Table 4.

Microbiology of ear discharge (ED) or middle ear fluid (MEF).

Author, Year of publication, Year of data,	Country, Population	Study design	Study Question Population - risk group, age	Diagnostic method	Specimen collection and transport method	Culture conditions, PCR included, serotype method	Results
Coleman 2018  2  Data 1972 to 2016  Search to 15/8/17	Australian Aboriginal communities (22) Alaskan (1) Greenlandic (2)	Review [PRISMA] See additional file for search strategy. Quality	Microbiology of OM in Indigenous children < 18 yo	NP at time of OM ED of CSOM MEF if OME	Table 2. Mostly culture. WHO methods not mentioned in review.	Culture Pathogens, some PCR	ED - Less otopathogens cultured cf molecular methods ED (CSOM): Ps.a and Sa MEF (OME): otopathogen < 20% NP: high otopathogen in both AOM & OME (no controls) = = 75%
Van Dyke 2017  3  GSK  Data 2006 to 2011	Including (%PCV7): Chile (2%) Columbia (18%) Mexico (42%) Sth Africa (9%) Thailand (0%) Venezuela (74%)	Pooled analysis of observational studies	Review of AOM Spn serotypes and NTHi. Children < 5yo with AOM	AOM: otoscopy and tympanometry. OME: type B tymp CSOM > 2w or > 6w	Tympanocentesis (AOMwoP) Ear discharge (AOMwiP) Amies <48hr.	Selective agars. Culture ± PCR. Quellung	Countries very similar. MEF or ED: Spn & NTHi ≫ S.pyogenes & Mcat 2006 to 2011: Spn: PCVVT+6A dec NTHi inc relative risk Sth Africa, Spain, Venezuela: NTHi < Spn
Lewnard 2017  4  (2004 to 2016)	Bedouin population survey	Retrospective analysis of clinical and microbiology data	Rates of clinical progression from NP carriage to MEF culture + ve in PCV-vaccinated vs PCV-non-vaccinated	ED MEF if required Chronic and acute cases	See Dagan 2000, Ben-Shimol 2016	Quellung	Progression from NPcarr to ED/MEF < 12 mo old: dec by 92% (Bedouin), 80% (Jewish) > 12 mo old: dec by 32% (Bedouin) 61% (Jewish)
Jervis-Bardy 2017  5  2004 to 2016	Australian Indigenous Remote communities	Review of OME surgeries in hospital and published data on ED microbiology.		ED from cases of AOMwiP CSOM MEF from OME	Mainly WHO methods for culture	Selective and non-selective media. qPCR	Culture: ED (AOMwiP): NTHi 31–57%, & Spn 4–35% ≫ Mcat 0–6%, Sa, Spy Bacterial Load predicts severity PCR: A. otitidis co-infection in OME (10/22 + ve for Aboriginal & non-Aboriginal children). PCR inc detection of NTHi, Spn & Mcat in ED. ED (CSOM): Ps.a 62%. NTHi (greater in << 6yo) MEF (OME in surgery canal sterilised): Ps.a, Sa 3 to 42% culture + ve. (1985, 2003, 2007)
Ilechukwu 2017  6  Data July & Sept 2007	Nigeria Hospital	Consecutive case series	Children 1mo to 17yo. N = 100 Exclusion: foreign bodies, Antibiotics < 2 weeks, OE	Any ED	Otoscopy, canal clean EtOH, swab. No STGG, no −70 °C.	Aerobic culture. Choc agar (candle jar). Cystine-Lactose-Electrolyte deficient (CLED) agar	53% Low SES. ED: 91% culture + ve. Acute ED: Sa 31% Proteus 25% Ps.a 23% Chronic ED: Proteus 39% Sa 28%. No Spn or Hi
Filipe 2017  7  Data 2016	Angola Hospital	Case series. Patient selection methods not specified	Traditional use of bird faeces to prevent ear secretions caused by primary ear infection All ages N = 188	ED related to OM	ED: Clean canal w EtOH. Swab in STGG −70 °C to Sweden	Culture (online techappendix - NA)	ED (CSOM): Alcaligens faecalis co-colonisation in 11%, mostly with Ps.a (50%) Fluoroquinolone R? Recommendation - change to colistin±oral amoxi-clav
