Copyright: ©Author(s) 2026.
World J Methodol. Sep 20, 2026; 16(3): 115598
Published online Sep 20, 2026. doi: 10.5662/wjm.115598
Published online Sep 20, 2026. doi: 10.5662/wjm.115598
Table 1 Association of demographic, microbiologic, and clinical variables associated with pathogen vs non-pathogen, n (%)
| Category | Parameter | Total (n = 145) | Non-pathogen (n = 14) | Pathogen (n = 131) | P value |
| Demographic variables, mean ± SD | Age (years) | 5042 ± 1635 | 5121 ± 1643 | 5034 ± 1640 | - |
| Gender | Male | 81 (559) | 10 (714) | 71 (542) | - |
| Female | 64 (441) | 4 (286) | 60 (458) | ||
| Site of clinical care | General medicine ward | 20 (138) | 5 (357) | 15 (115) | - |
| Medicine ICU | 71 (490) | 4 (286) | 67 (511) | ||
| Nephrology ward | 5 (34) | 0 (00) | 5 (38) | ||
| Pulmonary medicine | 49 (338) | 5 (357) | 44 (336) | ||
| Microbiological variables | - | ||||
| Sample | Aerobic culture | 131 (903) | 14 (1000) | 117 (893) | - |
| Multiplex PCR (Biofire FilmArray) | 14 (97) | 0 (00) | 14 (107) | ||
| Sputum | 24 (166) | 4 (28.6) | 20 (15.3) | - | |
| ET/TT | 96 (662) | 8 (57.1) | 88 (67.2) | - | |
| BAL | 25 (172) | 2 (14.3) | 23 (17.6) | - | |
| Organism (n = 195); aerobic culture (n = 158) | Acinetobacter baumannii | 58 (29.7) | 4 (25) | 54 (30.2) | - |
| Klebsiella pneumoniae | 55 (28.2) | 5 (31.3) | 50 (27.9) | - | |
| Pseudomonas aeruginosa | 23 (11.8) | 2 (12.5) | 21 (11.7) | - | |
| Escherichia coli | 5 (2.6) | 1 (6.3) | 4 (2.2) | ||
| Stenotrophomonas maltophilia | 4 (2.1) | 1 (6.3) | 3 (1.7) | ||
| Others | 13 (6.6) | 3 (18.8) | 10 (5.6) | ||
| Multiplex PCR (n = 37) | Acinetobacter baumannii; genes - IMP, VIM, NDM | 10 (5.1) | 0 (0.0) | 10 (5.6) | - |
| Pseudomonas aeruginosa; genes - NDM, VIM, IMP | 9 (4.6) | 0 (0.0) | 10 (5.0) | ||
| Klebsiella pneumoniae; genes - KPC, OXA - 48 | 6 (3.1) | 0 (0.0) | 6 (3.4) | ||
| Influenza virus | 4 (2.1) | 0 (0.0) | 4 (2.2) | ||
| Escherichia coli; genes - VIM, NDM | 3 (1.5) | 0 (0.0) | 3 (1.6) | ||
| Others | 5 (2.5) | 0 (0.0) | 5 (2.7) | ||
| Number of organisms positive/sample (n = 195) | 1 | 110 (759) | 12 (857) | 98 (748) | - |
| 2 | 27 (186) | 2 (143) | 25 (191) | - | |
| 3 | 3 (21) | 0 (00) | 3 (23) | - | |
| 4 | 4 (28) | 0 (00) | 4 (31) | - | |
| 6 | 1 (07) | 0 (00) | 1 (08) | - | |
| Same organism isolated from the local site and blood | 28 (193) | 0 (00) | 28 (214) | - | |
| Pathogen | 1 (71) | 131 (1000) | - | ||
| Clinical variables | Signs and symptoms of any localized site of infection | 138 (95.2) | 9 (643) | 129 (985) | < 00013 |
| Fever | 71 (51.4) | 4 (444) | 67 (519) | - | |
