Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae and Anopheles coluzzii.

Resistance to insecticides in Anopheles mosquitoes threatens the effectiveness of malaria control, but the genetics of resistance are only partially understood. We performed a large scale multi-country genome-wide association study of resistance to two widely used insecticides: deltamethrin and pirimiphos-methyl, using sequencing data from An. gambiae and An.

Recovery of metagenomic data from the microbiome using a reproducible snakemake pipeline: MINUUR.

Ongoing research of the mosquito microbiome aims to uncover novel strategies to reduce pathogen transmission. Sequencing costs, especially for metagenomics, are however still significant. A resource that is increasingly used to gain insights into host-associated microbiomes is the large amount of publicly available genomic data based on whole organisms like mosquitoes, which includes sequencing reads of the host-associated microbes and provides the opportunity to gain additional value from these initially host-focused sequencing projects.

Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in s.l.

Resistance to insecticides in mosquitoes threatens the effectiveness of the most widespread tools currently used to control malaria. The genetic underpinnings of resistance are still only partially understood, with much of the variance in resistance phenotype left unexplained. We performed a multi-country large scale genome-wide association study of resistance to two insecticides widely used in malaria control: deltamethrin and pirimiphos-methyl.

MDR Escherichia coli carrying CTX-M-24 (IncF[F-:A1:B32]) and KPC-2 (IncX3/IncU) plasmids isolated from community-acquired urinary trainfection in Brazil.

Acquired antibiotic resistance in bacteria has become an important worldwide challenge. Currently, several bacteria, including Escherichia coli, have multidrug resistance profiles. Genes such as bla CTX-M-24 and bla KPC-2 (carbapenemase) are widespread.

Whole genome sequencing of the multidrug-resistant isolated from a patient in Brazil.

Chryseobacterium indologenes is a non-glucose-fermenting Gram-negative bacillus. This emerging multidrug resistant opportunistic nosocomial pathogen can cause severe infections in neonates and immunocompromised patients. This study aimed to present the first detailed draft genome sequence of a multidrug-resistant strain isolated from the cerebrospinal fluid of an infant hospitalized at the Neonatal Intensive Care Unit of Brazilian Tertiary Hospital.

Linear plasmids in and other .

Linear plasmids are extrachromosomal DNA elements that have been found in a small number of bacterial species. To date, the only linear plasmids described in the family belong to , first found in Typhi. Here, we describe a collection of 12 isolates of the species complex in which we identified linear plasmids.

Multidrug-resistant Klebsiella pneumoniae: a retrospective study in Manaus, Brazil.

Klebsiella pneumoniae is an opportunistic pathogen that can cause several infections, mainly in hospitalised or immunocompromised individuals. The spread of K. pneumoniae emerging virulent and multidrug-resistant clones is a worldwide concern and its identification is crucial to control these strains especially in hospitals.

WHO Critical Priority Escherichia coli as One Health Challenge for a Post-Pandemic Scenario: Genomic Surveillance and Analysis of Current Trends in Brazil.

The dissemination of carbapenem-resistant and third generation cephalosporin-resistant pathogens is a critical issue that is no longer restricted to hospital settings. The rapid spread of critical priority pathogens in Brazil is notably worrying, considering its continental dimension, the diversity of international trade, livestock production, and human travel. We conducted a nationwide genomic investigation under a One Health perspective that included Escherichia coli strains isolated from humans and nonhuman sources, over 45 years (1974-2019).

Carbapenem-resistant IMP-1-producing Pseudocitrobacter vendiensis emerging in a hemodialysis unit.

Hemodialysis patients are at high risk for bloodstream infections associated with highest morbidity and mortality rates. Bacterial species not commonly related to such infections has been hardly identified by traditional methods. Pseudocitrobacter is a novel genus of the order Enterobacterales that is associated with carbapenemase genes and nosocomial infection.

Genomic insights of Acinetobacter baumannii ST374 reveal wide and increasing resistome and virulome.

