Identification of termites from Gabon using MALDI-TOF MS.

Termites are one of the most common pests that damage wood and other cellulosic materials. Although Africa has more varieties of termite species than any other continent, few entomological studies have been conducted in Gabon. Identifying termites poses significant difficulties for entomologists. The aim of this study was to evaluate the reliability and confirm the significance of MALDI-TOF MS in identifying fresh termites collected in equatorial Africa. A total of 108 termites were collected from 13 termite nests during a field mission in 2021 in Lekedi and Bongoville, Gabon. Termites were morphologically identified and subjected to MALDI-TOF MS, then molecular analyses using the COI and 12S rRNA genes. Four termite species were morphologically identified in this study: Pseudacanthotermes militaris, Macrotermes muelleri, Macrotermes nobilis, and Noditermes indoensis. However, when using molecular biology, only three species were identified, namely Macrotermes bellicosus, P. militaris, and N. indoensis, because the specimens initially identified as M. muelleri and M. nobilis were found to be M. bellicosus. The MALDI-TOF MS spectral profiles of the termites were all of good quality, with intra-species reproducibility and inter-species specificity. The spectra of 98 termites were blind tested against our upgraded database, which included the spectra of ten termite specimens. All tested spectra were correctly matched to their respective species, with log score values (LSVs) ranging from 1.649 to 2.592. The mean LSV was 2.215 ± 0.203, and the median was 2.241. However, 95.91% (94/98) of our spectra had LSVs above 1.8. This study demonstrates how a proteomic approach can overcome termites' molecular and morphological identification limitations and serve as a useful taxonomic tool.

Taxonogenomics of Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. new bacteria isolated from human stool microbiota.

Two new bacterial strains, Marseille-P2698T (CSUR P2698 = DSM 103,121) and Marseille-P2260T (CSUR P2260 = DSM 101,844 = SN18), were isolated from human stools by the culturomic method. We used the taxonogenomic approach to fully describe these two new bacterial strains. The Marseille-P2698T strain was a Gram-negative, motile, non-spore-forming, rod-shaped bacterium. The Marseille-P2260T strain was a Gram-positive, motile, spore-forming rod-shaped bacterium. Major fatty acids found in Marseille-P2698T were C15:0 iso (63%), C15:0 anteiso (11%), and C17:0 3-OH iso (8%). Those found in Marseille-P2260T strain were C16:00 (39%), C18:1n9 (16%) and C18:1n7 (14%). Strains Marseille-P2698T and Marseille-P2260T had 16S rRNA gene sequence similarities of 91.50% with Odoribacter laneusT, and of 90.98% and 95.07% with Odoribacter splanchnicusT and Eubacterium sulciT, respectively. The exhibited digital DNA-DNA Hybridization values lower than 20.7%, and Orthologous Average Nucleotide Identity values lower than 73% compared to their closest related bacterial species O. splanchnicusT and E. sulciT respectively. Phenotypic, biochemical, phylogenetic, and genomic results obtained by comparative analyses provided sufficient evidence that both of the two studied strains Marseille-P2698T and Marseille-P2260T are two new bacterial species and new bacterial genera for which the names Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. were proposed, respectively.

Screening of colistin-resistant bacteria in livestock animals from France.

Colistin is frequently used as a growth factor or treatment against infectious bacterial diseases in animals. The Veterinary Division of the European Medicines Agency (EMA) restricted colistin use as a second-line treatment to reduce colistin resistance. In 2020, 282 faecal samples were collected from chickens, cattle, sheep, goats, and pigs in the south of France. In order to track the emergence of mobilized colistin resistant (mcr) genes in pigs, 111 samples were re-collected in 2021 and included pig faeces, food, and water from the same location. All samples were cultured in a selective Lucie Bardet Jean-Marc Rolain (LBJMR) medium and colonies were identified using MALDI-TOF mass spectrometry and then antibiotic susceptibility tests were performed. PCR and Sanger sequencing were performed to screen for the presence of mcr genes. The selective culture revealed the presence of 397 bacteria corresponding to 35 different bacterial species including Gram-negative and Gram-positive. Pigs had the highest prevalence of colistin-resistant bacteria with an abundance of intrinsically colistin-resistant bacteria and from these samples one strain harbouring both mcr-1 and mcr-3 has been isolated. The second collection allowed us to identify 304 bacteria and revealed the spread of mcr-1 and mcr-3 in pigs. In the other samples, naturally, colistin-resistant bacteria were more frequent, nevertheless the mcr-1 variant was the most abundant gene found in chicken, sheep, and goat samples and one cattle sample was positive for the mcr-3 gene. Animals are potential reservoir of colistin-resistant bacteria which varies from one animal to another. Interventions and alternative options are required to reduce the emergence of colistin resistance and to avoid zoonotic transmissions.

