MRSA Causing Infections in Hospitals in Greater Metropolitan New York: Major Shift in the Dominant Clonal Type Between 1996 and 2014

A surveillance study in 1996 identified the USA100 clone (ST5/SCCmecII)-also known as the New York/Japan clone-as the most prevalent MRSA causing infections in 12 New York City hospitals. Here we update the epidemiology of MRSA in seven of the same hospitals eighteen years later in 2013/14. Most of the current MRSA isolates (78 of 121) belonged to the MRSA clone USA300 (CC8/SCCmecIV) but the USA100 clone-dominant in the 1996 survey-still remained the second most frequent MRSA (25 of the 121 isolates) causing 32% of blood stream infections. The USA300 clone was most common in skin and soft tissue infections (SSTIs) and was associated with 84.5% of SSTIs compared to 5% caused by the USA100 clone. Our data indicate that by 2013/14, the USA300 clone replaced the New York/Japan clone as the most frequent cause of MRSA infections in hospitals in Metropolitan New York. In parallel with this shift in the clonal type of MRSA, there was also a striking change in the types of MRSA infections from 1996 to 2014

MRSA Causing Infections in Hospitals in Greater Metropolitan New York: Major Shift in the Dominant Clonal Type between 1996 and 2014

A surveillance study in 1996 identified the USA100 clone (ST5/SCCmecII)–also known as the “New York/Japan” clone—as the most prevalent MRSA causing infections in 12 New York City hospitals. Here we update the epidemiology of MRSA in seven of the same hospitals eighteen years later in 2013/14. Most of the current MRSA isolates (78 of 121) belonged to the MRSA clone USA300 (CC8/SCCmecIV) but the USA100 clone–dominant in the 1996 survey–still remained the second most frequent MRSA (25 of the 121 isolates) causing 32% of blood stream infections. The USA300 clone was most common in skin and soft tissue infections (SSTIs) and was associated with 84.5% of SSTIs compared to 5% caused by the USA100 clone. Our data indicate that by 2013/14, the USA300 clone replaced the New York/Japan clone as the most frequent cause of MRSA infections in hospitals in Metropolitan New York. In parallel with this shift in the clonal type of MRSA, there was also a striking change in the types of MRSA infections from 1996 to 2014

A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia.

Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance

Serogrouping as a valid but incomplete method to diagnose diarrheagenic Escherichia coli

International audienc

Genetic Determinants of High-Level Oxacillin Resistance in Methicillin-Resistant Staphylococcus aureus

Free PMC Article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5971597/Erratum in: Correction for Pardos de la Gandara et al., "Genetic Determinants of High-Level Oxacillin Resistance in Methicillin-Resistant Staphylococcus aureus". Antimicrob Agents Chemother. 2018 Jun 26;62(7). pii: e01096-18. doi: 10.1128/AAC.01096-18. Print 2018 Jul. Disponível em: https://aac.asm.org/content/62/7/e01096-18.longMethicillin-resistant Staphylococcus aureus (MRSA) strains carry either a mecA- or a mecC-mediated mechanism of resistance to beta-lactam antibiotics, and the phenotypic expression of resistance shows extensive strain-to-strain variation. In recent communications, we identified the genetic determinants associated with the stringent stress response that play a major role in the antibiotic resistant phenotype of the historically earliest "archaic" clone of MRSA and in the mecC-carrying MRSA strain LGA251. Here, we sought to test whether or not the same genetic determinants also contribute to the resistant phenotype of highly and homogeneously resistant (H*R) derivatives of a major contemporary MRSA clone, USA300. We found that the resistance phenotype was linked to six genes (fruB, gmk, hpt, purB, prsA, and relA), which were most frequently targeted among the analyzed 20 H*R strains (one mutation per clone in 19 of the 20 H*R strains). Besides the strong parallels with our previous findings (five of the six genes matched), all but one of the repeatedly targeted genes were found to be linked to guanine metabolism, pointing to the key role that this pathway plays in defining the level of antibiotic resistance independent of the clonal type of MRSA.This work was financially supported by a US Public Health Service Award 2 R01 AI457838-15 and by project LISBOA-01-0145-FEDER-007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020-Programa Operacional Competitividade e Internacionalização (POCI), by national funds through FCTFundação para a Ciência e a Tecnologia and project ONEIDA (LISBOA-01-0145-FEDER016417) cofunded by FEEI-“Fundos Europeus Estruturais e de Investimento” from “Programa Operacional Regional Lisboa 2020,” and by national funds from FCT. M.P.D.L.G. was supported by PCORI grant CER-1402-10800 and by funds from the RB Roberts Bacterial Antibiotic Resistance Group (BARG). C.M. was supported by grant SFRH/BPD/111697/2015 from FCT.info:eu-repo/semantics/publishedVersio

