Hypermut 3: Identifying specific mutational patterns in a defined nucleotide context that allows multistate characters.

The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutation events in sequences relative to a reference.

Relationship between malaria vector survival, infectivity, and insecticide-treated net use in western Kenya.

Background: Significant effort and resources have been invested to control malaria transmission in sub-Saharan Africa, but it remains a major public health problem. For the parasite to be transmitted, the female Anopheles vector must survive 10-14 days following an infective bite to allow Plasmodium gametocytes to develop into infectious sporozoites. The goal of this study was to assess factors associated with wild-caught Anopheles survival and infection following host-seeking and indoor resting.

bistro: An R package for vector bloodmeal identification by short tandem repeat overlap.

Measuring vector-human contact in a natural setting can inform precise targeting of interventions to interrupt transmission of vector-borne diseases. One approach is to directly match human DNA in vector bloodmeals to the individuals who were bitten using genotype panels of discriminative short tandem repeats (STRs). Existing methods for matching STR profiles in bloodmeals to the people bitten preclude the ability to match most incomplete profiles and multi-source bloodmeals to bitten individuals.

Analytic optimization of Plasmodium falciparum marker gene haplotype recovery from amplicon deep sequencing of complex mixtures.

Molecular epidemiologic studies of malaria parasites and other pathogens commonly employ amplicon deep sequencing (AmpSeq) of marker genes derived from dried blood spots (DBS) to answer public health questions related to topics such as transmission and drug resistance. As these methods are increasingly employed to inform direct public health action, it is important to rigorously evaluate the risk of false positive and false negative haplotypes derived from clinically-relevant sample types. We performed a control experiment evaluating haplotype recovery from AmpSeq of 5 marker genes (ama1, csp, msp7, sera2, and trap) from DBS containing mixtures of DNA from 1 to 10 known P.

Identification of 2 Novel Subtypes of Hepatitis C Virus Genotype 8 and a Potential New Genotype Successfully Treated With Direct Acting Antivirals.

Background: Hepatitis C virus (HCV) has high genetic diversity and is classified into 8 genotypes and >90 subtypes, with some endemic to specific world regions. This could compromise direct-acting antiviral efficacy and global HCV elimination.

Methods: We characterized HCV subtypes "rare" in the United Kingdom (non-1a/1b/2b/3a/4d) by means of whole-genome sequencing via a national surveillance program.

Relationship between malaria vector survival, infectivity and insecticide treated net use in western Kenya.

Background: Much effort and resources have been invested to control malaria transmission in Sub-Saharan Africa, but it remains a major public health problem. For the disease to be transmitted from one person to another, the female vector must survive 10-14 days following an infective bite for the gametocytes to develop into infectious sporozoites which can be transmitted to the next person during a bloodmeal. The goal of this investigation was to assess factors associated with wild-caught Anopheles survival and infection following host-seeking and indoor resting.

bistro: An R package for vector bloodmeal identification by short tandem repeat overlap.

1. Measuring vector-human contact in a natural setting can inform precise targeting of interventions to interrupt transmission of vector-borne diseases. One approach is to directly match human DNA in vector bloodmeals to the individuals who were bitten using genotype panels of discriminative short tandem repeats (STRs).

Analytic optimization of marker gene haplotype recovery from amplicon deep sequencing of complex mixtures.

Molecular epidemiologic studies of malaria parasites commonly employ amplicon deep sequencing (AmpSeq) of marker genes derived from dried blood spots (DBS) to answer public health questions related to topics such as transmission and drug resistance. As these methods are increasingly employed to inform direct public health action, it is important to rigorously evaluate the risk of false positive and false negative haplotypes derived from clinically-relevant sample types. We performed a control experiment evaluating haplotype recovery from AmpSeq of 5 marker genes (, , , , and ) from DBS containing mixtures of DNA from 1 to 10 known reference strains across 3 parasite densities in triplicate (n=270 samples).

Distinct Origins and Transmission Pathways of across Three U.S. States.

Carbapenem-resistant (CRE) are among the most concerning antibiotic resistance threats due to high rates of multidrug resistance, transmissibility in health care settings, and high mortality rates. We evaluated the potential for regional genomic surveillance to track the spread of -carrying CRE (KPC-CRE) by using isolate collections from health care facilities in three U.S.

Risk Factors for Colistin-Resistant Carbapenem-Resistant in the Postacute Care Setting.

We assessed risk factors for colistin resistance among carbapenem-resistant (CRKP) from 375 patients in long-term acute care hospitals. Recent colistin or polymyxin B exposure was associated with increased odds of colistin resistance (adjusted odds ratio = 1.11 per day of exposure, 95% confidence interval = 1.

Plasmodium falciparum Genetic Diversity in Coincident Human and Mosquito Hosts.

Population genetic diversity of Plasmodium falciparum antigenic loci is high despite large bottlenecks in population size during the parasite life cycle. The prevalence of genetically distinct haplotypes at these loci, while well characterized in humans, has not been thoroughly compared between human and mosquito hosts. We assessed parasite haplotype prevalence, diversity, and evenness using human and mosquito P.