Basnet 2017  8  Data May 2015 to Jan 2016	Nepal Hospital ENT.	Prospective case series. Patient selection not specified.	N = 263 pus samples from 240 patients	Pus present - 151 chronic 65 acute pus	Hospital lab using standard protocol. Swab in peptone water.	BA, CA, Mannitol, MacConkey agars.	ED: 216 culture + ve Sa 36%, Ps.a 33%. All sens to Gent. All Ps.s sens to Imipenem. All Sa sens to Amikacin (co-trimox 55%) No Spn nor Hi -(even in acute type OM)
Sonsuwan 2016  9  Data 2008	Thailand Hospital Dept ORL	Prospective = = consecutive AOMwiP cases	Age 3mo – 5yo (mean 24mo) with AOMwiP N = 40	AOMwiP = = fever, pain, non-chronic. Exclusion: antibiotic treatment, tympanostomy tubes, pneumococcal or NTHi vaccine	ED swab	Culture & sensitivity Chocolate, Blood and MacConkey agars	ED: 100% culture + ve 13 organisms Hi 36%, Sa 26%, Spn 9% (no serotypes), Ps.a 11% Hi sensitivity amp 74% co-tri 47% Excluded coag -ve Staph
Shakoor 2016  10  Data 2004 to 2013	Pakistan Hospital laboratory data	Retrospective case series	Pre-Hib (2004 to 2008) versus post-Hib (2009 to 2013) vaccination. Children 0–24mo (n = 179) and 25–58mo (n = 98)	None. Ear pus, aspirate, MEF ear fluid.	Ear pus. Methods not specified.	Standard methods across multiple labs. No Hib test!	ED: 277/352 (79%) children were pathogen + ve. AGE: 0–24mo (n = 179), 134 (75%) monomicrobial, Spn 56% Hi 38% 25–58mo (n = 98), 68 (69%) monomicrobial, Spn 18% Hi 17%. Sa, Ps.a most common in both age groups, esp older. Post-Hib: n = 159. 33% polymicrobial. Sa 38%, Psa. 26%. Spn 27%, Hi 25%, Spy 6%
Ofogbu 2016  11  Abstract only, no date of data collection	SE Nigeria Hospital	Prospective. HIV+ vs age and sex-matched HIV-ve children mean age ~7yo & ~8yo	HIV+ vs HIV-ve micro of CSOM	Chronically discharging ears	ED swabs culture and sensitivity. No detail in abstract	NA	ED: Ps.a most prevalent in HIV + ve Fungal elements more common in HIV-ve
Leach 2016  12  Data Feb 2010 to Aug 2013	Northern Territory Aboriginal and Torres Strait Islander remote communities	Cross sectional comparison of vaccine groups. PHiD-CV10 vs PCV13	Children < 6yo	AOMwiP < 6w & perf < 6w CSOM > 6w & perf >2% Dry Perf Any TMP Otoscopy	WHO methods STGGB −70 °C	Selective and non-selective agar. Quellung	ED swabs collected from 51/511 children in PHiD-CV10 & 11/140 in PCV13 PHiD-CV10:PCV13 NTHi 36%:64% Spn 17%:43% Mc 8%:7% Sa 40%:7% Serotypes in ED: PHiD-CV10 = = 11A, 15A, 16F, 19F, 21, 22A, 35F PCV13 = = 33F, 1, 9N, 35B
Flasche 2016  13  Data 2009	Israel Bedouin. Hospital	Prospective daily first 4 patients in paediatric emergency. < 2yo	Value of NP carriage in < 5yo to monitor serotypes causing OM in < 2yo OM incidence.	acute symptoms (<7 days) necessitating a visit to clinic or hospital and resulting in MEF culture	NP swab in < 5yo MEF in < 2 yo via tympanocentesis. Swabs of MEF into Amies processed within 16hrs	Gent BA. Quellung	NP: in < 5yo - inc non-vaccine types (non-VT replacement). ED: in < 2yo - smaller inc in non-VT OM Suggests non-VT are less virulent than VT. Bedouin and Jewish - same trend. No NTHi reported No individual serotypes reported.
