Mauro Maria Colombo

Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs

Integrating and conjugative elements (ICEs) are one of the three principal types of self-transmissible mobile genetic elements in bacteria. ICEs, like plasmids, transfer via conjugation; but unlike plasmids and similar to many phages, these elements integrate into and replicate along with the host chromosome. Members of the SXT/R391 family of ICEs have been isolated from several species of gram-negative bacteria, including Vibrio cholerae, the cause of cholera, where they have been important vectors for disseminating genes conferring resistance to antibiotics. Here we developed a plasmid-based system to capture and isolate SXT/R391 ICEs for sequencing. Comparative analyses of the genomes of 13 SXT/R391 ICEs derived from diverse hosts and locations revealed that they contain 52 perfectly syntenic and nearly identical core genes that serve as a scaffold capable of mobilizing an array of variable DNA. Furthermore, selection pressure to maintain ICE mobility appears to have restricted insertions of variable DNA into intergenic sites that do not interrupt core functions. The variable genes confer diverse element-specific phenotypes, such as resistance to antibiotics. Functional analysis of a set of deletion mutants revealed that less than half of the conserved core genes are required for ICE mobility; the functions of most of the dispensable core genes are unknown. Several lines of evidence suggest that there has been extensive recombination between SXT/R391 ICEs, resulting in re-assortment of their respective variable gene content. Furthermore, our analyses suggest that there may be a network of phylogenetic relationships among sequences found in all types of mobile genetic elements.

New Cluster of Plasmid-Located Class 1 Integrons in Vibrio cholerae O1 and a dfrA15 Cassette-Containing Integron in Vibrio parahaemolyticus Isolated in Angola

ABSTRACT The resistance profile and its correlation with mobile genetic elements were investigated in 11 Vibrio cholerae O1 and 2 Vibrio parahaemolyticus clinical isolates, as well as in 1 V. cholerae O1 and 1 V. cholerae non-O1 environmental isolate, isolated between 1991 and 1996 in different provinces of Angola. All clinical isolates of V. cholerae O1 were resistant to ampicillin, chloramphenicol, trimethoprim, sulfamethoxazole, and tetracycline. They also contained a large conjugative plasmid (p3iANG) with a set of three class 1 integrons harboring dfrA15, blaP1, and qacH-aadA8 cassettes, which code for resistance to trimethoprim, beta-lactams, quaternary ammonium compounds, and aminoglycosides, clustered in a 19-kb region. Chloramphenicol (cat1), kanamycin (aph), sulfonamide (sul2), and tetracycline (tetG) resistance genes were also carried on the plasmid within the same 19-kb region. A chromosomal integron containing the dfrA15 cassette was also revealed in V. parahaemolyticus strains. SXT integrase genes were present in six V. cholerae isolates but apparently were not associated with known SXT-associated resistance genes. This study indicates that plasmids and integrons contributed mainly to the circulation of multiple-drug resistance determinants in Vibrio strains from Angola.

Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons

Circulation of mobile genetic elements linked to drug resistance spread was studied in Vibrio strains isolated from surface urban water (river and sea) and shellfish samples in 2002-2003 in Maputo, Mozambique. Class 1 integrons and integrating conjugative elements (ICE) were investigated by PCR and mating experiments in strains of major health interest: 10 Vibrio cholerae, six Vibrio parahaemolyticus, two Vibrio alginolyticus and one Vibrio fluvialis. Resistance to at least two antibiotics (predominantly beta-lactams) was detected in all the strains, with additional resistances to sulfamethoxazole, spectinomycin, streptomycin and/or trimethoprim. Class 1 integrons contributed partially to the expression of drug resistance and were found in five isolates: four V. cholerae (blaP1 cassette, one strain also contained the dfrA15 cassette) and one V. alginolyticus (aadA2 cassette). ICEs, apparently devoid of resistance genes, were found in eight V. cholerae, three V. parahaemolyticus and one V. fluvialis isolates. A wide variability was observed by molecular characterization of ICEs. Five ICEs were included in the SXT/R391 family and seven ICEs were not classified. Our results indicate that the SXT/R391 family and related ICEs comprise a large class of polymorphic genetic elements widely circulating in environmental Vibrio strains in Africa, beside those evidently linked to drug resistance in clinical isolates.

