scholarly journals Global evolutionary dynamics and resistome analysis of Clostridioides difficile ribotype 017

2021 ◽  
Author(s):  
Korakrit Imwattana ◽  
Papanin Putsathit ◽  
Teera Leepattarakit ◽  
Pattarachai Kiratisin ◽  
Thomas V Riley ◽  
...  
Keyword(s):  
Middle Ages ◽  
Evolutionary Dynamics ◽  
Tertiary Hospital ◽  
Multidrug Resistant ◽  
Genomic Diversity ◽  
Genomic Epidemiology ◽  
Clostridioides Difficile ◽  
Hospitalised Patients ◽  
Key Factor ◽  
The 1960S

Clostridioides difficile PCR ribotype (RT) 017 ranks among the most successful strains of C. difficile in the world. In the past three decades, it has caused outbreaks on four continents, more than other "epidemic strains", however, our understanding of the genomic epidemiology underpinning the spread of C. difficile RT 017 is limited. Here, we performed high-resolution phylogenomic and Bayesian evolutionary analyses on an updated and more representative dataset of 282 non-clonal C. difficile RT 017 isolates collected worldwide between 1981 and 2019. These analyses place an estimated time of global dissemination between 1953 and 1983 and identified the acquisition of the ermB-positive transposon Tn6194 as a key factor behind global emergence. This coincided with the introduction of clindamycin, a key inciter of C. difficile infection, into clinical practice in the 1960s. Based on the genomic data alone, the origin of C. difficile RT 017 could not be determined, however, geographical data and records of population movement suggest that C. difficile RT 017 had been moving between Asia and Europe since the Middle Ages and was later transported to North America around 1860 (95% CI: 1622 - 1954). A focused epidemiological study of 45 clinical C. difficile RT 017 genomes from a cluster in a tertiary hospital in Thailand revealed that the population consisted of two groups of multidrug-resistant (MDR) C. difficile RT 017 and a group of early, non-MDR C. difficile RT 017. The significant genomic diversity within each MDR group suggests that although they were all isolated from hospitalised patients, there was likely a reservoir of C. difficile RT 017 in the community that contributed to the spread of this pathogen.

scholarly journals First Genome Sequence of a Mexican Multidrug-Resistant Acinetobacter baumannii Isolate

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Lucía Graña-Miraglia ◽  
Luis Lozano ◽  
Semiramis Castro-Jaimes ◽  
Miguel A. Cevallos ◽  
Patricia Volkow ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Mexico City ◽  
Genome Sequence ◽  
Draft Genome ◽  
Tertiary Hospital ◽  
Multidrug Resistant ◽  
Genomic Diversity ◽  
Nosocomial Pathogen ◽  
Starting Point ◽  
Baumannii Isolate

Acinetobacter baumannii has emerged as an important nosocomial pathogen worldwide. Here, we present the draft genome of the first multidrug-resistant A. baumannii isolate, sampled from a tertiary hospital in Mexico City. This genome will provide a starting point for studying the genomic diversity of this species in Mexico.

scholarly journals Molecular epidemiology of community-onset Clostridioides difficile infections at a tertiary hospital in mainland China: A ten-year (2010-2019) retrospective study

2021 ◽  
Author(s):  
Yunbo Chen ◽  
Lihong Bu ◽  
Tao Lv ◽  
Lisi Zheng ◽  
Silan Gu ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Mainland China ◽  
Tertiary Hospital ◽  
Multidrug Resistant ◽  
Binary Toxin ◽  
Common Disease ◽  
High Genetic Diversity ◽  
Toxin Genes ◽  
Clostridioides Difficile ◽  
Community Onset

Abstract Background Clostridioides difficile infection (CDI) is an increasingly common disease in healthcare facilities and community settings. However, there are limited reports of community-onset CDI (CO-CDI) in China. We retrospectively analyzed the molecular epidemiology of CO-CDI at a tertiary hospital over a period of 10 years. Methods A total of 1307 stool samples from 1213 outpatients were tested by culturing. The presence of toxin genes (tcd A, tcd B, cdtA and cdtB) were confirmed by PCR. Toxigenic strains were typed using multilocus sequence typing (MLST). Susceptibility to 9 antimicrobials was evaluated using the E-test. Results Eighty-nine of 1213 outpatients (7.3%) had CO-CDI, 4 of these patients (4.5%) had one or more recurrence, and there were 95 strains of toxigenic C. difficile. Among these strains, 82 (86.3%) had the tcdA and tcdB genes (A + B+) and 5 of these 82 strains were positive for the binary toxin genes (cdtA and cdtB); the other 13 strains (13.7%) had the tcdB gene only (A-B+). There were 15 different STs and the most prevalent were ST-54 (23.2%), ST-35 (16.8%), and ST-2 (13.7%). All strains were susceptible to metronidazole and vancomycin, and had low resistance to moxifloxacin and tetracycline, but had high resistance to ciprofloxacin, clindamycin, and erythromycin. Twenty-three isolates (24.2%) were multidrug-resistant. Conclusions Outpatients with CDI were common during this period in our hospital. The C. difficile isolates had high genetic diversity. All isolates were susceptible to metronidazole and vancomycin, and nearly one quarter of all isolates had multidrug resistance.

