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2.2 Microbiology > Denise - Enterobacterales > Flashcards

Denise - Enterobacterales Flashcards

1
Q

Write about the enterobacterales species

A

Gram negative bacilli
Facultatively anaerobic
Ferment glucose
Reduce nitrate to nitirite
Oxidase negative
Weak catalase positive
Most motile
Some capsulated

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2
Q

List the eight enterobacterales

A

Lactose fermenters:
Escherichia
Citrobacter
Enterobacter
Klebsiella

Non lactose fermenters
Shigella
Proteus
Salmonella
Yersenia

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3
Q

Write about the four factors of enterobacter pathogenesis

A

Enteropathogens in the GIT

Uropathogens in the UTI

Opportunistice infections

HCAIs

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4
Q

Give some examples of opportunistic infections caused by enterobactet

A

Central nervous system infection (Escherichia)

Lower respiratory tract infection

Blood stream infection

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5
Q

What enterobacters can cause a lower respiratory tract infection

A

Klebsiella
Enterobacter
Escherichia

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6
Q

What enterobacters can cause bloodstream infections

A

Escherichia
Klebsiella
Enterobacter

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7
Q

What enterobacters can infect the GIT

A

Salmonella
Shigella
Escherichia
Yersinia

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8
Q

What HCAIs are caused by enterobacter

A

Blood stream infections
Catheter associated UTIs
Ventilator associated pneumonia
Antimicrobial resistance

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9
Q

What infections does Escherichia, Salmonella and Yersinia cause

A

infection within the GT and outside the GIT

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10
Q

What infections does Shigella cause

A

Primarily gastrointestinal

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11
Q

What infections does Klebsiella, Enteobacter and Citrobacter cause

A

Primarily extraintesitinal

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12
Q

what are sources of enterobacterales
(3)

A

Faeces from humans/animals containing pathogens/toxins

This is then ingested through food or liquid (milk or water) or on your fingers

Ingestion of organism and/or toxins

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13
Q

what happens upon ingestion of organisms and/or toxins

A

Organisms multiply and toxins produced but infection remains localised -> diarrhoea -> pathogen in faeces

Organisms invade or toxins are absorbed -> dissemination -> symptoms of systemic infection fever

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14
Q

How are faecal specimens processed in the lab

A

Evaluate specimens macroscopically based on appearance

Direct molecular detection is carried out - if positive then further testing is carried out

Enrichment broths and sub culturing onto selective plates

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15
Q

What investigation must be done for cryptosporidium/giardia faecal specimens

A

Smear microscopy

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16
Q

What treatment shous clostridium diff/perfringens and B. cereus feaces undergo?

A

Pretreatment
Alcohol shock
Toxin detection

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17
Q

Explain the conventional micro process of laboratory investigation of faeces

A

Faeces -> broth for 24 hours -> selective agar for 24 hours -> biochemical ID -> serotyping

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18
Q

Explain the contemporary micro process of laboratory investigation of faeces

A

Direct detection via Real Time PCR or EntericBio

Same day detection of target gene

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19
Q

Write about E. Coli

A

Common constituent of mammalian digestive tracts
Predominant facultative anaerobe
Essential for our well being:
- improves digesiton
- produces essential vitamins
- competitive exclusion

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20
Q

Write about the diversity of E. Coli: Seroty[es

A

Tradition classification made on the basis of presence of three antigens O, K and H antigens

A combination of O and H antigens have been identified and used to serotype E. Coli

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21
Q

Give some examples of E. Coli serotypes

A

O157:H7
O104:H4
O26
O103
O111

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22
Q

How does E. Coli acquire virulence genes

A

Horizontal gene transfer

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23
Q

What are the three steps of horizontal gene transfer

A

Transfer of virulence genes via plasmids
- Conjugation
- Transduction
- Transformation

Or transfer of virulence genes via bacteriophages

Change of vell to virulence

Virulence genes bringing about:
- adherence
- enterotoxins
- invasiveness
- cytotoxicity

