The Gram-Negative Bacilli Isolated from Caves—Sphingomonas paucimobilis and Hafnia alvei and a Review of Their Involvement in Human Infections
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cave Samples Collection and Bacterial Identification
2.1.1. Cave Samples Collection
2.1.2. Bacteriological Identification and Antibiotic Phenotype of the Cave Isolates
2.2. Search Strategy for Literature Review
References Collection, Screening, and Selection
2.3. Statistical Analysis
3. Results
3.1. The Cave Isolates
3.2. The Results of the Literature Review
3.2.1. Type of Studies
3.2.2. The Case Report and Literature Reviews
3.2.3. Type of Infections
3.2.4. The Bloodstream Infections
3.2.5. The Urinary Tract Infections
3.2.6. The Respiratory Tract Infections
3.2.7. The Pediatric Infections
3.2.8. The Studies with Healthy-Control Groups
3.2.9. The Microbiological Diagnostic Methods
3.3. The Innate or Natural Antibiotic Resistance
3.4. The Limitations of the Study
3.5. The Strength of the Study
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample Code | Cave | Bacterial Strain | Probability (%) * |
---|---|---|---|
PTDF1 | Topolniţa | Aerococcus viridans | 88 |
PLDF1 | Apă din Valea Leșului | Bacillus cereus/thuringiensis/mycoides | 89 |
PFDF5 | Ferice | Rhodococcus coprophilus/erythropolis/globerulus | 90 |
PFDF3 | Ferice | Bacillus cereus/thuringiensis/mycoides | 85 |
PCDF1 | Cloşani | Sphingomonas paucimobilis Geobacillus thermoleovorans | 94 |
92 | |||
PTSDF2 | Tăuşoare | Hafnia alvei Corynebacterium afermentans | 86 |
90 | |||
PMDF11 | Muierilor | Geobacillus toebii | 91 |
PMDF11A | Muierilor | Bacillus smithii | 88 |
PMDF11B | Muierilor | Bacillus cereus/thuringiensis/mycoides | 86 |
PMOS1 | Muierilor | Sphingomonas paucimobilis Bacillus smithii | 93 |
97 | |||
PMOS2 | Muierilor | Geobacillus toebi | 95 |
Antibiotic | S. paucimobilis PCDF1 | S. paucimobilis PMOS1 | H. alvei PTSDF2 | ||||||
---|---|---|---|---|---|---|---|---|---|
MIC 1 | CLSI 2 | EUCAST 8 | MIC | CLSI 2 | EUCAST 8 | MIC | CLSI | EUCAST 8 | |
Ticarcillin | 32 | I | <=8 | S | S | <=8 | - | S 5 | |
Ticarcillin/Clavulanic Acid | 16 | S | S | <=8 | - | S | <=8 | S | S |
Piperacillin | 32 | I 6 | I | <=4 | S | S | <=4 | S | S |
Piperacillin/Tazobactam | 16 | S | S | <=4 | S | S | 8 | S | S |
Ceftazidime | >=64 | R | R | 2 | S | S | 32 | R 7 | R |
Cefepime | >=64 | R | R | <=1 | S | S | <=1 | S | S |
Aztreonam | >=64 | - | (-) | 16 | - | I | 8 | R | |
Imipenem | 1 | S | S | 1 | S | 0.5 | S | S | |
Meropenem | <=0.25 | S | S | 0.5 | S | 4 | R | I | |
Amikacin | <=2 | S | S | <=2 | S | <=2 | S | S | |
Gentamicin | <=1 | S | IE 3 | <=1 | IE 3 | <=1 | S | S | |
Tobramycin | <=1 | S | S | <=1 | S | <=1 | S | S | |
Ciprofloxacin | <=0.25 | S | I | 2 | R | <=0.25 | S | S | |
Pefloxcin | - | - | - | - | - | - | - | - | - |
Minocycline | <=1 | S | S | <=1 | S | 8 | I | - | |
Colistin 4 | >=16 | R | R 9 | 8 | R | R 9 | >=16 | R | R 9 |