scholarly journals Genomic epidemiology of meticillin-resistant Staphylococcus aureus ST22 widespread in communities of the Gaza Strip, 2009

2018 ◽  
Vol 23 (34) ◽  
Author(s):  
Qiuzhi Chang ◽  
Izzeldin Abuelaish ◽  
Asaf Biber ◽  
Hanaa Jaber ◽  
Alanna Callendrello ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Evolutionary Dynamics ◽  
Gaza Strip ◽  
Genomic Diversity ◽  
Genomic Epidemiology ◽  
Recent Emergence ◽  
Close Relationship ◽  
History Of ◽  
The Gaza Strip ◽  
Toxic Shock Syndrome Toxin

Background Remarkably high carriage prevalence of a community-associated meticillin-resistant Staphylococcus aureus (MRSA) strain of sequence type (ST) 22 in the Gaza strip was reported in 2012. This strain is linked to the pandemic hospital-associated EMRSA-15. The origin and evolutionary history of ST22 in Gaza communities and the genomic elements contributing to its widespread predominance are unknown. Methods: We generated high-quality draft genomes of 61 ST22 isolates from Gaza communities and, along with 175 ST22 genomes from global sources, reconstructed the ST22 phylogeny and examined genotypes unique to the Gaza isolates. Results: The Gaza isolates do not exhibit a close relationship with hospital-associated ST22 isolates, but rather with a basal population from which EMRSA-15 emerged. There were two separate resistance acquisitions by the same MSSA lineage, followed by diversification of other genetic determinants. Nearly all isolates in the two distinct clades, one characterised by staphylococcal cassette chromosome mec (SCCmec) IVa and the other by SCCmec V and MSSA isolates, contain the toxic shock syndrome toxin-1 gene. Discussion: The genomic diversity of Gaza ST22 isolates is not consistent with recent emergence in the region. The results indicate that two divergent Gaza clones evolved separately from susceptible isolates. Researchers should not assume that isolates identified as ST22 in the community are examples of EMRSA-15 that have escaped their healthcare roots. Future surveillance of MRSA is essential to the understanding of ST22 evolutionary dynamics and to aid efforts to slow the further spread of this lineage.

scholarly journals Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli sequence type (ST)131 associated with bacteraemia in Wales, United Kingdom

2021 ◽  
Author(s):  
Rhys Thomas White ◽  
Matthew J Bull ◽  
Clare R Barker ◽  
Julie M Arnott ◽  
Mandy Wootton ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Multidrug Resistant ◽  
Geographic Region ◽  
Sequence Type ◽  
Genomic Diversity ◽  
Genomic Epidemiology ◽  
North Wales ◽  
Clade C ◽  
Tract Infections