Due to intestinal disease

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24
Q

Describe intestinal pathogenic E. Coli, what are the different strains causing intestinal infection
(6)

A

Enterotocigenic (ETEC)
Enteropathogenic (EPEC)
Enteroaggregative (EAEC)
Enteroinvasive (EIEC)/Shigella
Diffuse adhering (DAEC)
Shiga toxin producin (STEC) and other enterohemorrhagic (EHEC)

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25
What strain of E. Coli causes extraintestinal infection
ExPEC - uropathogenic - strains associated with neonatal meningitis
26
What infections does enterotoxigenic (ETEC) cause
Watery diarrheae
27
What infections does enteropathogenic (EPEC) cause
Watery diarrhear of lung duration Mostly in infants, often in developing countries
28
What infections does Enterohaemorrhagic E. Coli cause
EHEC
29
What infections does Enterohaemorrhagic E. Coli (EHEC) cause
Bloody diarrhea Haemorrhagic colitis and haemolytic uremic syndrome (HUS)
30
What does infection enteronvasive (EIEC) cause
Blood diarrhea
31
What infection does enteroadherant E. Coli (EAEC) cause
Persistent watery diarrhea in children and patients infected with HIV
32
Write about enteropathogenic E. Coli
Induces the formation of pedestals on the host cell surface Causes infantile diarrhoea mostly in the tropics Caused by poor hygiene
33
Explain the pathogenesis of Enteropathogenic E. Coli
Induces the formation of pedestals on the host cell surface Causes infantile diarrhoea mostly in the tropics Caused by poor hygiene Non invasive Does not produce toxins Adherence to intestinal mucosa Small intestine effacement Plasma encoded protein
34
What does enteropathogenic E. Coli secrete
Intimin and TIR
35
What does secretion of intimin and TIR by EPEC do
Destroys microvilli Loss of absorbtive surface Leads to diarrhoeae
36
Write about EnteroInvasive E. Coli (EIEC)
Inflammatory dysentry Bloody diarrhoea Large intestine Intracellular pathogen fever
37
Explain the pathogenesis of EIECs
Invades the basolateral surface - invasion plasmid antigen - Ipa gene Lateral spread Food, water and person-to- person transmission
38
Write about enterotoxigenic E. Coli
Non inflammatory Diarrhoae in children in developing countries Travellers Diarrhoea
39
Write about the pathogenicity of ETEC
Colonisation factor antigen LT heat-labile toxin activates adenylate cyclase-increases production of cAMP ST heat-stable toxin activates guanylate cyclase- increased production of cGMP Increased fluid secretion = diarrhoae
40
Write about EHEC
E. Coli 0157 Shiga toxin production Hemolysin LEE Mobile genetic elemets: - phages - genomic islands - plasmid
41
What infections does E. Coli 0157:H7 cause
Intestinal - asymptomatic - watery diarrhoea - haemorrhagic colitis Systemic - haemlytic uremic syndrom HUS Causes: - Thrombotic thrombocytopenic purpura (TTP) - kidney failure - haemolytic anaemia
42
What does infection of 0157:H7 cause
- Thrombotic thrombocytopenic purpura (TTP) - kidney failure - haemolytic anaemia
43
What is E. Coli 0157 called
EHEC STEC VTEC
44
Write about the epedemiology of STEC/VTEC infections
Ireland had the highest annual incidence of VTEC between 2009 and 2018 with the exception of 2011
45
Write about the day 1 investigation of E. Coli
Clinical sample = faeces Direct detection of shiga toxin genes by entericBio real time PCR Selective culture on day 1 is positive
46
What selective media should E. Coli be put up on
MacConkey for all E. Coli STEC - STEC chromagar - CTSMAC (Cefixime Tellurite sorbitol MacConkey)
47
Explain the use of Enteric Bio real time PCR for detection of VTEC/EHEC
Real-time detection of pathogens directly from faeces Without pre-enrichment DNA DNA extraction amplification and detection Rapid result 3 hours Day 1
48
Write about Enteric Bio Panels for Bacteria, what can we test for
