Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate

Novel multidrug resistance genomic islands and transposon carrying blaVEB-1 identified in mcr-positive Aeromonas strains from raw meat in China

OBJECTIVES

To characterize the genetic environments of ESBL gene blaVEB-1 in mcr-positive Aeromonas strains from raw meat in China.

METHODS

Whole genomes of Aeromonas strains were sequenced using the Illumina or Nanopore platforms. Genetic environments of blaVEB-1 were analysed using the BLAST program.

RESULTS

The blaVEB-1 gene was detected in five Aeromonas strains carrying the mcr-7-like gene. WGS revealed that all blaVEB-1 genes were located on Aeromonas chromosome, and were carried by two novel different genomic islands named Aeromonas veronii genomic islands AveGI1 and AveGI2, as well as one transposon named Tn7690. AveGI1 is a new member of the Salmonella genomic island 1 family, incorporated into the 3'-end of mnmE (trmE). AveGI2 is a novel genomic island that has a size of 23 180 bp and is incorporated into the 3'-end of syd. The MDR regions of AveGI1 and AveGI2 are two different class 1 integrons containing 10 and five resistance genes, respectively. Tn7690 is a Tn1722 derivative containing In4-type integron and Tn5393, which harbours 10 resistance genes and integrates into different positions on the chromosomes of three strains with the capacity for mobility.

CONCLUSIONS

We report chromosomally located novel MDR genomic islands and transposon that carry blaVEB-1 in mcr-positive Aeromonas strains. These genetic elements may mediate the spread of blaVEB-1 in Aeromonas, and may also evolve by capturing new antimicrobial resistance genes or other mobile genetic elements.

Multiple host colonization and differential expansion of multidrug-resistant ST25-Acinetobacter baumannii clades

The Acinetobacter baumannii clonal lineage ST25 has been identified in humans and animals and found associated with outbreaks globally. To highlight possible similarities among ST25 A. baumannii of animal and human origins and to gather clues on the dissemination and evolution of the ST25 lineage, we conducted a phylogenetic analysis on n = 106 human and n = 35 animal A. baumannii ST25 genomes, including 44 sequenced for this study. Resistance genes and their genetic background were analyzed, as well. ST25 genomes are clustered into four clades: two are widespread in South America, while the other two are largely distributed in Europe, Asia and America. One particular clade was found to include the most recent strains and the highest number of acquired antibiotic resistance genes. OXA-23-type carbapenemase was the most common. Other resistance genes such as blaNDM-1, blaPER-7, and armA were found embedded in complex chromosomal regions present in human isolates. Genomic similarity among multidrug resistant ST25 isolates of either animal or human origin was revealed, suggesting cross-contaminations between the two sectors. Tracking the clonal complex ST25 between humans and animals should provide new insights into the mode of dissemination of these bacteria, and should help defining strategies for preserving global health.

Overview of Salmonella Genomic Island 1-Related Elements Among Gamma-Proteobacteria Reveals Their Wide Distribution Among Environmental Species

The aim of this study was to perform an in silico analysis of the available whole-genome sequencing data to detect syntenic genomic islands (GIs) having homology to Salmonella genomic island 1 (SGI1), analyze the genetic variations of their backbone, and determine their relatedness. Eighty-nine non-redundant SGI1-related elements (SGI1-REs) were identified among gamma-proteobacteria. With the inclusion of the thirty-seven backbones characterized to date, seven clusters were identified based on integrase homology: SGI1, PGI1, PGI2, AGI1 clusters, and clusters 5, 6, and 7 composed of GIs mainly harbored by waterborne or marine bacteria, such as Vibrio, Shewanella, Halomonas, Idiomarina, Marinobacter, and Pseudohongiella. The integrase genes and the backbones of SGI1-REs from clusters 6 and 7, and from PGI1, PGI2, and AGI1 clusters differed significantly from those of the SGI1 cluster, suggesting a different ancestor. All backbones consisted of two parts: the part from attL to the origin of transfer (oriT) harbored the DNA recombination, transfer, and mobilization genes, and the part from oriT to attR differed among the clusters. The diversity of SGI1-REs resulted from the recombination events between GIs of the same or other families. The oriT appeared to be a high recombination site. The multi-drug resistant (MDR) region was located upstream of the resolvase gene. However, most SGI1-REs in Vibrio, Shewanella, and marine bacteria did not harbor any MDR region. These strains could constitute a reservoir of SGI1-REs that could be potential ancestors of SGI1-REs encountered in pathogenic bacteria. Furthermore, four SGI1-REs did not harbor a resolvase gene and therefore could not acquire an integron. The presence of mobilization genes and AcaCD binding sites indicated that their conjugative transfer could occur with helper plasmids. The plasticity of SGI1-REs contributes to bacterial adaptation and evolution. We propose a more relevant classification to categorize SGI1-REs into different clusters based on their integrase gene similarity.

Variants of Tn6924, a Novel Tn7 Family Transposon Carrying the blaNDM Metallo-β-Lactamase and 14 Copies of the aphA6 Amikacin Resistance Genes Found in Acinetobacter baumannii

Carbapenem resistance in Acinetobacter baumannii is primarily due to the global spread of two main clones that carry oxa23, oxa24, and oxa58. However, new carbapenem-resistant clones are emerging that are also resistant to a wide range of antibiotics. Strains belonging to ST85_IP (Institut Pasteur) carry the bla_NDM metallo-β-lactamase carbapenem resistance gene. Here, we completed the genome sequence of an ST85_IP strain, Cl300, recovered in 2015 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. Cl300 is highly resistant to meropenem and amikacin, and consistent with this, a copy of the bla_NDM carbapenem and 14 copies of the aphA6 amikacin resistance genes were found in the genome. Cl300 also contains the sul2 sulfonamide and the msr(E) macrolide resistance genes. All aphA6 copies and bla_NDM are in a novel 76-kb Tn7 family transposon designated Tn6924. Like Tn7, Tn6924 is bounded by 29-bp inverted repeats with additional TnsB binding sites at each end. Several variants of Tn6924 were found in a set of diverse strains, including ST85_IP strains as well as members of global clones 1 and 2. sul2 and msr(E) are in a 13.0-kb pseudocompound transposon (PCT) bounded by IS1008. ST85s represent a diverse group of strains, particularly in their antibiotic resistance gene content and the K and OC surface polysaccharide loci. Acquisition of Tn6924 by members of global clones indicates the significance of this transposon in spreading two clinically significant resistance genes, bla_NDM and aphA6.

