Rapid Increase of CTX-M-Producing Shigella sonnei Isolates in Switzerland Due to Spread of Common Plasmids and International Clones

ABSTRACT The Swiss Centre for Antibiotic Resistance (ANRESIS) has recently noted an increase of extended-spectrum cephalosporin-resistant (ESC-R) Shigella sonnei isolates nationwide (3.8% in 2016 versus 37.5% in 2019). To understand this phenomenon, we analyzed 25 representative isolates (of which 14 were ESC-R) collected in Switzerland during 2016 to 2019. Whole-genome sequencing was achieved using both the Illumina and the Nanopore platforms. Both ESC-R and extended-spectrum cephalosporin-susceptible isolates belonged to sequence type 152 (ST152). The ESC-R isolates carried blaCTX-M-3 in IncI1-pST57 (n = 5), blaCTX-M-15 in IncFII (F2:A-:B-) (n = 5), blaCTX-M-15 in IncI1-pST16, and blaCTX-M-27, blaCTX-M-55, or blaCTX-M-134 in other IncFII plasmids (n = 1 each). Plasmids having the same bla and Inc group exhibited high degrees of genetic identity to each other but also to plasmids previously reported in other Enterobacterales. Core-genome analysis showed that there were 4 main clusters, each of which included strains that differed by <58 single nucleotide variants (SNVs) and that consisted of both blaCTX-M-positive and blaCTX-M-negative isolates. Moreover, most isolates belonging to the same cluster shared an identical core-genome sequence type (cgST). For instance, cluster 1 included 4 isolates of cgST113036, of which only 3 harbored the IncI1-pST57 blaCTX-M-3-positive plasmid. The 25 S. sonnei isolates were also subjected to phylogenetic comparison with deposited international strains. As a result, matching isolates (isolates that had the same cgST and that differed by <8 SNVs) have been reported in the United Kingdom, the United States, France, and the Netherlands. Overall, our results suggest that some common S. sonnei clusters can spread between continents and can be imported into other nations after international trips. Such clusters include, in part, isolates that do not possess blaESBL-harboring plasmids, indicating their tendency to acquire them from other Enterobacterales.

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Singleton Sequence Type 382, an Emerging Clonal Group of Listeria monocytogenes Associated with Three Multistate Outbreaks Linked to Contaminated Stone Fruit, Caramel Apples, and Leafy Green Salad

Journal of Clinical Microbiology ◽

10.1128/jcm.02140-16 ◽

2017 ◽

Vol 55 (3) ◽

pp. 931-941 ◽

Cited By ~ 21

Author(s):

Yi Chen ◽

Yan Luo ◽

James Pettengill ◽

Ruth Timme ◽

David Melka ◽

...

Keyword(s):

Listeria Monocytogenes ◽

The United States ◽

Sequence Type ◽

Stone Fruit ◽

Nucleotide Polymorphisms ◽

Outbreak Strain ◽

Single Nucleotide ◽

Content Type ◽

Genomic Divergence ◽

Singleton Sequence

ABSTRACT Three multistate outbreaks between 2014 and 2016, involving case patients in and outside the United States, were linked to stone fruit, caramel apples, and packaged leafy green salad contaminated with Listeria monocytogenes singleton sequence type 382 (ST382), a serotype IVb-v1 clone with limited genomic divergence. Isolates from these outbreaks and other ST382 isolates not associated with these outbreaks were analyzed by whole-genome sequencing (WGS) analysis. The primary differences among ST382 strains were single nucleotide polymorphisms (SNPs). WGS analysis differentiated ST382 from a clonal complex 1 outbreak strain co-contaminating the caramel apples. WGS clustered food, environmental, and clinical isolates within each outbreak, and also differentiated among the three outbreak strains and epidemiologically unrelated ST382 isolates, which were indistinguishable by pulsed-field gel electrophoresis. ST382 appeared to be an emerging clone that began to diverge from its ancestor approximately 32 years before 2016. We estimated that there was 1.29 nucleotide substitution per genome (2.94 Mbp) per year for this clone.

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Emergence of Multidrug-Resistant Salmonella enterica Serovar Goldcoast Strains in Taiwan and International Spread of the ST358 Clone

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01122-19 ◽

2019 ◽

Vol 63 (10) ◽

Cited By ~ 3

Author(s):

Ying-Shu Liao ◽

Bo-Han Chen ◽

Yu-Ping Hong ◽

Ru-Hsiou Teng ◽

You-Wun Wang ◽

...