Shiga toxin (1) Shiga toxin 2 Salmonella/Shigella/Campylobacter Yersinia Vibrio Clostridium difficile
49
What parasites can we detect with enteric bio
Cryptosporidium/Giardia Entamoeba
50
What viruses can be detected with Enteric Bio
Norovirus, Rotavirus, Adenovirus
51
Where is the reference lab for VTEC/EHEC
Cherry Orchard
52
Write about VTEC isolation on CT SMAC agar
Sorbitol fermenters = pink e.g. non 0157H7 Non sorbitol fermenter = colourless e.g. O157H7
53
Write about STEC Chromagar
Detects most common Shiga-toxin E. Coli serotypes -> mauve colonies Other enterobacterales are coulerless, blue or inhibited
54
Write about the day 2 investigation of E. Coli
GNBs Oxidase negative Weak catalase positive Biochemical screen: IMVic Test
55
What is meant by the IMVic test
I: indole M: methyl red V: Voges-Proskauer iC: citrate
56
What are the biochemical IMVic results for E. Coli
I: produces indole M: methyl red positive V: negative iC: negative
57
Write about the indole test
 decompose the amino acid tryptophan to indole  accumulates in the medium  Inoculate a peptone water  Incubate 24 hrs @ 37  When indole is combined with Kovac’s Reagent  yellow to cherry red  an oily layer at the top of the broth.
58
Write about the methyl red test
 Methyl Red Test  detection of end products from the metabolism of glucose.  Inoculate a buffered glucose  the fermentation of glucose.  MR Positive: When the culture medium turns red after addition of methyl red  pH at or below 4.4
59
Write about Voges-Proskauer test
 Voges-Proskauer Test  detection of end products from the metabolism of glucose.  produce acetoin as the chief end product of glucose metabolism  Heavy inoculum  Add 40% KoH and alpha Napthol  Shake vigorously  Colour development within 15 mins  Voges-Proskauer negative
60
Write about Simmons Citrate
 Simmons Citrate Test  use citrate as sole carbon source Growth usually results in the bromothymol blue indicator, turning from green to blue. The alkaline carbonates and bicarbonates produced as by-products of citrate catabolism raise the pH of the medium to above 7.6
61
Write about all of the biochemical test results for E. Coli
 produces indole  methyl red positive  Voges-Proskauer negative  cannot use citrate as sole carbon source  Lactose Fermenter  produces lysine decarboxylase  ferments sorbitol except E. coli O157 H7  produce β-glucuronidase except E. coli O157 H7
62
What two methods of automated identification can be used for E. Coli
Vitek MaldiTOF
63
Write about use of Vitek for E. Coli
ID and sensitivity ID 64 individual substrate tests Colourmetric
64
Write about use of MaldiTOF for E. COli
Cannot differentiate between E. Coli and Shigella 93% of their genes are common
65
What are the four species of shigella studied
Shigella dysenteriae - serogroup A Shigella flexneri - serogroup B Shigella boydii - serogroup C Shigella sonnei - serogroup D
66
Which is the most serious shigella species
Shigella flexneri Shigella boydii Shigella sonnei is the most severe
67
Write about shigella species
Reservoir is humans Food = chicken, tuna and potato salad Spread via faecal-oral route through food, faeces, fingers, flies and fomites Fragile in human faeces Incubation time of 24-50 hours
68
What are the symptoms of shigella
Diarrhoeae Abdominal pain Fever Might become invasive
69
Write about shigella infection
Toxin mediated infection Shiga toxin (AB toxin) Bloody diarrhoea Infective does < 200 cells
70
Write about shigella epidemiology
8 shigellosis outbreaks in 2018 Large outbreak of shigellosis in 2017 in HSE
71
Write about the day 1 laboratory investigation of shigella
Faeces sample Direct Detection Selective culture
72
How is direct detection of shigella carried out
Real Time PCR EntericBio BD Max Syndromic Testing BioFire GI panel Shigella Ipa gene DNA detected on Day 1
73
What selective culture is used for shigella
XLD DCA
74
