ClonalFrameML: efficient inference of recombination in whole bacterial genomes

Novel ribotype/sequence type associations and diverse CRISPR-Cas systems in environmental Clostridioides difficile strains from northern Iraq

The environment is a natural reservoir of Clostridioides difficile, and here, we aimed to isolate the pathogen from seven locations in northern Iraq. Four of the sites yielded thirty-one isolates (ten from soils, twenty-one from sediments), which together represent ribotypes (RTs) 001 (five), 010 (five), 011 (two), 035 (two), 091 (eight), and 604 (nine). Twenty-five of the isolates (∼81%) are non-toxigenic, while six (∼19%) encode the toxin A and B genes. The genomes of eleven selected isolates represent six sequence types (STs): ST-3 (two), ST-15 (one), ST-107 (five), ST-137 (one), ST-177 (one), and ST-181 (one). Five novel RT/ST associations: RT011/ST-137, RT035/ST-107, RT091/ST-107, RT604/ST-177, and RT604/ST-181 were identified, and the first three are linked to RTs previously uncharacterized by multilocus sequence typing (MLST). Nine of the genomes belong to Clade 1, and two are closely related to the cryptic C-I clade. Diverse multiple prophages and CRISPR-Cas systems (class 1 subtype I-B1 and class 2 type V CRISPR-Cas systems) with spacers identical to other C. difficile phages and plasmids were detected in the genomes. Our data show the broader diversity that exists within environmental C. difficile strains from a much less studied location and their potential role in the evolution and emergence of new strains.

A clinical KPC-producing Klebsiella michiganensis strain carrying IncFII/IncFIA (HI1)/IncFIB (K) multiple replicon plasmid

Klebsiella michiganensis is an increasingly important bacterial pathogen causing nosocomial infections in clinical patients. In this study, we described the molecular and genomic characteristics of a carbapenem-resistant K. michiganensis strain KM166 cultured from a one-month premature baby's blood sample. KM166 showed lower biofilm forming ability in optical density (OD) than K. pneumoniae NTUH-K2044 (0.271 ± 0.027 vs. 0.595 ± 0.054, p = 0.001), and the median lethal dose (0.684 lg CFU/mL) was lower than K. pneumoniae strain NTUH-K2044 (6.679 lg CFU/mL). A IncFII/IncFIA(HI1)/IncFIB(K) multiple replicon plasmid in KM166 was identified carrying three replicon types. It has low homology to Escherichia coli pMRY09-581ECO_1 and the highest homology similarity to the INcFIA/INcFII(p14)-type plasmid in K. michiganensis strain fxq plasmid pB_KPC, suggesting that this multiple replicon plasmid was unlikely to have been transmitted from E. coli and probably a transfer of repFIB replicon genes from other K. michiganensis strains into the INcFIA/INcFII(p14)-type plasmid of KM166 had occurred. Mapping of the gene environment revealed that bla _KPC-2 in KM166 plasmid 3 had high identity and same Tn3-tnpR-IS481-bla _KPC-2-klcA_1 genomic context structure with K. pneumoniae strain JKP55, plasmid pKPC-J5501, and bla _KPC-2-carrying plasmid proved to be autonomously transferred under the help of mobile genetic elements into Escherichia coli 600 by plasmid conjugation experiment. In conclusion, we have characterized a K. michiganensis strain carrying multi-replicon IncFII/IncFIA(HI1)/IncFIB(K) plasmid and bla _KPC-2-carrying IncFII(p14)/IncFIA plasmid in this study, which provided insights about the evolutionary diversity of plasmids carried by K. michiganensis.

Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease

MOTIVATION

The ability to distinguish imported cases from locally acquired cases has important consequences for the selection of public health control strategies. Genomic data can be useful for this, for example, using a phylogeographic analysis in which genomic data from multiple locations are compared to determine likely migration events between locations. However, these methods typically require good samples of genomes from all locations, which is rarely available.

RESULTS

Here, we propose an alternative approach that only uses genomic data from a location of interest. By comparing each new case with previous cases from the same location, we are able to detect imported cases, as they have a different genealogical distribution than that of locally acquired cases. We show that, when variations in the size of the local population are accounted for, our method has good sensitivity and excellent specificity for the detection of imports. We applied our method to data simulated under the structured coalescent model and demonstrate relatively good performance even when the local population has the same size as the external population. Finally, we applied our method to several recent genomic datasets from both bacterial and viral pathogens, and show that it can, in a matter of seconds or minutes, deliver important insights on the number of imports to a geographically limited sample of a pathogen population.

AVAILABILITY AND IMPLEMENTATION

The R package DetectImports is freely available from https://github.com/xavierdidelot/DetectImports.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Phylogenetic Analysis of Bacterial Pathogen Genomes

The development of high-throughput sequencing technology has led to a significant reduction in the time and cost of sequencing whole genomes of bacterial pathogens. Studies can sequence and compare hundreds or even thousands of genomes within a given bacterial population. A phylogenetic tree is the most frequently used method of depicting the relationships between these bacterial pathogen genomes. However, the presence of homologous recombination in most bacterial pathogen species can invalidate the application of standard phylogenetic tools. Here we describe a method to produce phylogenetic analyses that accounts for the disruptive effect of recombination. This allows users to investigate the recombination events that have occurred, as well as to produce more meaningful phylogenetic analyses which recover the clonal genealogy representing the clonal relationships between genomes.

Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes

Fusobacterium necrophorum is a Gram-negative, filamentous anaerobe prevalent in the mucosal flora of animals and humans. It causes necrotic infections in cattle, resulting in a substantial economic impact on the cattle industry. Although infection severity and management differ within F. necrophorum species, little is known about F. necrophorum speciation and the genetic virulence determinants between strains. To characterize the clinical isolates, we performed whole-genome sequencing of four bovine isolates (8L1, 212, B17, and SM1216) and one human isolate (MK12). To determine the phylogenetic relationship and evolution pattern and investigate the presence of antimicrobial resistance genes (ARGs) and potential virulence genes of F. necrophorum, we also performed comparative genomics with publicly available Fusobacterium genomes. Using up-to-date bacterial core gene (UBCG) set analysis, we uncovered distinct Fusobacterium species and F. necrophorum subspecies clades. Pangenome analyses revealed a high level of diversity among Fusobacterium strains down to species levels. The output also identified 14 and 26 genes specific to F. necrophorum subsp. necrophorum and F. necrophorum subsp. funduliforme, respectively, which could be essential for bacterial survival under different environmental conditions. ClonalFrameML-based recombination analysis suggested that extensive recombination among accessory genes led to species divergence. Furthermore, the only strain of F. necrophorum with ARGs was F. necrophorum subsp. funduliforme B35, with acquired macrolide and tetracycline resistance genes. Our custom search revealed common virulence genes, including toxins, adhesion proteins, outer membrane proteins, cell envelope, type IV secretion system, ABC (ATP-binding cassette) transporters, and transporter proteins. A focused study on these genes could help identify major virulence genes and inform effective vaccination strategies against fusobacterial infections. IMPORTANCE Fusobacterium necrophorum is an anaerobic bacterium that causes liver abscesses in cattle with an annual incidence rate of 10% to 20%, resulting in a substantial economic impact on the cattle industry. The lack of definite biochemical tests makes it difficult to distinguish F. necrophorum subspecies phenotypically, where genomic characterization plays a significant role. However, due to the lack of a good reference genome for comparison, F. necrophorum subspecies-level identification represents a significant challenge. To overcome this challenge, we used comparative genomics to validate clinical test strains for subspecies-level identification. The findings of our study help predict specific clades of previously uncharacterized strains of F. necrophorum. Our study identifies both general and subspecies-specific virulence genes through a custom search-based analysis. The virulence genes identified in this study can be the focus of future studies aimed at evaluating their potential as vaccine targets to prevent fusobacterial infections in cattle.

Insights into Genomic Evolution and the Potential Genetic Basis of Klebsiella variicola subsp. variicola ZH07 Reveal Its Potential for Plant Growth Promotion and Autotoxin Degradation

The accumulation of autotoxins in soil causes continuous cropping obstacle stress in crops, and the bioremediation of autotoxins by microorganisms is an efficient process. In this study, strain ZH07 was isolated from the peanut rhizosphere and was found to be utilizing multiple autotoxins as its carbon sources. Based on its genomic characteristics and a phylogenetic analysis, ZH07 represents a member of Klebsiella variicola subsp. variicola. A comparative genomic analysis exhibited evolutionary dynamics exhibited by mobile genetic elements (MGEs), strain-specific genes, potential horizontal genes, and evolutionary constraints driven by purifying selection, which facilitated its genomic adaptation to rhizosphere soil. Genome mining revealed the potential genomic properties associated with plant growth promotion, such as nitrogen fixation, indole acetic acid synthesis, phosphonate solubilization and assimilation, siderophore production, and secondary metabolite synthesis. Moreover, abundant genes putatively responsible for the biodegradation of aromatic xenobiotics, including benzoic acid, cinnamic acid, vanillic acid, protocatechuic acid, phenylacetic acid, and p-hydroxybenzoic acid were also observed in the ZH07 genome. Compared to autotoxin stress alone, the combination of ZH07 application promoted peanut germination and seedling growth. Our analysis revealed the genetic adaptation of ZH07 to the rhizosphere environment and the potential genetic basis and effectiveness of the isolate to serve as a plant growth stimulator. IMPORTANCE Continuous cropping obstacles reduce the production and quality of agricultural products, and the application of rhizosphere beneficial microbes is an important strategy. Strain ZH07 showed autotoxin-degrading and plant growth-promoting capacities. The objectives of this study were to characterize its genomic evolution and the potential genetic basis of the autotoxin degradation and plant growth promotion. ZH07 represents a member of Klebsiella variicola subsp. variicola, based on genomic and phylogenetic analyses. Its genomic components have undergone different degrees of purifying selection, and the disparity in the evolutionary rate may be associated with its niche adaptation. A systematic analysis of the ZH07 genome identified the potential genetic basis that contributes to plant growth promotion and to aromatic xenobiotic biodegradation. This study demonstrates that plant growth-promoting rhizobacteria (PGPR) play important roles in autotoxin biodegradation and can be used as biofertilizers to enhance the growth of peanuts in response to continuous cropping obstacle stress.