IMPORTANCE To date, efforts to study the resistance mechanisms of carbapenem-resistant Acinetobacter baumannii have been largely focused on the two major globally distributed clones (GC1 and GC2). ST85 is an emerging sequence type, and unlike other clones, it is associated with the carriage of the bla_NDM gene. Here, we completed the genome sequence of an ST85 strain and showed that bla_NDM and 14 copies of the aphA6 amikacin resistance genes are in Tn6924, a novel Tn7 family transposon. Analysis of all publicly available ST85s predicted that all strains in the main lineage carry a variant of Tn6924. Variants of Tn6924 were also found in other clones, including GC1 and GC2. Tn6924 is an important mobile element given that it carries two clinically important resistance genes (bla_NDM and aphA6) and has spread to other clones. Therefore, outbreaks caused by ST85s should be studied and tracked.

Mobilisation of plasmid-mediated blaVEB-1 gene cassette into distinct genomic islands of Proteus mirabilis after ceftazidime exposure

OBJECTIVES

We sought to integrate a VEB-1-encoding gene cassette into the integron of the MDR region of genomic islands (GIs) harboured by Proteus mirabilis strains after antibiotic exposure.

METHODS

An IncP1 plasmid from Achromobacter xylosoxidans carrying the cassette array dfrA14-bla_VEB-1-aadB was introduced by conjugation into five strains of P. mirabilis: PmBRI, PmABB, PmSCO and Pm2CHAMA harbouring Salmonella GI 1 and PmESC harbouring Proteus GI 1. Circular intermediates of the cassettes were amplified by PCR. bla_VEB-harbouring P. mirabilis were exposed to increasing concentrations of ceftazidime each day. Presence of bla_VEB-1 in the GI was assessed by PCR. The complete MDR regions were mapped and sequenced in positive clones.

RESULTS

Circular intermediates were detected for dfrA14 and bla_VEB-1-aadB and dfrA14-bla_VEB-1-aadB cassettes arrays in A. xylosoxidans, and for aadA2 in P. mirabilis. Insertion of bla_VEB-1 into the GIs occurred under ceftazidime pressure. In all cases, the three cassettes from IncP1 were integrated. They replaced the cassette array of PmBRI, PmABB and PmSCO in which floRc, tet(A)G and bla_PSE-1 were conserved, whereas they replaced an integron and the IS26-flanked region in Pm2CHAMA. In PmESC, they only replaced aadB, with aadA2 being conserved. bla_VEB-1 integration occurred just after conjugation for Pm2CHAMA but required ceftazidime exposure for the other strains.

CONCLUSION

Homologous recombination of gene cassettes conferring resistance to clinically important antibiotics may occur under antibiotic pressure between an integron located on a plasmid and a co-resident GI. This feature participates in the acquisition, maintenance and spread of antibiotic resistance genes.

Identification of Proteus genomic island 2 variants in two clonal Proteus mirabilis isolates with coexistence of a novel genomic resistance island PmGRI1

OBJECTIVES

To characterize the MDR genomic islands (GIs) in Proteus mirabilis isolates.

METHODS

Two P. mirabilis strains (C55 and C74) of chicken origin were subjected to WGS (HiSeq and PacBio) and the MDR GIs were determined.

RESULTS

P. mirabilis strains C55 and C74 are clonal strains and harbour different Proteus genomic island 2 (PGI2) variants (PGI2-C55 and PGI2-C74). The MDR region of PGI2-C55 is composed of two class 1 integrons, separated by a region containing seven copies of IS26 and eight resistance genes, including blaCTX-M-3 and fosA3. The region in PGI2-C74 is a complete In4-type class 1 integron, harbouring five gene cassettes (dfrA16, blaCARB-2, aadA2, cmlA1 and aadA1). In addition, C55 and C74 carry an SXT/R391 integrative and conjugative element (ICEPmiJpn1), harbouring blaCMY-2, and a novel 50.46 kb genomic resistance island named PmGRI1-C55. PmGRI1-C55 harbours a tyrosine-type recombinase/integrase that might be responsible for the integration of PmGRI1-C55 at the 3' end of tRNA-Sec. It carries an MDR region derived from Tn2670 that harbours a Tn21 region and carries six resistance genes (catA1, blaTEM-1b, aphA1a, sul2, strA and strB). Blast analysis showed diverse PmGRI1 variants in P. mirabilis and Escherichia coli strains.

CONCLUSIONS

The finding of the two new PGI2 variants highlights that the homologous recombination between shared components of class 1 integrons and transposition by IS26 promote the diversity of MDR regions in PGI2. PmGRI1 is a new GI that carries various resistance genes identified in P. mirabilis and E. coli.

AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates

OBJECTIVES

To investigate the genomic context of a novel resistance island (RI) in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates and global isolates.

METHODS

Using a combination of long and short reads generated from the Oxford Nanopore and Illumina platforms, contiguous chromosomes and plasmid sequences were determined. BLAST-based analysis was used to identify the RI insertion target.

RESULTS

Genomes of four multiply antibiotic-resistant A. baumannii clinical strains, from a US hospital system, belonging to prevalent MLST ST2 (Pasteur scheme) and ST281 (Oxford scheme) clade F isolates were sequenced to completion. A class 1 integron carrying aadB (tobramycin resistance) and aadA2 (streptomycin/spectinomycin resistance) was identified. The class 1 integron was 6.8 kb, bounded by IS26 at both ends, and embedded in a new target location between an α/β-hydrolase and a reductase. Due to its novel insertion site and unique RI composition, we suggest naming this novel RI AbGRI4. Molecular analysis of global A. baumannii isolates identified multiple AbGRI4 RI variants in non-ST2 clonal lineages, including variations in the resistance gene cassettes, integron backbone and insertion breakpoints at the hydrolase gene.

CONCLUSIONS

A novel RI insertion target harbouring a class 1 integron was identified in a subgroup of ST2/ST281 clinical isolates. Variants of the RI suggested evolution and horizontal transfer of the RI across clonal lineages. Long- and short-read hybrid assembly technology completely resolved the genomic context of IS-bounded RIs, which was not possible using short reads alone.

Identification of a novel genomic resistance island PmGRI1-STP3 and an SXT/R391 integrative conjugative element in Proteus mirabilis of swine origin in China

OBJECTIVES

This study aimed to determine the genetic environment of antimicrobial resistance genes in Proteus mirabilis strain STP3 isolated from a diarrhoeic pig on a swine farm in Sichuan Province, China.

