Phylogenomics analysis of multidrug-resistant Elizabethkingia anophelis in industrial wastewater treatment plant.

AIMS: This study investigated the phylogenetic relatedness of multidrug-resistant Elizabethkingia anophelis recovered from an industrial wastewater treatment plant (WWTPi). METHODS AND RESULTS: The wastewater samples were plated in brain heart infusion agar (4 mg/L ceftazidime, 8 mg/L meropenem, and 2 mg/L polimixin). Four isolates recovered from four stages of WWTPi (influent, aeration, decantation, and treated effluent) were identified and evaluated of susceptibility profiles in the VITEK 2 system. These strains identified as E. meningoseptica were confirmed to be E. anophelis by whole genomic sequencing (Miseq-Illumina) and showed antimicrobial resistance genes of ß-lactams, aminoglycosides, and tetracycline's classes. The ribosomal multilocus sequence typing showed that they belong to the rST 65620 together with clinical strains. The phylogenomic tree revealed the similarity of our strains to those belonging to sublineage 11 and the single nucleotide polymorphism analysis confirmed that they belong to a single clade. CONCLUSIONS: To the best of our knowledge, this is the first study reporting the persistence of multidrug-resistant E. anophelis sublineage 11 along the wastewater treatment.

Occurrence of Klebsiella pneumoniae ST244 and ST11 extensively drug-resistant producing KPC, NDM, OXA-370 in wastewater, Brazil.

AIMS: To investigate the occurrence of carbapenem-resistant Klebsiella pneumoniae (CRKP) and their clonal relationships from hospital and municipal wastewater treatment plants (WWTPs). METHODS AND RESULTS: Eighteen Kl. pneumoniae strains recovered from three WWTPs were identified by matrix-assisted laser desorption-ionization-time of flight (MALDI-TOF). The antimicrobial susceptibility were evaluated by disk-diffusion and the carbapenemases production by Carbapenembac®. The carbapenemases genes were investigated by real-time PCR and the clonal relationship through multilocus sequence typing (MLST). Thirty nine % (7/18) of isolates were classified as multidrug-resistant (MDR), 61.1% (11/18) extensively drug-resistant (XDR), and 83.3% (15/18) showed carbapenemase activity. Three carbapenemase-encoding genes were found, blaKPC (55%), blaNDM (27.8%) and blaOXA-370 (11.1%) as well five sequencing types ST11, ST37, ST147, ST244, and ST281. ST11 and ST244, sharing four alleles were grouped into clonal complex 11 (CC11). CONCLUSIONS: Our results show the importance of monitoring antimicrobial resistance in WWTPs effluents to minimize the risk of spreading bacterial load and ARGs in aquatic ecosystems, using advanced treatment technologies to reduce these emerging pollutants at WWTPs.

Environmental genomic surveillance of SARS-CoV-2 in wastewater in Rio de Janeiro, Brazil.

Wastewater-based epidemiology can be a complementary approach for monitoring SARS-CoV-2 prevalence, diversity, and geographic distribution. It is a complementary approach regarding its prevalence and diversity, and geographic distribution. The study aimed to evaluate the genetic diversity of SARS-CoV-2 in two wastewater treatment plants (WWTPs) in Rio de Janeiro, Brazil. Samples were collected over a period of January to December 2021 and were concentrated with PEG8000 and the presence of SARS-CoV-2 was detected using E and N1 genes. Partial sequencing of the SARS-CoV-2 genomes resulted in the identification of variants of concern and variants of interest throughout the collection period. It was possible to identify the Mu, Delta, Gamma and Omicron variants in WWTP1; on the contrary, no variants were observed in WWTP2. To the best of our knowledge, we detected the variant Mu (B.1.621) containing characteristic mutations (S:E484K, S:N501Y) from WWTP, for the first time, in Brazil. Another Mu variant detected from clinical surveillance was announced one month after our finding. The detection of SARS-CoV-2 in wastewater can serve as a tool to monitor the prevalence and epidemiology in each community, helping to understand the spread of the virus among the population.

Genomic Analysis of Multidrug-Resistant Enterococcus faecium Harboring vanA Gene from Wastewater Treatment Plants.

