Phylogenomic Analysis of CTX-M-15-Positive Escherichia coli from Companion Animal Reveals Intercontinental Dissemination of ST90 Within a One Health Framework.

The global dissemination of extended-spectrum-ß-lactamase (ESBL)-producing Escherichia coli has been considered a critical issue within a One Health framework. The aim of this study was to perform a genomic investigation of an ESBL-producing E. coli strain belonging to the globally spread sequence type/clonal complex ST90/CC23, isolated from gastrointestinal tract of a dog, in Brazil. Besides CTX-M-15 ESBL, this E. coli isolate carried mutations conferring resistance to human and veterinary fluoroquinolones (GyrA [Ser83Leu, Asp87Asn], ParC [Ser80Ile] and ParE [Ser458Ala]), and resistance determinants to disinfectants and pesticides. Noteworthy, phylogenomic analysis revealed that this multidrug E. coli strain clustered with ST90 lineages isolated from human, dog, and livestock in Brazil. The phylogenetic tree also revealed that this E. coli strain shares a common ancestor with isolates from the United States, Russia, Germany, and China, highlighting the potential global spreading of this clone. In summary, we report genomic data of CTX-M-15-positive E.coli ST90 colonizing a pet. Colonization of companion animals by critical resistant pathogens highlights the need for close monitoring to better understand the epidemiology and genetic factors contributing for successful adaptation of global clones at the human-animal interface.

Genomic features of a polymyxin-resistant Klebsiella pneumoniae ST491 isolate co-harbouring blaCTX-M-8 and qnrE1 genes from a hospitalised cat in São Paulo, Brazil.

OBJECTIVES: Klebsiella pneumoniae has emerged as one of the major pathogens of humans and companion animals. Moreover, polymyxin resistance in K. pneumoniae is increasingly reported worldwide, mainly among extended-spectrum ß-lactamase (ESBL)- and/or carbapenemase-producing isolates. The aim of this study was to report the draft genome sequence of a polymyxin-resistant, ESBL-producing K. pneumoniae isolate (14CSI) from a hospitalised domestic cat in Brazil. METHODS: Whole-genome sequencing of strain 14CSI was performed on an Illumina NextSeq platform and the genome was de novo assembled using Velvet v.1.2.10. Data analysis was performed using bioinformatics tools available from the Center for Genomic Epidemiology and the Institut Pasteur database. RESULTS: The genome size of strain 14CSI was calculated at 5 260 459 bp, with a GC content of 57.3% and comprising 5294 total genes, 28 tRNAs, 7 rRNAs, 8 ncRNAs and 237 pseudogenes. Klebsiella pneumoniae strain 14CSI belongs to sequence type 491 (ST491), presents a mutation (A14S) in the mgrB gene and co-harbours blaCTX-M-8 and qnrE1 genes. Genes conferring resistance to heavy metals were further identified. CONCLUSION: This draft genome could be used as a reference sequence for comparative analysis of polymyxin-resistant and/or CTX-M-8-producing K. pneumoniae strains circulating at the human-animal interface.

Multidrug-resistant CTX-M-15-positive Klebsiella pneumoniae ST307 causing urinary tract infection in a dog in Brazil.

OBJECTIVES: Klebsiella pneumoniae sequence type 307 (ST307) has emerged as a new high-risk clone worldwide. The aim of this study was to report the draft genome sequence of a multidrug-resistant CTX-M-15-positive K. pneumoniae strain causing urinary tract infection in a companion animal in Brazil. METHODS: Whole-genome sequencing was performed on an Illumina NextSeq platform and the genome was de novo assembled using SPAdes. Data analysis was performed using online tools from the Center for Genomic Epidemiology. RESULTS: The genome size of K. pneumoniae strain PRETA was calculated at 5 450 575 bp, containing a total of 5355 protein-coding sequences. The strain was assigned to the high-risk ST307 and carried the clinically relevant blaCTX-M-15 gene, besides other genes conferring resistance to aminoglycosides, tetracyclines, quinolones, trimethoprim and fosfomycin. CONCLUSION: These data offer novel information for comparative genomic analyses in order to track the transmission dynamics and epidemiology of the newly emerging high-risk clone ST307.

Draft genome sequences of two fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST90 (ST23 complex) isolated from a calf and a dairy cow in South America.

OBJECTIVES: Farm animals have been recognised as important carriers and reservoirs of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli. The aim of this study was to report the draft genome sequences of two multidrug-resistant (MDR) CTX-M-15-producing E. coli strains (47VL and 13B) isolated from different bovine hosts (a calf and a dairy cow), housed separately in a commercial dairy farm in Brazil. METHODS: Total genomic DNA of the E. coli isolates was sequenced using an Illumina MiSeq paired-end 300-bp sequencing platform. Sequence reads were de novo assembled using the A5-miseq pipeline and polishing assembly in Geneious v.R9. The NCBI Prokaryotic Genome Annotation Pipeline v.3.2 was used for genome annotation, whereas whole-genome sequences were analysed using bioinformatic tools from the Center of Genomic Epidemiology and EnteroBase. RESULTS: E. coli 47VL generated a total of 3238770 and E. coli 13B a total of 1422808 paired-end reads of ca. 190× and ca. 80×, respectively. The resistome revealed that both isolates carried resistance genes to aminoglycosides, ß-lactams, macrolides, sulphonamides, trimethoprim and tetracycline. Comparative analyses revealed clonal relatedness. In fact, both isolates belonged to sequence type ST90 (clonal complex CC23) and phylogroup AxB1. CONCLUSION: To our knowledge, these are the first draft genome sequences of CTX-M-15-producing E. coli ST90 isolated from bovines in South America. These data can be used to elucidate genetic features that contribute to colonisation and adaptation of CTX-M-15-producing E. coli in dairy cattle.