METHODS

Strain STP3 was subjected to antimicrobial susceptibility testing. Illumina MiSeq (200× coverage) and Nanopore PromethION (100× coverage) platforms were used for genome sequencing. A conjugation experiment was performed to determine the transferability and stability of antimicrobial resistance genes in this strain.

RESULTS

The assembled circular genome of P. mirabilis STP3 was 4 115 975 bp with a GC content of 39.58%; no plasmid sequence was detected. A novel genomic resistance island (PmGRI1-STP3) and an SXT/R391 integrative conjugative element (ICE) variant (ICEPmiChnSTP3) were characterised in P. mirabilis STP3. PmGRI1-STP3 of 52.7 kb was located at the 3' end of tRNA-Sec and shared the greatest identity with PmGRI1-C55 (54% coverage, 99.99% identity). PmGRI1-STP3 carried 16 resistance genes, including the clinically important extended-spectrum β-lactamase (ESBL) gene bla_CTX-M-3. ICEPmiChnSTP3 was inserted into the prfC gene. It carried 18 resistance genes, including the rRNA methyltransferase gene cfr and the fluoroquinolone resistance gene aac(6')-Ib-cr. A class 2 integron (dfrA1-sat2-aadA1) was also identified on transposon Tn7. Mobilisation experiments indicated that ICEPmiChnSTP3 was conjugally mobilised to Escherichia coli. However, PmGRI1-STP3 appeared to lose its mobilisation ability.

CONCLUSION

The identification of two genomic islands (GIs) in this study suggested that genetic elements might be key mediators for resistance gene acquisition in P. mirabilis and that IS26-mediated rearrangements promote the diversity of GIs.

Genomic islands related to Salmonella genomic island 1; integrative mobilisable elements in trmE mobilised in trans by A/C plasmids

Salmonella genomic island 1 (SGI1), an integrative mobilisable element (IME), was first reported 20 years ago, in the multidrug resistant Salmonella Typhimurium DT104 clone. Since this first report, many variants and relatives have been found in Salmonella enterica and Proteus mirabilis. Thanks to whole genome sequencing, more and more complete sequences of SGI1-related elements (SGI1-REs) have been reported in these last few years among Gammaproteobacteria. Here, the genetic organisation and main features common to SGI1-REs are summarised to help to classify them. Their integrases belong to the tyrosine-recombinase family and target the 3'-end of the trmE gene. They share the same genetic organisation (integrase and excisionase genes, replicase module, SgaCD-like transcriptional activator genes, traN, traG, mpsB/mpsA genes) and they harbour AcaCD binding sites promoting their excision, replication and mobilisation in presence of A/C plasmid. SGI1-REs are mosaic structures suggesting that recombination events occurred between them. Most of them harbour a multiple antibiotic resistance (MAR) region and the plasticity of their MAR region show that SGI1-REs play a key role in antibiotic resistance and might help multiple antibiotic resistant bacteria to adapt to their environment. This might explain the emergence of clones with SGI1-REs.

IncC helper dependent plasmid-like replication of Salmonella Genomic Island 1

The Salmonella genomic island 1 (SGI1) and its variants are mobilized by IncA and IncC conjugative plasmids. SGI1-family elements and their helper plasmids are effective transporters of multidrug resistance determinants. SGI1 exploits the transfer apparatus of the helper plasmid and hijacks its activator complex, AcaCD, to trigger the expression of several SGI1 genes. In this way, SGI1 times its excision from the chromosome to the helper entry and expresses mating pore components that enhance SGI1 transfer. The SGI1-encoded T4SS components and the FlhDC-family activator proved to be interchangeable with their IncC-encoded homologs, indicating multiple interactions between SGI1 and its helpers. As a new aspect of this crosstalk, we report here the helper-induced replication of SGI1, which requires both activators, AcaCD and FlhDC_SGI1, and significantly increases the stability of SGI1 when coexists with the helper plasmid. We have identified the oriV_SGI1 and shown that S004-repA operon encodes for a translationally coupled leader protein and an IncN2/N3-related RepA that are expressed under the control of the AcaCD-responsive promoter P_S004. This replicon transiently maintains SGI1 as a 4–8-copy plasmid, not only stabilizing the island but also contributing to the fast displacement of the helper plasmid.

Replication of the Salmonella Genomic Island 1 (SGI1) triggered by helper IncC conjugative plasmids promotes incompatibility and plasmid loss

The mobilizable resistance island Salmonella genomic island 1 (SGI1) is specifically mobilized by IncA and IncC conjugative plasmids. SGI1, its variants and IncC plasmids propagate multidrug resistance in pathogenic enterobacteria such as Salmonella enterica serovars and Proteus mirabilis. SGI1 modifies and uses the conjugation apparatus encoded by the helper IncC plasmid, thus enhancing its own propagation. Remarkably, although SGI1 needs a coresident IncC plasmid to excise from the chromosome and transfer to a new host, these elements have been reported to be incompatible. Here, the stability of SGI1 and its helper IncC plasmid, each expressing a different fluorescent reporter protein, was monitored using fluorescence-activated cell sorting (FACS). Without selective pressure, 95% of the cells segregated into two subpopulations containing either SGI1 or the helper plasmid. Furthermore, FACS analysis revealed a high level of SGI1-specific fluorescence in IncC⁺ cells, suggesting that SGI1 undergoes active replication in the presence of the helper plasmid. SGI1 replication was confirmed by quantitative PCR assays, and extraction and restriction of its plasmid form. Deletion of genes involved in SGI1 excision from the chromosome allowed a stable coexistence of SGI1 with its helper plasmid without selective pressure. In addition, deletion of S003 (rep) or of a downstream putative iteron-based origin of replication, while allowing SGI1 excision, abolished its replication, alleviated the incompatibility with the helper plasmid and enabled its cotransfer to a new host. Like SGI1 excision functions, rep expression was found to be controlled by AcaCD, the master activator of IncC plasmid transfer. Transient SGI1 replication seems to be a key feature of the life cycle of this family of genomic islands. Sequence database analysis revealed that SGI1 variants encode either a replication initiator protein with a RepA_C domain, or an alternative replication protein with N-terminal replicase and primase C terminal 1 domains.

