Haemophilus influenzae Carriage among Healthy Children in Portugal, 2015–2019
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Study Design
2.3. Questionnaires
2.4. Sample Collection
2.5. Isolation of Putative Haemophilus influenzae
2.6. Preparation of DNA Templates for Serotyping
2.7. Serotyping
2.8. β-Lactamase Production and Minimum Inhibitory Concentration (MIC) Determination
2.9. DNA Extraction and Whole Genome Sequencing (WGS)
2.10. Whole Genome Sequencing Analysis
2.11. Accession Numbers
2.12. Statistical Analysis
3. Results
3.1. Population Characteristics
3.2. Colonization Rates and Capsular Type
3.3. β-Lactamase Production and Antimicrobial Susceptibility Testing
3.4. Whole Genome Sequencing (WGS)
3.5. Multilocus Sequence Typing (MLST)
3.6. Genetic Determinants of Antimicrobial Resistance
3.7. Virulence Associated Genes
3.8. Characterization of Cap Loci in H. influenzae and H. parainfluenzae
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Total | Year, n (%) | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Characteristic | 2015 | 2016 | 2018 | 2019 | ||||||
Participants | 1524 | 315 | 318 | 427 | 464 | |||||
Age group (months) a | ||||||||||
0–12 | 122 | (8.0) | 21 | (6.7) | 30 | (9.6) | 28 | (6.6) | 43 | (9.4) |
13–24 | 252 | (16.6) | 47 | (14.9) | 49 | (15.6) | 86 | (20.2) | 70 | (15.2) |
25–36 | 287 | (19.0) | 55 | (17.5) | 59 | (18.8) | 80 | (18.8) | 93 | (20.2) |
37–48 | 362 | (23.9) | 88 | (27.9) | 64 | (20.4) | 98 | (23.1) | 112 | (24.3) |
49–60 | 272 | (18.0) | 60 | (19.0) | 69 | (29) | 67 | (15.8) | 76 | (16.5) |
≥61 | 219 | (14.5) | 44 | (14.0) | 43 | (13.7) | 66 | (15.5) | 66 | (14.4) |
Gender | ||||||||||
Male | 817 | (53.6) | 163 | (51.8) | 171 | (53.8) | 234 | (54.8) | 249 | (53.7) |
Antimicrobial use | ||||||||||
At sampling b | 63 | (4.3) | 14 | (4.5) | 11 | (3.7) | 21 | (5.0) | 17 | (3.8) |
In previous month c | 246 | (17.6) | 45 | (15.6) | 48 | (17.8) | 73 | (18.1) | 80 | (18.5) |
In previous six months d | 503 | (36.1) | 94 | (33.0) | 90 | (31.4) | 167 | (42.8) | 152 | (35.3) |
H. influenzae Carriage | Total | Year, % (n/Total) | |||
---|---|---|---|---|---|
2015 | 2016 | 2018 | 2019 | ||
Global | 84.1 (1282/1524) | 88.6 (279/315) | 75.2 (239/318) | 90.6 (387/427) | 81.3 (377/464) |
by age group (months) a | |||||
0–12 | 83.6 (102/122) | 81.0 (17/21) | 73.3 (22/30) | 92.9 (26/28) | 86.0 (37/43) |
13–24 | 92.1 (232/252) | 91.5 (43/47) | 89.8 (44/49) | 95.3 (82/86) | 90.0 (63/70) |
25–36 | 86.4 (248/287) | 92.7 (51/59) | 81.4 (48/59) | 91.3 (73/80) | 81.7 (76/93) |
37–48 | 84.3 (305/362) | 92.0 (81/88) | 73.4 (47/64) | 89.8 (88/98) | 79.5 (89/112) |
49–60 | 82.4 (224/272) | 86.7 (52/60) | 76.8 (53/69) | 86.6 (58/67) | 80.3 (61/76) |
≥61 | 75.3 (165/219) | 79.5 (35/44) | 51.2 (22/43) | 90.9 (60/66) | 72.7 (48/66) |
by serotype | |||||
serotype a | 0.3 (4/1282) | 0.0 (0/279) | 0.0 (0/239) | 0.3 (1/387) | 0.8 (3/377) |
serotype b | 0.1(1/1282) | 0.0 (0/279) | 0.0 (0/239) | 0.0 (0/387) | 0.3 (1/377) |
serotype e | 1.1(14/1282) | 0.0 (0/279) | 2.9 (7/239) | 1.8 (7/387) | 0.0 (0/377) |
serotype f | 1.8 (23/1282) | 0.7 (2/279) | 5.9 (14/239) | 0.8 (3/387) | 1.0 (4/377) |
nonencapsulated | 96.7 (1240/1282) | 99.3 (277/279) | 91.2 (218/239) | 97.1 (376/387) | 97.9 (369/377) |
Antimicrobial Agent | β-Lactamase Producers (n = 96) a | Capsulated (n = 42) a | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
S (%) | I (%) | R (%) | S (%) | I (%) | R (%) | |||||||