Acquisition and Evolution of SXT-R391 Integrative Conjugative Elements in the Seventh-Pandemic Vibrio cholerae Lineage

ABSTRACT SXT-R391 Integrative conjugative elements (ICEs) are self-transmissible mobile genetic elements able to confer multidrug resistance and other adaptive features to bacterial hosts, including Vibrio cholerae, the causative agent of cholera. ICEs are arranged in a mosaic genetic structure composed of a conserved backbone interspersed with variable DNA clusters located in conserved hot spots. In this study, we investigated ICE acquisition and subsequent microevolution in pandemic V. cholerae. Ninety-six ICEs were retrieved from publicly available sequence databases from V. cholerae clinical strains and were compared to a set of reference ICEs. Comparative genomics highlighted the existence of five main ICE groups with a distinct genetic makeup, exemplified by ICEVchInd5, ICEVchMoz10, SXT, ICEVchInd6, and ICEVchBan11. ICEVchInd5 (the most frequent element, represented by 70 of 96 elements analyzed) displayed no sequence rearrangements and was characterized by 46 single nucleotide polymorphisms (SNPs). SNP analysis revealed that recent inter-ICE homologous recombination between ICEVchInd5 and other ICEs circulating in gammaproteobacteria generated ICEVchMoz10, ICEVchInd6, and ICEVchBan11. Bayesian phylogenetic analyses indicated that ICEVchInd5 and SXT were independently acquired by the current pandemic V. cholerae O1 and O139 lineages, respectively, within a period of only a few years. IMPORTANCE SXT-R391 ICEs have been recognized as key vectors of antibiotic resistance in the seventh-pandemic lineage of V. cholerae, which remains a major cause of mortality and morbidity on a global scale. ICEs were acquired only recently in this clade and are acknowledged to be major contributors to horizontal gene transfer and the acquisition of new traits in bacterial species. We have reconstructed the temporal dynamics of SXT-R391 ICE acquisition and spread and have identified subsequent recombination events generating significant diversity in ICEs currently circulating among V. cholerae clinical strains. Our results showed that acquisition of SXT-R391 ICEs provided the V. cholerae seventh-pandemic lineage not only with a multidrug resistance phenotype but also with a powerful molecular tool for rapidly accessing the pan-genome of a large number of gammaproteobacteria. SXT-R391 ICEs have been recognized as key vectors of antibiotic resistance in the seventh-pandemic lineage of V. cholerae, which remains a major cause of mortality and morbidity on a global scale. ICEs were acquired only recently in this clade and are acknowledged to be major contributors to horizontal gene transfer and the acquisition of new traits in bacterial species. We have reconstructed the temporal dynamics of SXT-R391 ICE acquisition and spread and have identified subsequent recombination events generating significant diversity in ICEs currently circulating among V. cholerae clinical strains. Our results showed that acquisition of SXT-R391 ICEs provided the V. cholerae seventh-pandemic lineage not only with a multidrug resistance phenotype but also with a powerful molecular tool for rapidly accessing the pan-genome of a large number of gammaproteobacteria.

Identification of Trichomonas vaginalis α-Actinin as the Most Common Immunogen Recognized by Sera of Women Exposed to the Parasite

A study on presence of antibodies to Trichomonis vaginalis in serum was done on a group of 500 pregnant, asymptomatic Angolan women. A serologic screening, done by ELISA, revealed that 41% of the women had IgG and IgM against the parasite. Analysis of sera by immunoblotting revealed that 94.4% of sera with anti-T. vaginalis IgG class antibodies were reactive against a common immunogenic protein of 115 kDa. The common immunogen was identified as the protozoan alpha-actinin. All sera recognizing the 115-kDa antigen were reactive against both native and recombinant T. vaginalis alpha-actinin and nonreactive against human alpha-actinin. The findings presented in this work offer a new tool for epidemiologic studies and open new perspectives for vaccination.

Origin of Vibrio cholerae in Haiti

As pointed out in the December, 2010, editorial, the ongoing cholera outbreak in Haiti placed this diarrhoeal infectious disease at the forefront of the global public health agenda. As of Dec 3, 2010, WHO reported 121 518 cases, and 2591 deaths associated with cholera infection. Since Haiti was not previously aff ected by cholera during the current seventh pandemic its population is more susceptible to Vibrio cholerae infection. The epidemic strain responsible for the outbreak was identifi ed as V cholerae O1 biotype El Tor, resistant to co-trimoxazole (trimethoprim– sulfamethoxazole), furazolidone, sulfafurazole, streptomycin, and nalidixic acid. We analysed the genome of three clonal isolates sequenced recently by the US Centers for Disease Control and Prevention (AELH00000000, AELI00000000, and AELJ00000000). The Haitian strains contain an integrative conjugative element (ICE) of the SXT/R391 family, a major drugresistance-spreading vector in bacteria, which is 99% identical to ICEVchInd5. This ICE, which confers resistance to co-trimoxazole, sulfafurazole, and streptomycin, was originally identifi ed in strains of V cholerae isolated in India, which are also resistant to nalidixic acid, and clonally belong to the most prevalent epidemic clade in the Indian subcontinent, represented by the reference strain CIRS101. The Haitian clone carries a genotype 7 ctxB gene coding for the cholera toxin subunit B. This genotype was described only in an altered El Tor V cholerae variant isolated during the harsh cholera epidemic in Orissa, India, in 2007. Whole-genome alignment and comparative genomic analysis of the Haitian strains, with the representative V cholerae O1 variants from Central America and Indian subcontinent, confi rmed that the Haitian strain is strictly phylogenetically related to CIRS101 from India. This strain is one of the highly virulent Indian V cholerae O1 that are gradually spreading all over the world; it is not surprising that this strain easily took advantage of the susceptibility of the Haitian people to the disease, and the poor sanitation caused by the earthquake in Haiti.