First Report of the Globally Disseminated IncX4 Plasmid Carrying the mcr-1 Gene in a Colistin-Resistant Escherichia coli Sequence Type 101 Isolate from a Human Infection in Brazil.

A colistin-resistant Escherichia coli strain was recovered from a patient with a diabetic foot infection in Brazil. Whole-genome analysis revealed that the E. coli isolate belonged to the widespread sequence type (ST) 101 and harbored the mcr-1 gene on an IncX4 plasmid that was highly similar to mcr-1-bearing IncX4 plasmids that were recently identified in Enterobacteriaceae from food, animal, and human samples recovered on different continents. These results suggest that self-transmissible IncX4-type plasmids may represent promiscuous plasmids contributing to the intercontinental spread of the mcr-1 gene.

Silent dissemination of colistin-resistant Escherichia coli in South America could contribute to the global spread of the mcr-1 gene.

During a Brazilian multicentric antimicrobial resistance surveillance study, colistin resistance was investigated in 4,620 Enterobacteriaceae isolated from human, animal, food and environmental samples collected from 2000 to 2016. We present evidence that mcr-1-positive Escherichia coli has been emerging in South America since at least 2012, supporting a previous report on the possible acquisition of mcr-1-harbouring E. coli by European travellers visiting Latin American countries.

Prevalência de anticorpos contra o vírus da arterite equina nas mesorregiões Noroeste, Centro Ocidental e Norte Central do Paraná / Prevalence of antibodies against equine viral arteritis virus in Northwest, Western Central and North Central Regions of the State of Paraná, Brazil

O objetivo deste estudo foi investigar a prevalência de anticorpos contra o vírus da arterite viral equina (EVAV) em equinos sadios criados nas mesorregiões Noroeste, Centro Ocidental e Norte Central do estado do Paraná. Após o cálculo do tamanho amostral, foram analisadas, utilizando a técnica de soroneutralização, amostras de soro sanguíneo de 653 equinos. Nenhum animal sororreagente foi encontrado nas mesorregiões Noroeste (0/236) e Centro Ocidental (0/99). Na mesorregião Norte Central a prevalência foi de 0,62% (2/318), totalizando 0,30%. Pode-se concluir que a arterite viral equina (AVE) ainda não representa um problema de importância epidemiológica nos equinos criados nas mesorregiões paranaenses estudadas.(AU)

The prevalence of antibodies against equine viral arteritis virus (EVAV) in healthy horses raised in Northwest, Western Central and North Central regions of the State of Paraná, Brazil was investigated. According to calculated sample size, serum samples of 653 horses were analyzed through standard virus neutralization test. No horse had antibodies to EVAV in Northwest (0/236) and in Western Central (0/99) regions. In North Central region frequency was 0.62% (2/318), with an overall prevalence of 0.30%. It can be concluded that EVA does not represent a problem of epidemiological importance in the studied regions of Paraná.(AU)

Limnology of a lateral lagoon system connected to a Neotropical reservoir (Rosana reservoir, São Paulo/Paraná, Brazil) / Limnologia de um sistema de lagoas laterais conectadas a um reservatório Neotropical (reservatório de Rosana, Estado de São Paulo/Paraná, Brasil)

The aim of this work was to perform a comparative analysis of four lateral lagoons and of the main channel of the Rosana Reservoir (Paranapanema river), southeast Brazil. The fieldwork was conducted during dry and rainy periods of 2004 and 2005. The analyzed variables were chlorophyll a, turbidity, total phosphorus, total nitrogen, dissolved nutrients (ammonium, nitrate, nitrite, phosphate and silicate), Secchi disk transparency, suspended solids, temperature, pH, dissolved oxygen and electrical conductivity. Intense summer rainfall provided a high input of allochthonous material into the system, resulting in conspicuous changes - high turbidity and nutrient concentrations and low transparency, especially in the reservoir channel. The cluster analysis showed a clear segregation between the reservoir sampling site and the lagoons. The results evidenced the strong influence of regional factors on the limnological structure and functioning of these environments. The alternation between dry and rainy periods changes significantly the characteristics of the main channel and lagoons, mainly due to the contribution of tributaries. Spatially, the system exhibited a remarkable limnological variability. This shows the need to consider these distinct habitats in regional conservation strategy, presently focused on terrestrial habitats.

O objetivo desse estudo foi realizar uma análise comparativa de quatro lagoas laterais e do canal principal do reservatório de Rosana (rio Paranapanema, Brasil). O trabalho de campo foi realizado no período de setembro e novembro de 2004 e janeiro, março, maio e agosto de 2005. As variáveis analisadas foram clorofila a, turbidez, fósforo e nitrogênio total, nutrientes dissolvidos (amônio, nitrato, nitrito, fosfato e silicato), transparência do disco de Secchi, sólidos em suspensão, temperatura, pH, oxigênio dissolvido e condutividade elétrica. As chuvas de verão forneceram grande quantidade de material alóctone ao sistema, o que resultou em mudanças conspícuas - elevada turbidez e altas concentrações de nutrientes, e diminuição da transparência, especialmente no canal do reservatório. A análise de agrupamento mostrou clara a distinção entre o ponto do reservatório e as lagoas laterais. Os resultados evidenciaram a forte influência dos fatores regionais para a estrutura e funcionamento limnológico desses ambientes. A alternância entre períodos de seca e chuva muda significativamente as características do canal do reservatório e das lagoas, principalmente pela contribuição dos rios tributários. Espacialmente, o sistema apresentou uma notável variabilidade limnológica. Isso demonstra a necessidade de se considerar estes habitats em estratégia de conservação regional, focada atualmente nos ecossistemas terrestres.