Rifampicin | - | - | - | - | - | - | - | - | - |
Trimethoprim/Sulfamethoxazole | <=20 | S | S | <=20 | S | <=20 | S | S |
Type of Infections (n = 447) | S. paucimobilis (n = 262) n (%) | H. alvei (n = 185) n (%) |
---|---|---|
BSI | 116 (44.27) | 20 (10.81) |
UTI | 4 (1.52) | 121 (65.41) |
respiratory tract infections | 17 (6.49) | 11 (5.94) |
bone or soft-tissue infections | 18 (6.87) | 7 (3.78) |
Intra-abdominal infections | 15 (5.72) | 25 (13.51) |
Head and neck infections | 20 (7.63) | 0 |
Ocular infections | 17 (6.49) | 0 |
Cardiovascular infections | 3 (1.15) | 0 |
Other types of infections | 52 (19.85) | 1 (0.54) |
t(14) = 0.49, p = 0.32 |
The Acquired Source (n = 136) | SP | HA |
---|---|---|
n (%) | n = 116 (%) | n = 20 (%) |
Hospital 50 (36.76) | 50 (43.10) | - |
Community 43 (31.62) | 43 (37.06) | - |
Not specified * 43 (31.62) | 23 (19.82) | 20 (100) |
The Underlying Conditions (n = 136) | SP | HA |
---|---|---|
n (%) | n = 116 (%) | n = 20 (%) |
malignancy 45 (33.08) | 44 (37.93) | 1 (5) |
diabetes mellitus 15 (11.02) | 15 (12.93) | - |
bacteremia associated with contaminated iv fentanyl 6 (4.41) | 6 (5.17) | - |
kidney transplant 6 (4.41) | - | 6 (30) |
prematurity 5 (3.67) | 4 (3.44) | 1 ** (5) |
surgery 3 (2.21) | 3 (2.59) | - |
Streptococcus pyogenes infections 2 (1.47) | 2 (1.72) | - |
end-stage renal disease 3 (2.21) | 3 (2.59) | |
HIV 2 (1.47) | 1 (0.86) | 1 (5) |
neonatal sepsis 2 (1.47) | 2 (1.72) | - |
burn injury 2 (1.47) | 2 (1.72) | - |
chronic obstructive pulmonary disease and steroid use 1 (0.74) | 1 (0.86) | - |
chronic steroid use 1 (0.74) | 1 (0.86) | - |
chylothorax 1 (0.74) | 1 (0.86) | - |
Down syndrome 1 (0.74) | 1 (0.86) | - |
duodenal atresia 1 (0.74) | 1 (0.86) | - |
epilepsy 1 (0.74) | 1 (0.86) | - |
imperforate anus 1 (0.74) | 1 (0.86) | - |
liver cirrhosis and alcoholism 1 (0.74) | 1 (0.86) | - |
liver transplantation 1 (0.74) | - | 1 (5) |
perforated appendicitis 1 (0.74) | 1 (0.86) | - |
pulmonary embolization and atrial fibrillation 1 (0.74) | 1 (0.86) | - |
septic arthritis 1 (0.74) | 1 (0.86) | - |
urethral stone 1 (0.74) | 1 (0.86) | - |
unclear 9 (6.62) | 3 (2.59) | 6 (30) |
No* 23 (16.91) | 19 (16.38) | 4 (20) |
Age Range | S. paucimobilis (n = 62) n (%) | H. alvei (n = 10) n (%) |
---|---|---|
0 day to 1 month | 11 (17.19) | 2 (20) |
1 month to 1 year | 10 (15.63) | 2 (20) |
1 to 3 years | 6 (9.38) | 1 (10) |
3 to 6 years | 11 (17.19) | 1 (10) |
6 to 12 years | 14 (21.88) | 3 (30) |
12 to 18 years | 10 (16.12) | 1 (10) |
t(10) = 7.84, p < 0.00001 |
Type of Infections (n = 447) | Pediatric (n = 72) | Adult (n = 375) | ||
---|---|---|---|---|
n (%) | SP n = 62 (%) | HA n = 10 (%) | SP n = 200 (%) | HA n = 175 (%) |
BSI 136 (30.42) | 55 (88.71) | 8 (80) | 61 (30.5) | 12 (6.85) |
primary bacteremia 69 (15.44) | 34 (54.83) | 4 (40) | 25 (12.5) | 6 (3.43) |
CR-BSI 19 (4.25) | 7 (11.29) | 0 | 12 (6) | 0 |
bacteremia associated with contaminated iv fentanyl 6 (1.34) | 0 | 0 | 6 (3) | 0 |
