Detection of the carbapenemase gene blaVIM-5 in members of the Pseudomonas putida group isolated from polluted Nigerian wetlands

Abstract There are increasing concerns about possible dissemination of clinically relevant antibiotic resistance genes, including genes encoding for carbapenemases in the environment. However, little is known about environmental distribution of antibiotic resistance in Africa. In this study, four polluted urban wetlands in Nigeria were investigated as potential reservoirs of carbapenem-resistant bacteria (CRB). CRB were isolated from the wetlands, characterized by Blue-Carba test, MIC determinations and whole genome sequencing (WGS). Nine of 65 bacterial isolates identified as members of the Pseudomonas putida group (P. plecoglossicida and P. guariconensis, respectively) harboured the metallo-beta-lactamase gene bla VIM-5. WGS revealed the bla VIM-5 in three novel Tn402-like class 1 integron structures containing the cassette arrays aadB|bla VIM-5|bla PSE-1, aadB|bla VIM-5|aadB|bla PSE-1, and bla VIM-5|aadB|tnpA|bla PSE-1|smr2|tnpA, respectively. Strains carrying the aadB|bla VIM-5|bla PSE-1 cassette also carried an identical integron without bla VIM-5. In addition, the strains harboured another Tn402-like class 1 integron carrying bcr2, several multidrug resistance efflux pumps, and at least one of ampC, aph(3”)-lb, aph(6)-ld, tetB, tetC, tetG, floR, and macAB. This is the first report of a carbapenemase gene in bacteria from environmental sources in Nigeria and the first report of bla VIM-5 in environmental bacteria isolates. This result underscores the role of the Nigerian environment as reservoir of bacteria carrying clinically relevant antibiotic resistance genes

Identification of Antibiotic Resistance Gene Hosts in Treatment Wetlands Using a Single-Cell Based High-Throughput Approach

Determining the prevalence of antimicrobial resistance (AMR) in non-clinical settings is vital for better management of the global AMR crisis. Untreated and even treated wastewaters are important sources that release AMR into the environment. Methodologically, it is difficult to generate a comprehensive in situ profile of antibiotic resistance gene hosts. Here, we used epicPCR (emulsion, paired isolation, and concatenation PCR) as a cultivation-independent method to reveal the host profiles of the AMR indicator genes intI1, sul1, sul2, and dfrA1 in two constructed wetlands treating municipal wastewater. Overall, the epicPCR analysis revealed a profile of AMR indicator gene hosts that is consistent with literature data from cultivation-based approaches. Most carriers of antibiotic resistance (AR) genes and likely of class 1 integrons belonged to the Gammaproteobateria, particularly the Burkholderiaceae and Rhodocyclaceae families, followed by members of the Campylobacterota, Desulfobacterota, and Firmicutes. The analysis also identified several novel hosts for the indicator genes widely distributed in the wetlands, including the genera Legionella and Ralstonia. Therefore, the application of epicPCR has produced an expanded insight into the in situ indicator gene host profile, while highlighting the role of the environment as a reservoir for AMR

Draft Genome Sequence of Magnetospirillum sp. Strain 15-1, a Denitrifying Toluene Degrader Isolated from a Planted Fixed-Bed Reactor

Here, we report the draft genome sequence of Magnetospirillum sp. 15-1. This strain was isolated from a planted fixed-bed reactor based on its ability to degrade toluene under anaerobic conditions. The genome assembly consists of 5.4 Mb in 28 contigs and 5,095 coding sequences containing the genes involved in anaerobic toluene degradation

High abundances of class 1 integrase and sulfonamide resistance genes, and characterisation of class 1 integron gene cassettes in four urban wetlands in Nigeria.

There is little information about environmental contamination with antibiotic resistance genes (ARG) in Sub-Saharan Africa, home to about 1 billion people. In this study we measured the abundance of three genes (sul1, sul2, and intI1) used as indicators of environmental contamination with ARGs in the sediments of four urban wetlands in southwestern Nigeria by qPCR. In addition, we characterised the variable regions of class 1 integrons in sulfamethoxazole/trimethoprim (SMX/TRI)-resistant bacteria isolated from the wetlands by PCR and DNA sequencing. The indicator ARGs were present in all wetlands with mean absolute copy numbers/gram of sediment ranging between 4.7x106 and 1.2x108 for sul1, 1.1x107 and 1x108 for sul2, and 5.3x105 and 1.9x107 for intI1. The relative abundances (ARG/16S rRNA copy number) ranged from about 10-3 to 10-1. These levels of ARG contamination were similar to those previously reported for polluted environments in other parts of the world. The integrase genes intI1 and intI2 were detected in 72% and 11.4% SMX/TRI-resistant isolates, respectively. Five different cassette array types (dfrA7; aadA2; aadA1|dfrA1; acc(6')lb-cr|arr3|dfrA27; arr3|acc(6')lb-cr|dfrA27) were detected among 34 (59.6%) intI1-positive isolates. No gene cassettes were found in the nine intI2-positive isolates. These results show that African urban ecosystems impacted by anthropogenic activities are reservoirs of bacteria harbouring transferable ARG

Fecal contamination of food, water, hands, and kitchen utensils at the household level in rural areas of Peru

The study described in this article evaluated sources of contamination of children's food and drinking water in rural households in the highlands of Peru. Samples from children's meals, drinking water, kitchen utensils, and caregivers' and children's hands were analyzed for total coliforms and E. coli counts using Petrifilm EC. Thermotolerant coliforms in water were measured using DelAgua test kits while diarrheagenic E. coli was identified using polymerase chain reaction methods (PCR). Thermotolerant coliforms were found in 48% of all water samples. E. coli was found on 23% of hands, 16% of utensils, and 4% of meals. Kitchen cloths were the item most frequently contaminated with total coliforms (89%) and E. coli (42%). Diarrheagenic E. coli was found in 33% of drinking water, 27% of meals, and on 23% of kitchen utensils. These findings indicate a need to develop hygiene interventions that focus on specific kitchen utensils and hand washing practices, to reduce the contamination of food, water, and the kitchen environment in these rural settings