Keyword(s):

Salmonella Enterica ◽

Genetic Relatedness ◽

The United States ◽

Multidrug Resistant ◽

Sequence Type ◽

Content Type ◽

The United Kingdom ◽

Routine Surveillance ◽

Antimicrobial Resistance Genes ◽

High Degree

ABSTRACT Salmonella enterica serovar Goldcoast infection was rare in Taiwan; it was not detected in routine surveillance from 2004 to 2013. This serovar was first identified in 2014, but the frequency of infection remained low until 2017. From 2014 to 2016, all but one isolate was pan-susceptible. S. Goldcoast infections abruptly increased in 2018, and all isolates were multidrug-resistant (MDR). All MDR isolates harbored an IncHI2 plasmid, and the majority carried 14 antimicrobial resistance genes, aac(3)-IId, aadA22, aph(3′)-Ia, aph(6)-Id, blaTEM-1B, blaCTX-M-55, lnu(F), floR, qnrS13, arr-2, sul2, sul3, tet(A), and dfrA14. S. Goldcoast strains recovered in Taiwan and 96 of 99 strains from Germany, the Netherlands, the United Kingdom, and the United States belonged to sequence type 358 (ST358). Whole-genome single-nucleotide polymorphism and core genome multilocus sequence type analyses revealed that all strains of the ST358 clone shared a high degree of genetic relatedness. The present study highlighted that a dramatic increase in S. Goldcoast infections followed the emergence of MDR strains and indicated that a genetically closely related S. Goldcoast ST358 clone may have widespread significance internationally.

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Genomic Investigation of the Emergence of Invasive Multidrug-Resistant Salmonella enterica Serovar Dublin in Humans and Animals in Canada

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00108-19 ◽

2019 ◽

Vol 63 (6) ◽

Cited By ~ 2

Author(s):

Chand S. Mangat ◽

Sadjia Bekal ◽

Brent P. Avery ◽

Geneviève Côté ◽

Danielle Daignault ◽

...

Keyword(s):

Salmonella Enterica ◽

Bloodstream Infections ◽

The United States ◽

Multidrug Resistant ◽

Phylogenomic Analysis ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Content Type ◽

Human Infections ◽

Integrated Program

ABSTRACT Salmonella enterica subsp. enterica serovar Dublin is a zoonotic pathogen that often leads to invasive bloodstream infections in humans that are multidrug resistant. Described here are the results of Canadian national surveillance of S. Dublin from 2003 to 2015 in humans and bovines, principally collected through the Canadian Integrated Program for Antibiotic Resistance Surveillance (CIPARS). An increase in human infections due to multidrug-resistant (MDR) S. Dublin was observed in 2010, many of which were bloodstream infections. Phylogenomic analysis of human and bovine isolates revealed a closely related network that differed by only 0 to 17 single nucleotide variants (SNVs), suggesting some potential transmission between humans and bovines. Phylogenomic comparison of global publicly available sequences of S. Dublin showed that Canadian isolates clustered closely with those from the United States. A high correlation between phenotypic and genotypic antimicrobial susceptibility was observed in Canadian isolates. IS26 replication was widespread among U.S. and Canadian isolates and caused the truncation and inactivation of the resistance genes strA and blaTEM-1B. A hybrid virulence and MDR plasmid (pN13-01125) isolated from a Canadian S. Dublin isolate was searched against NCBI SRA data of bacteria. The pN13-01125 coding sequences were found in 13 Salmonella serovars, but S. Dublin appears to be a specific reservoir. In summary, we have observed the rise of invasive MDR S. Dublin in humans in Canada and found that they are closely related to bovine isolates and to American isolates in their mobile and chromosomal contents.

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Population Structure of KPC-Producing Klebsiella pneumoniae Isolates from Midwestern U.S. Hospitals

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00125-14 ◽

2014 ◽

Vol 58 (8) ◽

pp. 4961-4965 ◽

Cited By ~ 56

Author(s):

Meredith S. Wright ◽

Federico Perez ◽

Lauren Brinkac ◽

Michael R. Jacobs ◽

Keith Kaye ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Capsular Polysaccharide ◽

Sequence Type ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Content Type ◽

Strain Diversity ◽

Carbapenem Resistant ◽

Genetic Context ◽

Over Time

ABSTRACTGenome sequencing of carbapenem-resistantKlebsiella pneumoniaeisolates from regional U.S. hospitals was used to characterize strain diversity and theblaKPCgenetic context. A phylogeny based on core single-nucleotide variants (SNVs) supports a division of sequence type 258 (ST258) into two distinct groups. The primary differences between the groups are in the capsular polysaccharide locus (cps) and their plasmid contents. A strict association between clade and KPC variant was found. TheblaKPCgene was found on variants of two plasmid backbones. This study indicates that highly similarK. pneumoniaesubpopulations coexist within the same hospitals over time.