What is the day 2,3 investigation of shigella
Day 2 = reading XLD and DCA agar Day 3 = biochemical ID, serotyping
75
Write about deoxycholate citrate agar
Selective factors include sodium deoxycholate and sodium citrate Differential factors are lactose and sodium ferric chloride Lactose fermenters = commensals = pink Shigella = NLF = pale Salmonella = NLF = pale with H2S positive black centre
76
Write about XLD media
Selective factor is sodium deoxycholate Differential factors are Xylose, lysine, H2S Lactose fermenters = commensals = yellow Shigella = xylose lysine = red Salmonella = red with black centre
77
Write about shigella on chrom GTI
Teal coloured colonies Non-H2S producing salmonellas will look the same
78
What are the basic characteristics of Shigella
GNBs Oxidase negative Weak catalase positive Non motile Late lactose fermenter
79
Write about biochemical results for shigella
Indole negative Methyl red positive Vogues negative Citrate negative urease negative Lysine decarboxylase negative
80
Where is the shigella reference lab
University Hospital Galway Salmonella and Shigella Listeria Reference Lab
81
What are the main reservoirs for salmonella
Foodborne - eggs Zoonotic - lizards Human - typhoid mary
82
What are the main species of salmonella studies
S. Typhimurium S. Enteritidis S. Typhi S. Paratyphi S. cholerae suis
83
What infection does S. cholerae suis cause
Septicaemia
84
What infection does S. enteriditis and S. typhimurium cause
Gastroenteritis
85
What infection does S, paratyphi and S, typhi cause
Parathyphoid fever or thyphoid fever Leads to enteric fever
86
What are the virulence factors of Salmonella
Peptidoglycan Fimbrae/Pilli Salmonella Pathogenicity islands Type 3 secretion system Flagellin Vi antigen of S, typhi
87
What is special about S. typhi
Vi antigen
88
How does S. enteritidis and S, typhimurium cause gastroenteritis
Invasion of M cell of intestine Passes into tissue Uptake by Neutrophils, dendritic cells and macrophages Limited dissemination i.e. they can't spread out of intestine
89
How does S. typhi and S. paratyphi cause typhoid fever
Invasion through M cells Macrophage uptake Intramacrophage replication System dissemination i.e. spread to other organs such as the gallbladder
90
How does S. typhi cause enteric fever
Uptake through small intestine Spread to other organs such as gallbladder and lymph nodes Gallbladder infection leads to cholecystitis and a carrier states Infection of small intestine caused inflammation and ulceration of intestinal which causes diarrheae and hemorrhage or performation
91
Explain what happens when S. typhi infects the lymphatic system (5)
S, typhi passes from small intestine into lymph Travels to lymph nodes Enters circulation via thoracic duct (bacteremia) + fever + malasie Infection of liver, spleen ,kidney, bone marrow etc (secondary bacteremia) Causes fever, slow pulse, enlarged liver and spleen ,rose spots and low WBC count
92
Write about Salmonella epidemiology
11 cases of S, Typhi many associated with travel 5 cases of S, paratyphi associated with India
93
Write about day 1 investigation of salmonella
Direct detection of Salmonella Inv gene Selective enrichment on selenite broth
94
How is direct detection of salmonella carried out
Real Time PCR EntericBio Syndromic testing BioFire GI panel Inv gene DNA detected
95
What selective agar is used for Salmonella
Selenite broth
96
What is the day 3 investigation for salmonella
XLS DCA Chromagar
97
What is the day 4 investigation of salmonella
Biochemical ID Serotyping
98
Write about samples for Salmonella
Cat 3 facilities required Enteric fever: - blood culture - faeces - urine - bone marrow aspirate Gastroenteritis - faeces
99
Write about selenite broth for Salmonella
