The Microbiology and Risk of Infection Following

Open, Agricultural Upper Extremity Injuries

Mir H. Ali, MD, PhD, Nathaniel A. Hoekzema, MD, Mohanand Bakleh, MD,
Alexander Y. Shin, MD, Douglas R. Osmon, MD

Purpose This study was designed to determine the microbiology and risk of infection following open, agricultural,
upper extremity injuries. Specifically, we sought to evaluate the microbiology of the wounds at the time of initial
treatment and the development of any subsequent infections, determine whether the development of subsequent
infection was related to injury severity, and clarify whether the microorganisms isolated at the time of initial
treatment and development of subsequent infection were susceptible to the initial antibiotic prophylaxis.
Methods A retrospective chart review of 214 patients was conducted.
Results The initial injuries were classified into 1 of 3 groups, with 1 being the least severe and 3 being the most severe.
Twenty-six were type 1 injuries, 94 type 2, and 94 type 3 injuries. Forty patients developed infection following the injury.
Seventeen had superficial wound infection, 16 had deep soft tissue infections, and 7 developed osteomyelitis. Six went on to
an amputation due to infection. Fifteen of the infections were polymicrobial. The number of patients who developed infection
in the first 6 months following injury was 2, 14, and 24 for type 1, 2, and 3 injuries respectively (p⫽.07).
Conclusions Empiric antimicrobial regimens for the management of infection requiring surgical debridement
following open upper extremity agricultural injury should be active against staphylococci, aerobic gram-negative
bacilli, and anaerobes, but not necessarily against fungi. These antibiotics ideally should be administered on initial
presentation of the patient to the emergency department. Prospective studies with emphasis on timely acquisition of
cultures and sensitivities are needed to determine optimal prophylactic antimicrobial therapy for these injuries and
directed antibiotic regimens for the infections that may develop. (J Hand Surg 2008;33A:87–93. Copyright © 2008
by the American Society for Surgery of the Hand.)
Type of study/level of evidence Prognostic II.
Key words Microbiology, upper extremity, agricultural trauma, infection, farm.

From the Department of Orthopedic Surgery, Mayo Clinic
College of Medicine, Rochester, MN; Department of
Orthopedic Surgery, Division of Hand Surgery, Mayo Clinic
College of Medicine, Rochester, MN; Division of Infectious
Diseases, Department of Medicine, Mayo Clinic College of
Medicine, Rochester, MN; Philadelphia Hand Center,
Philadelphia, PA; Dodge City Medical Center, Dodge City, KS.
Received for publication April 5, 2007; accepted in revised
form September 6, 2007.
This study was approved by Mayo Clinic Institutional
Review Board and Mayo Clinic Department of Orthopedic
Surgery Orthopedic Research Review Committee.
No benefits in any form have been received or will be
received from a commercial party related directly or
indirectly to the subject of this article.
Corresponding author: Alexander Y. Shin, MD,
Department of Orthopedic Surgery, Division of Hand
Surgery, 200 First St SW, Rochester, MN 55905;
e-mail: shin.alexander@mayo.edu.
0363-5023/08/33A01-0016$34.00/0
doi:10.1016/j.jhsa.2007.09.003
A
GRICULTURAL UPPER EXTREMITY injuries are
common and disabling injuries in rural America.1
The injuries that often occur after accidents with
high-power agricultural equipment compose a spectrum
from simple, relatively clean lacerations to mutilating
manure-, soil-, and crop-contaminated amputations (Fig. 1).
Crop and animal farms often harbor polymicrobial bacterial
as well as fungal organisms2,3 that are introduced into the
tissues of the upper extremity. Due to the complexity of
both the surgical and the medical management of these
injuries, it has been difficult to control infections, minimize
infectious complications, and achieve good functional results.
The wounds that result from agricultural injuries have
the potential to become infected with a myriad of aerobic,
anaerobic, and fungal organisms. In 1977, Fitzgerald and
Cooney4 reported their experience on the microbiology of
open, agricultural, upper extremity trauma. Injuries sustained
while handling farm implements tended to be colonized by
both aerobic gram-negative and gram-positive bacteria.4 The
gram-negative isolates were typically resistant to the initial
antibiotics used for antimicrobial treatment, with the
exception of gentamicin. The authors concluded that
parenteral prophylactic antibiotics at the time of initial