Increasing resistance to third-generation cephalosporins (3GCs) threatens public health, as these antimicrobials are prescribed as empirical therapies for systemic infections caused by Gram-negative bacteria. Resistance to 3GCs in urinary tract infections (UTIs) and bacteraemia is associated with the globally disseminated, multidrug-resistant, uropathogenic Escherichia coli sequence type (ST)131. This study combines the epidemiology of E.coli blood culture surveillance with whole-genome sequencing (WGS) to investigate ST131 associated with bacteraemia in Wales between 2013 and 2014. This population-based prospective genomic analysis investigated temporal, geographic, and genomic risk factors. To identify spatial clusters and lineage diversity, we contextualised 142 genomes collected from twenty hospitals, against a global ST131 population (n=181). All three major ST131 clades are represented across Wales, with clade C/H30 predominant (n=102/142, 71.8%). Consistent with global findings, Welsh strains of clade C/H30 contain β-lactamase genes from the blaCTX-M-1 group (n=65/102, 63.7%), which confers resistance to 3GCs. In Wales, the majority of clade C/H30 strains belonged to sub-clade C2/H30Rx (n=88/151, 58.3%), whereas sub-clade C1/H30R strains were less common (n=14/67, 20.9%). A sub-lineage unique to Wales was identified within the C2/H30Rx sub-clade (named GB-WLS.C2/H30Rx) and is defined by six non-recombinogenic single-nucleotide polymorphisms (SNPs), including a missense variant in febE (ferric enterobactin transport protein) and fryC (fructose-like permease IIC component), and the loss of the capsular biosynthesis genes encoding the K5 antigen. Bayesian analysis predicted that GB-WLS.C2/H30Rx diverged from a common ancestor (CA) most closely related to a Canadian strain between 1998 and 1999. Further, our analysis suggests a descendent of GB-WLS.C2/H30Rx arrived through an introduction to North Wales circa 2002, spread and persists in the geographic region, causing a cluster of cases (CA emerged circa 2009) with a maximum pair-wise distance of 30 non-recombinogenic SNPs. This limited genomic diversity likely depicts local transmission within the community in North Wales. This investigation emphasises the value of genomic epidemiology, allowing detection of suspected transmission clusters and the spread of genetically similar/identical strains in local areas. These analyses will enable targeted and timely public health interventions.

Gene flow, recombination, and positive selection in Stenotrophomonas maltophilia: mechanisms underlying the diversity of the widespread opportunistic pathogen

Genome ◽  
2016 ◽  
Vol 59 (12) ◽  
pp. 1063-1075 ◽  
Author(s):  
Dong Yu ◽  
Zhiqiu Yin ◽  
Beiping Li ◽  
Yuan Jin ◽  
Hongguang Ren ◽  
...  
Keyword(s):  
Positive Selection ◽  
Stenotrophomonas Maltophilia ◽  
Evolutionary Dynamics ◽  
Genotypic Diversity ◽  
Opportunistic Pathogen ◽  
Multidrug Resistant ◽  
Genomic Diversity ◽  
Genome Diversity ◽  
Evolutionary Mechanisms ◽  
A Genome

Stenotrophomonas maltophilia is a global multidrug-resistant human opportunistic pathogen in clinical environments. Stenotrophomonas maltophilia is also ubiquitous in aqueous environments, soil, and plants. Various molecular typing methods have revealed that S. maltophilia exhibits high levels of phenotypic and genotypic diversity. However, information regarding the genomic diversity within S. maltophilia and the corresponding genetic mechanisms resulting in said diversity remain scarce. The genome sequences of 17 S. maltophilia strains were selected to investigate the mechanisms contributing to genetic diversity at the genome level. The core and large pan-genomes of the species were first estimated, resulting in a large, open pan-genome. A species phylogeny was also reconstructed based on 344 orthologous genes with one copy per genome, and the contribution of four evolutionary mechanisms to the species genome diversity was quantified: 15%–35% of the genes showed evidence for recombination, 0%–25% of the genes in one genome were likely gained, 0%–44% of the genes in some genomes were likely lost, and less than 0.3% of the genes in a genome were under positive selection pressures. We observed that, among the four main mechanisms, homologous recombination plays a key role in maintaining diversity in S. maltophilia. In this study, we provide an overview of evolution in S. maltophilia to provide a better understanding of its evolutionary dynamics and its relationship with genome diversity.

scholarly journals A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile

2021 ◽  
Author(s):  
Korakrit Imwattana ◽  
César Rodríguez ◽  
Thomas V Riley ◽  
Daniel R Knight
Keyword(s):  
Antimicrobial Resistance ◽  
Strong Association ◽  
Tetracycline Resistance ◽  
Multidrug Resistant ◽  
Fluoroquinolone Resistance ◽  
Drug Resistant ◽  
Genomic Epidemiology ◽  
Clostridioides Difficile ◽  
Geographical Regions ◽  
Sequence Types