WGS-based surveillance has significantly improved the ability to track global spread and emergence of multidrug-resistant clones of clinically relevant pathogens. In this study, we performed the genomic characterization and comparative analysis of an Acinetobacter baumannii (strain Ac56) belonging to the sequence type ST374, which was isolated for the first time in Brazil, in 1996. Genomic analysis of Ac56 predicted a total of 5373 genes, with 3012 being identical across nine genomes of A.

Whole-Genome Analysis of a High-Risk Clone of ST147 Carrying Both and Genes in Peru.

The increasing prevalence and dissemination of carbapenemase-producing represent a serious concern for public health. We studied the genetic features of a multidrug-resistant isolate of high-risk clone ST147 coharboring -1 and recovered from a human clinical urine sample in 2017 in Peru. Whole-genome sequencing and conjugation assays identified and genes on two different conjugative plasmids, which belong to IncI2 and IncFIB/HI1B incompatibility groups, respectively.

A novel hypermucoviscous Klebsiella pneumoniae ST3994-K2 clone belonging to Clonal Group 86.

Emergent hypervirulent Klebsiella pneumoniae has been responsible for severe diseases, representing a serious threat to public health. We report the whole-genome sequencing of a novel ST3994-K2 clone, a single locus variant of ST86 K2, which is considered a worrying hypervirulent clone that emerged in several parts of the world. The strain K.

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex.

Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data.

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei.

Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S.

Multidrug-Resistant (MDR) Strains Isolated in a Brazilian Hospital Belong to New Clones.

is mainly associated with opportunistic infections and frequently identified as This misidentification implies a wrong epidemiology result as well as incorrect attribution to as the etiology of some severe infections. Recently, huge efforts have been made to study , however, the biological aspects of this species are still unclear. Here we characterized five strains initially identified as , with a Vitek-2 System and 16S rRNA sequencing.

Genomic data reveals the emergence of an IncQ1 small plasmid carrying bla in Escherichia coli of the pandemic sequence type 648.

Objectives: The global success of carbapenem-resistant pathogens has been attributed to large plasmids carrying bla genes circulating among high-risk clones. In this study, we sequenced the genome of a carbapenem-resistant Escherichia coli strain (Ec351) isolated from a human infection. Phylogenomic analysis based on single nucleotide polymorphisms (SNPs) as well as the comparative resistome and plasmidome of globally disseminated bla-positive E.

Endophytic Lifestyle of Global Clones of Extended-Spectrum β-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization?

The global spread of antibiotic-resistant bacteria and their resistance genes is a critical issue that is no longer restricted to hospital settings, but also represents a growing problem involving environmental and food safety. In this study, we have performed a microbiological and genomic investigation of critical priority pathogens resistant to broad-spectrum cephalosporins and showing endophytic lifestyles in fresh vegetables sold in a country with high endemicity of extended-spectrum β-lactamases (ESBLs). We report the isolation of international high-risk clones of CTX-M-15-producing , belonging to clonal complexes CC38 and CC648, and of complex CC307 from macerated tissue of surface-sterilized leaves of spinach, cabbage, arugula, and lettuce.

Detection of IncN-pST15 one-health plasmid harbouring bla in a hypermucoviscous Klebsiella pneumoniae CG258 isolated from an infected dog, Brazil.

The emergence and rapid spread of carbapenemase-producing Enterobacterales represents a serious public health concern. Critically, these global priority bacteria have begun to be reported in companion animals, implying a potential risk of cross-transmission between humans and pets. Using long-read (MinION) and short-read (Illumina) sequencing technologies, we have identified and characterized a hypermucoviscous KPC-2-producing Klebsiella pneumoniae strain belonging to the high-risk international clone ST11/CG258, in a dog with urinary tract infection.

Genomic insights of international clones of Haemophilus influenzae causing invasive infections in vaccinated and unvaccinated infants.

The emergence of invasive Haemophilus influenzae infections in vaccinated patient is a public health concern. We have investigated the genomic basis of invasiveness and possible vaccine failure in H. influenzae causing invasive disease in vaccinated and unvaccinated children in Brazil.