ICEVchInd5 is prevalent in epidemic Vibrio cholerae O1 El Tor strains isolated in India

Integrative conjugative elements (ICEs) of the SXT/R391 family are self-transmissible mobile elements mainly involved in antibiotic resistance spread among γ-Proteobacteria, including Vibrio cholerae. We demonstrated that the recently described ICEVchInd5 is prevailing in V. cholerae O1 clinical strains isolated in Wardha province (Maharashtra, India) from 1994 to 2005. Genetic characterization by ribotyping and multiple-locus SSR analysis proved the same clonal origin for V. cholerae O1 isolates in Wardha province over an 11-year period and was used to assess the correlation between strain and ICE content among ours and different Indian reference strains. In silico analysis showed the existence of at least 3 sibling ICEs of ICEVchInd5 in V. cholerae O1 El Tor reference strains, isolated in the Indian subcontinent after 1992.

New V. cholerae atypical El Tor variant emerged during the 2006 epidemic outbreak in Angola

BackgroundV. cholerae is the etiological agent of cholera, a major public health concern in most developing countries. Virulence of V. cholerae relies on the powerful cholera toxin, encoded by the CTX prophage. The emergence of new pathogenic variants in the recent years has been mostly associated with new CTX prophage rearrangements.ResultsIn this retrospective study, we show that the epidemic V. cholerae O1 El Tor strain responsible for the 2006 outbreak in Angola is clonally and genetically different from El Tor strains circulating in the 1990s in the same area. Strains from 2006 carry ICEVchAng3 of the SXT/R391 family. This ICE is associated with a narrower multidrug resistance profile compared to the one conferred by plasmid p3iANG to strains of the 1990s. The CTX prophage carried by 2006 El Tor strains is characterized by rstRET and ctxBCla alleles organized in a RS1-RS2-Core array on chromosome I. Interestingly, the newly emerging atypical strain belongs to a clade previously known to comprise only clinical isolates from the Indian subcontinent that also contain the same ICE of the SXT/R391 family.ConclusionsOur findings remark the appearance of a novel V. cholerae epidemic variant in Africa with a new CTXΦ arrangement previously described only in the Indian Subcontinent.

Phenotypic features and molecular characterization of plasmids in Salmonella abortusovis

Summary: The phenotypic and genotypic characteristics of 69 wild-type strains of Salmonella abortusovis from Sardinia and other Italian regions, representing four different epidemic outbreaks, were studied. Biochemical profiles, pathogenicity factors, resistance to antibacterial drugs and genomic organization were investigated. None of the strains tested showed any haemagglutination with different types of red blood cells, and electron microscopy revealed no fimbriae. Adhesivity to epithelial cells was present in all strains tested. Only 16% of the strains were resistant to streptomycin, and no other drug resistances were found. The restriction patterns of chromosomal DNA did not show heterogeneity and a high-molecular-mass (50-67 kb) plasmid was found in all strains. Restriction analysis of plasmid DNA from strains from different geographical areas, collected over a period of 30 years, showed a HindIII restriction profile characterized by two patterns, one with three fragments, stable and common to all strains, and a second polymorphic pattern with five fragments. The stable pattern included a 3·7 kb HindIII fragment that hybridized with a S. typhimurium probe containing a virulence region including the spvC and spvD genes. These studies allowed us to outline a genetic correlation among S. abortusovis isolated from different outbreaks.

Molecular characterization of enterotoxigenic and borderline oxacillin resistant Staphylococcus strains from ovine milk

Staphylococcal enterotoxins (SEs) produced by Staphylococcus spp. are superantigens responsible for food-poisoning and are associated to mobile genetic elements such as Staphylococcus aureus pathogenicity islands (SaPI). The presence of 13 enterotoxin genes (sea, seb, sec, sed, see, seg, seh, sei, sej, sel, sek, seq, and tst) was tested in 15 S. aureus and 24 coagulase-negative Staphylococcus (CNS) multi-resistant strains isolated from ovine milk in Sardinia. All CNS isolates were enterotoxin-negative, whereas co-presence of sec, sel and tst was observed in most of the S. aureus strains. One isolate of S. aureus was characterized by tst alone. A multiplex PCR assay aimed at discriminating between the integrase genes of pathogenicity islands SaPI2, SaPIbov1, and SaPIMW2 was developed. We demonstrated that strains harboring sec, sel and tst were associated with SaPIbov1, whereas the strain positive for tst was associated with SaPI2. Borderline oxacillin resistant S. aureus strains were also detected. RAPD analysis of the Staphylococcus strains showed that clonal relationships were correlated with pathogenic profiles.