Characterization of CRISPR-Cas Systems in Serratia marcescens Isolated from Rhynchophorus ferrugineus (Olivier, 1790) (Coleoptera: Curculionidae)

The CRISPR-Cas adaptive immune system has been attracting increasing scientific interest for biological functions and biotechnological applications. Data on the Serratia marcescens system are scarce. Here, we report a comprehensive characterisation of CRISPR-Cas systems identified in S. marcescens strains isolated as secondary symbionts of Rhynchophorus ferrugineus, also known as Red Palm Weevil (RPW), one of the most invasive pests of major cultivated palms. Whole genome sequencing was performed on four strains (S1, S5, S8, and S13), which were isolated from the reproductive apparatus of RPWs. Subtypes I-F and I-E were harboured by S5 and S8, respectively. No CRISPR-Cas system was detected in Si or S13. Two CRISPR arrays (4 and 51 spacers) were detected in S5 and three arrays (11, 31, and 30 spacers) were detected in S8. The CRISPR-Cas systems were located in the genomic region spanning from ybhR to phnP, as if this were the only region where CRISPR-Cas loci were acquired. This was confirmed by analyzing the S. marcescens complete genomes available in the NCBI database. This region defines a genomic hotspot for horizontally acquired genes and/or CRISPR-Cas systems. This study also supplies the first identification of subtype I-E in S. marcescens

Identification of pigmented Serratia marcescens symbiotically associated with Rhynchophorus ferrugineus Olivier (Coleoptera: Curculionidae)

To characterize red pigment-producing bacteria (RPPB) regularly released during oviposition by red palm weevil (RPW), RPPB were recovered from eggs deposited in apples supplied as substrate for oviposition. The presence of RPPB was also detected from gut, the reproductive apparatus of dissected adult and virgin insects and from pupal cases collected within infested palms. RPPB were also identified all along the tissue of these palms. Analysis of the 16S rDNA, gyrB, rpoB, recA, and groEL sequences assigned RPPB to the species Serratia marcescens. RPPB exhibited an antimicrobial activity assessed by the agar well diffusion method against a number of gram-positive and gram-negative bacteria. In this study, we first report the identification of a red pigment-producing S. marcescens as extracellular symbiont of RPW. Route of transmission, detection within different organs, and a wide spread along the infested palm tissue, suggested S. marcescens is present as extracellular symbiont in different developmental stages of the RPW. Additionally, the antimicrobial activity exhibited versus Bacillus spp., Paenibacillus spp., and Lysinibacillus spp., reported as insect pathogens and potential candidates for biocontrol agents, could ascribe for S. marcescens a potential protective role

Bioinformatic survey of CRISPR loci across 15 Serratia species

The Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins (CRISPR-Cas) system of prokaryotes is an adaptative immune defense mechanism to protect themselves from invading genetic elements (e.g., phages and plasmids). Studies that describe the genetic organization of these prokaryotic systems have mainly reported on the Enterobacteriaceae family (now reorganized within the order of Enterobacterales). For some genera, data on CRISPR-Cas systems remain poor, as in the case of Serratia (now part of the Yersiniaceae family) where data are limited to a few genomes of the species marcescens. This study describes the detection, in silico, of CRISPR loci in 146 Serratia complete genomes and 336 high-quality assemblies available for the species ficaria, fonticola, grimesii, inhibens, liquefaciens, marcescens, nematodiphila, odorifera, oryzae, plymuthica, proteomaculans, quinivorans, rubidaea, symbiotica, and ureilytica. Apart from subtypes I-E and I-F1 which had previously been identified in marcescens, we report that of I-C and the I-E unique locus 1, I-E*, and I-F1 unique locus 1. Analysis of the genomic contexts for CRISPR loci revealed mdtN-phnP as the region mostly shared (grimesii, inhibens, marcescens, nematodiphila, plymuthica, rubidaea, and Serratia sp.). Three new contexts detected in genomes of rubidaea and fonticola (puu genes-mnmA) and rubidaea (osmE-soxG and ampC-yebZ) were also found. The plasmid and/or phage origin of spacers was also established

Molecular epidemiology and origin of cholera reemergence

Abstract In 1994 a cholera epidemic occurred in Italy and Albania after more than a decade of case absence. To investigate genotypic characteristics and the origin of the epidemic strains, 110 Vibrio cholerae O1 El Tor isolates from Italy and Albania were studied by randomly amplified polymorphic DNA analysis (RAPD), BglI ribotyping, and pulsed-field gel electrophoresis (PFGE) of genomic DNA. The Italian and Albanian strains were all ribotype 6 and their RAPD and PFGE patterns were identical as well. These findings indicated that the 1994 isolates belonged to the same clone and that the clone was part of the larger global spread of epidemic ribotype 6 strains, which started in southern Asia in 1990

Diffusion and persistence of multidrug resistant salmonella typhimurium strains phage type DT120 in Southern Italy