| Cough | 88 (63.8) | 7 (778) | 81 (628) | - | |
| Expectoration | 105 (76.1) | 4 (444) | 101 (783) | 00363 | |
| Increasing oxygen requirement | 107 (77.5) | 3 (333) | 104 (806) | 00043 | |
| Tachypnoea | 97 (70.3) | 3 (333) | 94 (729) | 00203 | |
| Tachycardia | 68 (49.3) | 2 (222) | 66 (512) | - | |
| Chest pain | 4 (2.9) | 1 (111) | 3 (23) | - | |
| Increase in Sequential Organ Failure Assessment Score ≥ 2 (48 hours) | 111 (76.6) | 3 (214) | 108 (824) | < 00013 | |
| Risk factors for colonization | Invasive mechanical ventilation | 103 (71.0) | 7 (500) | 96 (733) | - |
| Recent hospitalization or antibiotic use within the past 90 days | 86 (59.3) | 8 (571) | 78 (595) | - | |
| Poor oral hygiene due to tobacco chewing, smoking, alcoholism, dry mouth, or chronic bedridden status | 56 (38.6) | 5 (357) | 51 (389) | - | |
| Chronic obstructive pulmonary disease | 31 (21.4) | 4 (286) | 27 (206) | - | |
| Tracheostomy | 25 (17.2) | 1 (71) | 24 (183) | - | |
| Prior isolation of the organism within one year of the incident | 22 (15.2) | 0 (00) | 22 (168) | - | |
| History of lower respiratory tract infection | 10 (6.9) | 2 (143) | 8 (61) | - | |
| Neuromuscular disorders | 7 (4.8) | 0 (00) | 7 (53) | - | |
| Bronchiectasis | 3 (2.1) | 1 (71) | 2 (15) | - | |
| Complications | Multiple organ dysfunction syndrome | 71 (49.0) | 4 (286) | 67 (511) | - |
| Ventilator-associated pneumonia | 43 (29.7) | 2 (143) | 55 (420) | 00442 | |
| Shock | 51 (35.2) | 0 (00) | 51 (389) | 00023 | |
| Bloodstream infections | 48 (33.1) | 2 (143) | 46 (351) | - | |
| Acute kidney injury | 16 (11.0) | 1 (71) | 15 (115) | - | |
| Patients on hemodialysis | 21 (14.5) | 0 (00) | 21 (160) | - | |
| Arrhythmias, including ventricular tachycardia and fibrillation | 5 (3.4) | 0 (00) | 5 (38) | - | |
| Bedsores | 7 (4.8) | 0 (00) | 7 (53) | - | |
| Comorbidities | Diabetes | 38 (418) | 3 (429) | 35 (417) | - |
| Hypertension | 41 (451) | 2 (28.6) | 39 (464) | - | |
| Chronic obstructive pulmonary disease | 26 (286) | 3 (42.9) | 23 (274) | - | |
| Coronary artery disease | 6 (66) | 0 (0.0) | 6 (71) | - | |
| Chronic liver disease | 3 (33) | 1 (14.3) | 2 (24) | - | |
| Chronic kidney disease | 20 (220) | 0 (0.0) | 20 (238) | - | |
| Malignancy | 5 (55) | 0 (0.0) | 5 (60) | - |
Table 2 Agreement for pathogen characterization between investigator and microbiologist, n (%)
| Characterization | Characterization by investigator | Cohen’s Kappa | ||||
| Non-pathogen | Pathogen | Total | k | P value | ||
| Characterization by microbiologist | Non-pathogen | 3 (2.1) | 2 (1.4) | 5 (3.4) | 0.28 | < 0.001 |