Comparative Genomics of Streptococcus oralis Identifies Large Scale Homologous Recombination and a Genetic Variant Associated with Infection

The viridans group streptococci (VGS) are a large consortium of commensal streptococci that colonize the human body. Many species within this group are opportunistic pathogens causing bacteremia and infective endocarditis (IE), yet little is known about why some strains cause invasive disease. Identification of virulence determinants is complicated by the difficulty of distinguishing between the closely related species of this group. Here, we analyzed genomic data from VGS that were isolated from blood cultures in patients with invasive infections and oral swabs of healthy volunteers and then determined the best-performing methods for species identification. Using whole-genome sequence data, we characterized the population structure of a diverse sample of Streptococcus oralis isolates and found evidence of frequent recombination. We used multiple genome-wide association study tools to identify candidate determinants of invasiveness. These tools gave consistent results, leading to the discovery of a single synonymous single nucleotide polymorphism (SNP) that was significantly associated with invasiveness. This SNP was within a previously undescribed gene that was conserved across the majority of VGS species. Using the growth in the presence of human serum and a simulated infective endocarditis vegetation model, we were unable to identify a phenotype for the enriched allele in laboratory assays, suggesting a phenotype may be specific to natural infection. These data highlighted the power of analyzing natural populations for gaining insight into pathogenicity, particularly for organisms with complex population structures like the VGS. IMPORTANCE The viridians group streptococci (VGS) are a large collection of closely related commensal streptococci, with many being opportunistic pathogens causing invasive diseases, such as bacteremia and infective endocarditis. Little is known about virulence determinants in these species, and there is a distinct lack of genomic information available for the VGS. In this study, we collected VGS isolates from invasive infections and healthy volunteers and performed whole-genome sequencing for a suite of downstream analyses. We focused on a diverse sample of Streptococcus oralis genomes and identified high rates of recombination in the population as well as a single genome variant highly enriched in invasive isolates. The variant lies within a previously uncharacterized gene, nrdM, which shared homology with the anaerobic ribonucleoside triphosphate reductase, nrdD, and was highly conserved among VGS. This work increased our knowledge of VGS genomics and indicated that differences in virulence potential among S. oralis isolates were, at least in part, genetically determined.

Clonal Spread of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 in Chinese Pediatric Patients

Klebsiella pneumoniae often causes life-threatening infections in patients globally. Despite its notability, little is known about potential nosocomial outbreak and spread of K. pneumoniae among pediatric patients in low- and middle-income countries. Ninety-eight K. pneumoniae strains isolated from pediatric patients in a large general hospital in China between February 2018 and May 2019 were subjected to nanopore and Illumina sequencing and genomic analysis to elucidate transmission and genetic diversity. The temporal distribution patterns of K. pneumoniae revealed a cluster of sequence type 11 (ST11) strains comprising two clades. Most inferred transmissions were of clade 1, which could be traced to a common ancestor dating to mid-2017. An infant in the coronary care unit played a central role, potentially seeding transmission clusters in other wards. Major genomic changes during the outbreak included chromosomal mutations associated with virulence and gains and losses of plasmids encoding resistance. In summary, we report a nosocomial outbreak among pediatric patients caused by clonal dissemination of KPC-2-producing ST11 K. pneumoniae. Our findings highlight the value of whole-genome sequencing during outbreak investigations and illustrate that transmission chains can be identified during hospital stays. IMPORTANCE We report a nosocomial outbreak among pediatric patients caused by clonal dissemination of blaKPC-2-carrying ST11 K. pneumoniae. Strains of various sequence types coexist in the complex hospital environment; the quick emergence and spread of ST11 strains were mainly due to the plasmid-mediated acquisition of resistance genes. The spread of hospital infection was highly associated with several specific wards, suggesting the importance of genomic surveillance on wards at high risk of infection.

Unsuspected Clonal Spread of Methicillin-Resistant Staphylococcus aureus Causing Bloodstream Infections in Hospitalized Adults Detected Using Whole Genome Sequencing

BACKGROUND

Though detection of transmission clusters of methicillin-resistant Staphylococcus aureus (MRSA) infections is a priority for infection control personnel in hospitals, the transmission dynamics of MRSA among hospitalized patients with bloodstream infections (BSIs) has not been thoroughly studied. Whole genome sequencing (WGS) of MRSA isolates for surveillance is valuable for detecting outbreaks in hospitals, but the bioinformatic approaches used are diverse and difficult to compare.

METHODS

We combined short-read WGS with genotypic, phenotypic, and epidemiological characteristics of 106 MRSA BSI isolates collected for routine microbiological diagnosis from inpatients in 2 hospitals over 12 months. Clinical data and hospitalization history were abstracted from electronic medical records. We compared 3 genome sequence alignment strategies to assess similarity in cluster ascertainment. We conducted logistic regression to measure the probability of predicting prior hospital overlap between clustered patient isolates by the genetic distance of their isolates.

RESULTS

While the 3 alignment approaches detected similar results, they showed some variation. A gene family-based alignment pipeline was most consistent across MRSA clonal complexes. We identified 9 unique clusters of closely related BSI isolates. Most BSIs were healthcare associated and community onset. Our logistic model showed that with 13 single-nucleotide polymorphisms, the likelihood that any 2 patients in a cluster had overlapped in a hospital was 50%.

CONCLUSIONS

Multiple clusters of closely related MRSA isolates can be identified using WGS among strains cultured from BSI in 2 hospitals. Genomic clustering of these infections suggests that transmission resulted from a mix of community spread and healthcare exposures long before BSI diagnosis.

Recombination events drives the emergence of Colombian Helicobacter pylori subpopulations with self-identity ancestry

Helicobacter pylori have coevolved with mankind since its origins, adapting to different human groups. In America, H. pylori has evolved into several subpopulations. We analysed the genome of 154 Colombian strains along with 1,091 strains from worldwide populations to discern the ancestry and adaption to Colombian people. Population structure and ancestry was inferred with FineStructure and ChromoPainter. Phylogenetic relationship and the relative effect of recombination were analysing the core SNPs. Also, a Fst index was calculated to identify the gene variants with the strongest fixation in the Colombian subpopulations compared to their parent population hspSWEurope. FineStructure allowed the identification of two Colombian subpopulations, the previously described hspSWEuropeColombia and a novel subpopulation named hspColombia, that included three subgroups following their geographic origin. Colombian subpopulations represent an admixture of European, African and Indigenous ancestry; although some genomes showed a high proportion of self identity, suggesting an advanced adaption to these mestizo Colombian groups. We found that recombination is more important that punctual mutations in H. pylori genome diversity, 13.9 more important in hspSWEurope, 12.5 in hspSWEColombia and 10.5 in hspColombia, reflecting the divergence of these subpopulations. Fst analysis identified 82 SNPs fixed in 26 genes of the hspColombia subpopulation that encode for outer membrane and central metabolism proteins. Strongest fixation indexes were identified in genes encoding HofC, HopE, FrpB-4 and Sialidase A. These findings demonstrate that H. pylori has evolved in Colombia to give rise to subpopulations with a self identity ancestry, reflected in allele changes on genes encoding for outer membrane proteins.

Gene flow and introgression are pervasive forces shaping the evolution of bacterial species

BACKGROUND

Although originally thought to evolve clonally, studies have revealed that most bacteria exchange DNA. However, it remains unclear to what extent gene flow shapes the evolution of bacterial genomes and maintains the cohesion of species.

RESULTS

Here, we analyze the patterns of gene flow within and between >2600 bacterial species. Our results show that fewer than 10% of bacterial species are truly clonal, indicating that purely asexual species are rare in nature. We further demonstrate that the taxonomic criterion of ~95% genome sequence identity routinely used to define bacterial species does not accurately represent a level of divergence that imposes an effective barrier to gene flow across bacterial species. Interruption of gene flow can occur at various sequence identities across lineages, generally from 90 to 98% genome identity. This likely explains why a ~95% genome sequence identity threshold has empirically been judged as a good approximation to define bacterial species. Our results support a universal mechanism where the availability of identical genomic DNA segments required to initiate homologous recombination is the primary determinant of gene flow and species boundaries in bacteria. We show that these barriers of gene flow remain porous since many distinct species maintain some level of gene flow, similar to introgression in sexual organisms.

