Ramon Loureiro Pimenta

Wastewater treatment plants (WWTPs) are important interfaces for the persistence and dissemination of antimicrobial resistance genes (ARGs) in the environment. This study investigated colistin resistance and the presence of mobile colistin resistance (mcr) genes in Enterobacterales isolated from a poultry slaughterhouse WWTP in Brazil. Samples were collected from raw sewage, an equalization tank, and treated effluent. A total of 27 Enterobacter spp. isolates were identified, of which 70.4% showed resistance to colistin (MIC range: 2 to ≥512 mg/L). PCR screening detected mcr-1 in two isolates and mcr-10 in three isolates distributed across all treatment stages, including the final effluent. Whole-genome sequencing of a representative isolate from treated effluent identified Enterobacter vonholyi ST3343, carrying a plasmid-borne mcr-10 gene on an ~107 kb IncFII(Yp) plasmid, along with additional resistance determinants. Phylogenetic analysis supported the classification of this gene as a novel allele, mcr-10.6. The persistence of a clonal lineage harboring mcr-10.6 throughout the treatment system indicates that conventional wastewater treatment may not effectively eliminate clinically relevant ARGs. These findings highlight treated effluent as a potential route for environmental dissemination of colistin resistance and reinforce the need for improved monitoring and mitigation strategies within a One Health framework.

Infectious bursal disease virus (IBDV) causes immunosuppression in broilers by affecting the bursa of Fabricius. IBDV strains were classified into seven genogroups based on the amino acid composition of the hypervariable region of the VP2 capsid protein. This study aimed to detect and genotype IBDV strains in bursal samples from broilers in Rio de Janeiro and evaluate the genetic variability of the vp2 gene. Sixty-five bursal tissue samples from broilers suspected to have IBD were collected from four farms in Rio de Janeiro and stored in RNAlater. RNA was extracted using TRIzol reagent, and genotyping was performed using RT-qPCR. The VP2 hypervariable region was amplified using conventional PCR, purified, and sequenced. Phylogenetic analysis was conducted using the maximum likelihood method with the Kimura 2-parameter substitution model. IBDV was detected in 75.38% (49/65) of the samples, with 8.16% (4/49) classified as very virulent (vvIBDV) and 91.84% (45/49) as non-vvIBDV strains. This study seems to be the first report of G-3 infection in the state of Rio de Janeiro. Sequence comparison identified multiple missense mutations, including 20 in genogroup 4 and eight in genogroup 3, relative to the reference strain Edgar-USA. The genetic distances among the isolates suggest potential viral evolution and adaptation. These findings highlight the genetic diversity of IBDV in this region and reinforce the importance of continuous molecular surveillance of the virus. The detection of vvIBDV in a previously unreported area underscores the need for monitoring strategies to mitigate the impact of emerging strains on poultry production. Further studies focusing on antigenic variation and vaccine efficacy are essential to ensure effective control of IBDV.

Poultry slaughterhouse wastewater (PSW) is a source of environmental pollutants, harboring pathogens and antibiotic resistance genes (ARGs). This study aimed to assess the effects of conventional biological treatment of PSW on the bacterial community and its efficiency in removing ARGs, as well as to evaluate the impact of its discharge on the receiving river. Samples were collected from raw sewage, treated effluent, and upstream and downstream river sites. Total metagenomic DNA was extracted for real-time PCR quantification of 16S rRNA, yccT gene (Escherichia coli), and ARGs, which were selected based on their ability to confer resistance to clinically relevant antibiotics and their prevalence in poultry-associated environments, including resistance to tetracyclines (tetM), beta-lactams (bla_TEM), sulfonamides (sul1), and quinolones (qnrS). Amplicon sequencing of 16S rRNA V3–V4 region was used to assess bacterial community structure. Treated effluent significantly altered the downstream microbiome, reducing bacterial richness by up to 72.3% and diversity by 25.4%. Effluent-associated phyla such as Pseudomonadota (37%), Bacillota (28%), and Bacteroidota (26%) became dominant in the downstream river samples. Enterobacterales increased after treatment, and E. coli increased by 2.93 logs downstream. All ARGs increased after treatment and remained elevated downstream, with qnrS and sul1 rising by 3.77 and 3.87 logs, respectively. These findings highlight PSW treatment plants as a potential point of selection and dissemination of antimicrobial resistance (AMR)-related bacteria and genes. Inefficient treatment contributes to shifts in river bacterial communities and the spread of AMR.

