Clinical and Bacterial Characteristics Associated with Glove and Gown Contamination by Carbapenem-Resistant Klebsiella pneumoniae in the Health Care Setting.

Carbapenem-resistant Klebsiella pneumoniae (CRKp) is a pathogen of significant concern to public health, as it has become increasingly associated with difficult-to-treat community-acquired and hospital-associated infections. Transmission of K. pneumoniae between patients through interactions with shared health care personnel (HCP) has been described as a source of infection in health care settings. However, it is not known whether specific lineages or isolates of K. pneumoniae are associated with increased transmission. Thus, we used whole-genome sequencing to analyze the genetic diversity of 166 carbapenem-resistant K. pneumoniae isolates from five U.S. hospitals in four states as part of a multicenter study examining risk factors for glove and gown contamination by carbapenem-resistant Enterobacterales (CRE). The CRKp isolates exhibited considerable genomic diversity with 58 multilocus sequence types (STs), including four newly designated STs. ST258 was the most prevalent ST, representing 31% (52/166) of the CRKp isolates, but was similarly prevalent among patients who had high, intermediate, and low CRKp transmission. Increased transmission was associated with clinical characteristics including a nasogastric (NG) tube or an endotracheal tube or tracheostomy (ETT/Trach). Overall, our findings provide important insight into the diversity of CRKp associated with transmission from patients to the gloves and gowns of HCP. These findings suggest that certain clinical characteristics and the presence of CRKp in the respiratory tract, rather than specific lineages or genetic content, are more often associated with increased transmission of CRKp from patients to HCP. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKp) is a significant public health concern that has contributed to the spread of carbapenem resistance and has been linked to high morbidity and mortality. Transmission of K. pneumoniae among patients through interactions with shared health care personnel (HCP) has been described as a source of infection in health care settings; however, it remains unknown whether particular bacterial characteristics are associated with increased CRKp transmission. Using comparative genomics, we demonstrate that CRKp isolates associated with high or intermediate transmission exhibit considerable genomic diversity, and there were no K. pneumoniae lineages or genes that were universally predictive of increased transmission. Our findings suggest that certain clinical characteristics and the presence of CRKp, rather than specific lineages or genetic content of CRKp, are more often associated with increased transmission of CRKp from patients to HCP.

Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli.

Escherichia coli is a frequent member of the healthy human gastrointestinal microbiota, as well as an important human pathogen. Previous studies have focused on the genomic diversity of the pathogenic E. coli and much remains unknown about the non-diarrheagenic E. coli residing in the human gut, particularly among young children in low and middle income countries. Also, gaining additional insight into non-diarrheagenic E. coli is important for understanding gut health as non-diarrheagenic E. coli can prevent infection by diarrheagenic bacteria. In this study we examine the genomic diversity of non-diarrheagenic fecal E. coli from male and female children with or without diarrhea from countries in sub-Saharan Africa and south Asia as part of the Global Enteric Multicenter Study (GEMS). We find that these E. coli exhibit considerable genetic diversity as they were identified in all E. coli phylogroups and an Escherichia cryptic clade. Although these fecal E. coli lack the characteristic virulence factors of diarrheagenic E. coli pathotypes, many exhibit remarkable genomic similarity to previously described diarrheagenic isolates with differences attributed to mobile elements. This raises an important question of whether these non-diarrheagenic fecal E. coli may have at one time possessed the mobile element-encoded virulence factors of diarrheagenic pathotypes or may have the potential to acquire these virulence factors.

Comparative Genomics Identifies Features Associated with Methicillin-Resistant Staphylococcus aureus (MRSA) Transmission in Hospital Settings.

Methicillin-resistant Staphylococcus aureus (MRSA) is a serious public health concern in the United States. Patients colonized and/or infected can transmit MRSA to healthcare workers and subsequent patients However, the components of this transmission chain are just becoming evident, including certain patient factors, specific patient-healthcare worker interactions, and microbial factors. We conducted a comparative genomic analysis of 388 isolates from four hospitals in three states: Maryland, California, and New York. Isolates from nasal surveillance or clinical cultures were categorized as high, moderate, or low transmission surrogate outcomes based on the number of times the species was identified on the gloves or gowns of healthcare providers. The comparative analyses included a single gene, multigene, and core genome phylogenetic analysis, as well as a genome-wide association analysis to identify molecular signatures associated with the observed transmission surrogate outcomes, geographic origin, or sample source of isolation. Based on the phylogenetic analysis, 95% (n = 372) of the MRSA isolates were from four well-described genomic clades, with most of the isolates being part of the USA300 containing clade (n = 187; 48%). Genome-wide association studies also identified genes that were exclusive or prevalent among specific geographic locations. The identified genes provide insights into the transmission dynamics of MRSA isolates providing additional insights into the basis of the geographical differences of MRSA for molecular diagnostics. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is considered a serious threat to public health and contributes to the dissemination of S. aureus in both the healthcare and community setting. Transmission of MRSA between patients via healthcare worker (HCW) has been described. However, what is not understood are the genetic determinants that contribute to the transmission of MRSA from patients to HCWs. In this study, we demonstrated that certain genes may be associated with transmission in the hospital setting.