CONCLUSIONS

Overall, bacterial evolution and speciation are likely shaped by similar forces driving the evolution of sexual organisms. Our findings support a model where the interruption of gene flow-although not necessarily the initial cause of speciation-leads to the establishment of permanent and irreversible species borders.

Genome-Wide Association Studies Identify an Association of Transferrin Binding Protein B Variation and Invasive Serogroup Y Meningococcal Disease in Older Adults

BACKGROUND

Neisseria meningitidis serogroup Y, especially ST-23 clonal complex (Y:cc23), represents a larger proportion of invasive meningococcal disease (IMD) in older adults compared to younger individuals. This study explored the meningococcal genetic variation underlying this association.

METHODS

Maximum-likelihood phylogenies and the pangenome were analyzed using whole-genome sequence (WGS) data from 200 Y:cc23 isolates in the Neisseria PubMLST database. Genome-wide association studies (GWAS) were performed on WGS data from 250 Y:cc23 isolates from individuals with IMD aged ≥65 years versus < 65 years.

RESULTS

Y:cc23 meningococcal variants did not cluster by age group or disease phenotype in phylogenetic analyses. Pangenome comparisons found no differences in presence or absence of genes in IMD isolates from the different age groups. GWAS identified differences in nucleotide polymorphisms within the transferrin-binding protein B (tbpB) gene in isolates from individuals ≥65 years of age. TbpB structure modelling suggests these may impact binding of human transferrin.

CONCLUSIONS

These data suggest differential iron scavenging capacity amongst Y:cc23 meningococci isolated from older compared to younger patients. Iron acquisition is essential for many bacterial pathogens including the meningococcus. These polymorphisms may facilitate colonization, thereby increasing the risk of disease in vulnerable older people with altered nasopharyngeal microbiomes and nutritional status.

The complete and closed genome of the facultative generalist Candidatus Endoriftia persephone from deep-sea hydrothermal vents

The mutualistic interactions between Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone (short Endoriftia) have been extensively researched. However, the closed Endoriftia genome is still lacking. Here, by employing single-molecule real-time sequencing we present the closed chromosomal sequence of Endoriftia. In contrast to theoretical predictions of enlarged and mobile genetic element-rich genomes related to facultative endosymbionts, the closed Endoriftia genome is streamlined with fewer than expected coding sequence regions, insertion-, prophage-sequences and transposase-coding sequences. Automated and manually curated functional analyses indicated that Endoriftia is more versatile regarding sulphur metabolism than previously reported. We identified the presence of two identical rRNA operons and two long CRISPR regions in the closed genome. Additionally, pangenome analyses revealed the presence of three types of secretion systems (II, IV and VI) in the different Endoriftia populations indicating lineage-specific adaptations. The in depth mobilome characterization identified the presence of shared genomic islands in the different Endoriftia drafts and in the closed genome, suggesting that the acquisition of foreign DNA predates the geographical dispersal of the different endosymbiont populations. Finally, we found no evidence of epigenetic regulation in Endoriftia, as revealed by gene screenings and absence of methylated modified base motifs in the genome. As a matter of fact, the restriction-modification system seems to be dysfunctional in Endoriftia, pointing to a higher importance of molecular memory-based immunity against phages via spacer incorporation into CRISPR system. The Endoriftia genome is the first closed tubeworm endosymbiont to date and will be valuable for future gene oriented and evolutionary comparative studies.

Emergence and Molecular Epidemiology of Campylobacter jejuni ST-2993 Associated with a Large Outbreak of Guillain-Barré Syndrome in Peru

Campylobacter jejuni infection is considered the most frequent factor associated with Guillain-Barré syndrome (GBS). In 2019, a large outbreak of GBS was detected in Peru, being associated with C. jejuni detected in stool samples from these patients. The aim of this study was to determine the molecular epidemiology of C. jejuni strains (ST-2993) associated with a large GBS outbreak in Peru. In this study, 26 C. jejuni strains belonging to the ST-2293, obtained from 2019 to 2020, were sequenced using Illumina technology. Five low-quality sequences were removed using bioinformatics, and 21 genomes (17 clinical strains and 4 chicken strains) were considered in the phylogenetic analysis and comparative genomics. Phylogenetic reconstruction, including genomes from international databases, showed a connection between Peruvian and Chinese GBS strains, both of them having lipooligosaccharides (LOS) locus genes related to molecular mimicry with gangliosides in peripheral nerves. Also, ST-2993 was detected in Amazon strains recovered many years before the 2019 outbreak, but with no epidemiological connection with GBS. Besides, a close relationship between human and chicken C. jejuni strains indicated chicken as one of the probable reservoirs. Finally, comparative genomics revealed differences between Chinese and Peruvian strains, including the presence of a prophage inserted into the genome. In conclusion, C. jejuni ST-2993 strains recovered from the GBS outbreak are closely related to Peruvian Amazon strains. Moreover, ST-2993 has been circulated in Peru since 2003 in the Peruvian Amazonia, showing the necessity to reinforce the epidemiological surveillance of C. jejuni to improve the prevention and control of future GBS outbreaks. IMPORTANCE This article describes the molecular epidemiology of C. jejuni strains (ST-2993) associated with a large Guillain-Barré Syndrome (GBS) outbreak in Peru, sequencing several strains recovered from GBS patients and chickens from 2019 to 2020. Phylogenetic analysis showed a connection between Peruvian and Chinese GBS strains, both of them having lipooligosaccharides (LOS) locus genes related to molecular mimicry with gangliosides in peripheral nerves. Also, ST-2993 strains were detected in isolates recovered many years before the 2019 outbreak, but with no epidemiological connection with GBS. Besides, a close relationship between human and chicken strains indicated those animals as a probable reservoir. This information will help to understand the real situation of GBS in Peru and its causal agent, C. jejuni ST-2993, showing the necessity to increase epidemiological tracking of these kinds of pathogens to detect them and avoid GBS outbreaks in the future.

Limited Transmission of Klebsiella pneumoniae among Humans, Animals, and the Environment in a Caribbean Island, Guadeloupe (French West Indies)

Guadeloupe (French West Indies), a Caribbean island, is an ideal place to study the reservoirs of the Klebsiella pneumoniae species complex (KpSC) and identify the routes of transmission between human and nonhuman sources due to its insularity, small population size, and small area. Here, we report an analysis of 590 biological samples, 546 KpSC isolates, and 331 genome sequences collected between January 2018 and May 2019. The KpSC appears to be common whatever the source. Extended-spectrum-β-lactamase (ESBL)-producing isolates (21.4%) belonged to K. pneumoniae sensu stricto (phylogroup Kp1), and all but one were recovered from the hospital setting. The distribution of species and phylogroups across the different niches was clearly nonrandom, with a distinct separation of Kp1 and Klebsiella variicola (Kp3). The most frequent sequence types (STs) (≥5 isolates) were previously recognized as high-risk multidrug-resistant (MDR) clones, namely, ST17, ST307, ST11, ST147, ST152, and ST45. Only 8 out of the 63 STs (12.7%) associated with human isolates were also found in nonhuman sources. A total of 22 KpSC isolates were defined as hypervirulent: 15 associated with human infections (9.8% of all human isolates), 4 (8.9%) associated with dogs, and 3 (15%) associated with pigs. Most of the human isolates (33.3%) belonged to the globally successful sublineage CG23-I. ST86 was the only clone shared by a human and a nonhuman (dog) source. Our work shows the limited transmission of KpSC isolates between human and nonhuman sources and points to the hospital setting as a cornerstone of the spread of MDR clones and antibiotic resistance genes. IMPORTANCE In this study, we characterized the presence and genomic features of isolates of the Klebsiella pneumoniae species complex (KpSC) from human and nonhuman sources in Guadeloupe (French West Indies) in order to identify the reservoirs and routes of transmission. This is the first study in an island environment, an ideal setting that limits the contribution of external imports. Our data showed the limited transmission of KpSC isolates between the different compartments. In contrast, we identified the hospital setting as the epicenter of antibiotic resistance due to the nosocomial spread of successful multidrug-resistant (MDR) K. pneumoniae clones and antibiotic resistance genes. Ecological barriers and/or limited exposure may restrict spread from the hospital setting to other reservoirs and vice versa. These results highlight the need for control strategies focused on health care centers, using genomic surveillance to limit the spread, particularly of high-risk clones, of this important group of MDR pathogens.

Molecular mechanisms leading to ceftolozane/tazobactam resistance in clinical isolates of Pseudomonas aeruginosa from five Latin American countries

Objectives

Identify molecular mechanisms responsible for the in vitro non-susceptibility to ceftolozane/tazobactam (TOL) in a group of 158 clinical isolates of Pseudomonas aeruginosa from five Latin American countries collected before the introduction of TOL into the clinical practice.