Antimicrobial resistance (AMR) plays an important role in the pathogenesis and spread of Clostridioides difficile infection (CDI), the leading healthcare-related gastrointestinal infection in the world. An association between AMR and CDI outbreaks is well documented, however, data is limited to a few 'epidemic' strains in specific geographical regions. Here, through detailed analysis of 10,330 publicly-available C. difficile genomes from strains isolated worldwide (spanning 270 multilocus sequence types (STs) across all known evolutionary clades), this study provides the first species-wide snapshot of AMR genomic epidemiology in C. difficile. Of the 10,330 C. difficile genomes, 4,532 (43.9%) in 89 STs across clades 1 - 5 carried at least one genotypic AMR determinants, with 901 genomes (8.7%) carrying AMR determinants for three or more antimicrobial classes (multidrug-resistant, MDR). No AMR genotype was identified in any strains belonging to the cryptic clades. C. difficile from Australia/New Zealand had the lowest AMR prevalence compared to strains from Asia, Europe and North America (p<0.0001). Based on the phylogenetic clade, AMR prevalence was higher in clades 2 (84.3%), 4 (81.5%) and 5 (64.8%) compared to other clades (collectively 26.9%) (p<0.0001). MDR prevalence was highest in clade 4 (61.6%) which was over three times higher than in clade 2, the clade with the second-highest MDR prevalence (18.3%). There was a strong association between specific AMR determinants and three major epidemic C. difficile STs: ST1 (clade 2) with fluoroquinolone resistance (mainly T82I substitution in GyrA) (p<0.0001), ST11 (clade 5) with tetracycline resistance (various tet-family genes) (p<0.0001) and ST37 (clade 4) with macrolide-lincosamide-streptogramin B (MLSB) resistance (mainly ermB) (p<0.0001) and MDR (p<0.0001). A novel and previously overlooked tetM-positive transposon termed Tn6944 was identified, predominantly among clade 2 strains. This study provides a comprehensive review of AMR in the global C. difficile population which may help in the early detection of drug-resistant C. difficile strains, and prevention of spread world-wide.

scholarly journals Accessory genomic epidemiology of co-circulating Acinetobacter baumannii clones

2021 ◽  
Author(s):  
Valeria Mateo-Estrada ◽  
Jose Luis Fernandez-Vazquez ◽  
Julia Moreno ◽  
Ismael Hernandez-Gonzalez ◽  
Eduardo Rodriguez-Noriega ◽  
...  
Keyword(s):  
Core Genome ◽  
Epidemiological Data ◽  
Tertiary Hospital ◽  
Multidrug Resistant ◽  
Molecular Dating ◽  
Accessory Genome ◽  
Genomic Epidemiology ◽  
Antimicrobial Susceptibility Tests ◽  
Genome Phylogeny ◽  
Susceptibility Tests

A. baumannii has become one of the most important multidrug resistant nosocomial pathogens all over the world. Nonetheless, very little is known about the diversity of A. baumannii lineages co-existing in hospital settings. Here, using whole-genome sequencing, epidemiological data and antimicrobial susceptibility tests, we uncover the transmission dynamics of extensive and multidrug resistant A. baumannii in a tertiary hospital for a decade. Our core genome phylogeny of almost 300 genomes suggests that there were several introductions of lineages from international clone 2 into the hospital. The molecular dating analysis shows that these introductions happened between 2004 and 2015. Furthermore, using the accessory genome, we show that these lineages were extensively disseminated across many wards in the hospital. Our results demonstrate that accessory genome variation can be a very powerful tool for conducting genomic epidemiology. We anticipate future studies employing the accessory genome as a phylogenomic marker over very short microevolutionary scales.

scholarly journals Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Danielle J. Ingle ◽  
Rebecca L. Ambrose ◽  
Sarah L. Baines ◽  
Sebastian Duchene ◽  
Anders Gonçalves da Silva ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Evolutionary Dynamics ◽  
Multidrug Resistant ◽  
Phenotypic Characterization ◽  
South East Asia ◽  
Genomic Epidemiology ◽  
The Third ◽  
Genetic Region ◽  
Evolutionary Event ◽  
Bacterial Fitness

AbstractSalmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergence and evolution of Salmonella 4,[5],12:i:- in Australia. We show that the interruption of the genetic region surrounding the phase II flagellin, FljB, causing a monophasic phenotype, represents a stepwise evolutionary event through the accumulation of mobile resistance elements with minimal impairment to bacterial fitness. We identify three lineages with different population dynamics and discrete antimicrobial resistance profiles emerged, likely reflecting differential antimicrobial selection pressures. Two lineages are associated with travel to South-East Asia and the third lineage is endemic to Australia. Moreover antimicrobial-resistant Salmonella 4,[5],12:i- lineages efficiently infected and survived in host phagocytes and epithelial cells without eliciting significant cellular cytotoxicity, suggesting a suppression of host immune response that may facilitate the persistence of Salmonella 4,[5],12:i:-.

