Genomic analysis of fluoroquinolone-resistant Leclercia adecarboxylata carrying the ISKpn19-orf-qnrS1-ΔIS3-blaLAP-2 module in a synanthropic pigeon, Brazil.

OBJECTIVES: The aim of this study was to perform a genomic investigation of a multiple fluoroquinolone-resistant Leclercia adecarboxylata strain isolated from a synanthropic pigeon in São Paulo, Brazil. METHODS: Whole-genome sequencing was performed using an Illumina platform, and in silico deep analyses of the resistome were performed. Comparative phylogenomics was conducted using a global collection of publicly available genomes of L. adecarboxylata strains isolated from human and animal hosts. RESULTS: L. adecarboxylata strain P62P1 displayed resistance to human (norfloxacin, ofloxacin, ciprofloxacin, and levofloxacin) and veterinary (enrofloxacin) fluoroquinolones. This multiple quinolone-resistant profile was associated with mutations in the gyrA (S83I) and parC (S80I) genes and the presence of the qnrS gene within an ISKpn19-orf-qnrS1-ΔIS3-blaLAP-2 module, previously identified in L. adecarboxylata strains isolated from pig feed and faeces in China. Genes associated with arsenic, silver, copper, and mercury resistance were also predicted. Phylogenomic analysis revealed clustering (378-496 single nucleotide polymorphism differences) with two L. adecarboxylata strains isolated from human and fish sources in China and Portugal, respectively. CONCLUSIONS: L. adecarboxylata is a Gram-negative bacterium of the Enterobacterales order and is considered an emergent opportunistic pathogen. Since L. adecarboxylata has adapted to human and animal hosts, genomic surveillance is highly recommended, in order to identify the emergence and spread of resistant lineages and high-risk clones. In this regard, this study provides genomic data that can help clarify the role of synanthropic animals in the dissemination of clinically relevant L. adecarboxylata within a One Health context.

One health clones of multidrug-resistant Escherichia coli carried by synanthropic animals in Brazil.

WHO priority pathogens have disseminated beyond hospital settings and are now being detected in urban and wild animals worldwide. In this regard, synanthropic animals such as urban pigeons (Columba livia) and rodents (Rattus rattus, Rattus norvegicus and Mus musculus) are of interest to public health due to their role as reservoirs of pathogens that can cause severe diseases. These animals usually live in highly contaminated environments and have frequent interactions with humans, domestic animals, and food chain, becoming sentinels of anthropogenic activities. In this study, we report genomic data of Escherichia coli strains selected for ceftriaxone and ciprofloxacin resistance, isolated from pigeons and black rats. Genomic analysis revealed the occurrence of international clones belonging to ST10, ST155, ST224 and ST457, carrying a broad resistome to beta-lactams, aminoglycosides, trimethoprim/sulfamethoxazole, fluoroquinolones, tetracyclines and/or phenicols. SNP-based phylogenomic investigation confirmed clonal relatedness with high-risk lineages circulating at the human-animal-environmental interface globally. Our results confirm the dissemination of WHO priority CTX-M-positive E. coli in urban rodents and pigeons in Brazil, highlighting potential of these animals as infection sources and hotspot for dissemination of clinically relevant pathogens and their resistance genes, which is a critical issue within a One Health perspective.

An Outbreak in Pigeons Caused by the Subgenotype VI.2.1.2 of Newcastle Disease Virus in Brazil.

Newcastle disease virus (NDV) can infect over 250 bird species with variable pathogenicity; it can also infect humans in rare cases. The present study investigated an outbreak in feral pigeons in São Paulo city, Brazil, in 2019. Affected birds displayed neurological signs, and hemorrhages were observed in different tissues. Histopathology changes with infiltration of mononuclear inflammatory cells were also found in the brain, kidney, proventriculus, heart, and spleen. NDV staining was detected by immunohistochemistry. Twenty-seven out of thirty-four tested samples (swabs and tissues) were positive for Newcastle disease virus by RT-qPCR test, targeting the M gene. One isolate, obtained from a pool of positive swab samples, was characterized by the intracerebral pathogenicity index (ICPI) and the hemagglutination inhibition (HI) tests. This isolate had an ICPI of 0.99, confirming a virulent NDV strain. The monoclonal antibody 617/161, which recognizes a distinct epitope in pigeon NDV strains, inhibited the isolate with an HI titer of 512. A complete genome of NDV was obtained using next-generation sequencing. Phylogenetic analysis based on the complete CDS F gene grouped the detected isolate with other viruses from subgenotype VI.2.1.2, class II, including one previously reported in Southern Brazil in 2014. This study reports a comprehensive characterization of the subgenotype VI.2.1.2, which seems to have been circulating in Brazilian urban areas since 2014. Due to the zoonotic risk of NDV, virus surveillance in feral pigeons should also be systematically performed in urban areas.