Genetic Determinants of High-Level Oxacillin Resistance in Methicillin-Resistant Staphylococcus aureus

Free PMC Article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5971597/Erratum in: Correction for Pardos de la Gandara et al., "Genetic Determinants of High-Level Oxacillin Resistance in Methicillin-Resistant Staphylococcus aureus". Antimicrob Agents Chemother. 2018 Jun 26;62(7). pii: e01096-18. doi: 10.1128/AAC.01096-18. Print 2018 Jul. Disponível em: https://aac.asm.org/content/62/7/e01096-18.longMethicillin-resistant Staphylococcus aureus (MRSA) strains carry either a mecA- or a mecC-mediated mechanism of resistance to beta-lactam antibiotics, and the phenotypic expression of resistance shows extensive strain-to-strain variation. In recent communications, we identified the genetic determinants associated with the stringent stress response that play a major role in the antibiotic resistant phenotype of the historically earliest "archaic" clone of MRSA and in the mecC-carrying MRSA strain LGA251. Here, we sought to test whether or not the same genetic determinants also contribute to the resistant phenotype of highly and homogeneously resistant (H*R) derivatives of a major contemporary MRSA clone, USA300. We found that the resistance phenotype was linked to six genes (fruB, gmk, hpt, purB, prsA, and relA), which were most frequently targeted among the analyzed 20 H*R strains (one mutation per clone in 19 of the 20 H*R strains). Besides the strong parallels with our previous findings (five of the six genes matched), all but one of the repeatedly targeted genes were found to be linked to guanine metabolism, pointing to the key role that this pathway plays in defining the level of antibiotic resistance independent of the clonal type of MRSA.This work was financially supported by a US Public Health Service Award 2 R01 AI457838-15 and by project LISBOA-01-0145-FEDER-007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020-Programa Operacional Competitividade e Internacionalização (POCI), by national funds through FCTFundação para a Ciência e a Tecnologia and project ONEIDA (LISBOA-01-0145-FEDER016417) cofunded by FEEI-“Fundos Europeus Estruturais e de Investimento” from “Programa Operacional Regional Lisboa 2020,” and by national funds from FCT. M.P.D.L.G. was supported by PCORI grant CER-1402-10800 and by funds from the RB Roberts Bacterial Antibiotic Resistance Group (BARG). C.M. was supported by grant SFRH/BPD/111697/2015 from FCT.info:eu-repo/semantics/publishedVersio

Contamination of street food with multidrug-resistant Salmonella, in Ouagadougou, Burkina Faso

