles/g mussel tissue. The performance characteristics of the method were satisfactory compared with numeric Codex criteria. Further, the method was applied to titanium-, chromium- and copper-based particles in mussels. The method demonstrates a new practical and cost-effective sample treatment, and streamlined, transparent, and reproducible data treatment for the routine surveillance of NPs in mussels.

The global prevalence of Cyclospora cayetanensis infection: A systematic review, meta-analysis, and meta-regression

Cyclospora cayetanensis (C. cayetanensis) is a significant pathogen that causes diarrheal illness and causes large foodborne diarrhea outbreaks in the USA and Canada. However, there is currently a lack of published meta-analysis on the prevalence of C. cayetanensis infection in the global population. A real estimation of a disease prevalence should always be done on the basis of studies designed for that purpose. We conducted a comprehensive search of various databases for articles pertaining to the prevalence of C. cayetanensis infection in humans, spanning from the inception of these databases to March 10, 2023. Utilizing a random effects model, we estimated the prevalence of C. cayetanensis infection in humans. Our analysis included a total of 150 datasets sourced from 42 different countries, which were ultimately selected for the final quantitative assessment. The prevalence of C. cayetanensis infection in humans worldwide was estimated to be 3.4 % (5636/166,611). Notably, Africa exhibited the highest prevalence rate at 5.9 % (606/11,068). Further subgroup analysis revealed a significantly higher infection rate in humans residing in low-income countries (7.6 %, 83/921) compared to those in lower-middle-income countries (4.8 %, 3280/48,852), upper-middle-income countries (2.9 %, 2194/99,419), and high-income countries (0.4 %, 79/17,419). The results indicate that the global prevalence of C. cayetanensis infection in humans is relatively low, despite its extensive geographical distribution and children were found to be more susceptible to C. cayetanensis infection compared to those adults. Sensitivity analysis revealed that one study significantly affects the prevalence of C. cayetanensis, which was adjusted to 2.9 % (4017/160,049; 95 % CI: 2.7–3.1 %) by excluding this study. The findings highlight the relatively high prevalence of C. cayetanensis infection in low-income countries and among humans with diarrhea, particularly in Africa. Consequently, routine surveillance for intestinal protozoa is crucial in these regions.

A measles IgM rapid diagnostic test to address challenges with national measles surveillance and response in Malaysia.

A lateral flow rapid diagnostic test (RDT) enables detection of measles specific immunoglobulin M (IgM) antibody in serum, capillary blood, and oral fluid with accuracy consistent with enzyme immunoassay (EIA). The objectives of the study were: 1) to assess measles RDT inter-reader agreement between two clinic staff; 2) to assess the sensitivity and specificity of the measles RDT relative to standard surveillance testing in a low transmission setting; 3) to evaluate the knowledge, attitudes, and practices of staff in clinics using the RDT; and 4) to assess the impact of RDT testing on the measles public health response in Malaysia. The clinic-based prospective evaluation included all suspected measles cases captured by routine measles surveillance at 34 purposely selected clinics in 15 health districts in Malaysia between September 2019 and June 2020, following day-long regional trainings on RDT use. Following informed consent, four specimens were collected from each suspected case, including those routinely collected for standard surveillance [serum for EIA and throat swabs for quantitative reverse transcriptase polymerase chain reaction (RT-qPCR)] together with capillary blood and oral fluid tested with RDTs during the study. RDT impact was evaluated by comparing the rapidity of measles public health response between the pre-RDT implementation (December 2018 to August 2019) and RDT implementation periods (September 2019 to June 2020). To assess knowledge, attitudes, and practices of RDT use, staff involved in the public health management of measles at the selected sites were surveyed. Among the 436 suspect cases, agreement of direct visual readings of measles RDT devices between two health clinic staff was 99% for capillary blood (k = 0.94) and 97% for oral fluid (k = 0.90) specimens. Of the total, 45 (10%) were positive by measles IgM EIA (n = 44, including five also positive by RT-qPCR) or RT-qPCR only (n = 1), and 38 were positive by RDT (using either capillary blood or oral fluid). Using measles IgM EIA or RT-qPCR as reference, RDT sensitivity using capillary blood was 43% (95% CI: 30%-58%) and specificity was 98% (95% CI: 96%-99%); using oral fluid, sensitivity (26%, 95% CI: 15%-40%) and specificity (97%, 95% CI: 94%-98%) were lower. Nine months after training, RDT knowledge was high among staff involved with the public health management of measles (average quiz score of 80%) and was highest among those who received formal training (88%), followed by those trained during supervisory visits (83%). During the RDT implementation period, the number of days from case confirmation until initiation of public response decreased by about 5 days. The measles IgM RDT shows >95% inter-reader agreement, high retention of RDT knowledge, and a more rapid public health response. However, despite ≥95% RDT specificity using capillary blood or oral fluid, RDT sensitivity was <45%. Higher-powered studies using highly specific IgM assays and systematic RT-qPCR for case confirmation are needed to establish the role of RDT in measles elimination settings.