Methods

Clinical isolates of P. aeruginosa (n = 504) were collected between January 2016 and October 2017 from 20 hospitals located in Argentina, Brazil, Chile, Colombia, and Mexico. Minimum inhibitory concentrations (MICs) to TOL were determined by standard broth microdilution and interpreted according to CLSI breakpoints. Initially, production of carbapenemases in TOL non-susceptible isolates was assessed by Rapidec® followed by qPCR to detect bla_KPC, bla_NDM-1, bla_VIM, and bla_IMP. Illumina® WGS was performed for isolates in which non-susceptibility to TOL was not mediated by carbapenemases.

Results

A total of 158 (31.3%) isolates were non-susceptible to TOL. In 74 (46.8%) of these isolates, non-susceptibility to TOL was explained by the production of at least one carbapenemase. WGS revealed that some isolates carried ESBLs, mutated bla_PDC and ampD, associated with decreased susceptibility to TOL.

Conclusion

Substitutions found in PDC and carbapenemase production were the most common presumed mechanisms of resistance to TOL detected in this study. This study shows that epidemiological surveillance is warranted to monitor the emergence of novel mechanisms of resistance to TOL that might compromise its clinical utility.

Emergence of a Novel Lineage and Wide Spread of a blaCTX-M-15/IncHI2/ST1 Plasmid among Nosocomial Enterobacter in Guadeloupe

Between April 2018 and August 2019, a total of 135 strains of Enterobacter cloacae complex (ECC) were randomly collected at the University Hospital Center of Guadeloupe to investigate the structure and diversity of the local bacterial population. These nosocomial isolates were initially identified genetically by the hsp60 typing method, which revealed the clinical relevance of E. xiangfangensis (n = 69). Overall, 57/94 of the third cephalosporin-resistant strains were characterized as extended-spectrum-β-lactamase (ESBL) producers, and their whole-genome was sequenced using Illumina technology to determine the clonal relatedness and diffusion of resistance genes. We found limited genetic diversity among sequence types (STs). ST114 (n = 13), ST1503 (n = 9), ST53 (n = 5) and ST113 (n = 4), which belong to three different Enterobacter species, were the most prevalent among the 57 ESBL producers. The blaCTXM-15 gene was the most prevalent ESBL determinant (56/57) and was in most cases associated with IncHI2/ST1 plasmid replicon carriage (36/57). To fully characterize this predominant blaCTXM-15/IncHI2/ST1 plasmid, four isolates from different lineages were also sequenced using Oxford Nanopore sequencing technology to generate long-reads. Hybrid sequence analyses confirmed the circulation of a well-conserved plasmid among ECC members. In addition, the novel ST1503 and its associated species (ECC taxon 4) were analyzed, in view of its high prevalence in nosocomial infections. These genetic observations confirmed the overall incidence of nosocomial ESBL Enterobacteriaceae infections acquired in this hospital during the study period, which was clearly higher in Guadeloupe (1.59/1000 hospitalization days) than in mainland France (0.52/1,000 hospitalization days). This project revealed issues and future challenges for the management and surveillance of nosocomial and multidrug-resistant Enterobacter in the Caribbean.

A scalable analytical approach from bacterial genomes to epidemiology

Recent years have seen a remarkable increase in the practicality of sequencing whole genomes from large numbers of bacterial isolates. The availability of this data has huge potential to deliver new insights into the evolution and epidemiology of bacterial pathogens, but the scalability of the analytical methodology has been lagging behind that of the sequencing technology. Here we present a step-by-step approach for such large-scale genomic epidemiology analyses, from bacterial genomes to epidemiological interpretations. A central component of this approach is the dated phylogeny, which is a phylogenetic tree with branch lengths measured in units of time. The construction of dated phylogenies from bacterial genomic data needs to account for the disruptive effect of recombination on phylogenetic relationships, and we describe how this can be achieved. Dated phylogenies can then be used to perform fine-scale or large-scale epidemiological analyses, depending on the proportion of cases for which genomes are available. A key feature of this approach is computational scalability and in particular the ability to process hundreds or thousands of genomes within a matter of hours. This is a clear advantage of the step-by-step approach described here. We discuss other advantages and disadvantages of the approach, as well as potential improvements and avenues for future research. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.

Detecting bacterial adaptation within individual microbiomes

The human microbiome harbours a large capacity for within-person adaptive mutations. Commensal bacterial strains can stably colonize a person for decades, and billions of mutations are generated daily within each person's microbiome. Adaptive mutations emerging during health might be driven by selective forces that vary across individuals, vary within an individual, or are completely novel to the human population. Mutations emerging within individual microbiomes might impact the immune system, the metabolism of nutrients or drugs, and the stability of the community to perturbations. Despite this potential, relatively little attention has been paid to the possibility of adaptive evolution within complex human-associated microbiomes. This review discusses the promise of studying within-microbiome adaptation, the conceptual and technical limitations that may have contributed to an underappreciation of adaptive de novo mutations occurring within microbiomes to date, and methods for detecting recent adaptive evolution. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.

Genome dynamics mediated by repetitive and mobile elements in Xanthomonas citri pv. durantae

Xanthomonas is a highly evolved group of phytopathogenic bacteria infecting nearly 400 host plants having vast genomic resources available with heterogenicity in representation from different species and pathovars. Unfortunately, the wealth of data is extremely biased and restricted to a few Xanthomonas pathogens that infect economically important plants, while those reported to infect the most diverse plants remain neglected. In the present study, we report the first complete genome sequence of Xanthomonas citri pv. durantae that was reported to infect Duranta repens L. or golden dewdrop, a hedge plant of ornamental importance native to the American region. Phylogenomic analysis with its closest relatives placed it amongst X. citri pv. citri A* pathotype strains and further comparative studies revealed various large unique genomic regions of chromosomal origin. The association of integrative and conjugative elements and prophages with unique genomic regions suggests the role of mobilome in genome dynamics. A large number of IS elements and transcription activator-like effectors encoding genes on each of the four plasmids indicate the further scope of diversification in Xanthomonas .

Genome-Wide Association Study of Listeria monocytogenes Isolates Causing Three Different Clinical Outcomes

Heterogeneity in virulence potential of L. monocytogenes subgroups have been associated with genetic elements that could provide advantages in certain environments to invade, multiply, and survive within a host. The presence of gene mutations has been found to be related to attenuated phenotypes, while the presence of groups of genes, such as pathogenicity islands (PI), has been associated with hypervirulent or stress-resistant clones. We evaluated 232 whole genome sequences from invasive listeriosis cases in human and ruminants from the US and Europe to identify genomic elements associated with strains causing three clinical outcomes: central nervous system (CNS) infections, maternal-neonatal (MN) infections, and systemic infections (SI). Phylogenetic relationships and virulence-associated genes were evaluated, and a gene-based and single nucleotide polymorphism (SNP)-based genome-wide association study (GWAS) were conducted in order to identify loci associated with the different clinical outcomes. The orthologous results indicated that genes of phage phiX174, transfer RNAs, and type I restriction-modification (RM) system genes along with SNPs in loci involved in environmental adaptation such as rpoB and a phosphotransferase system (PTS) were associated with one or more clinical outcomes. Detection of phenotype-specific candidate loci represents an approach that could narrow the group of genetic elements to be evaluated in future studies.

The natural history and genetic diversity of Haemophilus influenzae infecting the airways of adults with cystic fibrosis

Haemophilus influenzae is a Gram-negative pathobiont, frequently recovered from the airways of persons with cystic fibrosis (pwCF). Previous studies of H. influenzae infection dynamics and transmission in CF predominantly used molecular methods, lacking resolution. In this retrospective cohort study, representative yearly H. influenzae isolates from all pwCF attending the Calgary Adult CF Clinic with H. influenzae positive sputum cultures between 2002 and 2016 were typed by pulsed-field gel electrophoresis. Isolates with shared pulsotypes common to ≥ 2 pwCF were sequenced by Illumina MiSeq. Phylogenetic and pangenomic analyses were used to assess genetic relatedness within shared pulsotypes, and epidemiological investigations were performed to assess potential for healthcare associated transmission. H. influenzae infection was observed to be common (33% of patients followed) and dynamic in pwCF. Most infected pwCF exhibited serial infections with new pulsotypes (75% of pwCF with ≥ 2 positive cultures), with up to four distinct pulsotypes identified from individual patients. Prolonged infection by a single pulsotype was only rarely observed. Intra-patient genetic diversity was observed at the single-nucleotide polymorphism and gene content levels. Seven shared pulsotypes encompassing 39% of pwCF with H. influenzae infection were identified, but there was no evidence, within our sampling scheme, of direct patient-to-patient infection transmission.