Ampicillin | 0 | (0.0) | 0 | (0.0) | 96 | (100.0) | 37 | (88.1) | 0 | (0.0) | 5 | (11.9) |
Amoxicillin-clavulanic acid | 95 | (99.0) | 0 | (0.0) | 1 | (1.0) | 42 | (100.0) | 0 | (0.0) | 0 | (0.0) |
Cefepime | 93 | (96.9) | 0 | (0.0) | 3 | (3.1) | 41 | (97.6) | 0 | (0.0) | 1 | (2.4) |
Cefotaxime | 96 | (100.0) | 0 | (0.0) | 0 | (0.0) | 42 | (100.0) | 0 | (0.0) | 0 | (0.0) |
Cefuroxime | 0 | (0.0) | 87 | (90.6) | 9 | (9.4) | 0 | (0.0) | 40 | (95.2) | 2 | (4.8) |
Ciprofloxacin | 95 | (99.0) | 0 | (0.0) | 1 | (1.0) | 42 | (100.0) | 0 | (0.0) | 0 | (0.0) |
Chloramphenicol | 93 | (96.9) | 0 | (0.0) | 3 | (3.1) | 42 | (100.0) | 0 | (0.0) | 0 | (0.0) |
Meropenem | 96 | (100.0) | 0 | (0.0) | 0 | (0.0) | 42 | (100.0) | 0 | (0.0) | 0 | (0.0) |
Tetracycline | 94 | (97.9) | 0 | (0.0) | 2 | (2.1) | 42 | (100.0) | 0 | (0.0) | 0 | (0.0) |
Trimethoprim-sulfamethoxazole | 63 | (65.6) | 0 | (0.0) | 33 | (34.4) | 40 | (95.2) | 0 | (0.0) | 2 | (4.8) |
Rifampicin | 96 | (100.0) | 0 | (0.0) | 0 | (0.0) | 42 | (100.0) | 0 | (0.0) | 0 | (0.0) |
Strain Reference | Sampling Year | Genome Size (Mbp) | Genome Coverage | Number of Contigs | Serotype | Multilocus Sequence Typing | Phenotype Resistance Pattern | Antimicrobial Resistance Determinants | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
adk | atpG | frdB | fucK | mdh | pgi | recA | ST | Resistance Genotype | bla Gene | ftsI Allele | PBP3 Mutations a | folA Mutations a | folP Mutations a | |||||||
PT12096 | 2019 | 1.76 | 352 | 32 | a | 13 | 16 | 5 | 2 | 3 | 11 | 7 | 23 | - | - | nd | 46 | - | ||
PT12098 | 2019 | 1.76 | 323 | 30 | a | 13 | 16 | 5 | 2 | 3 | 11 | 7 | 23 | - | - | nd | 46 | - | ||
PT12114 | 2019 | 1.76 | 292 | 33 | a | 13 | 16 | 5 | 2 | 3 | 11 | 7 | 23 | - | - | nd | 46 | - | ||
PT11402 | 2018 | 1.76 | 27 | 46 | a | 13 | 16 | 5 | 2 | 3 | 11 | 7 | 23 | - | - | nd | 46 | - | ||
PT11856 | 2019 | 1.87 | 217 | 46 | b | 10 | 14 | 4 | 5 | 4 | 7 | 8 | 6 | - | - | nd | 10 | - | ||
PT10981 | 2016 | 1.85 | 243 | 33 | e | 18 | 6 | 3 | 7 | 10 | 28 | 12 | 18 | Amp, Cfx(I),SXT, BLP | BLP | bla TEM-1 | 55 | D350N | F154S | P64E |
PT10993 | 2016 | 1.84 | 287 | 37 | e | 18 | 6 | 3 | 7 | 10 | 28 | 12 | 18 | - | - | nd | 55 | D350N | ||
PT10998 | 2016 | 1.84 | 291 | 37 | e | 18 | 6 | 3 | 7 | 10 | 28 | 12 | 18 | - | - | nd | 55 | D350N | ||
PT11000 | 2016 | 1.84 | 307 | 31 | e | 18 | 6 | 3 | 18 | 10 | 28 | 12 | 122 | Cfx (I) | BLNAR IIb | nd | 2 | D350N M377I A502V N526K | ||
PT11005 | 2016 | 1.84 | 308 | 29 | e | 18 | 6 | 3 | 18 | 10 | 28 | 12 | 122 | Cfx | BLNAR IIb | nd | 2 | D350N M377I A502V N526K | ||
PT11022 | 2016 | 1.84 | 101 | 36 | e | 18 | 6 | 3 | 7 | 10 | 28 | 12 | 18 | Amp, Cfx(I),SXT, BLP | BLP | bla TEM-1 | 55 | D350N | F154S | P64E |
PT11039 | 2016 | 1.84 | 190 | 33 | e | 18 | 6 | 3 | 18 | 10 | 28 | 12 | 122 | Cfx | BLNAR IIb | nd | 2 | D350N M377I A502V N526K | ||
PT11370 | 2018 | 1.90 | 52 | 41 | e | 18 | 6 | 3 | 18 | 10 | 28 | 12 | 122 | Amp, Cfx(I), BLP | BLPACR | bla TEM-82 | 2 | D350N M377I A502V N526K | ||
PT11380 | 2018 | 1.84 | 43 | 32 | e | 18 | 6 | 3 | 7 | 10 | 28 | 12 | 18 | - | - | nd | 55 | D350N | ||
PT11407 | 2018 | 1.84 | 27 | 40 | e | 18 | 6 | 3 | 7 | 10 | 28 | 12 | 18 | - | - | nd | 55 | D350N | ||
PT11426 | 2018 | 1.84 | 32 | 31 | e | 18 | 6 | 3 | 7 | 10 | 28 | 12 | 18 | - | - | nd | 55 | D350N | ||
PT11437 | 2018 | 1.84 | 35 | 35 | e | 18 | 6 | 3 | 18 | 10 | 28 | 12 | 122 | Cfx (I) | BLNAR IIb | nd | 2 | D350N M377I A502V N526K | ||