Can “Soft” Advice from International Organizations Catalyze Natural Resource Sector Reform?

Abstract Can international organizations improve natural resource governance? The International Monetary Fund (IMF) is most noted for its role in crisis lending, where it can wield the “teeth” of loan suspensions to push for reforms. But IMF officials also spend a large amount of time conducting routine surveillance through Article IV consultations, which assess a country’s economic developments and provide non-binding recommendations. Do governments follow this “toothless” advice? To answer this question, we examine the content of all Article IV staff appraisals published between 2004 and 2019. Using text analysis and a difference-in-differences estimator, we find that resource-rich developing countries are more likely to adopt legislation reforming the oil, gas, and mining sectors in the wake of an Article IV appraisal that extensively discusses the natural resource sector and recommends natural resource governance reforms. Our results suggest that technocratic advice—a tool often overlooked in international organization scholarship—can lead to the adoption of policies that help ameliorate the resource curse.

Examining the impact and response to an outbreak of carbapenemase-producing Enterobacterales in a neonatal unit in the United Kingdom: An outbreak report.

Carbapenemase-producing Enterobacterales (CPE) are a group of Gram-negative bacteria causing global concern due to their resistance to carbapenems. In this report, we detail the learning points from a CPE outbreak in a tertiary neonatal unit (NU) in the UK. Routine surveillance screening (rectal swabs) of babies on the NU identified a potential cluster of CPE carriage. Samples were sent to a reference laboratory for confirmatory testing. Environmental screening and cot mapping were undertaken to determine movements of babies within the unit. Regular audits of cleaning standards, hand hygiene, and maternal hygiene when expressing breast milk were carried out. The outbreak lasted 19weeks. During the outbreak, there were 360 admissions, with 11 babies being colonised with the outbreak strain. Once the outbreak was declared, there were enhanced Infection Prevention and Control (IPC) precautions (including increased environmental and equipment cleaning frequency). CPE screening frequency was increased and cot capacity was reduced. Hand hygiene compliance improved from 92% at the start of the outbreak to 100% by its close. Cleaning standards remained compliant. Maternal hygiene standards varied from 78% to 100%, but no cross-infection links were identified. Environmental screening was negative. No route of cross-infection was identified. Notably, no babies developed invasive CPE infection. This is the first report of a CPE outbreak in a UK NU. Although no specific mode of cross-transmission was identified and the outbreak's end cannot be attributed to any single intervention, the bundle of interventions proved successful after a 5-month period.

Utility of Routine Surveillance Head Computed Tomography After Receiving Therapeutic Anticoagulation in Patients with Acute Traumatic Intracranial Hemorrhage

