| Literature DB >> 35401464 |
Rong Zhang1, Yan Zhuang1, Zheng-Hui Xiao2, Cai-Yun Li3, Fan Zhang1, Wei-Qing Huang1, Min Zhang1, Xiao-Ming Peng1, Chao Liu3.
Abstract
Microbial infections cause significant morbidity and mortality in neonates. Metagenomic next-generation sequencing is a hypothesis-free and culture-free test that enables broad identification of pathogens and antimicrobial resistance genes directly from clinical samples within 24 h. In this study, we used mNGS for etiological diagnosis and monitoring the efficacy of antibiotic treatment in a cohort of neonatal patients with severe infections. The median age was 19.5 (3-52) days, median gestational age was 37.96 (31-40+3) weeks, and the median birth weight was 3,261 (1,300-4,300) g. The types of infectious diseases included pneumonia, sepsis, and meningitis. mNGS reported microbial findings in all cases, which led to changes in antibiotic treatment. These included cases of Mycobacterium tuberculosis, Legionella pneumophila, and Bacillus cereus. Eight of ten infants recovered after antibiotic adjustment and showed normal development during follow-up. On the other hand, neurological retardation was seen in two infants with meningitis. mNGS enabled etiological diagnosis and guided antibiotic therapy when all conventional methods failed to discover the culprit. It has the potential to cut down the overall cost and burden of disease management in neonatal infections.Entities:
Keywords: Bacillus cereus; Legionella pneumophila; Mycobacterium tuberculosis; metagenomic next-generation sequencing; neonatal infections
Year: 2022 PMID: 35401464 PMCID: PMC8989347 DOI: 10.3389/fmicb.2022.855988
Source DB: PubMed Journal: Front Microbiol ISSN: 1664-302X Impact factor: 5.640
Clinical characteristics of the 10 patients.
| Patient no./Sex/Age, d | Infection data | Initial signs | RF | CF | NA | LOS in NICU, d | Final diagnosis | ||
|---|---|---|---|---|---|---|---|---|---|
| CRP (mg/dl) | PCT (ng/ml) | IL-6 (pg/ml) | |||||||
| 1/M/19 | 205.08 | 16.44 | 1,387 | fever, tachypnea | + | + | − | 19 |
|
| 2/F/4 | >320 | 1.07 | 181.5 | fever, cough, dyspnea | + | + | − | 33 |
|
| 3/F/2 | 206.68 | >100 | >5,000 | cough, fever | + | + | − | 26 |
|
| 4/F/38 | 3.74 | 0.16 | 13.46 | spasmodic cough | + | − | − | 11 |
|
| 5/M/52 | 41.84 | 0.17 | 76.92 | fever, abdominal distention | + | − | − | 83 |
|
| 6/M/5 | 98.46 | 2.32 | 165.8 | fever, cyanosis | + | + | + | 47 |
|
| 7/M/23 | 33.06 | 0.31 | 101.0 | cough, fever, tachypnea | + | − | + | 43 |
|
| 8/M/7 | 122.59 | >100 | >5,000 | fever, convulsion | + | + | + | 40 |
|
| 9/M/3 | 192.9 | 12.18 | 324.1 | fever, convulsion | − | − | + | 26 |
|
| 10/F/15 | 168.1 | 18.12 | 23.06 | fever, dyspnea, convulsion | + | + | + | 13 |
|
F, female; M, male; CRP, C-reactive protein; PCT, Procalcitonin; IL-6, cinterleukin 6; RF, Respiratory failure; CF, Circulatory failure; NA, Neurological abnormality; LOS, length of stay; and NICU, neonatal intensive care unit.
mNGS findings of the 10 patients.
