Enterobacterales - Jan 9 PDF

Enterobacterales Thanks to Dr. Yang Yu MD PhD FRCPC for original slide deck Agenda Introduction and Overview General Characteristics of Enterobacterales Medically Important Species Diagnosis and Treatment Prevention and Control  Learning Objectives...

Enterobacterales Thanks to Dr. Yang Yu MD PhD FRCPC for original slide deck Agenda Introduction and Overview General Characteristics of Enterobacterales Medically Important Species Diagnosis and Treatment Prevention and Control  Learning Objectives Describe the general characteristics of the Enterobacterales order, including basic biochemical testing feature, microscopic Gram staining characteristics, macroscopic appearance on culture media. Describe the methods for the detection of Enterobacterales in clinical specimens; pros and cons of culture vs. culture-independent testing. List some common solid culture media for the Enterobacterales, including blood, MacConkey, xylose-lysine-deoxycholate (XLD), Salmonella-Shigella (SS), Hektoen enteric agar. Describe the importance of STEC infection, and identify the available methods for STEC lab diagnosis Describe Salmonella infection including typhoid, non-typhoid infection, diagnosis; prevention of typhoid fever. Describe antimicrobial resistant features among Enterobacterales; impact of antimicrobial resistance on therapeutic and infection prevention and control (IPAC) Describe food-borne infection surveillance and outbreak investigation. General Characteristics of Enterobacterales  Gram-Negative Coccobacilli Enterobacterales N. meningitis ·Pseudomonas  Enterobacterales Gram negative bacilli – More than 50 genera, hundreds of species Common characteristics – Aerobic and facultative anaerobic growth – Non-spore forming – Ferment glucose (acid ±gas) – Reduce nitrate (NO3) to nitrite (NO2) – Catalase positive – Oxidase negative  Enterobacterales Ubiquitous – Soil, water, vegetation – Gut flora of all animals and humans Some strict human pathogens – Salmonella typhi, Yersinia pestis Some opportunistic pathogens – Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis Some flora that can acquire pathogenic genes – Escherichia coli diarrhea Traditional Bacterial Identification Medically Important Species  Medically Important Species "bacter" Escherichia coli "-al He Klebsiella pneumoniae, Klebsiella oxytoca generally indica I Proteus mirabilis gram-neg Salmonella enterica Shigella sonnei, Shigella flexneri Yersinia pestis, Yersinia enterocolitica Citrobacter freundii, Citrobacter koseri Enterobacter aerogenes, Enterobacter cloacae Morganella morganii Serratia marcescens  Escherichia coli Part of the flora of human and animal GI tract – Opportunistic pathogens Associated with a variety of diseases, including – Gastroenteritis Some strains can cause watery diarrhea with vomiting, dehydration, and low-grade fever, Some serotypes associated with greater virulence causing bloody diarrhea with abdominal cramps ± fever (e.g., hemorrhagic colitis and hemolytic uremic syndrome caused by E. coli O157 ). – Extraintestinal infections Urinary tract infection (UTI), Neonatal sepsis/ meningitis, Bacteremia, Hospital acquired infection (HAI), e.g., ventilator-associated pneumonia  E. coli Associated with Gastroenteritis Organism Site Disease Pathogenesis Enterotoxigenic E. Small bowel Traveler’s diarrhea, infant Plasmid-mediated coli (ETEC) diarrhea in developing water secretion countries; Enteropathogenic E. Small bowel Infant diarrhea in developing Plasmid-mediated coli countries; disruption of (EPEC) microvillus Enteroaggregative E. Small bowel Infant diarrhea in Plasmid-mediated coli (EAEC) developing and probably adherence of developed countries; bacteria traveler’s diarrhea Shiga toxin-producing Large bowel Bloody diarrhea, Shiga toxin (stx1, E. coli (STEC) HUS (hemolytic uremic stx2) syndrome) Enteroinvasive E. coli Large bowel Bloody diarrhea Plasmid-mediated (EIEC) cell invasion Shiga toxin-producing E.coli (STEC) Nomenclature – Shiga toxin–producing E. coli (STEC), – Verocytotoxin-producing E. coli (VTEC), – Enterohemorrhagic E. coli (EHEC). All members of the STEC producing Shiga toxin 1 (Stx1) and/ or 2 (Stx2).  Shiga toxin-producing E.coli (STEC) The most common serotype associated with human disease is O157:H7 – 2000 Walkerton outbreak after breakdowns in the local water system. Non O157 strains are aware of causing severe gastroenteritis/ HUS/ outbreak – 2011 outbreak of E. coli O104:H4 in Germany and France – 2007 E. coli O121 that was linked to various flour and flour products several provinces of Canada  STEC infection – Ranges from mild uncomplicated diarrhea to hemorrhagic colitis with severe abdominal pain and bloody diarrhea. – Severe complication: hemolytic uremic syndrome (HUS), characterized by acute renal failure, thrombocytopenia, and microangiopathic hemolytic anemia – HUS occurs in 10-15% of children younger than 10 years old. – Food-borne and water-borne (undercooked ground beef, unpasteurized milk or fruit juices, contaminated water or uncooked vegetables). Some studies have shown that administering antibiotics to patients with STEC infections might increase their risk of developing HUS. Antibiotics are not recommended for patients with suspected STEC infections until complete diagnostic testing can be performed and STEC infection is ruled out.  