Enterobactericeae Lecture Notes PDF

Enterobacterales, Campylobacterales and Vibrionales Dr Jenny Ritchie Dept of Microbial Sciences [email protected] Module aims To describe the str...

Enterobacterales, Campylobacterales and Vibrionales Dr Jenny Ritchie Dept of Microbial Sciences [email protected] Module aims To describe the structural, physiological, biochemical and genetic characteristics of the major groups of bacteria and animal viruses To describe the diseases caused by bacteria and protozoa To examine virulence mechanisms in pathogenic bacteria and protozoa To examine the role and effects of bacteria and protozoa in the environment Thorough knowledge of a wide range of bacterial species Dr Jenny Ritchie September 2023 1 Position in phylogenetic tree Order Enterobacterales Today Family: Enterobacteriaceae (Genera: Salmonella, Escherichia, Shigella) Family: Yersiniaceae (Genus: Yersinia Order Vibrionales (Genus: Vibrio) Tomorrow Order Campylobacterales Genera: Campylobacter, Helicobacter Phylum: Proteobacteria https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.001485 Dr Jenny Ritchie September 2023 2 Order: Enterobacterales General morphological and biochemical characteristics emended family Enterobacteriaceae 29 genera including type genus Escherichia, as well as other genera e.g. Salmonella, Klebsiella, Enterobacter Optimum temperature 37 °C Gram-negative, non-spore forming rods Facultative anaerobes Catalase positive Oxidase negative Nitrate reductase positive G+C content 38-60% genome size ~5 Mbp Motile, via peritrichous flagella (a few exceptions) Dr Jenny Ritchie September 2023 3  Enterobactericeae: common aspects Habitats: gastrointestinal tract of hosts including humans, animals and insects Widespread contamination of environment: sewage, soil, water, plants, food Routes of infection: oral, via wounds, urinary tract, respiratory tract Disease patterns: diarrhoea, sepsis, urinary tract, CNS and brain Among the most pathogenic and most often encountered organisms……. Dr Jenny Ritchie September 2023 4 Genus: Salmonella Classification of Salmonella species is complex 2 species 7 subspecies >2,600 serovars Some serovars are host-restricted e.g. Typhi (human). Abortusovis (sheep) Most serovars infect a wide range of hosts e.g. Typhimurium Dr Jenny Ritchie September 2023 5  Genus Salmonella: general characteristics Non-lactose fermenter (E. coli ferments lactose but Shigella does not) Indole test negative (E. coli positive; Shigella variable) Various selective medias can distinguish XLD media Salmonella from E. coli / Shigella by: E. coli – yellow Salmonella – black H2S production Shigella - red Acid production during carbohydrate fermentation e.g. XLD media, SS media Salmonella-Shigella (SS) media Dr Jenny Ritchie September 2023 6 Typhoidal Salmonella : impact & disease Typhoid fever (S. Typhi) ~ 15 million new cases each year, with about 1% deaths 1st phase: slow fever, rose spots, mild, bacteraemia 2nd phase: organism reaches gallbladder, formation of ulcers, haemorrhage, death (20%) Typhoid state “muttering delirium” or “coma vigil” (picking at bedclothes and imaginary objects) Enteric fever (S. Paratyphi) → similar to typhoid fever but less severe; rare ‘Rose spots’ Wain et al. (2014) Typhoid fever. The Lancet 385:1136-1145. GBD 2017 Typhoid and Paratyphoid collaborators (2019) Dr Jenny Ritchie September 2023 7  Non-typhoid Salmonella (NTS): impact Global burden ~94 million cases (155,000 deaths) each year, of which about 80 million were estimated as foodborne origin UK data: 8-9,000 confirmed cases per year Predominant serovars: Salmonella Enteritidis Salmonella Typhimurium Salmonella Heidelberg Salmonella Newport NTS causes self-limiting enteritis in healthy individuals Can be invasive (iNTS) in regions with immunocompromised / malnourished individuals e.g. in sub-Saharan Africa Hume et al. (2017) Swiss army pathogen: the Salmonella entry toolkit. Front. Cellular Infect. Microbiol. 