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Molecular Features of Community-Associated Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains in the United States

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.03321-14 ◽

2014 ◽

Vol 58 (11) ◽

pp. 6953-6957 ◽

Cited By ~ 5

Author(s):

Fupin Hu ◽

Jessica A. O'Hara ◽

Jesabel I. Rivera ◽

Yohei Doi

Keyword(s):

United States ◽

Escherichia Coli ◽

Restriction Analysis ◽

The United States ◽

Sequence Type ◽

Content Type ◽

Molecular Features ◽

Extended Spectrum ◽

Sequence Types ◽

Replicon Type

ABSTRACTWe characterized 30 community-associated extended-spectrum-β-lactamase-producingEscherichia coliisolates collected from five hospitals in the United States. Nineteen sequence types were identified. All sequence type 131 (ST131) isolates had thefimH30 allele. IncFII-FIA-FIB was the most common replicon type among theblaCTX-M-carrying plasmids, followed by IncFII-FIA and IncA/C. Restriction analysis of the IncFII-FIA-FIB and IncFII-FIA plasmids yielded related profiles for plasmids originating from different hospitals. The plasmids containingblaCTX-MorblaSHVwere stably maintained after serial passages.

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Molecular Epidemiological Analysis of Escherichia coli Sequence Type ST131 (O25:H4) andblaCTX-M-15among Extended-Spectrum-β-Lactamase-Producing E. coli from the United States, 2000 to 2009

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.05824-11 ◽

2012 ◽

Vol 56 (5) ◽

pp. 2364-2370 ◽

Cited By ~ 83

Author(s):

James R. Johnson ◽

Carl Urban ◽

Scott J. Weissman ◽

James H. Jorgensen ◽

James S. Lewis ◽

...

Keyword(s):

United States ◽

Escherichia Coli ◽

Antimicrobial Resistance ◽

The United States ◽

Sequence Type ◽

Fluoroquinolone Resistance ◽

Convenience Sample ◽

Content Type ◽

E Coli ◽

Extended Spectrum

ABSTRACTEscherichia colisequence type ST131 (from phylogenetic group B2), often carrying the extended-spectrum-β-lactamase (ESBL) geneblaCTX-M-15, is an emerging globally disseminated pathogen that has received comparatively little attention in the United States. Accordingly, a convenience sample of 351 ESBL-producingE. coliisolates from 15 U.S. centers (collected in 2000 to 2009) underwent PCR-based phylotyping and detection of ST131 andblaCTX-M-15. A total of 200 isolates, comprising 4 groups of 50 isolates each that were (i)blaCTX-M-15negative non-ST131, (ii)blaCTX-M-15positive non-ST131, (iii)blaCTX-M-15negative ST131, or (iv)blaCTX-M-15positive ST131, also underwent virulence genotyping, antimicrobial susceptibility testing, and pulsed-field gel electrophoresis (PFGE). Overall, 201 (57%) isolates exhibitedblaCTX-M-15, whereas 165 (47%) were ST131. ST131 accounted for 56% ofblaCTX-M-15-positive- versus 35% ofblaCTX-M-15-negative isolates (P< 0.001). Whereas ST131 accounted for 94% of the 175 total group B2 isolates, non-ST131 isolates were phylogenetically distributed byblaCTX-M-15status, with groups A (blaCTX-M-15-positive isolates) and D (blaCTX-M-15-negative isolates) predominating. BothblaCTX-M-15and ST131 occurred at all participating centers, were recovered from children and adults, increased significantly in prevalence post-2003, and were associated with molecularly inferred virulence. Compared with non-ST131 isolates, ST131 isolates had higher virulence scores, distinctive virulence profiles, and more-homogeneous PFGE profiles.blaCTX-M-15was associated with extensive antimicrobial resistance and ST131 with fluoroquinolone resistance. Thus,E. coliST131 andblaCTX-M-15are emergent, widely distributed, and predominant among ESBL-positiveE. colistrains in the United States, among children and adults alike. Enhanced virulence and antimicrobial resistance have likely promoted the epidemiological success of these emerging public health threats.

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Characteristics of Escherichia coli Sequence Type 131 Isolates That Produce Extended-Spectrum β-Lactamases: Global Distribution of theH30-Rx Sublineage

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02428-14 ◽

2014 ◽

Vol 58 (7) ◽

pp. 3762-3767 ◽

Cited By ~ 46

Author(s):

Gisele Peirano ◽

Akke K. van der Bij ◽

Joshua L. Freeman ◽

Laurent Poirel ◽

Patrice Nordmann ◽

...