urosepsis 10 (2.24) | 3 (4.83) | 1 (10) | 0 | 6 (3.43) |
pneumonia 4 (0.89) | 1 (1.61) | 0 | 3 (1.5) | 0 |
meningitis 2 (0.45) | 0 | 1 (10) | 1 (0.5) | 0 |
bone or soft tissue infections 5 (1.12) | 0 | 0 | 5 (2.5) | 0 |
intra-abdominal infections * 6 (1.34) | 1 (1.61) | 2 (20) | 3 (1.5) | 0 |
unspecified 15 (3.35) | 9 (14.52) | 0 | 6 (3) | 0 |
UTI 125 (27.96) | 0 | 0 | 4 (2) | 121 (69.14) |
Respiratory tract infections 28 (6.26) | 1 (1.61) | 0 | 16 (8) | 11 (6.29) |
ventilator-associated pneumonia 1(0.22) | 0 | 0 | 0 | 1 (0.57) |
empyema 1(0.22) | 0 | 0 | 1 (0.5) | 0 |
airway inflammation 1(0.22) | 1 (1.61) | 0 | 0 | 0 |
unspecified 25 (5.6) | 0 | 0 | 15 (7.5) | 10 (5.71) |
Bone or soft tissue infections 25 (5.6) | 2 (3.23) | 1 (10) | 16 (8) | 6 (3.43) |
cellulitis 2 (0.45) | 0 | 0 | 2 (1) | 0 |
otomastoiditis 1 (0.22) | 1 (1.61) | 0 | 0 | 0 |
osteomyelitis and septic arthritis 1 (0.22) | 1 (1.61) | 0 | 0 | 0 |
septic arthritis 1 (0.22) | 0 | 0 | 1 (0.5) | 0 |
osteomyelitis 2 (0.45) | 0 | 0 | 2 (1) | 0 |
deep infection, open fracture 1(0.22) | 0 | 1 | 0 | 0 |
focal myositis 1(0.22) | 0 | 0 | 1 (0.5) | 0 |
necrotizing fasciitis 1(0.22) | 0 | 0 | 0 | 1 (0.57) |
unspecified soft tissue infections 15(3.36) | 0 | 0 | 10 (5) | 5 (2.86) |
Intra-abdominal infections 40 (8.94) | 1 (1.61) | 1 (10) | 14 (7) | 24 (13.71) |
peritoneal dialysis-associated peritonitis 14 (3.13) | 1 (1.61) | 0 | 13 (6.5) | 0 |
diarrhea 19 (4.25) | 0 | 1 (10) | 0 | 18 (10.29) |
cholecystitis 1(0.22) | 0 | 0 | 0 | 1 (0.57) |
intra-abdominal abscess and peritoneal dialysis related peritonitis 1 (0.22) | 0 | 0 | 1 (0.5) | 0 |
unspecified 5 (1.12) | 0 | 0 | 0 | 5 (2.86) |
Head and neck infections 20 (4.47) | 3 (4.84) | 0 | 17 (8.5) | 0 |
brain abscess 1 (0.22) | 1 (1.61) | 0 | 0 | 0 |
cervical adenitis 1 (0.22) | 1 (1.61) | 0 | 0 | 0 |
central nervous system infections 6 (1.34) | 1 (1.61) | 0 | 5 (2.5) | 0 |
unspecified 12 (2.68) | 0 | 0 | 12 (6) | 0 |
Ocular infections 17 (3.8) | 0 | 0 | 17 (8.5) | 0 |
endophthalmitis 3 (0.67) | 0 | 0 | 3 (1.5) | 0 |
neurotrophic keratitis 1 (0.22) | 0 | 0 | 1 (0.5) | 0 |
ocular contaminations 13 (2.9) | 0 | 0 | 13 (6.5) | 0 |
Cardiovascular infections 3 (0.67) | 0 | 0 | 3 (1.5) | 0 |
cardiac implantable electronic device infection 1 (0.22) | 0 | 0 | 1 (0.5) | 0 |
endocarditis 1 (0.22) | 0 | 0 | 1 (0.5) | 0 |
acute phlebitis 1(0.22) | 0 | 0 | 1 (0.5) | 0 |
Other types of infections 53 (11.86) | 0 | 0 | 52 (26) | 1 (0.57) |
periodontal disease 51 (11.41) | 0 | 0 | 51 (25.5) | 0 |
bromhidrosis 1 (0.22) | 0 | 0 | 1 (0.5) | 0 |
unclear (body fluid) 1 (0.22) | 0 | 0 | 0 | 1 (0.57) |
t-test, p-value | t(16) = 0.95, p = 0.18 | t(16) = 0.19, p = 0.42 | ||
F-ratio, p-value | F = 1.61, p = 0.21 |
Reported Underlying Conditions (n = 447) | Pediatric (n = 72) | Adult (n = 375) | ||
---|---|---|---|---|
n (%) | SP n = 62 (%) | HA n = 10 (%) | SP n = 200 (%) | HA n = 175 (%) |
Malignancy 50 (11.19) | 22 (35.48) | 1 (10) | 27 (13.5) | 0 |