Genomic Evolution of ST11 Carbapenem-Resistant Klebsiella pneumoniae from 2011 to 2020 Based on Data from the Pathosystems Resource Integration Center

(1) Objective: ST11 carbapenem-resistant Klebsiella pneumoniae (CRKP) is widespread throughout the world, and the mechanisms for the transmission and evolution of major serotypes, ST11-KL47 and ST11-KL64, were analyzed to investigate the global distribution and evolutionary characteristics of ST11 CRKP; (2) Methods: The Pathosystems Resource Integration Center (PATRIC) database was downloaded and all K. pneumoniae from 2011 to 2020 were screened to obtain ST11 CRKP genome assemblies with basic information. The relationship of serotype evolution between KL47 and KL64 was then investigated using statistical and bioinformatic analysis; (3) Results: In total, 386 ST11 CRKP isolates were included for analysis. Blood (31.09%, 120/386), respiratory tract (23.06%, 89/386), and feces (20.21%, 78/386) were the major sources of samples. China was the leading country where ST11 CRKP was isolated. KL47 and KL64 were found to be the most prevalent serotypes. ST11-KL64 CRKP [median 78(P25~P75: 72~79.25)] had remarkably more virulence genes than the KL47 [median 63(P25~P75: 63~69)], and the distinction was statistically significant (p < 0.001). A differential comparison of virulence genes between KL47 and KL64 revealed 35 differential virulence genes, including rmpA/rmpA2, iucABCD, iutA, etc. The comparison of the recombination of serotype-determining regions between the two serotypes revealed that KL64 CRKP carried more nucleotide sequences in the CD1-VR2-CD2 region than KL47 CRKP. More nucleotide sequences added approximately 303 base pairs (bp) with higher GC content (58.14%), which might facilitate the evolution of the serotype toward KL64; (4) Conclusions: KL47 and KL64 have become the predominant serotypes of ST11 CRKP. KL64 CRKP carries more virulence genes than KL47 and has increased by approximately 303 bp through recombinant mutations, thus facilitating the evolution of KL47 to KL64. Stricter infection prevention and control measures should be developed to deal with the epidemic transmission of ST11-KL64 CRKP.

Genomic sequence of the non-pathogen Neisseria sp. strain MA1-1 with antibiotic resistance and virulence factors isolated from a head and neck cancer patient

Recent research has claimed virulence factors or antimicrobial resistance in commensal or non-pathogenic Neisseria spp. This study aimed to isolate and analyze commensal microorganisms related to the genus Neisseria from the oral cavity of a patient with head and neck cancer. We successfully isolated strain MA1-1 and identified its functional gene contents. Although strain MA1-1 was related to Neisseria flava based on 16S rRNA gene sequence similarity, genomic relatedness analysis revealed that strain MA1-1 was closely related to Neisseria mucosa, reported as a commensal Neisseria species. The strain MA1-1 genome harbored genes for microaerobic respiration and the complete core metabolic pathway with few transporters for nutrients. A number of genes have been associated with virulence factors and resistance to various antibiotics. In addition, the comparative genomic analysis showed that most genes identified in the strain MA1-1 were shared with other Neisseria spp. including two well-known pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. This indicates that the gene content of intra-members of the genus Neisseria has been evolutionarily conserved and is stable, with no gene recombination with other microbes in the host. Finally, this study provides more fundamental interpretations for the complete gene sequence of commensal Neisseria spp. and will contribute to advancing public health knowledge.

Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape

Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses1-4. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral evolution5. Here, we use a new phylogenomic method to search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. In a 1.6 million sample tree from May 2021, we identify 589 recombination events, which indicate that around 2.7% of sequenced SARS-CoV-2 genomes have detectable recombinant ancestry. Recombination breakpoints are inferred to occur disproportionately in the 3' portion of the genome that contains the spike protein. Our results highlight the need for timely analyses of recombination for pinpointing the emergence of recombinant lineages with the potential to increase transmissibility or virulence of the virus. We anticipate that this approach will empower comprehensive real-time tracking of viral recombination during the SARS-CoV-2 pandemic and beyond.

Genomic elements located in the accessory repertoire drive the adaptation to biocides in Listeria monocytogenes strains from different ecological niches

In response to the massive use of biocides for controlling Listeria monocytogenes (hereafter Lm) contaminations along the food chain, strains showing biocide tolerance emerged. Here, accessory genomic elements were associated with biocide tolerance through pangenome-wide associations performed on 197 Lm strains from different lineages, ecological, geographical and temporal origins. Mobile elements, including prophage-related loci, the Tn6188_qacH transposon and pLMST6_emrC plasmid, were widespread across lineage I and II food strains and associated with tolerance to benzalkonium-chloride (BC), a quaternary ammonium compound (QAC) widely used in food processing. The pLMST6_emrC was also associated with tolerance to another QAC, the didecyldimethylammonium-chloride, displaying a pleiotropic effect. While no associations were detected for chemically reactive biocides (alcohols and chlorines), genes encoding for cell-surface proteins were associated with BC or polymeric biguanide tolerance. The latter was restricted to lineage I strains from animal and the environment. In conclusion, different genetic markers, with polygenic nature or not, appear to have driven the Lm adaptation to biocide, especially in food strains but also from animal and the environment. These markers could aid to monitor and predict the spread of biocide tolerant Lm genotypes across different ecological niches, finally reducing the risk of such strains in food industrial settings.

First experience of implementing Candida auris real-time PCR for surveillance in the UK: detection of multiple introductions with two international clades and improved patient outcomes

BACKGROUND

Candida auris has been associated with rapid transmission and high mortality. A novel PCR-based surveillance programme was initiated at a London teaching hospital from January 2018. The results of this implementation until March 2019 are presented along with the clinical, transmission and phylogenetic characteristics encountered in that setting.

METHODS

A real-time PCR assay for C. auris was developed, validated, and implemented for direct use on skin swabs and urine. Environmental swabs were also tested by PCR as an emergency outbreak-control measure. Clinical risk factors and outcomes of patients were determined. Environmental dispersal was assessed using 24 h settle plate cultures around nine colonized patients followed by air sampling around one colonized patient during high- and low-turbulence activities. Sequencing was performed using Illumina HiSeq and maximum likelihood phylogenies were constructed using rapid bootstrap analysis.

RESULTS

Twenty-one C. auris colonized patients were identified. Median turnaround time of colonization detection reduced from 141 h (5.8 days) to approximately 24 h enabling rapid infection-control precautions. Settle plates detected 70-600 cfu/m² around colonized patients over 24 h and air sampling suggested dispersal during turbulent activities. C. auris DNA was detected from 35.7% environmental swabs. Despite being in a high-risk setting, no patients developed invasive infection. Sequencing analysis of isolates from this centre identified two introductions of the South Asian (Clade I) and one of the South African (Clade III) strain.

CONCLUSION

The PCR offers a rapid, scalable method of screening and supports clinical risk reduction in settings likely to encounter multiple introductions.

Metagenomic data from cerebrospinal fluid permits tracing the origin and spread of Neisseria meningitidis CC4821 in China

Metagenomic next-generation sequencing (mNGS) is useful for difficult to cultivate pathogens. Here, we use cerebrospinal fluid mNGS to diagnose invasive meningococcal disease. The complete genome sequences of Neisseria meningitidis were assembled using N. meningitidis of ST4821-serotype C isolated from four patients. To investigate the phylogeny, 165 CC4821 N. meningitidis genomes from 1972 to 2017 were also included. The core genome accumulated variation at a rate of 4.84×10⁻⁸ substitutions/nucleotide site/year. CC4821 differentiated into four sub-lineages during evolution (A, B, C, and D). While evolving from sub-lineage A (early stage) to sub-lineage D (late stage), the ST and CC4821 serotype converged into the ST4821-serotype C clone. Most strains of sub-lineage D were isolated from invasive meningococcal disease, with increasing resistance to quinolones. Phylogeographic analysis suggests that CC4821 has spread across 14 countries. Thus, the selective pressure of quinolones may cause CC4821 to converge evolutionarily, making it more invasive and facilitating its spread.

Metagenomic data from cerebrospinal fluid was used to genotype Neisseria meningitidis in patients with invasive meningococcal disease and trace the origin of the pathobiont, providing a phylogeographic analysis of the strain’s evolution in China and its global spread.

Genetic ancestry and population structure of vaccinia virus

Vaccinia virus (VACV) was used for smallpox eradication, but its ultimate origin remains unknown. The genetic relationships among vaccine stocks are also poorly understood. We analyzed 63 vaccine strains with different origin, as well horsepox virus (HPXV). Results indicated the genetic diversity of VACV is intermediate between variola and cowpox viruses, and that mutation contributed more than recombination to VACV evolution. STRUCTURE identified 9 contributing subpopulations and showed that the lowest drift was experienced by the ancestry components of Tian Tan and HPXV/Mütter/Mulford genomes. Subpopulations that experienced very strong drift include those that contributed the ancestry of MVA and IHD-W, in good agreement with the very long passage history of these vaccines. Another highly drifted population contributed the full ancestry of viruses sampled from human/cattle infections in Brazil and, partially, to IOC clones, strongly suggesting that the recurrent infections in Brazil derive from the spillback of IOC to the feral state.