Draft Genome Sequences of Two Enteroinvasive Escherichia coli Strains Representative of Major Enteroinvasive E. coli Clades.

There are six described pathotypes of Escherichia coli that cause significant clinical illness in humans. Enteroinvasive E. coli (EIEC) strains have been shown to be separated into three phylogenomic clades. To add to a limited body of EIEC genomic data, we report two high-quality draft genome sequences representing different EIEC phylogenomic clades.

Draft Genome Sequences of Five Diverse Klebsiella Species Isolates from Intensive Care Unit Patients.

We have examined the draft genomes of five isolates from two different Klebsiella species obtained from intensive care unit patients at two geographically distributed hospitals to examine the genomic diversity of hospital-acquired organisms in this understudied population.

Genome Sequences of Four Shigella boydii Strains Representative of the Major S. boydii Clades.

There are four bacterial species in the genus Shigella that cause shigellosis or dysentery. Shigella boydii is one of the least studied Shigella species but has been shown to be separated into three phylogenomic clades. Here, we report four complete reference sequences of the S. boydii phylogenomic clades.

Examination of Staphylococcus aureus Isolates from the Gloves and Gowns of Intensive Care Unit Health Care Workers.

Interactions with health care workers are often thought to be associated with the spread of microbes in the hospital setting. We have examined the genomic diversity of methicillin-resistant Staphylococcus aureus isolates from the gloves and gowns of health care workers from four hospitals in three states.

Examination of 189 Campylobacter Species Isolates from the Global Enteric Multicenter Study.

We have examined the draft genomes of 189 Campylobacter species isolates from the Global Enteric Multicenter Study, in which Campylobacter species were identified as significant pathogens.

Comparative genomic analysis provides insight into the phylogeny and virulence of atypical enteropathogenic Escherichia coli strains from Brazil.

BACKGROUND: Atypical enteropathogenic Escherichia coli (aEPEC) are one of the most frequent intestinal E. coli pathotypes isolated from diarrheal patients in Brazil. Isolates of aEPEC contain the locus of enterocyte effacement, but lack the genes of the bundle-forming pilus of typical EPEC, and the Shiga toxin of enterohemorrhagic E. coli (EHEC). The objective of this study was to evaluate the phylogeny and the gene content of Brazilian aEPEC genomes compared to a global aEPEC collection. METHODOLOGY: Single nucleotide polymorphism (SNP)-based phylogenomic analysis was used to compare 106 sequenced Brazilian aEPEC with 221 aEPEC obtained from other geographic origins. Additionally, Large-Scale BLAST Score Ratio was used to determine the shared versus unique gene content of the aEPEC studied. PRINCIPAL FINDINGS: Phylogenomic analysis demonstrated the 106 Brazilian aEPEC were present in phylogroups B1 (47.2%, 50/106), B2 (23.6%, 25/106), A (22.6%, 24/106), and E (6.6%, 7/106). Identification of EPEC and EHEC phylogenomic lineages demonstrated that 42.5% (45/106) of the Brazilian aEPEC were in four of the previously defined lineages: EPEC10 (17.9%, 19/106), EPEC9 (10.4%, 11/106), EHEC2 (7.5%, 8/106) and EPEC7 (6.6%, 7/106). Interestingly, an additional 28.3% (30/106) of the Brazilian aEPEC were identified in five novel lineages: EPEC11 (14.2%, 15/106), EPEC12 (4.7%, 5/106), EPEC13 (1.9%, 2/106), EPEC14 (5.7%, 6/106) and EPEC15 (1.9%, 2/106). We identified 246 genes that were more frequent among the aEPEC isolates from Brazil compared to the global aEPEC collection, including espG2, espT and espC (P<0.001). Moreover, the nleF gene was more frequently identified among Brazilian aEPEC isolates obtained from diarrheagenic patients when compared to healthy subjects (69.7% vs 41.2%, P<0.05). CONCLUSION: The current study demonstrates significant genomic diversity among aEPEC from Brazil, with the identification of Brazilian aEPEC isolates to five novel EPEC lineages. The greater prevalence of some virulence genes among Brazilian aEPEC genomes could be important to the specific virulence strategies used by aEPEC in Brazil to cause diarrheal disease.