scholarly journals Molecular Epidemiology of Community-Onset Clostridioides Difficile Infections At A Tertiary Hospital In Mainland China: A Ten-Year (2010-2019) Retrospective Study

2021 ◽  
Author(s):  
Yunbo Chen ◽  
Lihong Bu ◽  
Tao Lv ◽  
Lisi Zheng ◽  
Silan Gu ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Mainland China ◽  
Tertiary Hospital ◽  
Multidrug Resistant ◽  
Binary Toxin ◽  
Common Disease ◽  
High Genetic Diversity ◽  
Toxin Genes ◽  
Clostridioides Difficile ◽  
Community Onset

Abstract Background: Clostridioides difficile infection (CDI) is an increasingly common disease in healthcare facilities and community settings. However, there are limited reports of community-onset CDI (CO-CDI) in China. We retrospectively analyzed the molecular epidemiology of CO-CDI at a tertiary hospital over a period of 10 years. A total of 1307 stool samples from 1213 outpatients were tested by culturing. The presence of toxin genes (tcdA, tcdB, cdtA, and cdtB) were confirmed by PCR. Toxigenic strains were typed using multilocus sequence typing (MLST). Susceptibility to 9 antimicrobials was evaluated using the E-test.Results: Eighty-nine of 1213 outpatients (7.3%) had CO-CDI, 4 of these patients (4.5%) had one or more recurrence, and there were 95 strains of toxigenic C. difficile. Among these strains, 82 (86.3%) had the tcdA and tcdB genes (A+B+) and 5 of these 82 strains were positive for the binary toxin genes (cdtA and cdtB); the other 13 strains (13.7%) had the tcdB gene only (A−B+). There were 15 different STs, and the most prevalent were ST-54 (23.2%), ST-35 (16.8%), and ST-2 (13.7%). All strains were susceptible to metronidazole and vancomycin, and had low resistance to moxifloxacin and tetracycline, but had high resistance to ciprofloxacin, clindamycin, and erythromycin. Twenty-three isolates (24.2%) were multidrug-resistant.Conclusions: Outpatients with CDI were common during this period in our hospital. The C. difficile isolates had high genetic diversity. All isolates were susceptible to metronidazole and vancomycin, and nearly one quarter of all isolates had multidrug resistance.

scholarly journals Antimicrobial susceptibility, serotype distribution, virulence profile and molecular typing of piliated clinical isolates of pneumococci from east coast, Peninsular Malaysia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nurul Diana Dzaraly ◽  
Mohd Nasir Mohd Desa ◽  
AbdulRahman Muthanna ◽  
Siti Norbaya Masri ◽  
Niazlin Mohd Taib ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Antimicrobial Susceptibility ◽  
East Coast ◽  
Tertiary Hospital ◽  
Multidrug Resistant ◽  
Peninsular Malaysia ◽  
Clinical Isolates ◽  
Serotype Distribution ◽  
Antimicrobial Susceptibility Test ◽  
Conjugate Vaccines

AbstractPilus has been recently associated with pneumococcal pathogenesis in humans. The information regarding piliated isolates in Malaysia is scarce, especially in the less developed states on the east coast of Peninsular Malaysia. Therefore, we studied the characteristics of pneumococci, including the piliated isolates, in relation to antimicrobial susceptibility, serotypes, and genotypes at a major tertiary hospital on the east coast of Peninsular Malaysia. A total of 100 clinical isolates collected between September 2017 and December 2019 were subjected to serotyping, antimicrobial susceptibility test, and detection of pneumococcal virulence and pilus genes. Multilocus sequence typing (MLST) and phylogenetic analysis were performed only for piliated strains. The most frequent serotypes were 14 (17%), 6A/B (16%), 23F (12%), 19A (11%), and 19F (11%). The majority of isolates were resistant to erythromycin (42%), tetracycline (37%), and trimethoprim-sulfamethoxazole (24%). Piliated isolates occurred in a proportion of 19%; 47.3% of them were multidrug-resistant (MDR) and a majority had serotype 19F. This study showed ST236 was the most predominant sequence type (ST) among piliated isolates, which was related to PMEN clone Taiwan19F-14 (CC271). In the phylogenetic analysis, the piliated isolates were grouped into three major clades supported with 100% bootstrap values. Most piliated isolates belonged to internationally disseminated clones of S. pneumoniae, but pneumococcal conjugate vaccines (PCVs) have the potential to control them.

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