Identification of Genetic and Chemical Factors Affecting Type III Secretion System Expression in Pseudomonas syringae pv. actinidiae Biovar 3 Using a Luciferase Reporter Construct

The type III secretion system (T3SS) is a key factor in the pathogenesis of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3), the causal agent of a global kiwifruit bacterial canker pandemic. To monitor the T3SS expression levels in Psa3, we constructed a luciferase reporter plasmid-expressing HrpA_Psa3-NLuc fusion protein. The expression of HrpA-NLuc was induced in hrp-inducing conditions whereas the level of luciferase activity correlated with the expression of hrp/hrc genes in Psa3 confirmed the reliability of the reporter construct. Based on the readout of the NLuc reporter construct, three small molecule compounds 4-methoxy-cinnamic acid, sulforaphane, and ferulic acid were determined as T3SS inhibitors in Psa3, whereas sodium acetate was determined to be a T3SS inducer. Moreover, the aqueous extract of fruit inhibited the accumulation of HrpA-NLuc in Psa3 in medium and in planta. Additionally, the T3SS inhibitors suppress Psa3 virulence, whereas the T3SS inducer promotes Psa3 virulence on kiwifruit. Thus, our findings may provide clues to why the fruit is not infected by Psa3, and the Psa3 T3SS inhibitors have potential as alternatives to current nonspecific antimicrobials for disease management.

The impact of genetic recombination on pathogenic Leptospira

Leptospirosis is the most common zoonosis worldwide, and is increasingly common in poor urban communities, where there is inadequate sewage disposal and abundance of domestic and peridomestic animals. There are many risk factors associated with the disease, such as contaminated water exposure, close contact with animals, floods, recreational activities related to water, wet agriculture. The symptoms of leptospirosis are common to other infectious diseases and, if not treated, it can lead to meningitis, liver failure, kidney damage and death. Leptospirosis is caused by 38 pathogenic species of Leptospira, which are divided in almost 30 serogroups and more than 300 serovars. The serological classification (serogroups and serovars) is based on the expression of distinct lipopolysaccharide (LPS) antigens. These antigens are also associated to protective immunity; antibodies against a serovar protect from any member of the same serovar. Serologic and phylogenetic analyses are not congruent probably due to genetic recombination of LPS genes among different leptospiral species. To analyze the importance of recombination in leptospiral evolution, we performed a gene-by-gene tree topology comparison on closed genomes available in public databases at two levels: among core genomes of pathogenic species (34 recombinant among 1213 core genes), and among core genomes of L. interrogans isolates (178/798). We found that most recombinant genes code for proteins involved in translation, ribosomal structure and biogenesis, but also for cell wall, membrane and envelope biogenesis. Besides, our final results showed that half of LPS genes are recombinant (18/36). This is relevant because serovar classification and vaccine development are based on these epitopes. The frequent recombination of LPS-associated genes suggests that natural selection is promoting the survival of recombinant lineages. These results may help understanding the factors that make Leptospira a successful pathogen.

Coastal Transient Niches Shape the Microdiversity Pattern of a Bacterioplankton Population with Reduced Genomes

Globally dominant marine bacterioplankton lineages are often limited in metabolic versatility, owing to their extensive genome reductions, and thus cannot take advantage of transient nutrient patches. It is therefore perplexing how the nutrient-poor bulk seawater sustains the pelagic streamlined lineages, each containing numerous populations. Here, we sequenced the genomes of 33 isolates of the recently discovered CHUG lineage (~2.6 Mbp), which have some of the smallest genomes in the globally abundant Roseobacter group (commonly over 4 Mbp). These genome-reduced bacteria were isolated from a transient habitat: seawater surrounding the brown alga, Sargassum hemiphyllum. Population genomic analyses showed that: (i) these isolates, despite sharing identical 16S rRNA genes, were differentiated into several genetically isolated populations through successive speciation events; (ii) only the first speciation event led to the genetic separation of both core and accessory genomes; and (iii) populations resulting from this event are differentiated at many loci involved in carbon utilization and oxygen respiration, corroborated by BiOLOG phenotype microarray assays and oxygen uptake kinetics experiments, respectively. These differentiated traits match well with the dynamic nature of the macroalgal seawater, in which the quantity and quality of carbon sources and the concentration of oxygen likely vary spatially and temporally, though other habitats, like fresh organic aggregates, cannot be ruled out. Our study implies that transient habitats in the overall nutrient-poor ocean can shape the microdiversity and population structure of genome-reduced bacterioplankton lineages.

Helicobacter pylori genomes reveal Paleolithic human migration to the east end of Asia

A virulence bacterium, Helicobacter pylori, evolved parallel to its host human, therefore, can work as a marker for tracing the human migration. We found H. pylori strains indigenous in the southernmost islands of Japanese Archipelago, Okinawa, and defined them as hspOkinawa and hpRyukyu. Genome data of the strains revealed that hspOkinawa diverged from other East Asian strains about 20,000 years ago, and that hpRyukyu diverged about 45,000 years ago. The closest strains of hpRyukyu were found from Afghanistan, Punjab, and Nepal, which suggest this strain originated in the central Asia and traveled across the Eurasian continent during Paleolithic era. The divergence date of hpRyukyu corresponds with human fossil records in Okinawa. Although it is controversial from human DNA analyses whether descendants of the Paleolithic migrants remain in the modern Japanese population, this study reveals that the bacterium of Paleolithic origin remains in the stomachs of current Japanese.

A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin

From a historically rare serotype, Salmonella enterica subsp. enterica Dublin slowly became one of the most prevalent Salmonella in cattle and raw milk cheese in some regions of France. We present a retrospective genomic analysis of 480 S. Dublin isolates to address the context, evolutionary dynamics, local diversity and the genesis processes of regional S. Dublin outbreaks events between 2015 and 2017. Samples were clustered and assessed for correlation against metadata including isolation date, isolation matrices, geographical origin and epidemiological hypotheses. Significant findings can be drawn from this work. We found that the geographical distance was a major factor explaining genetic groups in the early stages of the cheese production processes (animals, farms) while down-the-line transformation steps were more likely to host genomic diversity. This supports the hypothesis of a generalised local persistence of strains from animal to finished products, with occasional migration. We also observed that the bacterial surveillance is representative of diversity, while targeted investigations without genomics evidence often included unrelated isolates. Combining both approaches in phylogeography methods allows a better representation of the dynamics, of outbreaks.

Core genes can have higher recombination rates than accessory genes within global microbial populations

Recombination is essential to microbial evolution, and is involved in the spread of antibiotic resistance, antigenic variation, and adaptation to the host niche. However, assessing the impact of homologous recombination on accessory genes which are only present in a subset of strains of a given species remains challenging due to their complex phylogenetic relationships. Quantifying homologous recombination for accessory genes (which are important for niche-specific adaptations) in comparison to core genes (which are present in all strains and have essential functions) is critical to understanding how selection acts on variation to shape species diversity and genome structures of bacteria. Here, we apply a computationally efficient, non-phylogenetic approach to measure homologous recombination rates in the core and accessory genome using >100,000 whole genome sequences from Streptococcus pneumoniae and several additional species. By analyzing diverse sets of sequence clusters, we show that core genes often have higher recombination rates than accessory genes, and for some bacterial species the associated effect sizes for these differences are pronounced. In a subset of species, we find that gene frequency and homologous recombination rate are positively correlated. For S. pneumoniae and several additional species, we find that while the recombination rate is higher for the core genome, the mutational divergence is lower, indicating that divergence-based homologous recombination barriers could contribute to differences in recombination rates between the core and accessory genome. Homologous recombination may therefore play a key role in increasing the efficiency of selection in the most conserved parts of the genome.

Analysis of bacterial diversity and genetic evolution of Lacticaseibacillus paracasei isolates in fermentation pit mud

AIMS

Since little is known about the genetic diversity of lactic acid bacteria (LAB) isolates from the fermentation pit mud (FPM), we sought to evaluate the bacterial structure, identify the LAB isolates and investigate the genotype and genetic diversity of the LAB isolates.

METHODS AND RESULTS

Using high-throughput MiSeq sequencing, we identified seven dominant bacterial genera in FPM. Lactobacillus had the highest abundance. We isolated 55 LAB strains. These isolates were all identified as Lacticaseibacillus paracasei. Using an extant multilocus sequence typing (MLST) scheme, isolates were assigned to 18 sequence types (STs) and three clonal complexes. ST1, the largest group, mainly comprised FPM isolates. Niche-specific ST2 to ST18 only contained FPM isolates. Isolates could be divided into four lineages, with most assigned to Lineage 1. Only one FPM isolate was classified as L. paracasei subsp. paracasei. Other isolates could not be classified at the subspecies level using the seven MLST loci.

CONCLUSIONS

Lactobacilli account for a high proportion of bacteria in pit mud. Based on the traditional culture method, L. paracasei was the dominant species, and these isolates exhibit a high ethanol tolerance, high intraspecific diversity and specific genetic profiles.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study described the characterization of FPM bacterial diversity, giving an insight into the genetic diversity of L. paracasei strains present in FPM.