Examination of 388 Staphylococcus aureus Isolates from Intensive Care Unit Patients.

We have examined the draft genomes of 388 methicillin-resistant Staphylococcus aureus isolates obtained from intensive care unit patients at three geographically distributed hospitals to determine genomic diversity associated with potential health care worker-associated transmission.

Responses of the Human Gut Escherichia coli Population to Pathogen and Antibiotic Disturbances.

Studies of Escherichia coli in the human gastrointestinal tract have focused on pathogens, such as diarrhea-causing enterotoxigenic E. coli (ETEC), while overlooking the resident, nonpathogenic E. coli community. Relatively few genomes of nonpathogenic E. coli strains are available for comparative genomic analysis, and the ecology of these strains is poorly understood. This study examined the diversity and dynamics of resident human gastrointestinal E. coli communities in the face of the ecological challenges presented by pathogen (ETEC) challenge, as well as of antibiotic treatment. Whole-genome sequences obtained from E. coli isolates from before, during, and after ETEC challenge were used in phylogenomic and comparative genomic analyses to examine the diversity of the resident E. coli communities, as well as the dynamics of the challenge strain, H10407, a well-studied ETEC strain (serotype O78:H11) that produces both heat-labile and heat-stable enterotoxins. ETEC failed to become the dominant E. coli clone in two of the six challenge subjects, each of whom exhibited limited or no clinical presentation of diarrhea. The E. coli communities of the remaining four subjects became ETEC dominant during the challenge but reverted to their original, subject-specific populations following antibiotic treatment, suggesting resiliency of the resident E. coli population following major ecological disruptions. This resiliency is likely due in part to the abundance of antibiotic-resistant ST131 E. coli strains in the resident populations. This report provides valuable insights into the potential interactions of members of the gastrointestinal microbiome and its responses to challenge by an external pathogen and by antibiotic exposure. IMPORTANCE Research on human-associated E. coli tends to focus on pathogens, such as enterotoxigenic E. coli (ETEC) strains, which are a leading cause of diarrhea in developing countries. However, the severity of disease caused by these pathogens is thought to be influenced by the microbiome. The nonpathogenic E. coli community that resides in the human gastrointestinal tract may play a role in pathogen colonization and disease severity and may become a reservoir for virulence and antibiotic resistance genes. Our study used whole-genome sequencing of E. coli before, during, and after challenge with an archetype ETEC isolate, H10407, and antibiotic treatment to explore the diversity and resiliency of the resident E. coli population in response to the ecological disturbances caused by pathogen invasion and antibiotic treatment.

H-NST induces LEE expression and the formation of attaching and effacing lesions in enterohemorrhagic Escherichia coli.

BACKGROUND: Enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli are important causes of morbidity and mortality worldwide. These enteric pathogens contain a type III secretion system (T3SS) responsible for the attaching and effacing (A/E) lesion phenotype. The T3SS is encoded by the locus of enterocyte effacement (LEE) pathogenicity island. The H-NS-mediated repression of LEE expression is counteracted by Ler, the major activator of virulence gene expression in A/E pathogens. A regulator present in EPEC, H-NST, positively affects expression of H-NS regulon members in E. coli K-12, although the effect of H-NST on LEE expression and virulence of A/E pathogens has yet-to-be determined. RESULTS: We examine the effect of H-NST on LEE expression and A/E lesion formation on intestinal epithelial cells. We find that H-NST positively affects the levels of LEE-encoded proteins independently of ler and induces A/E lesion formation. We demonstrate H-NST binding to regulatory regions of LEE1 and LEE3, the first report of DNA-binding by H-NST. We characterize H-NST mutants substituted at conserved residues including Ala16 and residues Arg60 and Arg63, which are part of a potential DNA-binding domain. The single mutants A16V, A16L, R60Q and the double mutant R60Q/R63Q exhibit a decreased effect on LEE expression and A/E lesion formation. DNA mobility shift assays reveal that these residues are important for H-NST to bind regulatory LEE DNA targets. H-NST positively affects Ler binding to LEE DNA in the presence of H-NS, and thereby potentially helps Ler displace H-NS bound to DNA. CONCLUSIONS: H-NST induces LEE expression and A/E lesion formation likely by counteracting H-NS-mediated repression. We demonstrate that H-NST binds to DNA and identify arginine residues that are functionally important for DNA-binding. Our study suggests that H-NST provides an additional means for A/E pathogens to alleviate repression of virulence gene expression by H-NS to promote virulence capabilities.