E. coli Associated with Extraintestinal Infections UTI – Pathogens originate in the colon, contaminate the urethra, ascend into the bladder, and may migrate to the kidney or prostate. – Uropathogen strains (UPEC) able to produce adhesins (primarily P pili, AAF/I, AAF/III, and Dr ) that bind to cells lining the bladder and upper urinary tract (preventing elimination of the bacteria in voided urine) and hemolysin HlyA that lyses erythrocytes and other cell types (leading to cytokine release and stimulation of an inflammatory response). Neonatal meningitis – Approximately 75% of the E. coli strains possess the K1 capsular antigen. Septicemia – Most commonly originates from UTI (urosepsis); or – Infections in the GI tract (e.g., intestinal leakage leading to an intraabdominal infection)  Salmonella species The genus Salmonella has two species: Salmonella enterica and S. bongari Salmonella enterica accounts for almost all human infections. >2500 serotypes (serovars) The individual species listed are actually a serovar of Salmonella enterica, e.g. Salmonella Typhi is actually Salmonella enterica, serovar typhi  Salmonella species Salmonellae are primary pathogens of almost all animals. Animals are the main source of nontyphoidal human salmonellosis via fecal-oral spread due to ingestion of food, water, milk contaminated by human or animal excreta. Humans are the only known reservoir for Salmonella Typhi Clinical types of Salmonella infections – Gastroenteritis – Septicemia – Typhoid fever – Chronic carriage – Focal infections: osteomyelitis, meningitis, brain abscess, endocarditis Typhoid (Enteric) Fever  Shigella species Four species: S. dysenteriae, Shigella flexneri, Shigella boydii, and Shigella sonnei. DNA analysis has determined that these four species are actually biogroups within the species E. coli. S. dysenteriae strains produce Shiga toxin, can mediate damage to the glomerular endothelial cells, resulting in renal failure (HUS). Humans are the only reservoir for Shigella.  Shigella species Shigellosis is transmitted person to person by the fecal-oral route, primarily by people with contaminated hands and less commonly in water or food. Common in children younger than 10 years old, or in male homosexual adults. Shigellosis is characterized by abdominal cramps, diarrhea, fever, and bloody stools. Antibiotic therapy is beneficial.  Yersinia species Three human pathogens of genus Yersinia: – Y. pestis, – Y. enterocolitica, – Y. pseudotuberculosis. Y. pestis is the pathogen for plague (endemic and pandemics) Is spread among rats or between rats and humans by infected fleas. The two clinical manifestations of Y. pestis infection are bubonic plague and pneumonic plague.  Yersinia species Y. enterocolitica and Y. pseudotuberculosis cause gastroenteritis 2/3 are enterocolitis involves the terminal ileum and, if the mesenteric lymph nodes become enlarged, can mimic acute appendicitis, esp. in children. Infection associated with ingestion of contaminated food products or water. incubation period of 1 to 10 days (average, 4 to 6 days) Presentation: diarrhea, fever, and abdominal pain. May develop a chronic form for months. Other manifestations seen in adults are septicemia, arthritis, intraabdominal abscess, hepatitis, and osteomyelitis. Y. enterocolitica reported to cause blood transfusion–related bacteremia and endotoxic shock (Yersinia sp. can grow at 4° C) Other Enterobacteria  Klebsiella species K. pneumoniae and Klebsiella oxytoca: two commonly isolated bacteria causing community- or hospital-acquired primary lobar pneumonia. Members of the genus Klebsiella have a prominent capsule that is responsible for the mucoid appearance of isolated colonies and the enhanced virulence of the organisms in vivo. Other clinical infections: wound and soft-tissue infections, UTIs, sepsis.  Klebsiella species K. granulomatis is the etiologic agent of granuloma inguinale (donovanosis), a granulomatous disease affecting the genitalia and inguinal area. Shiga toxin-producing E.coli (STEC) Timely diagnosis of STEC in critical – Culture Sorbitol MacConkey [SMAC] or CHROMagar – EIA to detect the Shiga toxins – Molecular assays (e.g. PCR) stx genes  Diagnosis Specimens: stool, blood, urine, bone marrow (typhoid fever)… Culture: blood agar, MacConkey, other selective media MacConkey Culture-independent methods Diagnosis and Treatment  Antimicrobial susceptibility Some infections might not need antibiotic therapy: STEC, Salmonella gastroenteritis in immunocompetent host Antibiotic resistance increasing among the Enterobacterales organisms: – Extended-spectrum β-lactamases (ESBL), – Carbapenem-resistant Enterobacteriaceae (CRE) (Heck Yes) AmpC - Prevention and Control  Enteric infection prevention Education (e.g. safe food handling/ preparation) The introduction of appropriate infection-control procedures (e.g., hand washing, proper disposal of soiled diapers and linens) Vaccine (Salmonella) – Injectable – Oral Water treatment Food safety  Surveillance Programs Nationally notifiable in all provinces and territories. Canada uses different surveillance systems to monitor cases of food-borne illness. – FoodNet Canada – the National Enteric Surveillance Program (NESP) – the Canadian Notifiable Disease Surveillance System – PulseNet Canada  Pathogen Laboratory Surveillance Programs Whole genome sequencing (WGS) www.cdc.gov/pulsenet/pdf/Genome-Sequencing-508c.pdf