Origin, Phylogeny, and Transmission of the Epidemic Clone ST208 of Carbapenem-Resistant Acinetobacter baumannii on a Global Scale

Carbapenem-resistant Acinetobacter baumannii (CRAB) is an opportunistic pathogen that has become a global threat. The dissemination of global clone 2 (GC2) CRAB has been well documented. Oxford sequence type (ST) 208 is one of the most prevalent lineages of A. baumannii GC2; however, its evolution and phylogeny are unclear. We collected 45 representative ST208 isolates from 14 cities in China between 1999 and 2018. Moreover, 411 ST208 genome sequences were downloaded from the GenBank database for comparison. The global ST208 phylogeny showed that ST208 might have originated from North America and subsequently evolved into two clades. Notably, the widespread OXA-23-producing ST208 A. baumannii was correlated with the transposon structure and dynamics of replicative transposition, and the Tn2009 tandem structure of five copies of blaOXA-23 and potential circular intermediate of Tn2009 were first detected. Furthermore, 15 Chinese ST208 isolates carried GR25 pABTJ1-like plasmids, which contained blaOXA-23 and have only been found in China in the last decade. In conclusion, our work suggests that replicative transposition contributes to the evolution and transmission of OXA-23-producing ST208 A. baumannii and highlights the new challenges posed by the epidemiological surveillance of globally distributed clonal groups via whole genome sequencing. IMPORTANCE ST208 as one of the most prevalent lineages of CRAB has caused several difficult-to-treat infections and outbreaks around the world. However, few studies have focused on evaluating the genetic background differences of ST208 A. baumannii isolated from very distant geographic regions. A comprehensive genomic analysis of 456 clinical strains of ST208 A. baumannii from a wide temporal and geographic range was performed in this study. Moreover, the mechanisms leading to the horizontal transfer of blaOXA-23 in ST208 A. baumannii are poorly understood. We first describe experimental evidence of the potential circular intermediate of Tn2009, and the Tn2009 tandem structure of five copies of blaOXA-23 was first detected. The interbacterial transfer of genetic elements carrying resistance to last-line antibiotic carbapenems highlights the essential need to enhance epidemiologic surveillance.

Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA

Mobile genetic elements (MGEs) are agents of horizontal gene transfer in bacteria, but can also be vertically inherited by daughter cells. Establishing the dynamics that led to contemporary patterns of MGEs in bacterial genomes is central to predicting the emergence and evolution of novel and resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex (CC) 398 is the dominant MRSA in European livestock and a growing cause of human infections. Previous studies have identified three categories of MGEs whose presence or absence distinguishes livestock-associated CC398 from a closely related and less antibiotic-resistant human-associated population. Here, we fully characterise the evolutionary dynamics of these MGEs using a collection of 1180 CC398 genomes, sampled from livestock and humans, over 27 years. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably inherited for 57 years. This was followed by the acquisition of a type V SCCmec that carries methicillin, tetracycline, and heavy metal resistance genes, which has been maintained for 35 years, with occasional truncations and replacements with type IV SCCmec. In contrast, a class of prophages that carry a human immune evasion gene cluster and that are largely absent from livestock-associated CC398 have been repeatedly gained and lost in both human- and livestock-associated CC398. These contrasting dynamics mean that when livestock-associated MRSA is transmitted to humans, adaptation to the human host outpaces loss of antibiotic resistance. In addition, the stable inheritance of resistance-associated MGEs suggests that the impact of ongoing reductions in antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to be realised.

Genomic Diversity of Hospital-Acquired Infections Revealed through Prospective Whole-Genome Sequencing-Based Surveillance

Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of health care resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAIs using prospective whole-genome sequencing-based surveillance of bacterial pathogens collected from hospitalized patients. Here, we describe the diversity of bacteria sampled from hospitalized patients at a single center, as revealed through systematic analysis of bacterial isolate genomes. We sequenced the genomes of 3,004 bacterial isolates from hospitalized patients collected over a 25-month period. We identified bacteria belonging to 97 distinct species, which were distributed among 14 groups of related species. Within these groups, isolates could be distinguished from one another by both average nucleotide identity (ANI) and principal-component analysis of accessory genes (PCA-A). Core genome genetic distances and rates of evolution varied among species, which has practical implications for defining shared ancestry during outbreaks and for our broader understanding of the origins of bacterial strains and species. Finally, antimicrobial resistance genes and putative mobile genetic elements were frequently observed, and our systematic analysis revealed patterns of occurrence across the different species sampled from our hospital. Overall, this study shows how understanding the population structure of diverse pathogens circulating in a single health care setting can improve the discriminatory power of genomic epidemiology studies and can help define the processes leading to strain and species differentiation. IMPORTANCE Hospitalized patients are at increased risk of becoming infected with antibiotic-resistant organisms. We used whole-genome sequencing to survey and compare over 3,000 clinical bacterial isolates collected from hospitalized patients at a large medical center over a 2-year period. We identified nearly 100 different bacterial species, which we divided into 14 different groups of related species. When we examined how genetic relatedness differed between species, we found that different species were likely evolving at different rates within our hospital. This is significant because the identification of bacterial outbreaks in the hospital currently relies on genetic similarity cutoffs, which are often applied uniformly across organisms. Finally, we found that antibiotic resistance genes and mobile genetic elements were abundant and were shared among the bacterial isolates we sampled. Overall, this study provides an in-depth view of the genomic diversity and evolutionary processes of bacteria sampled from hospitalized patients, as well as genetic similarity estimates that can inform hospital outbreak detection and prevention efforts.

Changes in the Genotypic Characteristics of Community-Acquired Methicillin-Resistant Staphylococcus aureus Collected in 244 Medical Facilities in Japan between 2010 and 2018: a Nationwide Surveillance

Although community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged worldwide, no nationwide CA-MRSA surveillance has been conducted in Japan to determine the changes in its molecular characteristics over time. We aimed to characterize the molecular epidemiology of Panton-Valentine leucocidin (PVL)-positive CA-MRSA strains collected from across Japan in the past decade. We isolated 1,770 MRSA strains from the skin and pus samples of outpatients of 244 medical facilities in 31 prefectures between 2010 and 2018 (2010, 2012, 2014, 2016, and 2018). Regions, hospitals, and periods in which strains were isolated and patient age group and sex were tabulated. Staphylococcal cassette chromosome mec (SCCmec) typing, detection of virulence factor genes, and antimicrobial susceptibility testing were performed. Whole-genome analysis was performed for the PVL-positive strains isolated in 2018. All strains harbored the mecA gene. Compared to that in 2010, the percentage of SCCmec type IV increased in 2018, with a corresponding increase in the proportion of PVL-positive strains (10% to 26%). Of the isolates obtained in 2018, clonal complex 8 (CC8) was dominant among PVL-positive strains. Core-genome single-nucleotide polymorphism analysis, using whole-genome sequencing, suggested that the CC8 PVL-positive strains spread throughout Japan over the last decade. Furthermore, a unique ST22 clone carrying both the PVL- and toxic shock syndrome toxin-1-encoding genes has emerged. We demonstrated that the molecular epidemiology of CA-MRSA in Japan differs from that in Europe and the United States; thus, it is crucial to monitor the trend of changes in CA-MRSA characteristics in Japan.

IMPORTANCE Community-associated MRSA, which is a multidrug-resistant organism and can cause infections in otherwise-healthy individuals, has become a global problem. This paper describes a nationwide surveillance conducted in Japan to investigate changes in molecular epidemiological characteristics of CA-MRSA over the past decade and provides a detailed review of the characteristics of Panton-Valentine leucocidin (PVL)-positive strains isolated in 2018. Although CA-MRSA is rare in Japan to date, we found that the isolation of PVL-positive strains has been increasing over the past decade. In particular, the PVL-positive strains wherein CC8 was dominant exhibited high interstrain similarity, suggesting that a limited number of clones have spread over the past decade. Furthermore, a unique ST22 clone carrying both PVL-encoding and toxic shock syndrome toxin-1-encoding genes has emerged. This study shows that various changes can be observed when molecular epidemiological analysis, combined with next-generation sequencing, is conducted over a long period.

Genome, genetic evolution, and environmental adaptation mechanisms of Schizophyllum commune in deep subseafloor coal-bearing sediments

To understand the genomic evolution and adaptation strategies of fungi to subseafloor sedimentary environments, we de novo assembled the genome of Schizophyllum commune strain 20R-7-F01 isolated from ∼2.0 km-deep, ∼20-millionyearsago (Mya) coal-bearing sediments. Phylogenomics study revealed a differentiation time of 28-73 Mya between this strain and the terrestrial type-strain H4-8, in line with sediment age records. Comparative genome analyses showed that FunK1 protein kinase, NmrA family, and transposons in this strain are significantly expanded, possibly linking to the environmental adaptation and persistence in sediment for over millions of years. Re-sequencing study of 14 S. commune strains sampled from different habitats revealed that subseafloor strains have much lower nucleotide diversity, substitution rate, and homologous recombination rate than other strains, reflecting that the growth and/or reproduction of subseafloor strains are extremely slow. Our data provide new insights into the adaptation and long-term survival of the fungi in the subseafloor sedimentary biosphere.