| Patient#/gestation age, wk | Conventional method results | mNGS results | Therapy | Follow-up (Mo)/outcome | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Culture | Antigen | PCR | Sample | TAT (h) | Initial Host index | Pathogens | IR | Initial Microbial index | FR | Final Host index | Final Microbial index | Antibiotics, d | Other | ||
| 1/39 | Sputum/Blood/CSF(−) | Respiratory/TORCH (−) | Blood | 13 | 28826.85 |
| 59 | 10723.30 | ND | / | / | Isoniazid/ rifampicin/pyrazinamide,67 | Ventilation 7d | 3/recovered | |
| 2/40 | Sputum/Blood/CSF/BALF(−) | Respiratory/TORCH (−) | Blood | 22.5 | 29143.69 |
| 361 | 13653.88 | NF | 29485.81 | NF | Erythromycin,19 | Plasma transfusion Ventilation 12d | 2/recovered | |
| 3/40+3 | Sputum( | Respiratory/TORCH (−) | Blood | 41.7 | 28392.78 |
| 110 | 10994.57 | NF | 21320.92 | NF | Amikacin/Ceftazidime/Linezolid,24 | Ventilation 3d | 5/recovered | |
| 4/38+1 | Sputum/Blood (−) | Respiratory/TORCH (−) | Sputum | 40.7 | 26006.36 |
| 1,330 | 13036.10 | NF | 19779.90 | NF | Erythromycin,11 | Salbutamol nebulization | 5/recovered | |
| 5/31 | Sputum/Blood (−) | TORCH (−) | Sputum | 21 | 26180.42 |
| 65 | 8430.86 | 6 | 22020.46 | 1784.12 | Erythromycin,7 | Bishop’s fistula of ileum and santulli fistulaVentilation 10d PICC 30d | 4/recovered | |
| 6/39+1 | Sputum/Blood (−) | Respiratory/TORCH (−) | Sputum | 18 | 27934.48 |
| 1,286 | 15876.97 | NF | 26254.30 | NF | Oxacillin/Vancomycin,14 | Repair of VSD and PFO, ligation of PDA Ventilation 10d | 4/recovered | |
| 7/40+1 | Sputum/Blood/CSF(−) | Blood | 17.7 | 23752.90 | 6/12 | 2661.86/3543.13 | ND | / | / | Vancomycin/Acyclovir,43 | NCPAP 4d DEX 4d | 2/recovered | |||
| CSF | 17.7 | 31468.11 |
| 32/1 | 12767.09/7773.50 | 4/11 | 28348.48 | 7672.03/9126.95 | |||||||
| 8/39+5 | Sputum/blood/CSF(−) | Respiratory/TORCH(−) | blood | 43.5 | 27536.51 |
| NF | / | ND | / | / | Meropenem/Cefotaxime,40 | phenobarbitone 7d/midazolam 3d/prednisone 7d | 1/recovered | |
| CSF | 43.5 | 31482.51 |
| 13 | 9777.09 | NF | 25699.22 | NF | |||||||
| 9/38+3 | Sputum/blood/CSF/stool(−) | Respiratory/TORCH(−) | blood | / | / | / | ND | / | ND | / | / | Penicillin,26 | phenobarbitone 16d/midazolam 3d DEX 4d | 1/encephalomalacia in left side of brain | |
| CSF | 18.6 | 27271.33 |
| 15,611 | 15390.84 | NF | 27033.76 | NF | |||||||
| 10/34+2 | Sputum/blood/CSF(−) | Blood | 21 | 32275.98 |
| 4 | 9508.34 | ND | / | / | Gentamicin/Vancomycin,17 | Ventilation 3d phenobarbitone 8d | 1/diffused encephalomalacia | ||
| CSF | 21 | 29712.14 |
| 61 | 9559.24 | 2 | 24454.21 | 804.66 | |||||||
wk, week; CSF, cerebral spinal fluid; MP, Mycoplasma pneumonia; TORCH, Toxoplasma, Rubella, cytomegalovirus, herpes, and others; Respiratory, including influenza A/B virus, parainfluenza virus, adenovirus, and respiratory syncytial virus; RSV, respiratory syncytial virus; EV, Enterovirus; CA, Coxsackie Virus; TAT, turn-around time; Mtb, Mycobacterium tuberculosis; LP, Legionella pneumophila; Mcat, Moraxella catarrhalis; CT, Chlamydia trachomatis; UP, Ureaplasma parvum; S. mitis, Streptococcus mitis; S. pasteuri, Streptococcus pasteuri; HHV-5, Human betaherpesvirus 5; E. coli, Escherichia coli; GBS, Streptococcus agalactiae; B. cereus, Bacillus cereus; IR, Initial reads; FR, Finial reads; NF, not found; ND, not done; PICC, peripherally inserted central catheter; VSD, ventricular septal defect; PFO, patent foramen ovale; PDA, patent ductus arteriosus; DEX, dexamethasone; and Mo, months.
Figure 1Chest computed tomography image of patient 1 showing many miliary nodules (arrowheads) can be seen in both lungs.
Figure 2The treatment course in Mycobacterium tuberculosis case. CRP, C-reactive protein; NICU, neonatal intensive care unit; and NIPPV, non-invasive positive pressure ventilation.
Figure 3Diagnosis of L. pneumophila infection by means of Unbiased Next-Generation Sequencing (mNGS) and 16s ribosomal RNA (rRNA) sequencing. The relative abundance of L. pneumophila from the patient’s bronchoalveolar lavage fluid (BALF) by mNGS and 16s rRNA sequencing (A). Sequence reads mapped to L. pneumophila by mNGS data (B).
Figure 4The treatment course in Legionella pneumophila case. CRP, C-reactive protein; NICU, neonatal intensive care unit; L. pneumophila, Legionella pneumophila.
Figure 5The treatment course in Bacillus cereus case. CRP, C-reactive protein; CSF, cerebral spinal fluid; NICU, neonatal intensive care unit; B. cereus, Bacillus cereus; and NCPAP, nasal continuous positive airway pressure.