The Salmonella genomic island 1 (SGI1) and its variants propagate multidrug resistance in several species of human and animal pathogens with the help of IncA and IncC conjugative plasmids that are absolutely required for SGI1 dissemination. These helper plasmids are known to trigger the excision of SGI1 from the chromosome. Here, we found that IncC plasmids also trigger the replication of the excised, circular form of SGI1 by enabling the expression of an SGI1-borne replication initiator gene. In return, high-copy replication of SGI1 interferes with the persistence of the IncC plasmid and prevents its cotransfer into a recipient cell, thereby allowing integration and stabilization of SGI1 into the chromosome of the new host. This finding is important to better understand the complex interactions between SGI1-like elements and their helper plasmids that lead to widespread and highly efficient propagation of multidrug resistance genes to a broad range of human and animal pathogens.

Assessing the benefits of composting poultry manure in reducing antimicrobial residues, pathogenic bacteria, and antimicrobial resistance genes: a field-scale study

The poultry industry in the European Union produces 13 million tons of manure annually, which represents a major health and environmental challenge. Composting is an environmental-friendly technique for the management of manure, but there are few studies about antibiotic residues and antimicrobial resistances at a field scale. The goal of this study was to determine if the composting of poultry manure at a field scale would result in the reduction of antibiotic residues, pathogenic bacteria, and antibiotic resistance genes (ARGs) in the final fertilizer product. A 10-week composting of poultry manure spiked with enrofloxacin, doxycycline, and ciprofloxacin was performed. The determination of antibiotics residues and 22 selected ARGs was carried out together with the identification of bacteria by metagenomics. In the case of ciprofloxacin and doxycycline, a 90% decrease was observed after composting for 3 weeks. Sixteen ARGs were detected at the beginning of the experiment; 12 of them decreased from week 0 to week 10 (reduction of 73.7-99.99%). The presence of potentially pathogenic bacteria, such as, Campylobacter coli or commensal bacteria such as Escherichia coli decreases along the composting process. In conclusion, 10-week composting of poultry manure promotes the reduction of antibiotic residues and most of the ARGs and pathogenic bacteria.

New insights regarding Acinetobacter genomic island-related elements

The objective of this study was to mobilise the Acinetobacter genomic island 1-A (AGI1-A) from Enterobacter hormaechei EclCSP2185 (E. cloacae complex) and to search for the distribution and structure of AGI1-related elements in the NCBI database. AGI1-A was transferred to Escherichia coli. Analysis of the attachment (att) sites could locate the possible recombination crossover in the att sequences at position 10-11 (GG) in the last 18 bp of trmE. In silico detection of AGI backbones in the WGS database identified AGI variants in Salmonella enterica (83 strains), Vibrio cholerae (33), E. hormaechei (12), Acinetobacter baumannii (2), most belonging to prevalent clones (ST40, ST69, ST114 and ST25, respectively), but also in E. coli (1) and Klebsiella pneumoniae (1). Two groups of backbone were identified: one similar to AGI1, the other with a short segment from a Shewanella element upstream of ORF A022. The MDR regions were inserted by transposition at the res site in four different positions ATAGG (A. baumannii), CATAG (S. enterica and V. cholerae), TAGGT (S. enterica and K. pneumoniae) and TGCAC (S. enterica) representing four different lineages. In some V. cholerae, E. hormaechei and E. coli, deletion events occurred that eliminated part of the backbone at the left junction. Analysis of the right junction identified a fifth lineage in V. cholerae and E. hormaechei (CCATA). In conclusion, based on the position of the MDR region, AGI-related elements belonged to five groups of closely related genomic islands (AGI1-AGI5), with differences in backbones that evolved independently over time.

Identification of a mobilizable, multidrug-resistant genomic island in Myroides odoratimimus isolated from Tibetan pasture

Strains of the environmental bacterium Myroides odoratimimus can cause human infections. However, treating M. odoratimimus infections can be difficult because of multidrug resistance in this organism. In this study, we isolated strain M. odoratimimus G13 from pastureland in Tibet, China. The minimum inhibitory concentration analysis suggested that strain G13 has resistance to multiple antibiotics, with an MIC for tetracycline of 168 mg/L. Whole-genome sequencing and bioinformatic analysis revealed that the genome of G13 was rich in virulence factor-encoding genes and antibiotic resistance genes (ARGs). The mobilizable genomic island MGI1313 was also identified and characterized, and six resistance genes related to four types of antibiotics were annotated in MGI1313. Conjugation assays indicated that MGI1313 could be transferred from G13 to Escherichia coli 25DN by horizontal gene transfer, resulting in multidrug-resistant E. coli conjugants. In conclusion, multidrug-resistant M. odoratimimus G13 and the mobility of MGI1313 raise the risk of difficult-to-treat bacterial infections and should be under close surveillance.

Genomic characterization of antibiotic resistance-encoding genes in clinical isolates of Vibrio cholerae non-O1/non-O139 strains from Kolkata, India: generation of novel types of genomic islands containing plural antibiotic resistance genes

Non-O1/non-O139 nontoxigenic Vibrio cholerae associated with cholera-like diarrhea has been reported in Kolkata, India. However, the property involved in the pathogenicity of these strains has remained unclear. The character of 25 non-O1/non-O139 nontoxigenic V. cholerae isolated during 8 years from 2007 to 2014 in Kolkata was examined. Determination of the serogroup showed that the serogroups O6, O10, O35, O36, O39, and O70 were represented by two strains in each serogroup, and the remaining isolates belonged to different serogroups. To clarify the character of antibiotic resistance of these isolates, an antibiotic resistance test and the gene analysis were performed. According to antimicrobial drug susceptibility testing, 13 strains were classified as drug resistant. Among them, 10 strains were quinolone resistant and 6 of the 13 strains were resistant to more than three antibiotics. To define the genetic background of the antibiotic character of these strains, whole-genome sequences of these strains were determined. From the analysis of these sequences, it becomes clear that all quinolone resistance isolates have mutations in quinolone resistance-determining regions. Further research on the genome sequence showed that four strains possess Class 1 integrons in their genomes, and that three of the four integrons are found to be located in their genomic islands. These genomic islands are novel types. This indicates that various integrons containing drug resistance genes are spreading among V. cholerae non-O1/non-O139 strains through the action of newly generated genomic islands.