Keyword(s):

Escherichia Coli ◽

United Arab Emirates ◽

The United States ◽

Multidrug Resistant ◽

Sequence Type ◽

Global Distribution ◽

Phylogenetic Groups ◽

Content Type ◽

Specific Pcr ◽

Extended Spectrum

ABSTRACTWe designed a study to describe the characteristics of sequence type 131 (ST131) lineages, including theH30-Rx sublineage, among a global collection of extended-spectrum β-lactamase (ESBL)-producingEscherichia coliisolates from 9 countries collected from 2000 to 2011. A total of 240 nonrepeat isolates from Canada, the United States, Brazil, the Netherlands, France, the United Arab Emirates (UAE), India, South Africa, and New Zealand were included. Established PCR, sequencing, and typing methods were used to define ST131 lineages,H30 andH30-Rx phylogenetic groups,gyrAandparCmutations, virotypes, and plasmid-mediated quinolone resistance determinants. The majority of the isolates produced CTX-M-15 withaac(6′)-lb-cr, belonged to phylogenetic group B2, and were positive for theH30 lineage with thegyrA1ABandparC1aABmutations. ST131 showed 15 distinct pulsotypes; 43% of the isolates belonged to four pulsotypes, with a global distribution. Seventy-five percent of the ST131 isolates belonged toH30-Rx; this sublineage was present in all the countries and was associated with multidrug resistance,blaCTX-M-15,aac(6′)-lb-cr, and virotypes A and C. TheH41 lineage was negative for the ST131pabBallele-specific PCR. The multidrug-resistantH30-Rx sublineage poses an important public health threat due to its global distribution, association with virotype C, and high prevalence among ST131 isolates that produce CTX-M-15.

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Microevolution ofStreptococcus agalactiaeST-261 from Australia Indicates Dissemination via Imported Tilapia and Ongoing Adaptation to Marine Hosts or Environment

Applied and Environmental Microbiology ◽

10.1128/aem.00859-18 ◽

2018 ◽

Vol 84 (16) ◽

Cited By ~ 13

Author(s):

Minami Kawasaki ◽

Jerome Delamare-Deboutteville ◽

Rachel O. Bowater ◽

Mark J. Walker ◽

Scott Beatson ◽

...

Keyword(s):

Streptococcus Agalactiae ◽

Core Genome ◽

Minimum Spanning Tree ◽

Vaccine Development ◽

The United States ◽

Wild Fish ◽

Clinical Isolates ◽

Global Trade ◽

Content Type ◽

Wide Range

ABSTRACTStreptococcus agalactiae(group BStreptococcus[GBS]) causes disease in a wide range of animals. The serotype Ib lineage is highly adapted to aquatic hosts, exhibiting substantial genome reduction compared with terrestrial conspecifics. Here, we sequence genomes from 40 GBS isolates, including 25 isolates from wild fish and captive stingrays in Australia, six local veterinary or human clinical isolates, and nine isolates from farmed tilapia in Honduras, and compared them with 42 genomes from public databases. Phylogenetic analysis based on nonrecombinant core-genome single nucleotide polymorphisms (SNPs) indicated that aquatic serotype Ib isolates from Queensland were distantly related to local veterinary and human clinical isolates. In contrast, Australian aquatic isolates are most closely related to a tilapia isolate from Israel, differing by only 63 core-genome SNPs. A consensus minimum spanning tree based on core-genome SNPs indicates the dissemination of sequence type 261 (ST-261) from an ancestral tilapia strain, which is congruent with several introductions of tilapia into Australia from Israel during the 1970s and 1980s. Pangenome analysis identified 1,440 genes as core, with the majority being dispensable or strain specific, with non-protein-coding intergenic regions (IGRs) divided among core and strain-specific genes. Aquatic serotype Ib strains have lost many virulence factors during adaptation, but six adhesins were well conserved across the aquatic isolates and might be critical for virulence in fish and for targets in vaccine development. The close relationship among recent ST-261 isolates from Ghana, the United States, and China with the Israeli tilapia isolate from 1988 implicates the global trade in tilapia seed for aquaculture in the widespread dissemination of serotype Ib fish-adapted GBS.IMPORTANCEStreptococcus agalactiae(GBS) is a significant pathogen of humans and animals. Some lineages have become adapted to particular hosts, and serotype Ib is highly specialized to fish. Here, we show that this lineage is likely to have been distributed widely by the global trade in tilapia for aquaculture, with probable introduction into Australia in the 1970s and subsequent dissemination in wild fish populations. We report here the variability in the polysaccharide capsule among this lineage but identify a cohort of common surface proteins that may be a focus of future vaccine development to reduce the biosecurity risk in international fish trade.