International audienceBackgroundGastrointestinal infections are a global public health problem. In Burkina Faso, West Africa, exposure to Salmonella through the consumption of unhygienic street food represents a major risk of infection requiring detailed evaluation.MethodsBetween June 2017 and July 2018, we sampled 201 street food stalls, in 11 geographic sectors of Ouagadougou, Burkina Faso. We checked for Salmonella contamination in 201 sandwiches (one per seller), according to the ISO 6579:2002 standard. All Salmonella isolates were characterized by serotyping and antimicrobial susceptibility testing, and whole-genome sequencing was performed on a subset of isolates, to investigate their phylogenetic relationships and antimicrobial resistance determinants.ResultsThe prevalence of Salmonella enterica was 17.9% (36/201) and the Salmonella isolates belonged to 16 different serotypes, the most frequent being Kentucky, Derby and Tennessee, with five isolates each. Six Salmonella isolates from serotypes Brancaster and Kentucky were multidrug-resistant (MDR). Whole-genome sequencing revealed that four of these MDR isolates belonged to the emergent S. enterica serotype Kentucky clone ST198-X1 and to an invasive lineage of S. enterica serotype Enteritidis (West African clade).ConclusionThis study reveals a high prevalence of Salmonella spp. in sandwiches sold in Ouagadougou. The presence of MDR Salmonella in food on sale detected in this study is also matter of concern

Multidrug-Resistant Salmonella enterica Serotype Typhi, Gulf of Guinea Region, Africa

International audienceWe identified 3 lineages among multidrug-resistant (MDR) Salmonella enterica serotype Typhi isolates in the Gulf of Guinea region in Africa during the 2000s. However, the MDR H58 haplotype, which predominates in southern Asia and Kenya, was not identified. MDR quinolone-susceptible isolates contained a 190-kb incHI1 pST2 plasmid or a 50-kb incN pST3 plasmid

Rapid emergence of extensively drug-resistant Shigella sonnei in France

International audienceShigella sonnei, the main cause of bacillary dysentery in high-income countries,has become increasingly resistant to antibiotics. We monitored the anti-microbial susceptibility of 7121 S. sonnei isolates collected in France between2005 and 2021. We detected a dramatic increase in the proportion of isolatessimultaneously resistant to ciprofloxacin (CIP), third-generation cephalos-porins (3GCs) and azithromycin (AZM) from 2015. Our genomic analysis of164 such extensively drug-resistant (XDR) isolates identified 13 differentclusters within CIP-resistant sublineage 3.6.1, which was selected in South Asia∼15 years ago. AZM resistance was subsequently acquired, principally throughIncFII (pKSR100-like) plasmids. The last step in the development of theXDR phenotype involved various extended-spectrum beta-lactamase genes(blaCTX-M-3, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, and blaCTX-M-134) carried bydifferent plasmids (IncFII, IncI1, IncB/O/K/Z) or even integrated into thechromosome, and encoding resistance to 3GCs. This rapid emergence of XDRS. sonnei, including an international epidemic strain, is alarming, and goodlaboratory-based surveillance of shigellosis will be crucial for informeddecision-making and appropriate public health action

ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies

International audienceShigella is one of the commonest causes of diarrhoea worldwide and a major public health problem. Shigella serotyping is based on a standardized scheme that splits Shigella strains into four serogroups and 60 serotypes on the basis of biochemical tests and O-antigen structures. This conventional serotyping method is laborious, time-consuming, impossible to automate, and requires a high level of expertise. Whole-genome sequencing (WGS) is becoming more affordable and is now used for routine surveillance, opening up possibilities for the development of much-needed accurate rapid typing methods. Here, we describe ShigaPass, a new in silico tool for predicting Shigella serotypes from WGS assemblies on the basis of rfb gene cluster DNA sequences, phage and plasmid-encoded O-antigen modification genes, seven housekeeping genes (EnteroBase’s MLST scheme), fliC alleles and clustered regularly interspaced short palindromic repeats (CRISPR) spacers. Using 4879 genomes, including 4716 reference strains and clinical isolates of Shigella characterized with a panel of biochemical tests and serotyped by slide agglutination, we show here that ShigaPass outperforms all existing in silico tools, particularly for the identification of Shigella boydii and Shigella dysenteriae serotypes, with a correct serotype assignment rate of 98.5 % and a sensitivity rate (i.e. ability to make any prediction) of 100 %