Fungicides enhanced the abundance of antibiotic resistance genes in greenhouse soil

Long-term substantial application of fungicides in greenhouse cultivation led to residual pollution in soils and then altered soil microbial community. However, it is unclear whether residual fungicides could affect the diversity and abundance of antibiotic resistance genes (ARGs) in greenhouse soils. Here, the dissipation of fungicides and its impact on the abundance of ARGs were determined using shotgun metagenomic sequencing in the greenhouse and mountain soils under laboratory conditions. Our results showed the greenhouse soils harbored more diverse and abundant ARGs than the mountain soils. The application of carbendazim, azoxystrobin, and chlorothalonil could increase the abundance of total ARGs in the greenhouse soils, especially for those dominant ARG subtypes including sul2, sul1, aadA, tet(L), tetA(G), and tetX2. The abundant ARGs were significantly correlated with mobile genetic elements (MGEs, e.g. intI1and R485) in the greenhouse soils but no significant relationship in the mountain soils. Meanwhile, the co-occurrence patterns of ARGs and MGEs, e.g., sul2 and R485, sul1 and transposase, were further verified via the genetic arrangement of genes on the metagenome-assembled contigs in the greenhouse soils. Additionally, host tracking analysis indicated that ARGs were mainly carried by enterobacteria in the greenhouse soils but actinomyces in the mountain soils. These findings confirmed that some fungicides might serve as the co-selectors of ARGs and elevated their abundance via MGEs-mediated horizontal gene transfer in the greenhouse soils.

Abundance of mobile genetic elements in an Acinetobacter lwoffii strain isolated from Transylvanian honey sample

Based on phylogenetic analyses, strain M2a isolated from honey, an unexpected source of acinetobacters, was classified as Acinetobacter lwoffii. The genome of this strain is strikingly crowded with mobile genetic elements. It harbours more than 250 IS elements of 15 IS-families, several unit and compound transposons and 15 different plasmids. These IS elements, including 30 newly identified ones, could be classified into at least 53 IS species. Regarding the plasmids, 13 of the 15 belong to the Rep-3 superfamily and only one plasmid, belonging to the “Low-GC” family, possesses a seemingly complete conjugative system. The other plasmids, with one exception, have a mobilization region of common pattern, consisting of the divergent mobA/mobL-family and mobS-, mobC- or traD-like genes separated by an oriT-like sequence. Although two plasmids of M2a are almost identical to those of A. lwoffi strains isolated from gold mine or Pleistocene sediments, most of them have no close relatives. The presence of numerous plasmid-borne and chromosomal metal resistance determinants suggests that M2a previously has also evolved in a metal-polluted environment. The numerous, possibly transferable, plasmids and the outstanding number of transposable elements may reflect the high potential of M2a for rapid evolution.

Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae

Salmonella genomic island 1 (SGI1) is an integrative mobilisable element that plays an important role in the capture and spread of multiple drug resistance. To date, SGI1 has been found in clinical isolates of Salmonella enterica serovars, Proteus mirabilis, Morganella morganii, Acinetobacter baumannii, Providencia stuartii, Enterobacter spp, and recently in Escherichia coli. SGI1 preferentially targets the 3´-end of trmE, a conserved gene found in the Enterobacteriaceae and among members of the Gammaproteobacteria. It is, therefore, hypothesised that SGI1 and SGI1-related elements (SGI1-REs) may have been acquired by diverse bacterial genera. Here, Bitsliced Genomic Signature Indexes (BIGSI) was used to screen the NCBI Sequence Read Archive (SRA) for putative SGI1-REs in Gammaproteobacteria. Novel SGI-REs were identified in diverse genera including Cronobacter spp, Klebsiella spp, and Vibrio spp and in two additional isolates of Escherichia coli. An extensively drug-resistant human clonal lineage of Klebsiella pneumoniae carrying an SGI1-RE in the United Kingdom and an SGI1-RE that lacks a class 1 integron were also identified. These findings provide insight into the origins of this diverse family of clinically important genomic islands and expand the knowledge of the potential host range of SGI1-REs within the Gammaproteobacteria.

Multidrug resistance genes are associated with a 42-kb island TGI1 carrying a complex class 1 integron in Trueperella pyogenes

OBJECTIVES

This research was conducted to ascertain the context and location of the antibiotic resistance determinants in a multiple antibiotic-resistant Trueperella pyogenes isolate TP1.

METHODS

The genome was sequenced using PacBio RS II, and the filtered data were assembled using Canu. Sequences were annotated on the basis of those in GenBank, and the genomic island (GI) of the TP1 was predicted by IslandPath-DIMOB.

RESULTS

TP1 as a multiple antibiotic-resistant isolate was recovered at Jilin Province (China) in 2017 from a dairy cow with pneumonia. TP1 exhibited resistance to aminoglycosides (gentamicin and amikacin), macrolides (erythromycin), lincosamides (clindamycin), sulfonamides (sulfamonomethoxine), tetracyclines (tetracycline and doxycycline) and chloramphenicols (chloramphenicol and florfenicol). An antibiotic resistance gene clustered together with the aadB, aadA1, cmlA5 and cmlA6 resistance genes located on a 7-kilobase (kb) multidrug-resistant (MDR) region, constituting a complex class 1 integron. The MDR region was located at one end of a 42-kb GI, and IS6100Δ1 mediated a genetic rearrangement with the complex class 1 integron-like SGI1 and formed a composite transposon. Furthermore, the tetW gene was located outside the four GIs consistent with tetracycline and doxycycline resistance. The ermD gene positioned in the front end of the 42-kb GI played an important role in mediating acquired erythromycin and clindamycin resistance.

CONCLUSIONS

Multiple resistance genes are located in a complex class 1 integron within a 42-kb T. pyogenes genomic island (TGI1), leading to TP1 multiple drug resistance. In comparison with SG1 families, TGI1 possesses versatile gene distribution and specific gene context for it upstream and downstream, and it represents a new lineage of genomic resistance islands.

SGI0, a relative of Salmonella genomic islands SGI1 and SGI2, lacking a class 1 integron, found in Proteus mirabilis

Several groups of integrative mobilizable elements (IMEs) that harbour a class 1 integron carrying antibiotic resistance genes have been found at the 3'-end of the chromosomal trmE gene. Here, a new IME, designated SGI0, was found in trmE in the sequenced and assembled genome of a French clinical, multiply antibiotic resistant Proteus mirabilis strain, Pm1LENAR. SGI0 shares the same gene content as the backbones of SGI1 and SGI2 (overall 97.6% and 97.7% nucleotide identity, respectively) but it lacks a class 1 integron. However, SGI0 is a mosaic made up of segments with >98.5% identity to SGI1 and SGI2 interspersed with segments sharing 74-95% identity indicating that further diverged backbone types exist and that recombination between them is occurring. The structure of SGI1-V, here re-named SGI-V, which lacks two SGI1 (S023 and S024) backbone genes and includes a group of additional genes in the backbone, was re-examined. In regions shared with SGI1, the backbones shared 97.3% overall identity with the differences distributed in patches with various levels of identity. The class 1 integron is also in a slightly different position with the target site duplication AAATT instead of ACTTG for SGI1 and variants, indicating that it was acquired independently. The Pm1LENAR resistance genes are in the chromosome, in Tn7 and an ISEcp1-mobilised segment.