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Genomic Investigation Reveals Contaminated Detergent as the Source of an Extended-Spectrum-β-Lactamase-Producing Klebsiella michiganensis Outbreak in a Neonatal Unit

Journal of Clinical Microbiology ◽

10.1128/jcm.01980-19 ◽

2020 ◽

Vol 58 (5) ◽

Cited By ~ 1

Author(s):

Paul Chapman ◽

Brian M. Forde ◽

Leah W. Roberts ◽

Haakon Bergh ◽

Debra Vesey ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Klebsiella Oxytoca ◽

Multidrug Resistant ◽

Hospital Environment ◽

Nucleotide Polymorphism ◽

Taxonomic Assignment ◽

Single Nucleotide ◽

Content Type ◽

Extended Spectrum ◽

Antimicrobial Resistance Genes

ABSTRACT Klebsiella species are problematic pathogens in neonatal units and may cause outbreaks, for which the sources of transmission may be challenging to elucidate. We describe the use of whole-genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lactamase (ESBL)-producing Klebsiella michiganensis colonizing neonates. Ceftriaxone-resistant Klebsiella spp. isolated from neonates (or their mothers) and the hospital environment were included. Short-read sequencing (Illumina) and long-read sequencing (MinION; Oxford Nanopore Technologies) were used to confirm species taxonomy, to identify antimicrobial resistance genes, and to determine phylogenetic relationships using single-nucleotide polymorphism profiling. A total of 21 organisms (10 patient-derived isolates and 11 environmental isolates) were sequenced. Standard laboratory methods identified the outbreak strain as an ESBL-producing Klebsiella oxytoca, but taxonomic assignment from WGS data suggested closer identity to Klebsiella michiganensis. Strains isolated from multiple detergent-dispensing bottles were either identical or closely related by single-nucleotide polymorphism comparison. Detergent bottles contaminated by K. michiganensis had been used for washing milk expression equipment. No new cases were identified once the detergent bottles were removed. Environmental reservoirs may be an important source in outbreaks of multidrug-resistant organisms. WGS, in conjunction with traditional epidemiological investigation, can be instrumental in revealing routes of transmission and guiding infection control responses.

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Serotype and Genotype (Multilocus Sequence Type) ofStreptococcus suisIsolates from the United States Serve as Predictors of Pathotype

Journal of Clinical Microbiology ◽

10.1128/jcm.00377-19 ◽

2019 ◽

Vol 57 (9) ◽

Cited By ~ 12

Author(s):

April A. Estrada ◽

Marcelo Gottschalk ◽

Stephanie Rossow ◽

Aaron Rendahl ◽

Connie Gebhart ◽

...

Keyword(s):

United States ◽

Odds Ratio ◽

Clinical Information ◽

The United States ◽

Growing Pigs ◽

Sequence Type ◽

Primary Methods ◽

Content Type ◽

History Of ◽

Sequence Types

ABSTRACTStreptococcus suisis a significant cause of mortality in piglets and growing pigs worldwide. The species contains pathogenic and commensal strains, with pathogenic strains causing meningitis, arthritis, endocarditis, polyserositis, and septicemia. Serotyping and multilocus sequence typing (MLST) are primary methods to differentiate strains, but the information is limited for strains found in the United States. The objective of this study was to characterize the diversity of 208S. suisisolates collected between 2014 and 2017 across North America (mainly the United States) by serotyping and MLST and to investigate associations between subtype and pathotype classifications (pathogenic, possibly opportunistic, and commensal), based on clinical information and site of isolation. Twenty serotypes were identified, and the predominant serotypes were 1/2 and 7. Fifty-eight sequence types (STs) were identified, and the predominant ST was ST28. Associations among serotypes, STs, and pathotypes were investigated using odds ratio and clustering analyses. Evaluation of serotype and ST with pathotype identified a majority of isolates of serotypes 1, 1/2, 2, 7, 14, and 23 and ST1, ST13, ST25, ST28, ST29, ST94, ST108, ST117, ST225, ST373, ST961, and ST977 as associated with the pathogenic pathotype. Serotypes 21 and 31, ST750, and ST821 were associated with the commensal pathotype, which is composed of isolates from farms with no known history ofS. suis-associated disease. Our study demonstrates the use of serotyping and MLST to differentiate pathogenic from commensal isolates and establish links between pathotype and subtype, thus increasing the knowledge aboutS. suisstrains circulating in the United States.

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