PT11452 | 2018 | 1.84 | 25 | 43 | e | 18 | 6 | 3 | 18 | 10 | 28 | 12 | 122 | Cfx (I) | BLNAR IIb | nd | 2 | D350N M377I A502V N526K | ||
PT11544 | 2018 | 1.84 | 33 | 39 | e | 18 | 6 | 3 | 18 | 10 | 28 | 12 | 122 | Cfx (I) | BLNAR IIb | nd | 2 | D350N M377I A502V N526K | ||
PT10674 | 2015 | 1.81 | 262 | 21 | f | 22 | 19 | 11 | 11 | 86 | 19 | 15 | 2346 | Cfx (I), Cpe | - | nd | 6 | D350N | ||
PT10786 | 2015 | 1.81 | 222 | 23 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT10821 | 2016 | 1.81 | 290 | 20 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT10923 | 2016 | 1.81 | 195 | 21 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT10955 | 2016 | 1.81 | 266 | 22 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT10964 | 2016 | 1.81 | 319 | 25 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT10978 | 2016 | 1.81 | 335 | 22 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT10980 | 2016 | 1.81 | 236 | 24 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT10991 | 2016 | 1.81 | 238 | 23 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT11001 | 2016 | 1.81 | 324 | 25 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT11017 | 2016 | 1.81 | 258 | 22 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT11021 | 2016 | 1.81 | 91 | 21 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT11098 | 2016 | 1.81 | 78 | 24 | f | 22 | 19 | 140 | 11 | 22 | 19 | 15 | 973 | - | - | nd | 6 | D350N | ||
PT11104 | 2016 | 1.81 | 75 | 24 | f | 22 | 19 | 140 | 11 | 22 | 19 | 15 | 973 | - | - | nd | 6 | D350N | ||
PT11317 | 2016 | 1.81 | 73 | 24 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT11321 | 2016 | 1.81 | 66 | 21 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT11400 | 2018 | 1.81 | 53 | 21 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT11546 | 2018 | 1.81 | 37 | 29 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | - | - | nd | 6 | D350N | ||
PT11703 | 2018 | 1.81 | 156 | 20 | f | 22 | 19 | 140 | 11 | 22 | 19 | 15 | 973 | Cip | - | nd | 6 | D350N | ||
PT12019 | 2019 | 1.81 | 308 | 23 | f | 22 | 19 | 11 | 11 | 22 | 19 | 15 | 124 | Amp, Cfx(I), BLP | BLP | bla TEM-1 | 6 | D350N | ||
PT12088 | 2019 | 1.81 | 286 | 22 | f | 22 | 19 | 140 | 11 | 22 | 19 | 15 | 973 | - | - | nd | 6 | D350N | ||
PT12152 | 2019 | 1.81 | 298 | 21 | f | 22 | 19 | 140 | 11 | 22 | 19 | 15 | 973 | - | - | nd | 6 | D350N | ||
PT11604 | 2018 | 1.84 | 84 | 101 | NT | 1 | 8 | 1 | 14 | 22 | 14 | 13 | 145 | Amp, Aug, Cfx, Cpe, SXT, BLP | BLPACR | bla TEM-1 | 24 | D350N A502T N526K | F154S | P64E |
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Bajanca-Lavado, M.P.; Cavaco, L.; Fernandes, M.; Touret, T.; Candeias, C.; Simões, A.S.; Sá-Leão, R. Haemophilus influenzae Carriage among Healthy Children in Portugal, 2015–2019. Microorganisms 2022, 10, 1964. https://doi.org/10.3390/microorganisms10101964
Bajanca-Lavado MP, Cavaco L, Fernandes M, Touret T, Candeias C, Simões AS, Sá-Leão R. Haemophilus influenzae Carriage among Healthy Children in Portugal, 2015–2019. Microorganisms. 2022; 10(10):1964. https://doi.org/10.3390/microorganisms10101964
Chicago/Turabian StyleBajanca-Lavado, Maria Paula, Luís Cavaco, Mariana Fernandes, Tiago Touret, Catarina Candeias, Alexandra S. Simões, and Raquel Sá-Leão. 2022. "Haemophilus influenzae Carriage among Healthy Children in Portugal, 2015–2019" Microorganisms 10, no. 10: 1964. https://doi.org/10.3390/microorganisms10101964