Concurrent pigeon paramyxovirus-1 and Acinetobacter baumannii infection in a fatal case of pneumonia

Figures & data

Figure 1. Timeline of the clinical course of the patient and identification of the causative pathogen.

Figure 2. Chest radiographs during the clinical course. Bilateral ground-glass opacity and consolidation were observed on day 9 (Dec 26, Panel A) and worsened on day 11 (Dec 28, Panel B). Bilateral lung involvement was slightly relieved on day 14 (Dec 31, Panel C) after methylprednisolone was administrated on day 11. Bilateral ground-glass opacity and consolidation continued till day 16 (Jan 2, Panel D) and day 18 (Jan 4, Panel E) and relieved slightly on day 20 (Jan 6, Panel F).

Table 1. Clinical blood biochemistry tests and gas analysis.

	Normal range	Days after illness onset
		3	9	11	14	17	20
Number of white blood cells (×10^9 /L)	3.5-9.5	7.04	8.43	11.57		10.17	10.29
Proportion of neutrophils (%)	40–75		94.5	95.5	96	94	96.7
Proportion of lymphocytes (%)	20–50		3.7	3.2	2.5	3.8	1.7
Neutrophils count (×10^9 /L)	1.8–6.3	6.26	7.97	11.05	9.06	9.56	9.95
Lymphocytes (×10^9 /L)	1.1–3.2	0.44	0.31	0.37	0.24	0.39	0.18
C-reactive protein (nmol/L)	0–10			164.52	148.78	144.88
Alanine aminotransferase(U/L)	9–50	37	30	29.8	45.8	39.6	42.6
Aspartate aminotransferase (U/L)	15–40	34	36	58.4	67.2	57	56.4
Alkaline phosphatase (U/L)	45–125			95	202.2	172.8	192
Total protein (g/L)	65–85		49	44.2	49.7	47.5	50.5
Globin (g/L)	20–40			21.5	22.9	22.4	23.4
Albumin (g/L)	40–55	32.5	24.7	22.7	26.8	25.1	27.1
D-dimer (mg/L)	0–0.55			4.7	> 20	14.8
Uric Acid (μmol/L)	149–446			131	117		282
Creatinine (μmol/L)	44–105	80	62.5	59.44	62.5		123.7
Procalcitonin (ng/ml)	0–0.5		0.335	1.511	1.218	1.24	46.754
FiO2%	21–100		40	85	45	60	75
PaCO2 (mmHg)	35–45		35	59	51	43	108
PaO2 (mmHg)	80–100		67	55	63	57	58
PaO2/FiO2 (mmHg)	400–500		167.5	64.7	140	140	77.3
pH	7.35–7.45		7.46	7.29	7.3	7.47	7.16

Abbreviations: FiO₂%: fraction of inspired oxygen; PaCO₂: partial pressure of carbon dioxide; PaO₂: arterial partial pressure of oxygen.

Table 2. Complications, treatment, and clinical outcome of the patients.

Signs and treatment
Fever	Yes
Temperature on admission (°C)	36.4
Highest temperature (°C)	39.8
Complications
Failure of respiratory function	Yes
Septic shock	Yes
Heart failure	Yes
Liver failure	Yes
Oxygen treatment	Yes
Bacterial co-infection	Yes (Acinetobacter baumannii in blood culture)
Antibiotic treatment	Yes
Days 1–8	Moxifloxacin, ganciclovir, and then switched to cefperazone-Sulbactam and levofloxacin (does unknown)
Days 9–19	Imipenem (1 g given intravenously every 8 h)
	Moxifloxacin (one 0.4 g dose given intravenously)
Days 19–20	Vancomycin (0.5 g given intravenously every 12 h)
	Piperacillin/Tazobactam (4.5 g given intravenously every 8 h)
Day 21	Meropenem (1 g given intravenously every 12 h)
Glucocorticoid treatment
Days 11–20	Methylprednisolone (40 mg given intravenously every 12 h)
Antiviral treatment
Days 10–18	Ganciclovi (0.35 g given intravenously every 12 h)
Days 11–18	Oseltamivir (75 mg given orally twice a day)
Days 18–21	Arbidol (three 0.2 g doses given orally)
Antifungal treatment
Days 19–20	Micafungin Sodium (one 100 mg dose given intravenously)
Intravenous albumin therapy	10 g (day 9-11)

Figure 3. Metagenomic analysis of the clean reads after host sequences were removed. (A) The complete genome of reference APMV-1 strain pigeon/China/SDLC/2011 was fully covered by 3,289 reads with a mean depth of 31.2×. (B) taxa assignment of the clean reads using MEGAN software. Taxa and the number of their assigned reads were labelled in the polygenetic tree. The pie chart showed Acinetobacter baumannii contributed the most reads, followed by pigeon APMV-1 virus, among the reads of microorganism origin.

Figure 4. Phylogenetic classification of the APMV-1 virus using the full-length nucleotide sequence of the fusion gene, according to the phylogenetic classification system suggested by Dimitrov et al. [21]. The patient’s APMV-1 virus clustered with pigeon strains isolated in north China and belonged to genotype VI.2.1. Pigeon strains from China were labelled with a green triangle and the patient’s APMV-1 strain was labelled with a red circle. The cleavage sites of the fusion protein were aligned for several strains shown in the bottom-right corner, from which multiple basic amino acids were observed, indicating high virulence of the patient’s strain to poultry. Strain name abbreviations: Human/NY, Avian paramyxovirus 1 from the lethal human case of pneumonia reported by Goebel, et al. [15]; Human/SD, APMV-1 strain from our case occurred in Shangdong province in China; pigeon/1344, pigeon/Qinghai/1344/2017; pigeon/TJ2017, pigeon/China/TJ201; Pigeon/190610, Pigeon/Shandong/190610-2/2019; Pigeon/3P3, Pigeon/Shandong/3P3/2018.

Dimitrov KM, Abolnik C, Afonso CL, et al. Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus. Infect Genet Evol. 2019;74:103917.

 PubMed Web of Science ®Google Scholar

Goebel SJ, Taylor J, Barr BC, et al. Isolation of avian paramyxovirus 1 from a patient with a lethal case of pneumonia. J Virol. 2007;81(22):12709–12714.

 PubMed Web of Science ®Google Scholar

Data availability statement

Sequences are available via the National Genomics Data Center (BioProject number PRJCA006351under accession CRA004864).