7:article 348 Balasubramanian et al. (2018) Human vaccines and Immunotherapeutics https://doi.org/10.1080/21645515.2018.1504717 Dr Jenny Ritchie September 2023 8  NT Salmonella: infection and pathogenesis Despite differences in disease outcome, all Salmonella must cross epithelial barrier to colonise the host cross epithelium via phagocytic cells (M cells, DCs) or direct uptake targets macrophages, or re-invades epithelial cells from basolateral side may evade killing by inducing macrophage apoptosis / manipulate for bacterial replication severe disease results from systemic spread and bacteraemia Dr Jenny Ritchie September 2023 9  Main Salmonella virulence factor: Type 3 secretion systems (T3SSs) – encoded on Salmonella pathogenicity island (SPI) SPI1 – encodes genes T3SS = molecular necessary for invasion ‘syringe’ that transfers of intestinal epithelial proteins (effectors) cells and induction of from bacterial intestinal secretory and cytoplasm to host cell inflammatory responses SPI2 – encodes genes essential for intracellular replication and necessary for establishment of systemic infection beyond the intestinal epithelium Dr Jenny Ritchie September 2023 10  Vehicles of NTS Salmonella infection in UK Route: faecal-oral transmission Predominantly poultry and poultry products but many foods have been associated with infection an unusual vector! 2007, S. Senftenberg 2013, S. Agona basil 2010, S. Bareilly 2019, Salmonella?? curry leaves bean sprouts cucumber UK: meat, milk, UK: pre-1980s Eggs! sausages and even chocolate! 5/5/22 – 101 cases linked to ‘Kinder’ outbreak, most in children < 5 years old 11 Dr Jenny Ritchie September 2023  Genus: Escherichia Escherichia genus – E. coli first isolated 1919, Theodor Escherich Five species: E. albertii, E. coli, E. fergusonii, E. hermannii, E. vulneris E. coli colonises mammalian GI tract a few hours after birth and maintains regular presence over lifetime Of >700 different serotypes (O,H,K), most are harmless Pathogenic strains are assigned to ‘pathotypes’ based on the type of disease they cause and the virulence factors they harbour Dr Jenny Ritchie September 2023 12  E. coli pathotypes associated with disease Gastrointestinal disease intestinal infections Attaching and effacing Enteroaggregative Shiga toxin-producing E. coli E. coli Enteroinvasive E. coli (STEC) or (EAggEC) E. coli Enterohaemorrhagic (EIEC) E. coli (EHEC) Enteropathogenic Enterotoxigenic E. coli E. coli (EPEC) (ETEC) uropathogenic meningitis-associated E. coli E. coli (UPEC) septicaemic E. coli (MNEC) Urinary tract (SEPEC) Meningitis infections (UTIs) extra-intestinal infections Dr Jenny Ritchie September 2023 13  Urinary tract infections (UTIs) 50% of women get a UTI in their lifetime 75% of UTIs are caused by uropathogenic E. coli (UPEC) UTI infection: 14x more common in females (shorter urethra) In the pre-antibiotic era, 15% of UTI Flores-Mireles et al. Nature Reviews cases were fatal Microbiology 13:269–284 (2015) Types of UTI include: asymptomatic bacteriuria (1% normally, 20% elderly) cystitis (bladder infection) pyelonephritis (upper ureter infection, kidney infection) Dr Jenny Ritchie September 2023 14  Mechanism of UPEC infection Intestine of healthy individuals contains UPEC Periurethral contamination with UPEC can occur after a bowel movement or be propelled into the bladder during sexual intercourse For infection, P fimbriae must bind to the P blood group antigen, which is found in 99% of people (D- galactose-D-galactose) Flores-Mireles et al. Nature Reviews Microbiology 13:269–284 (2015) https://doi.org/10.3389/fmicb.2017.01566 Dr Jenny Ritchie September 2023 15  Meningitis-associated E. coli (MNEC) Affects 1 in every 2,000 – 4,000 infants Major cause of CNS infections in infants < 1 month old Primary bloodstream infection with secondary distribution to the central nervous system (CNS) is the mechanistic basis of infection 80% of E. coli strains involved synthesize K-1 capsular antigens K-1 antigen is a major virulence factor (homopolymer of sialic acid) K-1 strains are common in the GI tract of pregnant women and new- borns Dr Jenny Ritchie September 2023 16  Intestinal pathogenic E. coli common cause of gastrointestinal infections (1 in 5 people affected each year in UK) transmitted by infected food and water (or via person-to-person) symptoms vary depending on pathotype: mild watery diarrhoea………………….….typically ETEC dysentery………………………………………...typically EIEC severe bloody diarrhoea…………………..typically EHEC persistent diarrhoea………………………….typically EPEC, EAggEC vomiting, abdominal pain, fever……..