IntroductionPatients with traumatic intracranial hemorrhage (tICH) are at increased risk of venous thromboembolism and may require anticoagulation. We evaluated the utility of surveillance computed tomography (CT) in patients with tICH who required therapeutic anticoagulation. MethodsThis single institution, retrospective study included adult patients with tICH who required anticoagulation within 4-weeks and had a surveillance head CT within 24-hours of reaching therapeutic anticoagulation levels. The primary outcome was hematoma expansion (HE) detected by the surveillance CT. Secondary outcomes included 1) changes in management in patients with HE on the surveillance head CT, 2) HE in the absence of clinical changes, and 3) mortality due to HE. We also compared mortality between patients who did and did not have a surveillance CT. ResultsOf 175 patients, 5 (2.9%) were found to have HE. Most (n=4, 80%) had changes in management including anticoagulation discontinuation (n=4), reversal (n=1), and operative management (n=1). Two patients developed symptoms or exam changes prior to the head CT. Of the 3 patients (1.7%) without preceding exam changes, each had only very minor HE and did not require operative management. No patient experienced mortality directly attributed to HE. There was no difference in mortality between patients who did and those who did not have a surveillance scan. ConclusionsOur findings suggest that most patients with tICH who are started on anticoagulation could be followed clinically, and providers may reserve CT imaging for patients with changes in exam/symptoms or those who have a poor clinical examination to follow.

Pleiotropic Role of Rainbow Trout CXCRs in Response to Disease and Environment: Insights from Transcriptional Signatures and Structure Analysis.

Chemokines are cytokines with chemoattractant capacities that exert their physiological functions through the binding of chemokine receptors. Thus, chemokine and receptor complexes exert important roles in regulating development and homeostasis during routine immune surveillance and inflammation. Compared to mammals, the physiology and structure of chemokine receptors in fish have not been systematically studied. Furthermore, the salmonid-specific whole genome duplication has significantly increased the number of functional paralogs of chemokine receptors. In this context, in the current study, trout exhibited 17 cxcr genes, including 12 newly identified and 5 previously identified receptors. Interestingly, gene expression of brain cxcr1 and cxcr4, kidney cxcr3 and cxcr4, and spleen cxcr3, cxcr4, and cxcr5 subtypes were altered by bacterial infection, whereas brain cxcr1, kidney cxcr1 and cxcr7, and liver cxcr2, cxcr3, and cxcr4 subtypes were changed in response to environmental changes. Based on protein structures predicted by ColabFold, the conserved amino acids in binding pockets between trout CXCR4.1 subtypes and human CXCR4 were also analyzed. Our study is valuable from a comparative point of view, providing new insights into the identification and physiology of salmonid chemokine receptors.

Utilization of Patient-Specific Characteristics and Competing Risks to Tailor the Duration of Surveillance Imaging After Surgery for Renal Cell Carcinoma

Purpose: The appropriate duration of follow-up after surgical resection of renal cell carcinoma (RCC) remains incompletely defined. To better inform on this time line, we investigate when an individual's risk of RCC recurrence becomes less significant than their risk of non-RCC death. Materials and Methods: We identified 1672 patients who underwent surgery for M0 RCC between 1999 and 2018. Patients were stratified by pathologic stage, histology, age, and Eastern Cooperative Oncology Group (ECOG) performance status. Cumulative incidence functions were estimated for RCC recurrence and non-RCC death using Fine and Gray models. Follow-up durations were estimated as the time point at which the cumulative incidence of non-RCC death exceeded that of RCC recurrence. Results: At a median follow-up of 2.1 years (IQR 0.6-5.1 years), a total of 272 recurrences (16.3%) and 234 non-RCC deaths (14.0%) occurred. The fitted model showed significant associations of stage with RCC recurrence and of age and ECOG with non-RCC death. For 50-year-old patients with pT1aN0-x clear cell and ECOG 0, the incidence of non-RCC death exceeded that of recurrence after 4.4 years. However, if such patients had an ECOG status of 1 or 2 to 4, the incidence of non-RCC death exceeded that of recurrence at 30 days, suggesting that routine oncologic surveillance may not be necessary. Alternatively, regardless of ECOG status, the incidence of non-RCC death failed to exceed that of recurrence for &gt;13.9 years in all patients age 50 with &gt; pT3aN0-x clear cell thereby suggesting longer surveillance than currently recommended. Conclusion: Modeling competing risks of RCC recurrence and non-RCC death provide patient-specific estimates when follow-up may be reasonably discontinued.

Detection of Invasive Anopheles stephensi Mosquitoes through Molecular Surveillance, Ghana.