The emergence of vancomycin-resistant Enterococcus faecium (Efm) harboring vanA gene and multidrug-resistant determinants is a relevant public health concern. It is an opportunistic pathogen responsible for nosocomial infections widely distributed in the environment, including wastewater treatment plants (WWTPs). Our study addresses a genomic investigation of vanA-carrying Efm from WWTPs in Brazil. Samples from five WWTPs supplied with sewage from different sources were evaluated. Here we present whole-genome sequencing of eight vanA-Efm isolates performed on Illumina MiSeq platform. All these isolates presented multidrug-resistant profile, and five strains were from treated wastewater. Multiple antimicrobial resistance genes (ARGs) were found, such as aph(3')-IIIa, ant(6')-Ia, erm(B), and msrC, some of them being allocated in plasmids. The virulence profile was predominantly constituted by efaAfm and acm genes and all isolates, except for one, were predicted as human pathogens. Multilocus sequence typing analysis revealed a new allele and five different STs, three previously described (ST32, ST168, and ST253) and two novel ones (ST1893 and ST1894). Six strains belonged to CC17, often associated with hospital outbreaks. As far as our knowledge, no genomic studies of vanA-Efm recovered from WWTPs revealed isolates belonging to CC17 in Brazil. Therefore, our findings point to the environmental spread of Efm carrying multiple ARGs.

Perfil de resistência aos antibióticos e prevalência dos genes qacEΔ1 e sul1 em Pseudomonas aeruginosa de efluente hospitalar / Antibiotic resistance pattern and prevalence of qacEΔ1 and sul1 genes in Pseudomonas aeruginosa from hospital wastewater

Introdução: Efluentes hospitalares representam riscos à saúde pública e ambiental devido à presença de microrganismos patogênicos, drogas e produtos químicos. Pseudomonas aeruginosa é um patógeno oportunista frequentemente encontrado no ambiente hospitalar. Objetivo: Avaliar o resistoma de isolados de P. aeruginosa da estação de tratamento de esgoto hospitalar (ETEH) de um complexo hospitalar na cidade do Rio de Janeiro. Método: Vinte isolados dos cinco estágios da ETEH foram identificados como P. aeruginosa pelo sequenciamento do gene 16S rRNA. A suscetibilidade aos antibióticos foi determinada segundo o CLSI e os genes qacEΔ1 e sul1 foram detectados pela PCR. Resíduos de sulfonamidas foram pesquisados por cromatografia líquida de alta eficiência acoplada à espectrometria de massas sequencial. Resultados: Foi demonstrada a presença de sulfametoxazol em nível inferior a 50 ng∙L−1, resistência às sulfonamidas (80%) seguida pelas quinolonas (50%) e 13 perfis de suscetibilidade aos antimicrobianos. Os genes qacEΔ1-sul1 foram detectados em 100% dos isolados, sugerindo a presença de integrons de classe 1 em toda a ETEH. Conclusões: Os resultados sinalizaram limitações no tratamento e a propagação de genes de resistência nas etapas da ETEH. Esses dados contribuem com órgãos competentes no desenho de ações preventivas frente aos impactos negativos à saúde pública.

Introduction: Hospital effluents may pose great environmental risk due to the presence of pathogenic microorganisms, drugs and chemical components. Pseudomonas aeruginosa is an opportunistic pathogen frequently found in hospital environment. Objective: To evaluate the resistome of P. aeruginosa from the hospital wastewater treatment plant (HWTP) in a hospital complex of Rio de Janeiro city. Method: Twenty isolates from the five stages of the HWTP were identified as P. aeruginosa by 16S rRNA gene sequencing analysis. Susceptibility to antibiotics was determined according to CLSI and qacEΔ1 and sul1 genes were detected by PCR. Sulphonamide residues were investigated by high performance liquid chromatography coupled to sequential mass spectrometry. Results: The sulfamethoxazole has been demonstrated at a level below 50 ng L-1. Sulfonamide resistance (80%) has been demonstrated followed by quinolone class (50%) and 13 susceptibility patterns to antimicrobials. The qacEΔ1-sul1 genes were detected in 100% of isolates suggesting the presence of class 1 integrons in the whole HWTP. Conclusions: The results signalized limitations of HWTP and propagation of resistance genes in all stages of the HWTP. These data also contribute to the environmental sanitary surveillance in the design of prevention actions against negative impact on the public health.