Sixty-two multidrug resistant Salmonella enterica serovar Typhimurium strains isolated from 255 clinical strains collected in Southern Italy in 2006–2008 were characterised for antimicrobial resistance genes, pulsotype, and phage type.Most strains (83.9%) were resistant to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (resistance pattern ACSSuT) encoded in 88.5% by the PSE-1, floR, aadA2, sul1, and tet(G) gene cluster harboured by the Salmonella Genomic Island (SGI1). In 11.5% of strains, the resistance was encoded by the InH-like integron (OXA-30-aadA1) and the catA1, sul1, and tet(B) genes. STYMXB.0061 (75%) and DT120 (84.6%) were the prevalent pulsotype and phage type identified in these strains, respectively. Five other resistance patterns were also found either in single or in a low number of isolates with TEM, dfrA12, strAB, sul2, tet(A), and tet(B) encoding for the associated ampicillin, trimethoprim, streptomycin, sulfamethoxazole, and tetracycline resistances, respectively. The pandemic DT104 clone, resistance pattern ACSSuT encoded by SGI1, has largely been identified in Italy since 1992, while strains DT120, resistance pattern ACSSuT (encoded by SGI1), have never been previously reported in Italy. In Europe, clinical S. Typhimurium strains DT120 have mainly been reported from sporadic outbreaks linked to the consumption of pork products.However, none of these strains were STYMXB.0061 and the antimicrobial resistance was not linked to SGI1.Theprevalent identification and persistence ofDT120 isolates would suggest, in Southern Italy, a phage type shifting of the pandemic DT104 clone pulsotype STYMXB.0061.Additionally, these findings raise epidemiological concern about the potential diffusion of these emerging multidrug resistant (SGI linked) DT120 strains

“Ectomosphere”: Insects and Microorganism Interactions

This study focuses on interacting with insects and their ectosymbiont (lato sensu) microorganisms for environmentally safe plant production and protection. Some cases help compare insect-bearing, -driving, or -spreading relevant ectosymbiont microorganisms to endosymbionts’ behaviour. Ectosymbiotic bacteria can interact with insects by allowing them to improve the value of their pabula. In addition, some bacteria are essential for creating ecological niches that can host the development of pests. Insect-borne plant pathogens include bacteria, viruses, and fungi. These pathogens interact with their vectors to enhance reciprocal fitness. Knowing vector-phoront interaction could considerably increase chances for outbreak management, notably when sustained by quarantine vector ectosymbiont pathogens, such as the actual Xylella fastidiosa Mediterranean invasion episode. Insect pathogenic viruses have a close evolutionary relationship with their hosts, also being highly specific and obligate parasites. Sixteen virus families have been reported to infect insects and may be involved in the biological control of specific pests, including some economic weevils. Insects and fungi are among the most widespread organisms in nature and interact with each other, establishing symbiotic relationships ranging from mutualism to antagonism. The associations can influence the extent to which interacting organisms can exert their effects on plants and the proper management practices. Sustainable pest management also relies on entomopathogenic fungi; research on these species starts from their isolation from insect carcasses, followed by identification using conventional light or electron microscopy techniques. Thanks to the development of omics sciences, it is possible to identify entomopathogenic fungi with evolutionary histories that are less-shared with the target insect and can be proposed as pest antagonists. Many interesting omics can help detect the presence of entomopathogens in different natural matrices, such as soil or plants. The same techniques will help localize ectosymbionts, localization of recesses, or specialized morphological adaptation, greatly supporting the robust interpretation of the symbiont role. The manipulation and modulation of ectosymbionts could be a more promising way to counteract pests and borne pathogens, mitigating the impact of formulates and reducing food insecurity due to the lesser impact of direct damage and diseases. The promise has a preventive intent for more manageable and broader implications for pests, comparing what we can obtain using simpler, less-specific techniques and a less comprehensive approach to Integrated Pest Management (IPM).The present work acknowledges the support from: European Union’s Horizon 2020 research and innovation programme under Grant Agreements No. 635646-POnTE “Pest Organisms Threatening Europe”, No. 727987-XF-ACTORS “Xylella Fastidiosa Active Containment Through a multidisciplinary-Oriented Research Strategy”, Grant number 952337-MycoTWIN “Enhancing Research and Innovation Capacity of Tubitak MAM Food Institute on Management of Mycotoxigenic Fungi and Mycotoxins”, and CURE-Xf, H2020-Marie Sklodowska-Curie Actions—Research and Innovation Staff Exchange. Reference number: 634353, coordinated by CIHEAM Bari. The EU Funding Agency is not responsible for any use that may be made of the information it contains. European Union’s StopMedWaste “Innovative Sustainable technologies TO extend the shelf-life of Perishable MEDiterranean fresh fruit, vegetables and aromatic plants and to reduce WASTE” a PRIMA project ID: 1556. European Union’s Euphresco BasicS “Basic substances as an environmentally friendly alternative to synthetic pesticides for plant protection” project ID: 2020-C-353. The work was partially carried out in the framework of the National Projects: RIGENERA, granted by MASAF n. 207631, 9 May 2022, and GENFORAGRIS, granted by MASAF n. 207631, 9 May 2022; and regional projects “Laboratory network for the selection, characterisation and conservation of germplasm and for preventing the spread of economically-relevant and quarantine pests (SELGE) No. 14”, founded by the Apulia Region, PO FESR 2007–2013—Axis I, Line of intervention 1.2., Action 1.2.1; Research for Innovation (REFIN) POR Puglia 2014–2020 Project: 8C6E699D, and PON AIM, COD. AIM 1809249-Attività 1 Linea 1

Genomic history of the seventh pandemic of cholera in Africa.

The seventh cholera pandemic has heavily affected Africa, although the origin and continental spread of the disease remain undefined. We used genomic data from 1070 Vibrio cholerae O1 isolates, across 45 African countries and over a 49-year period, to show that past epidemics were attributable to a single expanded lineage. This lineage was introduced at least 11 times since 1970, into two main regions, West Africa and East/Southern Africa, causing epidemics that lasted up to 28 years. The last five introductions into Africa, all from Asia, involved multidrug-resistant sublineages that replaced antibiotic-susceptible sublineages after 2000. This phylogenetic framework describes the periodicity of lineage introduction and the stable routes of cholera spread, which should inform the rational design of control measures for cholera in Africa

Editorial for the Special Issue “Antimicrobial Resistance and Genetic Elements in Bacteria”

Throughout human history, bacterial infections have been an omnipresent threat, which have, on occasion, resulted in devastating pandemics affecting humanity [...