| Pathogen | 11 (7.6) | 129 (90.3) | 140 (96.6) | |||
| Total | 14 (9.7) | 131 (90.3) | 145 (100.0) | |||
Table 3 Comparison of variables across the investigator’s classification of respiratory isolates
| Parameters | Pathogenic commensal | Pathogenic colonizer | Pathogenic direct | Non-pathogenic commensal | Non-pathogenic colonizer | Non-pathogenic contaminants | P value |
| Age (years), mean ± SD | 40.00 ± 19.52 | 50.67 ± 16.46 | 50.20 ± 16.10 | 30.00 ± 0 | 58.40 ± 5.90 | 49.38 ± 19.40 | 0.5591 |
| Gender: Male (%) | 33.3 | 49.5 | 76.0 | 100.0 | 80.0 | 62.5 | 0.0952 |
| Gender: Female (%) | 66.7 | 50.5 | 24.0 | 0.0 | 20.0 | 37.5 | 0.0952 |
| Sample type: Sputum (n = 24) | 100 | 0 | 68.0 | 100 | 0 | 37.5 | < 0.001 |
| Sample type: ET/TT (n = 96) | 0 | 84.5 | 4.0 | 0 | 80.0 | 50.0 | < 0.001 |
| Sample type: BAL (n = 25) | 0 | 15.5 | 28.0 | 0 | 20.0 | 12.5 | < 0.001 |
| Fever (%) | 33.3 | 43.6 | 88 | 0 | 33.3 | 50 | < 0.001 |
| Cough (%) | 66.7 | 56.4 | 88 | 0 | 66.7 | 83.3 | 0.0182 |
| Increasing oxygen requirement, n (%) | 1 (33.3) | 87 (86.1) | 16 (64.0) | 0 (0) | 1 (33.3) | 2 (33.3) | < 0.0012 |
| Increase in Sequential Organ Failure Assessment score ≥ 2 (%) | 66.7 | 85.4 | 72.0 | 0 | 0 | 37.5 | < 0.001 |
| Shock (%) | 0 | 43.7 | 24.0 | 0 | 0 | 0 | 0.009 |
| Multiple organ dysfunction syndrome (%) | 0 | 55.3 | 40.0 | 0 | 40.0 | 25.0 | 0.122 |
| VAP (%) | 0 | 48.5 | 20.0 | 0 | 20.0 | 12.5 | 0.011 |
| Risk factors | |||||||
| Mechanical ventilation (%) | 0 | 93.2 | 0 | 0 | 100.0 | 25.0 | < 0.001 |
| Recent hospitalizations/antibiotics (%) | 66.7 | 69.9 | 16.0 | 0 | 100.0 | 37.5 | < 0.001 |
| Poor oral hygiene (%) | 66.7 | 45.6 | 8.0 | 0 | 60.0 | 25.0 | 0.001 |
| Chronic obstructive pulmonary disease (%) | 33.3 | 24.3 | 4.0 | 0 | 60.0 | 12.5 | 0.030 |
| Bronchiectasis (%) | 66.7 | 0 | 0 | 0 | 20.0 | 0 | < 0.001 |
| Tracheostomy (%) | 0 | 23.3 | 0 | 0 | 20.0 | 0 | 0.030 |
| Response to treatment | < 0.001 | ||||||
| Improved | 100 | 43.70 | 80.00 | - | - | - | |
| No response | 0 | 56.30 | 20.00 | - | - | - | |
| Not treated | - | - | - | 100.00 | 80.00 | 87.50 | |
| Stable (non-pathogen) with treatment | 0 | 20.00 | 12.50 | ||||
| Outcome: Mortality (%) | 0 | 50.6 | 16.0 | 0 | 0 | 14.3 | 0.001 |
- Citation: Sahu S, Omar BJ, Bairwa M, Sharma P, Sahu P, Panda PK. Stepwise model to differentiate pathogenic from non-pathogenic organisms in lower-respiratory isolates: Effectiveness and feasibility prospective cohort study. World J Methodol 2026; 16(3): 115598
- URL: https://www.wjgnet.com/2222-0682/full/v16/i3/115598.htm
- DOI: https://dx.doi.org/10.5662/wjm.115598