Selenite broth Enhances culture yield by reducing growth of faecal coliforms and faecal streptococci. Take sub-cultures of broth from the upper third of the broth column should be at least 5 cm in depth. Better for enrichment of Salmonella Typhi 37 not exceeding 18 hours
100
Write about XLD agar for Salmonella
 Lactose Fermenters Commensals yellow  Shigella xylose Lysiene red  Salmonella red with black centres
101
Write about DCA agar for Salmonella
 Lactose Fermenters Commensals pink  Non-lactose fermenters are colourless pale  Shigella NLF pale  Salmonella NLF pale  Many Salmonella spp H2 S pos
102
Write about Bismith Sulphite agar for Samonella
 S Typhi and Paratyphi  BS and Brilliant Green Selective
103
Write about Salmonella on Chromagar
Teal coloured colonies with black centres
104
What are the basic characterisations for Salmonella
Motile Non Lactose Fermenter Oxidase Negative Weak Catalase Positive GNB
105
Write about the biochemical results for Salmonella
 I : negative  M: positive  V: negative  iC: positive  urease negative  lysine decarboxylase positive
106
What are the components of the lysine decarboxylase test
Glucose Lysine Bromocresol Purple
107
Write about the Kauffman-White Classification of Salmonella
 Differentiates isolates based on surface antigens  First "O" antigen type is determined- associated with LPS of outer membrane  Then the "H" antigen is determined- associated with flagella  Salmonella exist in two phases; a motile (specific) phase and a non-motile (nonspecific phase  Different "H" antigens are produced depending on the phase in which the salmonella is found
108
What are the three main Salmonella antigens
O-somatic cell wall antigens H-flagellar antigens Vi-antigens (enteric fever strains)
109
What do we do with a confirmed salmonella case
Whole genome sequencing Antimicrobial resistance
110
Write about whole genome sequencing for salmonella
Done for: - serology - antimicrobial susceptibility - epidemiological typing - outbreak investigation
111
Write about the antimicrobial resistance in Salmonella
 21% MDR  3 or more antimicrobials  1/3 profile of resistance to ampicillin, sulphonamide and tetracycline (ASuT) were mainly monophasic S. Typhimurium  1 ESBL  S.Brandenburg
112
What are the three most important yersinia species
Yersinia pestis Yersinia enterocolitica (foodborne) Yersinia pseudotuberculosis
113
Write about yersinia pestis infection
Plague - caused by yersinia pestis Bubonic plague
114
Write about bubonic plague
Swollen and painfil axillary (arm pit) and inguinal (groin) lymph nodes (buboes) Transmitted from mammalian reservoirs by flea bites or contact with contaminated animal tissues If infection spread to lung from lymph it caused pneumonic plague Person-to person spread
115
Write about yersinia enterocolitica infection
Enterocolitis Causes enterocolitis with diarrhoeae fever abdominal pain Invasion of the ileum Necrosis of the Peyers Patches Inflammation of the mesenteric lymph nodes 1/4 of children develop blood diarrhoea Appendicitis type syndrome in children BSI in elderly 6 cases in 2018
116
Write about yersinia spread
Reservoir: animals, rats, pets, soil, lakes Food: milk, PORK, poultyr, shellfish, vegetables Psychotrophic growth at 4 degrees Cold chain food products hazards Enteric zoonosis Incubation time 24-36 hours
117
What are symptoms of Enteric zoonosis
Diarrhoea Vomiting Fever Headache Pseudoappendicitis
118
Write about day 1 yersinia investigation
Direct detection via: - rela time PCR - BD max - Syndromic testing - BioFire GI panel Yersenia gene DNA detected Selective culture on CIN agar
119
What are the basic characteristics of yersinia
GNBs Oxidase negative Weak catalase positive Motile at 25 not 37 Non lactose fermenter
120
What is CIN agar
Selective for yersinia Cefsulodin, irgasan, novobiocin agar
121
What are the biochemical results for Yersinia
Indole positive Methyl red negative Vogues positive Citrate negative Urease positive Lysine negative Ornithine decarboxylase positive