The overuse of antimicrobials in poultry has led to the development and dissemination of multidrug-resistant bacteria in the poultry industry. One of the most effective mechanisms of resistance found in Escherichia coli is the production of extended-spectrum β-lactamases (ESBL); there are several ESBLs, including the TEM, SHV, and CTX-M families. This resistance mechanism and the risks associated with transmitting these resistant microorganisms between animals, the environment, and humans can occur through direct contact and consumption of infected animals. This study aimed to determine the prevalence of E. coli in samples isolated from three broiler farms in Rio de Janeiro, Brazil, and screen the isolates for ESBL genes. The findings of this study demonstrated the presence of ESBL-producing E. coli in all farms studied. The findings of this study highlight the urgency for a program to monitor the poultry industry value chains at the regional level to control the spread of antimicrobial resistance. Therefore, we recommend that the enzyme subtypes produced by bacterial isolates should be determined to effectively characterize the distribution of genes related to antimicrobial resistance. O uso excessivo de antimicrobianos em frangos de corte tem contribuído para o desenvolvimento e disseminação de bactérias multirresistentes, e um dos mais relevantes mecanismos de resistência encontrados em Escherichia coli é a produção de enzimas denominadas β-lactamases de espectro estendido (ESBL). CTX-M, SHV e TEM são as β-lactamases mais comumente encontradas nesta espécie e as ESBL mais prevalentes globalmente. Esse mecanismo de resistência e o risco associado à transmissão desses microrganismos resistentes entre animais, meio ambiente e seres humanos se devem principalmente ao contato direto e ao consumo de origem animal. Este trabalho buscou elucidar a prevalência de E. coli em amostras de três granjas de frangos de corte localizadas no Rio de Janeiro, Brasil, e caracterizá-las de acordo com seu genótipo. O estudo demonstrou uma presença consistente de E. coli produtora de ESBL com presença abundante do gene blaSHV nos isolados de todas as fazendas estudadas. Deste modo, este estudo teve como objetivo contribuir com dados epidemiológicos relativos à distribuição de genes relacionados às β-lactamases na produção animal, conscientizando sobre a transmissão desses microrganismos resistentes entre animais, meio ambiente e seres humanos contribuindo com dados epidemiológicos e de sua importância em uma perspectiva de saúde única.

The contribution of the animal environments to the worsening of the global antimicrobial resistance framework is related to the use of antimicrobials in subtherapeutic doses and, for long periods, establishing ideal conditions for the circulation of resistance genes, which can be transmitted to pathogens adapted to the human microbiota. The study of the animal environment as conducive to the acceleration of resistance evolution is an emerging and critical area for understanding the development and dissemination of resistance genes among the circulating bacteria. The connection between people, animals, and the environment allows us to consider antimicrobial resistance in an approach within the “One Health” concept, which provides a global strategy for expanding collaboration and interdisciplinary communication. This chapter will highlight the emergence of colistin resistance, a great challenge in antimicrobial resistance field. Also, it will focus on some agents included in the priority list of superbugs of the World Health Organization (WHO) or correlated species already identified in veterinary medicine, such as the critical superbugs; priority level 1, Carbapenem-resistant Acinetobacter baumannii, Carbapenem-resistant Pseudomonas aeruginosa, and ESBL-producing Carbapenemic-resistant Enterobacteriaceae; and the high-priority, level 2, methicillin-resistant Staphylococcus aureus (MRSA).