Listeria monocytogenes: Investigation of Fitness in Soil Does Not Support the Relevance of Ecotypes

Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes the serious foodborne illness listeriosis. Although soil is a primary reservoir and a central habitat for Lm, little information is available on the genetic features underlying the fitness of Lm strains in this complex habitat. The aim of this study was to identify (i) correlations between the strains fitness in soil, their origin and their phylogenetic position (ii) identify genetic markers allowing Lm to survive in the soil. To this end, we assembled a balanced panel of 216 Lm strains isolated from three major ecological compartments (outdoor environment, animal hosts, and food) and from 33 clonal complexes occurring worldwide. The ability of the 216 strains to survive in soil was tested phenotypically. Hierarchical clustering identified three phenotypic groups according to the survival rate (SR): phenotype 1 “poor survivors” (SR &lt; 2%), phenotype 2 “moderate survivors” (2% &lt; SR &lt; 5%) and phenotype 3 “good survivors” (SR &gt; 5%). Survival in soil depended neither on strains’ origin nor on their phylogenetic position. Genome-wide-association studies demonstrated that a greater number of genes specifically associated with a good survival in soil was found in lineage II strains (57 genes) than in lineage I strains (28 genes). Soil fitness was mainly associated with variations in genes (i) coding membrane proteins, transcription regulators, and stress resistance genes in both lineages (ii) coding proteins related to motility and (iii) of the category “phage-related genes.” The cumulative effect of these small genomic variations resulted in significant increase of soil fitness.

High Prevalence of bla CTXM-1/IncI1-Iγ/ST3 Plasmids in Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Collected From Domestic Animals in Guadeloupe (French West Indies)

Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) have been classified in the group of resistant bacteria of highest priority. We determined the prevalence of ESBL-E collected in feces from household and shelter pets in Guadeloupe (French West Indies). A single rectal swab was taken from 125 dogs and 60 cats between June and September 2019. The prevalence of fecal carriage of ESBL-E was 7.6% (14/185, 95% CI: 4.2-12.4), within the range observed worldwide. The only risk factor associated with a higher prevalence of ESBL-E rectal carriage was a stay in a shelter, suggesting that refuges could be hotspots for their acquisition. All but one (Klebsiella pneumoniae from a cat) were Escherichia coli. We noted the presence of a bla _CTX-M-1/IncI1-Iγ/sequence type (ST3) plasmid in 11 ESBL-producing E. coli isolates belonging to ST328 (n = 6), ST155 (n = 4) and ST953 (n = 1). A bla _CTX-M-15 gene was identified in the three remaining ESBL-E isolates. The bla _CTX-M-1 and most of the antimicrobial resistance genes were present in a well-conserved large conjugative IncI1-Iγ/ST3 plasmid characterized by two accessory regions containing antibiotic resistance genes. The plasmid has been detected worldwide in E. coli isolates from humans and several animal species, such as food-producing animals, wild birds and pets, and from the environment. This study shows the potential role of pets as a reservoir of antimicrobial-resistant bacteria or genes for humans and underlines the importance of basic hygiene measures by owners of companion animals.

Current Methods for Recombination Detection in Bacteria

The role of genetic exchanges, i.e., homologous recombination (HR) and horizontal gene transfer (HGT), in bacteria cannot be overestimated for it is a pivotal mechanism leading to their evolution and adaptation, thus, tracking the signs of recombination and HGT events is importance both for fundamental and applied science. To date, dozens of bioinformatics tools for revealing recombination signals are available, however, their pros and cons as well as the spectra of solvable tasks have not yet been systematically reviewed. Moreover, there are two major groups of software. One aims to infer evidence of HR, while the other only deals with horizontal gene transfer (HGT). However, despite seemingly different goals, all the methods use similar algorithmic approaches, and the processes are interconnected in terms of genomic evolution influencing each other. In this review, we propose a classification of novel instruments for both HR and HGT detection based on the genomic consequences of recombination. In this context, we summarize available methodologies paying particular attention to the type of traceable events for which a certain program has been designed.

Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health

Non-typhoidal Salmonella enterica is a common cause of diarrhoeal disease; in humans, consumption of contaminated poultry meat is believed to be a major source. Brazil is the world's largest exporter of chicken meat globally, and previous studies have indicated the introduction of Salmonella serovars through imported food products from Brazil. Here we provide an in-depth genomic characterisation and evolutionary analysis to investigate the most prevalent serovars and antimicrobial resistance (AMR) in Brazilian chickens and assess the impact to public health of products contaminated with S. enterica imported into the United Kingdom from Brazil. To do so, we examine 183 Salmonella genomes from chickens in Brazil and 357 genomes from humans, domestic poultry and imported Brazilian poultry products isolated in the United Kingdom. S. enterica serovars Heidelberg and Minnesota were the most prevalent serovars in Brazil and in meat products imported from Brazil into the UK. We extended our analysis to include 1,259 publicly available Salmonella Heidelberg and Salmonella Minnesota genomes for context. The Brazil genomes form clades distinct from global isolates, with temporal analysis suggesting emergence of these Salmonella Heidelberg and Salmonella Minnesota clades in the early 2000s, around the time of the 2003 introduction of the Enteritidis vaccine in Brazilian poultry. Analysis showed genomes within the Salmonella Heidelberg and Salmonella Minnesota clades shared resistance to sulphonamides, tetracyclines and beta-lactams conferred by sul2, tetA and blaCMY-2 genes, not widely observed in other co-circulating serovars despite similar selection pressures. The sul2 and tetA genes were concomitantly carried on IncC plasmids, whereas blaCMY-2 was either co-located with the sul2 and tetA genes on IncC plasmids or independently on IncI1 plasmids. Long-term surveillance data collected in the UK showed no increase in the incidence of Salmonella Heidelberg or Salmonella Minnesota in human cases of clinical disease in the UK following the increase of these two serovars in Brazilian poultry. In addition, almost all of the small number of UK-derived genomes which cluster with the Brazilian poultry-derived sequences could either be attributed to human cases with a recent history of foreign travel or were from imported Brazilian food products. These findings indicate that even should Salmonella from imported Brazilian poultry products reach UK consumers, they are very unlikely to be causing disease. No evidence of the Brazilian strains of Salmonella Heidelberg or Salmonella Minnesota were observed in UK domestic chickens. These findings suggest that introduction of the Salmonella Enteritidis vaccine, in addition to increasing antimicrobial use, could have resulted in replacement of salmonellae in Brazilian poultry flocks with serovars that are more drug resistant, but less associated with disease in humans in the UK. The plasmids conferring resistance to beta-lactams, sulphonamides and tetracyclines likely conferred a competitive advantage to the Salmonella Minnesota and Salmonella Heidelberg serovars in this setting of high antimicrobial use, but the apparent lack of transfer to other serovars present in the same setting suggests barriers to horizontal gene transfer that could be exploited in intervention strategies to reduce AMR. The insights obtained reinforce the importance of One Health genomic surveillance.

The population genetics of the causative agent of snake fungal disease indicate recent introductions to the USA

Snake fungal disease (SFD; ophidiomycosis), caused by the pathogen Ophidiomyces ophiodiicola (Oo), has been documented in wild snakes in North America and Eurasia, and is considered an emerging disease in the eastern United States of America. However, a lack of historical disease data has made it challenging to determine whether Oo is a recent arrival to the USA or whether SFD emergence is due to other factors. Here, we examined the genomes of 82 Oo strains to determine the pathogen’s history in the eastern USA. Oo strains from the USA formed a clade (Clade II) distinct from European strains (Clade I), and molecular dating indicated that these clades diverged too recently (approximately 2,000 years ago) for transcontinental dispersal of Oo to have occurred via natural snake movements across Beringia. A lack of nonrecombinant intermediates between clonal lineages in Clade II indicates that Oo has actually been introduced multiple times to North America from an unsampled source population, and molecular dating indicates that several of these introductions occurred within the last few hundred years. Molecular dating also indicated that the most common Clade II clonal lineages have expanded recently in the USA, with time of most recent common ancestor mean estimates ranging from 1985 to 2007 CE. The presence of Clade II in captive snakes worldwide demonstrates a potential mechanism of introduction and highlights that additional incursions are likely unless action is taken to reduce the risk of pathogen translocation and spillover into wild snake populations.

Snake fungal disease is an emerging disease in eastern North America, but the origins of the disease have been unclear. This study uses population genetic data to show that the fungus that causes the disease was introduced multiple times to North America over the last few hundred years.

Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment

Very little is known about how microbiome interactions shape the horizontal transfer of antibiotic resistance genes in aquacultural environment. To this end, we first conducted 16S rRNA gene amplicon sequencing to monitor the dynamics of bacterial community compositions in one shrimp farm from 2019 to 2020. Next, co-occurrence analysis was then conducted to reveal the interactions network between Vibrio spp. and other species. Subsequently, 21 V. parahaemolyticus isolates and 15 related bacterial species were selected for whole-genome sequencing (WGS). The 16S rDNA amplicon sequencing results identified a remarkable increase of Vibrio and Providencia in September-2019 and a significant rise of Enterobacter and Shewanella in Septtember-2020. Co-occurrence analysis revealed that Vibrio spp. positively interacted with the above species, leading to the sequencing of their isolates to further understand the sharing of the resistant genomic islands (GIs). Subsequent pan-genomic analysis of V. parahaemolyticus genomes identified 278 horizontally transferred genes in 10 GIs, most of which were associated with antibiotic resistance, virulence, and fitness of metabolism. Most of the GIs have also been identified in Providencia, and Enterobacter, suggesting that exchange of genetic traits might occur in V. parahaemolyticus and other cooperative species in a specific niche. No genetic exchange was found between the species with negative relationships. The knowledge generated from this study would greatly improve our capacity to predict and mitigate the emergence of new resistant population and provide practical guidance on the microbial management during the aquacultural activities.