…all? haemolytic uraemic syndrome (HUS)…only EHEC Different pathotypes cause very different illnesses Dr Jenny Ritchie September 2023 17  Intestinal pathogenic E. coli ETEC EIEC EAggEC Dysentery, bloody Diarrhoea (persistent) Watery diarrhoea diarrhoea High infectious dose High infectious dose 1010 High infectious dose 106- organisms 106 organisms 1010 organisms Site of damage - small Site of damage – colon; Site of damage – colon; extracellular intestine; extracellular intracellular Toxins: LT and ST Toxins: SPATEs Toxins: none (proteases), enterotoxins Colonisation factor Colonisation factor Colonisation factor e.g. fimbriae e.g. pINV (T3SS) e.g. fimbrial & afimbrial Treatment: adhesins Self-limiting; oral Treatment: rehydration; antibiotics (e.g. Oral rehydration; Antibiotics Treatment: fluoroquinolones) (e.g. azithromycin) Self-limiting; oral rehydration; antibiotics (e.g. rarely) Dr Jenny Ritchie September 2023 18 Intestinal pathogenic E. coli EPEC EHEC/STEC Diarrhoea Bloody diarrhoea, kidney disease High infectious dose 108-1010 organisms Low infectious dose 50-500 organisms Site of damage - colon; extracellular Site of damage - colon; LEE contains genes coding for extracellular type 3 secretion system Toxins: proteases (T3SS) Toxins: Shiga toxin (Stx) Colonisation factor T3SS enables bacterium to e.g. A/E lesion (LEE Colonisation factor export proteins directly into pathogenicity island) e.g. A/E lesion (LEE host cell pathogenicity island) Treatment: EPEC/EHEC export their own Self-limiting, oral Treatment: receptor called Tir, which rehydration; antibiotics None at present interacts with outer (rarely) membrane protein called intimin, to form an A/E lesion Dr Jenny Ritchie September 2023 19 Genus Shigella Genetic features 4 Shigella species (based on serological typing) A: S. dysenteriae – most severe, (ancient) cause of epidemics B: S. flexneri – most frequent, 60% cases in developed world C: S. boydii – confined to Indian sub-continent D: S. sonnei – mildest infection, developed world (main species) Phylogenetic typing (16S rRNA) now shows that Shigella spp. and E. coli are a single species but the clinical community has kept the original designation Dr Jenny Ritchie September 2023 20  Shigella spp. disease impact >190 million cases of shigellosis annually worldwide, causing at least 70,000 deaths Current global epidemiological burden for shigellosis is attributed to S. flexneri and S. sonnei Shigella is able to induce sustained transmissions in close contact communities e.g. Orthodox Jewish communities in UK e.g. Men who have sex with men (MSM community) Treatment: Shigella spp. are becoming increasingly resistant to antibiotics Recommended first-line treatment for shigellosis is fluoroquinolones, such as ciprofloxacin Dr Jenny Ritchie September 2023 21  Shigella transmission and disease Shigella is a human-only pathogen Transmits by faecal-oral route and person-person spread Shigellosis (dysentery) – clinical presentation of Shigella infection aggressive watery or mucoid/bloody diarrhoea, fever and stomach cramps begins 1-2 days after ingestion of organism and in immunocompetent individuals will resolve in 5-7 days; affects mostly children < 5 years Low infectious dose (10-100 organisms) Dr Jenny Ritchie September 2023 22  Shigella pathogenesis Clinical disease reflects Shigella invasion and destruction of the large intestine epithelium Shigella crosses epithelium via M cells and induces uptake by macrophages Shigella kills macrophages & escapes to reach the epithelium’s basolateral surface Back inside the epithelial cell, the bacterium induces lysis of the phagosome in which they are contained, and begins to disseminate intracellularly Dr Jenny Ritchie September 2023 23  Actin tail-based intracellular dissemination of Shigella spp. https://www.youtube.com/watch?v=HAqAWJOP8Ko Dr Jenny Ritchie September 2023 24  Shigella virulence factors Plasmid-borne factors (pINV) Entry region – codes for type 3 secretion system (T3SS), which allows the bacterium to inject proteins directly into the host cell T3SS is pivotal to infection Chromosomal factors SHI-1 – enterotoxins (SigA, Pic, Set1A,1bB SHI-2 – siderophores (IucA-D, IutA) SHI-3 – siderophores (IucA-D, IutA) SHI-O – serotype conversion/O-antigen Stx-phage p27 – shiga toxin Dr Jenny Ritchie September 2023 25  Order: Enterobacterales General morphological and biochemical characteristics emended family Enterobacteriaceae 29 genera including type genus Escherichia Optimum temperature 37 °C Gram-negative, non-spore forming rods Facultative anaerobes Catalase positive Oxidase negative Nitrate reductase positive G+C content 38-60% genome size ~5 Mbp Motile, via peritrichous flagella (a few exceptions) family Yersiniaceae 7 genera including type genus Yersinia Optimum temperature 28-29°C Some lack nitrate reductase G+C content ~47%; genome size 4.6 Mbp Non-motile at 37°C (with all but Y. pestis motile by peritrichous flagella below 30°C) Dr Jenny Ritchie September 2023 26  Genera: Yersinia 17 Yersinia species → 3 species are pathogenic to humans or animals: Y. enterocolitica self-limiting gastroenteritis