Complex Class 1 Integron in a Clinical Escherichia coli Strain From Vietnam Carrying Both mcr-1 and bla NDM-1

The co-production of MCR and carbapenemase in Enterobacteriaceae has been previously reported. Here, we describe a clinical strain of Escherichia coli from Vietnam carrying both mcr-1 and bla _NDM-1. Whole-genome sequencing showed that the genome of this strain consists of a 4,975,832-bp chromosome and four plasmids. The mcr-1 and bla _NDM-1 genes are located on IncI2 and IncA/C2-type plasmids, respectively. Genetic analysis revealed the presence of a multidrug-resistant region with the structure of a novel complex class 1 integron including a class 1 integron region bearing two 5' conserved segments and one 3' conserved segment and two complete structures of ISCR1. The complex integron contains aminoglycoside resistance genes aadA2, aadB, strA, strB, and aphA6, quinolone resistance gene qnrA1, extended-spectrum β-lactamase gene bla _{OXA- 4}, and a Tn125-like transposon bearing bla _NDM-1. In addition, the dfrA12-gcuF-aadA2-cmlA1-aadA1-qacH gene cassette array belonging to the sul3-type integron was also identified, but the region found downstream of the gene cassette array is the IS440-tet(M)-IS26 element instead of the sul3 gene. The results further support that Enterobacteriaceae isolates co-harboring mcr and bla _NDM are widely being distributed. The structural characteristics of the complex integron reveal that ISCR1 elements play an important role in the mobilization of bla _NDM-1 and the development of multidrug-resistant regions.

IS26-Mediated Genetic Rearrangements in Salmonella Genomic Island 1 of Proteus mirabilis

Salmonella genomic island 1 (SGI1) is an integrative mobilizable element integrated into the chromosome of bacteria, which plays an important role in the dissemination of antimicrobial resistance genes. Lots of SGI1 variants are found mainly in Salmonella enterica and Proteus mirabilis. In this study, a total of 157 S. enterica and 132 P. mirabilis strains were collected from food-producing animals in Sichuan Province of China between December 2016 and November 2017. Detection of the SGI1 integrase gene showed that three S. enterica and five P. mirabilis strains were positive for SGI1, which displayed different multidrug resistance profiles. Five different SGI1 variants, including two novel variants (SGI1-PmBC1123 and SGI1-PmSC1111), were characterized by whole genome sequencing and PCR linkage. In two novel SGI1 variants, IS26-mediated rearrangements resulted in large sequence inversions of the MDR regions extending outside the SGI1 backbone. The sul3-type III class 1 integron (5′CS-sat-psp-aadA2-cmlA1-aadA1-qacH-IS440-sul3) and gene cassettes aac(6′)-Ib-cr-bla_OXA–1-catB3-arr-3 are found in SGI1-PmSC1111. Mobilization experiments indicated that three known variants were conjugally mobilized in trans to Escherichia coli with the help of a conjugative IncC plasmid. However, the two novel variants seemed to lose the mobilization, which might result from the sequence inversion of partial SGI1 backbone. The identification of the two novel SGI1 variants in this study suggested that IS26-mediated rearrangements promote the diversity of SGI1.

Salmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate

Salmonella genomic island 1 (SGI1) is an integrative genetic island first described in Salmonella enterica serovars Typhimurium DT104 and Agona in 2000. Variants of it have since been described in multiple serovars of S. enterica, as well as in Proteus mirabilis, Acinetobacter baumannii, Morganella morganii, and several other genera. The island typically confers resistance to older, first-generation antimicrobials; however, some variants carry blaNDM-1, blaVEB-6, and blaCTX-M15 genes that encode resistance to frontline, clinically important antibiotics, including third-generation cephalosporins. Genome sequencing studies of avian pathogenic Escherichia coli (APEC) identified a sequence type 117 (ST117) isolate (AVC96) with genetic features found in SGI1. The complete genome sequence of AVC96 was assembled from a combination of Illumina and single-molecule real-time (SMRT) sequence data. Analysis of the AVC96 chromosome identified a variant of SGI1-B located 18 bp from the 3' end of trmE, also known as the attB site, a known hot spot for the integration of genomic islands. This is the first report of SGI1 in wild-type E. coli The variant, here named SGI1-B-Ec1, was otherwise unremarkable, apart from the identification of ISEc43 in open reading frame (ORF) S023.IMPORTANCE SGI1 and variants of it carry a variety of antimicrobial resistance genes, including those conferring resistance to extended-spectrum β-lactams and carbapenems, and have been found in diverse S. enterica serovars, Acinetobacter baumannii, and other members of the Enterobacteriaceae SGI1 integrates into Gram-negative pathogenic bacteria by targeting a conserved site 18 bp from the 3' end of trmE For the first time, we describe a novel variant of SGI1 in an avian pathogenic Escherichia coli isolate. The presence of SGI1 in E. coli is significant because it represents yet another lateral gene transfer mechanism to enhancing the capacity of E. coli to acquire and propagate antimicrobial resistance and putative virulence genes. This finding underscores the importance of whole-genome sequencing (WGS) to microbial genomic epidemiology, particularly within a One Health context. Further studies are needed to determine how widespread SGI1 and variants of it may be in Australia.

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S.enterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S.enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylogeographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase (gyrA) and DNA topoisomerase IV (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. enterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions, which appear to have hampered previous attempts to trace the clone’s evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results indicate that most MDR S. enterica serotype Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials. This article contains data hosted by Microreact.