The invasive Anopheles stephensi mosquito has rapidly expanded in range in Africa over the past decade. Consistent with World Health Organization guidelines, routine entomologic surveillance of malaria vectors in Accra, Ghana, now includes morphologic and molecular surveillance of An. stephensi mosquitoes. We report detection of An. stephensi mosquitoes in Ghana.

Whole Genome Sequence-Based Analyses of Drug Resistance Characteristics, Genetic Diversity, and Transmission Dynamics of Drug-Resistant Mycobacterium tuberculosis in Urumqi City.

This study aims to analyze the drug resistance spectrum, genetic diversity, and transmission dynamics to provide a basis for the prevention and control of drug-resistant (DR) tuberculosis (TB) epidemics. This retrospective study is based on routine national drug resistance surveillance. The demographic, epidemiological, and clinical information on DR-TB patients from 2016 to 2021 was collected and used for phenotypic drug susceptibility testing and whole-genome sequencing. It was indicated that L2.2.1 was the dominant lineage in Urumqi. The drug resistance spectrum in Urumqi was narrow, which means more drug combinations can be used for clinical treatment. Furthermore, mutations identification of drug-resistance gene katG, rpoB, embA/B, rrs, rpsL, eis, gyrA/B, folC and tryA are important for clinical drug use. However, mutations in cross-resistance genes rrs have limited guidance for clinical selection of KM, CPM and AK. Moreover, there is an increased risk of cluster transmission of DR-TB, and the difference in clustering rate among L2, L3, and L4 was not statistically significant (χ2 = 2.6410, p = 0.2670). In the Urumqi, DR-TB has a complex prevalence state, a narrow drug resistance spectrum, and a high clustering rate and burden of drug resistance. To reduce the burden of DR-TB, related research should be strengthened, and the development of prevention, control, and treatment strategies should be accelerated.

Patterns of Non-influenza Respiratory Viruses Among Severe Acute Respiratory Infection Cases in Burkina Faso: A Surveillance Study.

Although influenza viruses cause only one-fifth of severe acute respiratory infections (SARI) in Burkina Faso, the other viral causes of SARI remain poorly investigated to inform clinical and preventive decision making. Between 2016 and 2019, we prospectively enrolled inpatients meeting the World Health Organization (WHO) case definition of SARI in Burkina Faso. Results of viral etiologies among inpatients tested negative for influenza using the Fast Track Diagnostics Respiratory Kits (FTD-33) were reported. Of 1541 specimens tested, at least one respiratory virus was detected in 76.1% of the 1231 specimens negative for influenza virus. Human rhinoviruses (hRVs) were the most detected pathogens (476; 38.7%), followed by human adenoviruses (hAdV) (17.1%, 210/1231), human respiratory syncytial virus (hRSV) (15.4%, 189/1231), enterovirus (EnV) (11.2%, 138/1231), human bocavirus (hBoV) (7.9%, 97/1231), parainfluenza 3 (hPIV3) (6.1%, 75/1231), human metapneumovirus (hMPV) (6.0%,74/1321), parainfluenza 4 (hPIV4) (4.1%, 51/1231), human coronavirus OC43 (hCoV-OC43) (3.4%, 42/1231), human coronavirus HKU1(hCoV-HKU1) (2.7%, 33/1231), human coronavirus NL63 (hCoV-NL63) (2.5%, 31/1231), parainfluenza 1 (hPIV1) (2.0%, 25/1231), parainfluenza 2 (hPIV2) (1.8%, 22/1231), human parechovirus (PeV) (1.1%, 14/1231), and human coronavirus 229E (hCoV-229E) (0.9%, 11/1231). Among SARI cases, infants aged 1-4 years were mostly affected (50.7%; 622/1231), followed by those <1 year of age (35.7%; 438/1231). Most detected pathogens had year-long circulation patterns, with seasonal peaks mainly observed during the cold and dry seasons. Several non-influenza viruses are cause of SARI in Burkina Faso. The integration of the most common pathogens into the routine influenza surveillance system might be beneficial.