DeAntonio 2016  14  Data 2002 to 2011	Developing and newly industrialised. Assume hospitals	Systematic Review Epidemiology and aetiology.	Children < 6yo	Any OM Studies reporting pathogens causing OM	No details	No details	TABLE 3 ED 2002 Nigeria: AOM n = 53. Spn 9%, Hi 7%, Sa 25% 2001 Ethiopia: CSOM n = 63 Sa 8% 2004 India: CSOM n = 278 Ps.a 10% (<2yo) 2006 Turkey; AOM n = 120 Spn 36–38%, Hi 16–24%
Ben-Shimol 2016  15  Data 2004 to 2015	Israel Bedouin Population based	active surveillance	< 3 yo N = 7475	All OM episodes submitted for MEF.	See Ben-Shimol 2014, Dagan 2000. Amies processed within 12hrs	Non-selective agar for Spn, NTHi, Mc, GAS, culture -ve.	MEF: 64% culture + ve. Spn 30%. NTHi 26%. Spn+NTHi 12%. Other 5% Spn-OM incidence dec in both Bedouin & Jewish children (−22%,−36%) NTHi-OM dec in Bedouins (−17%) OM-other inc (53%) OM-ve dec in Bedouin (−29%)
Madhi 2016  17  Data May 2009 to April 2010	Sth Africa Hospital	Primary Health Care prospective	AOM in HIV ± in 3mo to 5yo, n = 260 episodes in 248 children	AOM symptoms + bulging… or otorrhoea	NPA - Viral PCR MEF - ED or tympanocentesis culture. Amies transport < 16hrs.	Selective agar. Quellung.	ED or MEF: Bacteria 54%. Hi 31%. Spn 20%, Sa 16%, Mc 5%, GAS 1.5%. Spn non-sus 64% 19F 23%>19A 11% = 15B11%. Resp viruses 74% cases. Rhinovirus 38% ± bacteria HIV + ve = = HIV-ve
Aho 2016  18  Data 2005 to 2009	Papua New Guinea Community	RCT of PCV7 in neonatal, infant and control groups.	Birth to 18 months of age Spn infection in ED of 49 episodes of AOMwiP or CSOM (n = 13, 20, 16) in 36 children (all fully vaccinated)	Purulent ear discharge on examination	WHO method in STGGB −70 °C	WHO methods. Selective agar. Semi-Q. Quellung	ED: Spn isolates in ED 46% (6/13), 65% (13/20) and 50% (8/16) in neonatal, infant and control vaccine groups. 27 Spn isolates. VT = 1,1, & 3. Non-VT 6,10,4. 19A in 7/33 PCV7 gps vs 1/16 controls.
Nwokoye 2015  16  Data no date	Nigeria Hospital (13mo)	Prospective case series	212 children 6mo to 10y with OM requiring treatment. 130 AOM (61%) 82 CSOM	AOM acute pain +fluid+opaque+dec mobility. Probably AOMwiP and CSOM current and previous ED	No details	ED aerobic + anaerobic culture. Refer to Nwokoye 2012 (not on Pubmed)	< 1 yo peak incidence of AOM & CSOM. ED: AOM = 55%, CSOM = 45% Aerobes in AOMwiP: Hi (12), Mc (8), Sa (66), Spn (32) GAS (6)
Leach 2015  19  Data 2008 to 2011	Northern Territory Aboriginal and Torres Strait Islander. Remote community.	Cross-sectional survey. ED from AOMwiP or CSOM in PCV7 vs PHiDCV10 era	PCV7: 60 children, 85 perforations. PHiD-CV10: 47 children, 59 perforations.	Otoscopy and tympanometry	WHO method in STGGB	CNA, BVCCA. Filter if swarming Proteus spp. Spn, NTHi, Mcat, Sa	ED: PCV7 : PHiD-CV10 Spn 25% : 18% NTHi 61% : 34% (p = 0.008) Serotypes in ED 12 serotypes in the PCV7 group: 10A (n = 4), 7F (n = 2), 11C (n = 2) and one each of 10F, 12F, 16F, 17F, 19A, 19F, 23F, 6A and 6C. The hierarchy of 7 serotypes in the PHiD-CV10 group: 11A(n = 2) and one each of 15A, 16F, 19F, 21, 22A and 35F.
Jervis-Bardy 2015  20  May-June 2014	Australian Aboriginal Alice Springs General Hospital ENT	Baseline for OME RCT	Mean age 5.4 yrs	Bilateral OME + HL + type B tympanogram. NP, MEF, Adenoid N = 11	WHO method in STGGB −80 °C	16S rRNA No culture	3 sites. N = 8 with sufficient bacterial biomass for microbiome analysis. Si variation in microbial diversity by site. Common to all sites: Mc, Hi, Sp. MEF: less diversity Ao & HI. Ao not in NP or adenoid.
Ding 2015  21  Jan 2011 to Dec 2013	China, Suzhou Hospital	Prospective cases	All children < 18yrs with AOMwiP N = 229. CSOM excluded	AOM confirmed by Otolaryngologist	MEF culture. Immediate plating.	Gentamicin BA, CA only	ED or MEF: 159(69%) + ve for bact pathogens. Spn 47%, Sa 19%, Hi 7% 19F>19A predominant = = 80%
Chirwa 2015  22  July-Sept 2013	Malawi Hospital (ENT)	Cross sectional descriptive CSOM random sampling	Mean age 18 yrs. 2 to 64 yo. N = 104	CSOM > 2w mostly purulent, scant in 53%	ED. Transported in anaerobic jar	Aerobic - BA, MacConkey, CA. no details for Spn, NTHi or Mc Anaerobic	ED: P. mirabilis 29%, Sa 20%, Ec 8% Anaerobes 35%