Identification and Characterization of oriT and Two Mobilization Genes Required for Conjugative Transfer of Salmonella Genomic Island 1

The integrative mobilizable elements of SGI1-family considerably contribute to the spread of resistance to critically important antibiotics among enteric bacteria. Even though many aspects of SGI1 mobilization by IncA and IncC plasmids have been explored, the basic transfer elements such as oriT and self-encoded mobilization proteins remain undiscovered. Here we describe the mobilization region of SGI1 that is well conserved throughout the family and carries the oriT _SGI1 and two genes, mpsA and mpsB (originally annotated as S020 and S019, respectively) that are essential for the conjugative transfer of SGI1. OriT _SGI1, which is located in the vicinity of the two mobilization genes proved to be a 125-bp GC-rich sequence with several important inverted repeat motifs. The mobilization proteins MpsA and MpsB are expressed from a bicistronic mRNA, although MpsB can be produced from its own mRNA as well. The protein structure predictions imply that MpsA belongs to the lambda tyrosine recombinase family, while MpsB resembles the N-terminal core DNA binding domains of these enzymes. The results suggest that MpsA may act as an atypical relaxase, which needs MpsB for SGI1 transfer. Although the helper plasmid-encoded relaxase proved not to be essential for SGI1 transfer, it appeared to be important to achieve the high transfer rate of the island observed with the IncA/IncC-SGI1 system.

Production of the K16 capsular polysaccharide by Acinetobacter baumannii ST25 isolate D4 involves a novel glycosyltransferase encoded in the KL16 gene cluster

A new capsular polysaccharide (CPS) biosynthesis gene cluster, KL16, was found in the genome sequence of a clinical Acinetobacter baumannii ST25 isolate, D4. The variable part of KL16 contains a module of genes for synthesis of 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid (5,7-di-N-acetylpseudaminic acid, Pse5Ac7Ac), a gene encoding ItrA3 that initiates the CPS synthesis with d-GlcpNAc, and two glycosyltransferase (Gtr) genes. The K16 CPS was studied by sugar analysis and Smith degradation along with 1D and 2D ¹H and ¹³C NMR spectroscopy, and shown to be built up of linear trisaccharide repeats containing d-galactose (d-Gal), N-acetyl-d-glucosamine (d-GlcNAc), and Pse5Ac7Ac. The d-Galp residue is linked to the d-GlcpNAc initiating sugar via a β-(1 → 3) linkage evidently formed by a Gtr5 variant, Gtr5_K16, encoded in KL16. This reveals an altered or relaxed substrate specificity of this variant as the majority of Gtr5-type glycosyltransferases have previously been shown to form a β-d-Galp-(1 → 3)-d-GalpNAc linkage. The β-Psep5Ac7Ac-(2 → 4)-d-Galp linkage is predicted to be formed by the other glycosyltransferase, Gtr37, which does not match members of any known glycosyltransferase family.

Identification and Characterization of New Resistance-Conferring SGI1s (Salmonella Genomic Island 1) in Proteus mirabilis

Salmonella genomic island 1 (SGI1) is a resistance-conferring chromosomal genomic island that contains an antibiotic resistance gene cluster. The international spread of SGI1-containing strains drew attention to the role of genomic islands in the dissemination of antibiotic resistance genes in Salmonella and other Gram-negative bacteria. In this study, five SGI1 variants conferring multidrug and heavy metal resistance were identified and characterized in Proteus mirabilis strains: SGI1-PmCAU, SGI1-PmABB, SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48. The genetic structures of SGI1-PmCAU and SGI1-PmABB were identical to previously reported SGI1s, while structural analysis showed that SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48 are new SGI1 variants. SGI1-PmJN16 is derived from SGI1-Z with the MDR region containing a new gene cassette array dfrA12-orfF-aadA2-qacEΔ1-sul1-chrA-orf1. SGI1-PmJN40 has an unprecedented structure that contains two right direct repeat sequences separated by a transcriptional regulator-rich DNA fragment, and is predicted to form two different extrachromosomal mobilizable DNA circles for dissemination. SGI1-PmJN48 lacks a common ORF S044, and its right junction region exhibits a unique genetic organization due to the reverse integration of a P. mirabilis chromosomal gene cluster and the insertion of part of a P. mirabilis plasmid, making it the largest known SGI1 to date (189.1 kb). Further mobility functional analysis suggested that these SGIs can be excised from the chromosome for transfer between bacteria, which promotes the horizontal transfer of antibiotic and heavy metal resistance genes. The identification and characterization of the new SGI1 variants in this work suggested the diversity of SGI1 structures and their significant roles in the evolution of bacteria.

Mobile Genetic Elements Associated with Antimicrobial Resistance

Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.

PGI2 Is a Novel SGI1-Relative Multidrug-Resistant Genomic Island Characterized in Proteus mirabilis

A novel 61,578-bp genomic island named Proteus genomic island 2 (PGI2) was characterized in Proteus mirabilis of swine origin in China. The 23.85-kb backbone of PGI2 is related to those of Salmonella genomic island 1 and Acinetobacter genomic island 1. The multidrug resistance (MDR) region of PGI2 is a complex class 1 integron containing 14 different resistance genes. PGI2 was conjugally mobilized in trans to Escherichia coli in the presence of a conjugative IncC helper plasmid.

Dissemination and loss of a biofilm-related genomic island in marine Pseudoalteromonas mediated by integrative and conjugative elements

Acquisition of genomic islands (GIs) plays a central role in the diversification and adaptation of bacteria. Some GIs can be mobilized in trans by integrative and conjugative elements (ICEs) or conjugative plasmids if the GIs carry specific transfer-related sequences. However, the transfer mechanism of GIs lacking such elements remains largely unexplored. Here, we investigated the transmissibility of a GI found in a coral-associated marine bacterium. This GI does not carry genes with transfer functions, but it carries four genes required for robust biofilm formation. Notably, this GI is inserted in the integration site for SXT/R391 ICEs. We demonstrated that acquisition of an SXT/R391 ICE results in either a tandem GI/ICE arrangement or the complete displacement of the GI. The GI displacement by the ICE greatly reduces biofilm formation. In contrast, the tandem integration of the ICE with the GI in cis allows the GI to hijack the transfer machinery of the ICE to excise, transfer and re-integrate into a new host. Collectively, our findings reveal that the integration of an ICE into a GI integration site enables rapid genome dynamics and a new mechanism by which SXT/R391 ICEs can augment genome plasticity.

Genomic characterization of an extensively-drug resistance Salmonella enterica serotype Indiana strain harboring blaNDM-1 gene isolated from a chicken carcass in China

OBJECTIVES

The objective of this study was to genetically characterize the antimicrobial resistance mechanisms of Salmonella enterica serotype Indiana C629 isolated from a chicken carcass in China in 2014.