Y. pseudotuberculosis self-limiting gastroenteritis usually without diarrhoea rare but more likely to become systemic Y. pestis pneumonic and bubonic plague Dr Jenny Ritchie September 2023 27  Y. enterocolitica / pseudotuberculosis: disease and impact ~100 cases/year foodborne infection worldwide, low mortality rate self-limiting acute gastroenteritis and mesenteric lymphadenitis that mimics acute appendicitis symptoms: fever, vomiting, abdominal pain (localised to right hand side), diarrhoea most common in individuals < 7 years old rare systemic or rheumatologically (joint) complications Treatment Usually self-limiting – supportive care only Antibiotics on occasion of sepsis (e.g. fluoroquinolones) Dr Jenny Ritchie September 2023 28  Y. pestis: impact Causative agent of plague Huge impact on society since 6th century 100s of millions have died Historically caused major pandemics e.g. Black Death (1347-1352) originated in Asia and spread to the Crimea, then Europe and Russia a quarter of Europe’s population were killed (25 million) Today WHO reports 1-2,000 cases per year globally (8-10% mortality) Dr Jenny Ritchie September 2023 29  Plague exists as a disease of wild rodents and can be transmitted to humans by fleas enzootic cycle wild rodent (maintenance) reservoir little host mortality epizootic cycle (amplifying hosts) droplet disease aerosol direct transmission inhalation ingestion secondary wounds, bites plague pneumonia primary plague pneumonia bubonic plague Dr Jenny Ritchie September 2023 30  Clinical aspects of plague Bubonic plague Y. pestis transported to regional lymph nodes (LN) but survives and grows in normal unactivated macrophages Massive proliferation in LN causes inflammatory response (bubo) Death 60% Disease may stop Buboes Septicaemic plague (black death) Y. pestis escapes LN and spreads to bloodstream, lysis of bacteria releases LPS, causing septic shock Death virtually 100% Disease progression Pneumonic plague Y. pestis invades lung macrophages, organism is Black death survivor now transmitted in aerosols (highly contagious) Dr Jenny Ritchie September 2023 31 Yersinia use M cells to enter the host but remain extracellular on macrophages Despite different routes of host entry, all pathogenic Yersinia cross the epithelial barrier Yersinia does this via M (microfold) cells -specialised epithelial cells of mucosal-associated lymphoid tissue (MALT) Yersinia quickly traffics to lymph nodes or tissues, and establishes Yersinia spreads systematically by accessing the bloodstream and colonising deep tissue sites, such as liver and spleen Sansonetti (2004) Nature reviews Immunology 4: 953-964 Dr Jenny Ritchie September 2023 Davis (2018) Front. Cell. Infect. Microbiol. 32  Yersinia virulence factors Type 3 secretion system (T3SS) is found in all pathogenic Yersinia Y. pestis has acquired additional plasmid DNA that encodes for factors that enable colonization and transmission via the flea vector and survival in blood but has lost motility and cell adhesive properties to enable colonisation of mammalian host. Dr Jenny Ritchie September 2023 33  References for further reading Octavia and Lan (2014) The Family Enterobacteriaceae. In: The Prokaryotes – gammaproteobacteria, Chapter 13, 226-283. Editors: E. Rosenberg et al. Sprineger-Verlag, Berlin Heidelberg. Croxen et al., (2013) Recent advances in understanding enteric pathogenic Escherichia coli. Clinical Microbiology reviews 26(4)822-880. https://cmr.asm.org/content/cmr/26/4/822.full.pdf Eng et al., (2015) Salmonella: A review on pathogenesis, epidemiology and antibiotic resistance, Frontiers in Life Science, 8:3, 284-293, https://www.tandfonline.com/doi/full/10.1080/21553769.2015.1051243 Davis (2018) All Yersinia are not created equal: phenotypic adaptation to distinct niches within mammalian tissues. Front. Cell. Infect. Microbiol. | https://doi.org/10.3389/fcimb.2018.00261 Demeure et al. (2019)Yersinia pestis and plague: an updated view on evolution, virulence determinants, immune subversion, vaccination, and diagnostics Genes & Immunity volume 20, pages357–370. https://www.nature.com/articles/s41435-019-0065-0 Baker and The (2018) Recent insights into Shigella: a major contributor to the global diarrhoeal disease burden. Curr. Opin. Infect. Dis 31:449-454 doi: 10.1097/QCO.0000000000000475 Mattock and Blocker (2017) How do the virulence factors of Shigella work together to cause disease? Frontiers in Cellular and Infection Microbiology 7 article 64. https://pubmed.ncbi.nlm.nih.gov/28393050/ Dr Jenny Ritchie September 2023 34