122
What three things caus urinary tract infections
UroPathogens Escherichia Proteus
123
Give an example of a urpathogen
E. Coli UPEC
124
Write about EPEC
80% of UTIs Endogenous infection
125
How can EPEC cause an infection
Contamination of urethral with EPEC from gut Colonisation of urethra with migration towards bladder Colonisation and invasion of bladder mediated by pili and adhesion Inflammatory response in bladder and fibrinogen accumulation in the catheter Neutrophil infiltration Bacterial multiplication and immune system subverison Biofilm formation Epithelial damage by bacterial toxins and proteases Ascension to the kidneys Colonisation of the kidneys Host tissue damage by bacterial toxins Bacteraemia
126
Write about Chromagar
E. coli - dark pink to red Enterococcus - turquoise blue Klebsiella, Enterobacter, Citrobacter - metallic blue Proteus - brown hali Pseudomonas - cream/translucent S. aureus -> golden/opaque S. saprophyticus -> pink small
127
Write about UPEC biochemical tests
Indole positive Methyl red positive Vogees negative Citrate negative urease negative Lysine dacarb positive Dulcitol positive Lactose positive
128
Write about proteus
Second most common cause of UTI Proteus mirabilis Sample = mid stream urine
129
Write about isolation of proteus
Not fastidious Highly motile-form 'swarm' No swarm on macConkey (NLF) Chromogenic UTI medium brown
130
Write about the biochemical results for proteus mirabilis
Indole negative MR positive VP negative Citrate positive Urease positive Lysine decarboxylase - Dulcitol - Lactose - Phenylalanine postiive
131
Write about extra intestinal E. Coli
Neonatal meningitis - 30% caused by E. Coli not HCAI Bloodsteam infection - progression from UTI
132
What are the two main enterobacters involved in HCAI
Klebsiella pneumonia Enterobacter species
133
How do you remember the HCAIs
ESKAPE Enterococcus faecium S. aureus K. pneumoniae Acinetobacter baumannii P. aeruginosa Enterobacter species
134
What are the four main HCAIs
Central line associated blood stream infections Catheter associated UTI Ventilator associated pneumonia Antimicrobial resistance
135
Write about Klebsiella species
Commensal but frequently an opportunistic pathogen causing BSI, HCAI UTI, VAP pneumoniae Specimens: blood, urine, sputum Screen for carriage -> rectal swabs and faeces
136
Write about Klebsiella antimicrobial resistance
Carbapenemase producing enterobacterales CPE
137
What are the basic characteristics of Klebsiella
Not fastidious Mucoid colonies Basic characterisation (GNBs Ox negative weak cat positive)
138
Write about the Klebsiella Biochemical tests
Indole negative MR negative VP positive Citrate postiive Urease V positive (K. pneumo) Lysine decarboxylase + Dulcitol +
139
Write about enterobacter species
 Opportunistic Infections  Health Care Acquired Infection  Antimicrobial Treatment  Catheters  Invasive Procedures  Burns/ wounds  Pneumonia  UT
140
Write about Enterobacter ID
LF on MacConkey Non fastidious GNB Oxidase negative Weak catalase postiive API or Vitek can be used
141
What are the biochemical results for enterobacter
Indole negative MR negative VP positive Citrate postiive Urease negative Lysine decarboxylase negative Dulcitol negative
142
Write about citrobacter species
 Inhabitant of soil and water and found in GIT  Citrobacter freundii- main pathogen  Healthcare-associated infection, UTI, bacteraemia
143
What are the biochemical results for citrobacter species
I : produces indole -  M: methyl red positive +  V: Voges-Proskauer negative -  iC: cannot use citrate as sole carbon source +  Urease -  Lysine Decarboxylase -  Dulcitol –  Lactose + LF
144
Look at slide 100 to learn biochemical tests
Look at slide 100 to learn biochemical tests

2.2 Microbiology (60 decks)

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