Characterization of resistance to newer antimicrobials among carbapenem-resistant in the post-acute-care setting.

We assessed susceptibility patterns to newer antimicrobial agents among clinical carbapenem-resistant (CRKP) isolates from patients in long-term acute-care hospitals (LTACHs) from 2014 to 2015. Meropenem-vaborbactam and imipenem-relebactam nonsusceptibility were observed among 9.9% and 9.

Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research.

Inspired by well-established material and pedagogy provided by The Carpentries (Wilson, 2016), we developed a two-day workshop curriculum that teaches introductory R programming for managing, analyzing, plotting and reporting data using packages from the tidyverse (Wickham et al., 2019), the Unix shell, version control with git, and GitHub. While the official Software Carpentry curriculum is comprehensive, we found that it contains too much content for a two-day workshop.

regentrans: a framework and R package for using genomics to study regional pathogen transmission.

Increasing evidence of regional pathogen transmission networks highlights the importance of investigating the dissemination of multidrug-resistant organisms (MDROs) across a region to identify where transmission is occurring and how pathogens move across regions. We developed a framework for investigating MDRO regional transmission dynamics using whole-genome sequencing data and created regentrans, an easy-to-use, open source R package that implements these methods (https://github.com/Snitkin-Lab-Umich/regentrans).

mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines.

Machine learning (ML) for classification and prediction based on a set of features is used to make decisions in healthcare, economics, criminal justice and more. However, implementing an ML pipeline including preprocessing, model selection, and evaluation can be time-consuming, confusing, and difficult. Here, we present mikropml (prononced "meek-ROPE em el"), an easy-to-use R package that implements ML pipelines using regression, support vector machines, decision trees, random forest, or gradient-boosted trees.

Regional Spread of blaNDM-1-Containing Klebsiella pneumoniae ST147 in Post-Acute Care Facilities.

Background: Carbapenem-resistant Enterobacterales (CRE) harboring blaKPC have been endemic in Chicago-area healthcare networks for more than a decade. During 2016-2019, a series of regional point-prevalence surveys identified increasing prevalence of blaNDM-containing CRE in multiple long-term acute care hospitals (LTACHs) and ventilator-capable skilled nursing facilities (vSNFs). We performed a genomic epidemiology investigation of blaNDM-producing CRE to understand their regional emergence and spread.

Patient and Microbial Genomic Factors Associated with Carbapenem-Resistant Klebsiella pneumoniae Extraintestinal Colonization and Infection.

Carbapenem-resistant (CRKP) is a critical-priority antibiotic resistance threat that has emerged over the past several decades, spread across the globe, and accumulated resistance to last-line antibiotic agents. While CRKP infections are associated with high mortality, only a subset of patients acquiring CRKP extraintestinal colonization will develop clinical infection. Here, we sought to ascertain the relative importance of patient characteristics and CRKP genetic background in determining patient risk of infection.

prewas: data pre-processing for more informative bacterial GWAS.

While variant identification pipelines are becoming increasingly standardized, less attention has been paid to the pre-processing of variants prior to their use in bacterial genome-wide association studies (bGWAS). Three nuances of variant pre-processing that impact downstream identification of genetic associations include the separation of variants at multiallelic sites, separation of variants in overlapping genes, and referencing of variants relative to ancestral alleles. Here we demonstrate the importance of these variant pre-processing steps on diverse bacterial genomic datasets and present prewas, an R package, that standardizes the pre-processing of multiallelic sites, overlapping genes, and reference alleles before bGWAS.

Application of Combined Genomic and Transfer Analyses to Identify Factors Mediating Regional Spread of Antibiotic-resistant Bacterial Lineages.

Background: Patients entering nursing facilities (NFs) are frequently colonized with antibiotic-resistant organisms (AROs). To understand the determinants of ARO colonization on NF admission, we applied whole-genome sequencing to track the spread of 4 ARO species across regional NFs and evaluated patient-level characteristics and transfer acute care hospitals (ACHs) as risk factors for colonization.

Methods: Patients from 6 NFs (n = 584) were surveyed for methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis/faecium (VREfc/VREfm), and ciprofloxacin-resistant Escherichia coli (CipREc) colonization.

Whole-Genome Sequencing To Identify Drivers of Carbapenem-Resistant Klebsiella pneumoniae Transmission within and between Regional Long-Term Acute-Care Hospitals.

Carbapenem-resistant (CRKP) is an antibiotic resistance threat of the highest priority. Given the limited treatment options for this multidrug-resistant organism (MDRO), there is an urgent need for targeted strategies to prevent transmission. Here, we applied whole-genome sequencing to a comprehensive collection of clinical isolates to reconstruct regional transmission pathways and analyzed this transmission network in the context of statewide patient transfer data and patient-level clinical data to identify drivers of regional transmission.

Integrated genomic and interfacility patient-transfer data reveal the transmission pathways of multidrug-resistant in a regional outbreak.

Development of effective strategies to limit the proliferation of multidrug-resistant organisms requires a thorough understanding of how such organisms spread among health care facilities. We sought to uncover the chains of transmission underlying a 2008 U.S.