Chronic heart disease 8 (1.78) | 0 | 0 | 8 (4) | 0 |
Chronic renal disease 25 (5.59) | 2 (3.22) | 0 | 16 (8) | 7 (4) |
Chronic liver disease 5 (1.12) | 0 | 1 (10) | 4 (2) | 0 |
Chronic pulmonary disease 7 (1.57) | 0 | 0 | 7 (3.5) | 0 |
Congenital malformation 2 (0.45) (duodenal atresia, imperforate anus) | 2 (3.22) | 0 | 0 | 0 |
Genetic disorders 3 (0.67) (Down syndrome, cystic fibrosis) | 2 (3.22) | 0 | 1(0.5) | 0 |
Diabetes mellitus 15 (3.36) | 0 | 0 | 15 (7.5) | 0 |
Surgery 4 (0.89) (cardiovascular surgery, neurosurgery, cataract extraction) | 0 | 0 | 3 (1.5) | 1 (0.57) |
Trauma 7 (1.57) (burn injury, penetrating globe injury, history of fracture, remote foreign body aspiration during the dental procedure) | 1 (1.61) | 1 (10) | 5 (2.5) | 0 |
Prematurity * 6 (1.34) | 5 (8.06) | 1 (10) | 0 | 0 |
Multiple conditions ** 8 (1.79) | 0 | 0 | 8 (4) | 0 |
other infections 11 (2.46) (HIV, Streptococcus pyogenes, abdominal infections due to perforated appendicitis, septic arthritis, neonatal sepsis, significant dysbiosis associated COVID-19) | 4 (6.45) | 1 (10) | 5 (2.5) | 1 (0.57) |
Other conditions 16 (3.58) (red eye, chylothorax, epilepsy, respiratory distress) | 1(1.61) | 0 | 15 (7.5) | 0 |
Chronic steroid use or alcohol abuse *** 10 (2.24) | 0 | 0 | 10 (5) | 0 |
No underlying conditions reported 80 (17.9) | 22 (35.48) | 5 (50) | 1(0.5) | 52 (29.71) |
Unclear or not specify 190 (42.51) | 1(1.61) | 0 | 75 (37.5) | 114 (65.14) |
t-test, p-value | t(32) = −0.503, p = 0.31 | t(32) = 0.37, p = 0.35 | ||
F-ratio, p-value | F = 1.56, p = 0.21 |
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Ionescu, M.I.; Neagoe, D.Ș.; Crăciun, A.M.; Moldovan, O.T. The Gram-Negative Bacilli Isolated from Caves—Sphingomonas paucimobilis and Hafnia alvei and a Review of Their Involvement in Human Infections. Int. J. Environ. Res. Public Health 2022, 19, 2324. https://doi.org/10.3390/ijerph19042324
Ionescu MI, Neagoe DȘ, Crăciun AM, Moldovan OT. The Gram-Negative Bacilli Isolated from Caves—Sphingomonas paucimobilis and Hafnia alvei and a Review of Their Involvement in Human Infections. International Journal of Environmental Research and Public Health. 2022; 19(4):2324. https://doi.org/10.3390/ijerph19042324
Chicago/Turabian StyleIonescu, Mihaela Ileana, Dan Ștefan Neagoe, Alexandra Marioara Crăciun, and Oana Teodora Moldovan. 2022. "The Gram-Negative Bacilli Isolated from Caves—Sphingomonas paucimobilis and Hafnia alvei and a Review of Their Involvement in Human Infections" International Journal of Environmental Research and Public Health 19, no. 4: 2324. https://doi.org/10.3390/ijerph19042324
APA StyleIonescu, M. I., Neagoe, D. Ș., Crăciun, A. M., & Moldovan, O. T. (2022). The Gram-Negative Bacilli Isolated from Caves—Sphingomonas paucimobilis and Hafnia alvei and a Review of Their Involvement in Human Infections. International Journal of Environmental Research and Public Health, 19(4), 2324. https://doi.org/10.3390/ijerph19042324