METHODS

Antimicrobial susceptibility against a panel of 23 antimicrobial agents was carried out on Salmonella enterica serotype Indiana C629 and assessed according to CLSI standards. Whole-genome sequencing of this isolate was conducted to obtain the complete genome of S. Indiana.

RESULTS

Salmonella Indiana C629 expressed an XDR phenotype being resistant to more than 20 antimicrobial agents, including imipenem and meropenem. From the analysis of the resistance mechanisms, two mutations were identified in subunit A of DNA gyrase within the quinolone resistance determining region, in addition to the acquisition of mobile efflux pumps encoding oqxA/B/R. Additionally, four beta-lactamases resistance genes (bla_CTX-M-65, bla_TEM-1, bla_OXA-1, and bla_NDM-1), five aminoglycosides resistance genes (aac(3)-IV, aac(6')-Ib-cr, aadA2, aadA5, and aph(4)-Ia), two phenicol resistance genes (catB3 and floR), and five trimethoprim/sulfamethoxazole resistance genes (sul1/2/3 and dfrA12/17) were also identified. A total of 191 virulence genes were identified. Among them, 57 belonged to type-three secretion system (T3SS) encoding genes, 55 belonged to fimbrial adherence encoding genes, and 39 belonged to flagella-encoding genes CONCLUSIONS: This study demonstrated that multi-resistance mechanisms consistent with an XDR-phenotype, along with various virulence encoding genes of a S. Indiana strain in China These findings highlight the importance of cooperation among different sectors in order to monitor the spread of resistant pathogens among food animal, foods of animal origin and human beings that might further take measures to protect consumers' health.

Lessons from the Environmental Antibiotic Resistome

Antibiotic resistance is a global public health issue of growing proportions. All antibiotics are susceptible to resistance. The evidence is now clear that the environment is the single largest source and reservoir of resistance. Soil, aquatic, atmospheric, animal-associated, and built ecosystems are home to microbes that harbor antibiotic resistance elements and the means to mobilize them. The diversity and abundance of resistance in the environment is consistent with the ancient origins of antibiotics and a variety of studies support a long natural history of associated resistance. The implications are clear: Understanding the evolution of resistance in the environment, its diversity, and mechanisms is essential to the management of our existing and future antibiotic resources.

Determination and Analysis of the Putative AcaCD-Responsive Promoters of Salmonella Genomic Island 1

The integrative genomic island SGI1 and its variants confer multidrug resistance in numerous Salmonella enterica serovariants and several Proteus mirabilis and Acinetobacter strains. SGI1 is mobilized by the IncA/C family plasmids. The island exploits not only the conjugation apparatus of the plasmid, but also utilizes the plasmid-encoded master regulator AcaCD to induce the excision and formation of its transfer-competent form, which is a key step in the horizontal transfer of SGI1. Triggering of SGI1 excision occurs via the AcaCD-dependent activation of xis gene expression. AcaCD binds in P_xis to an unusually long recognition sequence. Beside the P_xis promoter, upstream regions of four additional SGI1 genes, S004, S005, S012 and S018, also contain putative AcaCD-binding sites. Furthermore, SGI1 also encodes an AcaCD-related activator, FlhDC_SGI1, which has no known function. Here, we have analysed the functionality of the putative AcaCD-dependent promoter regions and proved their activation by either AcaCD or FlhDC_SGI1. Moreover, we provide evidence that both activators act on the same binding site in P_xis and that FlhDC_SGI1 is able to complement the acaCD deletion of the IncA/C family plasmid R16a. We determined the transcription start sites for the AcaCD-responsive promoters and showed that orf S004 is expressed probably from a different start codon than predicted earlier. Additionally, expression of S003 from promoter P_S004 was ruled out. P_xis and the four SGI1 promoters examined here also lack obvious -35 promoter box and their promoter profile is consistent with the class II-type activation pathway. Although the role of the four additionally analysed AcaCD/FlhDC_SGI1-controlled genes in transfer and/or maintenance of SGI1 is not yet clear, the conservation of the whole region suggests the existence of some selection for their functionality.

Unmasking the ancestral activity of integron integrases reveals a smooth evolutionary transition during functional innovation

Tyrosine (Y)-recombinases have evolved to deliver mechanistically different reactions on a variety of substrates, but these evolutionary transitions are poorly understood. Among them, integron integrases are hybrid systems recombining single- and double-stranded DNA partners. These reactions are asymmetric and need a replicative resolution pathway, an exception to the canonical second strand exchange model of Y-recombinases. Integron integrases possess a specific domain for this specialized pathway. Here we show that despite this, integrases are still capable of efficiently operating the ancestral second strand exchange in symmetrical reactions between double-stranded substrates. During these reactions, both strands are reactive and Holliday junction resolution can follow either pathway. A novel deep-sequencing approach allows mapping of the crossover point for the second strand exchange. The persistence of the ancestral activity in integrases illustrates their robustness and shows that innovation towards new recombination substrates and resolution pathways was a smooth evolutionary process.

The integron integrases have evolved to perform recombination of single and double stranded DNA. Here the authors show that the ancestral pathway is still functional at double stranded sites, revealing the evolution towards the modern resolution pathway.

Phylogenetic and genomic diversity in isolates from the globally distributed Acinetobacter baumannii ST25 lineage

Acinetobacter baumannii is a globally distributed nosocomial pathogen that has gained interest due to its resistance to most currently used antimicrobials. Whole genome sequencing (WGS) and phylogenetics has begun to reveal the global genetic diversity of this pathogen. The evolution of A. baumannii has largely been defined by recombination, punctuated by the emergence and proliferation of defined clonal lineages. In this study we sequenced seven genomes from the sequence type (ST)25 lineage and compared them to 12 ST25 genomes deposited in public databases. A recombination analysis identified multiple genomic regions that are homoplasious in the ST25 phylogeny, indicating active or historical recombination. Genes associated with antimicrobial resistance were differentially distributed between ST25 genomes, which matched our laboratory-based antimicrobial susceptibility typing. Differences were also observed in biofilm formation between ST25 isolates, which were demonstrated to produce significantly more extensive biofilm than an isolate from the ST1 clonal lineage. These results demonstrate that within A. baumannii, even a fairly recently derived monophyletic lineage can still exhibit significant genotypic and phenotypic diversity. These results have implications for associating outbreaks with sequence typing as well as understanding mechanisms behind the global propagation of successful A. baumannii lineages.