Mobile Colistin Resistance (mcr) Genes in Cats and Dogs and Their Zoonotic Transmission Risks.

Background: Pets, especially cats and dogs, represent a great potential for zoonotic transmission, leading to major health problems. The purpose of this systematic review was to present the latest developments concerning colistin resistance through mcr genes in pets. The current study also highlights the health risks of the transmission of colistin resistance between pets and humans. Methods: We conducted a systematic review on mcr-positive bacteria in pets and studies reporting their zoonotic transmission to humans. Bibliographic research queries were performed on the following databases: Google Scholar, PubMed, Scopus, Microsoft Academic, and Web of Science. Articles of interest were selected using the PRISMA guideline principles. Results: The analyzed articles from the investigated databases described the presence of mcr gene variants in pets including mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-8, mcr-9, and mcr-10. Among these articles, four studies reported potential zoonotic transmission of mcr genes between pets and humans. The epidemiological analysis revealed that dogs and cats can be colonized by mcr genes that are beginning to spread in different countries worldwide. Overall, reported articles on this subject highlight the high risk of zoonotic transmission of colistin resistance genes between pets and their owners. Conclusions: This review demonstrated the spread of mcr genes in pets and their transmission to humans, indicating the need for further measures to control this significant threat to public health. Therefore, we suggest here some strategies against this threat such as avoiding zoonotic transmission.

Screening of Colistin-Resistant Bacteria in Domestic Pets from France.

BACKGROUND: Pets are the closest animals to humans with a considerable risk of zoonotic transmission. This study aimed to screen colistin-resistant bacteria from stools of dogs and cats from Marseille, France. Screening of mcr genes in pets has never been reported in France. METHODS: Fecal samples (n = 157) were cultivated on the selective Lucie-Bardet Jean-Marc-Rolain medium (LBJMR). Bacteria were identified using Microflex LS MALDI-TOF. The antibiotic resistance phenotype was investigated for several antibiotics (ß-lactams, aminoside, cephalosporine, tetracycline, and sulfonamide). PCR techniques were performed to detect mcr genes. RESULTS: A total of 218 bacteria were identified. For cats, intrinsically colistin-resistant bacteria were significantly higher than mcr-1 gene carriers (n = 4). Dogs had more bacteria with the mcr-1 gene (n = 10). Furthermore, cats had a high prevalence of Gram-positive bacteria (GPB), whereas dogs had GNB equal to GPB. The diversity of identified bacteria was due to the constitution of the pets' microorganisms. Even though colistin use is monitored in France, pets harbor various colistin-resistant bacteria. Additionally, in this geographical area, bacteria bearing mcr-1 gene from dogs and cats were detected for the first time. CONCLUSIONS: The current study opens a new perspective: the spread of colistin resistance is independent of colistin use. What are the most factors related to the emergence of colistin resistance? The surveillance of pets must be considered a priority to avoid the spread of mcr genes. It is important to know the contribution that pets make to the pool of multidrug-resistant mcr-1-containing bacteria.

Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France.

OBJECTIVES: Colistin is considered a last-resort antibiotic against carbapenem-resistant isolates. Currently, this antibiotic is facing the emergence of mobilised colistin resistance (mcr) genes, which confer colistin resistance. This study conducted genomic characterisation of an atypical multidrug-resistant Escherichia coli harbouring two mcr genes in France. Samples collected from a pig farm in Avignon (Vaucluse department) were subjected to molecular screening targeting mcr variants. METHODS: Samples were cultured on selective Lucie-Bardet-Jean-Marc-Rolain medium. Growing bacteria were identified using MALDI-TOF, followed by antibiotic susceptibility testing. Whole-genome sequencing and bioinformatic genome analysis were performed. RESULTS: Selective culture of stools revealed the presence of an E. coli strain named Q4552 harbouring mcr-1.1 and mcr-3.5 genes, which is also resistant to 14 antibiotics. Genome sequencing and assembly yielded a complete and circular chromosome and eight different plasmids. Sequence analysis demonstrated an integration of a mobile genetic element carrying mcr-1.1 in the chromosome, whereas mcr-3.5 was in the plasmid and its resistome was composed of 22 resistance genes. The Q4552 strain was identified as an ST-843 clone that belonged to the clonal complex Cplx-568 and is the only ST type of this cplx-568 that has been isolated from animals, humans, and the environment. CONCLUSION: We report the first co-occurrence of mcr-1 and mcr-3 genes in France from a pathogenic E. coli isolated from a pig. Because this clone (ST-843) has been reported in zoonotic transmissions, programs to monitor the bacterium are urgently required to avoid its spread and zoonotic transmission to humans.