©  ASSH 䉬 Published by Elsevier, Inc. 䉬 87

88 MICROBIOLOGY OF UPPER EXTREMITY FARM TRAUMA
FIGURE 1: Clinical example of contaminated, near amputation of a
patient working with a corn auger.
management of the injury were ineffective in preventing
subsequent clinical infections and, therefore, did not seem to
be indicated in farm implement–related injuries.
Agricultural-related injuries are not limited to adults but
also affect children. A study of 68 children injured on farms
found that predominantly aerobic gram-negative organisms,
group D streptococci, and anaerobic organisms were isolated
in cultures of specimens obtained from wounds at the time
of initial injury.5 Infection was more often associated with
severe injuries of the large bones of the extremities than
with amputation injuries of the digit. The authors concluded
that early, aggressive surgical debridement and antimicrobial
therapy guided by tissue culture and in vitro susceptibility
testing at the time of debridement is optimal because of
polymicrobial invasion of the injured, vascularly
compromised tissue.
The purpose of this study was to determine the
microbiology and risk of infection following open,
agricultural, upper extremity injuries. Specifically, we sought
to evaluate the microbiology of the wounds at the time of
initial treatment and development of any subsequent
infections, determine whether the development of
subsequent infection was related to injury severity, and
clarify whether the microorganisms isolated at the time of
initial treatment and development of subsequent infection
were susceptible to the initial antibiotic prophylaxis.
MATERIALS AND METHODS
After internal review board approval, all patients with open,
agricultural upper extremity injuries were identified using a
Midwestern, level 1 hospital emergency department
database. Between January 1992 and December 2002, 232
patients were identified who met the inclusion criteria of an
open wound, upper extremity involvement, agricultural
injury, initial treatment at our facility, and who consented to
have their medical records reviewed. Eighteen patients were
subsequently excluded for not having an open injury or for
failure or refusal to consent to have their medical records
reviewed, yielding 214 patients that were studied.
JHS 䉬 Vol A, January 
We conducted a retrospective review of the medical
record. Information including patient demographics, injury
date, injury severity and etiology, antibiotic use, surgical
treatment, infection complications, and culture results were
collected.
A three-tier classification scheme (1–3) was devised,
based on the extent of injury to the involved limb, amount
of soft tissue damage, compromised vascularity, and wound
contamination (1 being the least severe and 3 being most
severe). This grading system is a variation of the Gustilo and
Anderson classification system for long bone fractures.6,7
The emergency department and surgical descriptions of each
injury were reviewed and categorized into 1 of the 3 types
of injury (Table 1).
Wound cultures were obtained according to the treating
surgeon’s discretion at the time of initial injury. Patients
who developed clinical wound infection were identified,
and their infections were classified as superficial infection,
deep soft tissue infection, or osteomyelitis. Superficial soft
tissue infections were limited to infections involving the skin
and overlying fat tissues (ie, cellulitis). Deep soft tissue
infections involved the fascia and underlying soft tissues such
as muscles and tendons. Osteomyelitis was identified when
bone was in communication with infected soft tissues and
subject to confirmation with gram stain, culture, or
pathology.8 Cultures were obtained in those patients with
infection who demonstrated clinical signs and symptoms of
infection and returned to the operating room for further
debridement.
The usual routine prophylaxis utilized during this period
of study at this medical center was a first-generation
cephalosporin with an aminoglycoside, with or without
additional intravenous penicillin G. There was no standard
protocol in place, however, for antimicrobial prophylaxis
during this time period. In patients who had initial cultures
obtained within 24 hours of injury or who developed
subsequent wound infection, the prophylactic regimen was
reviewed by our infectious diseases physician (D.R.O.). The
known in vitro activity of the prophylactic antibiotics used
were compared to the culture and in vitro susceptibility
results of tissue and wound cultures taken in the first 24
hours after the injury, as well as those obtained at the time
of treatment/debridement of any subsequent infection.
Patient Demographics
The mean patient age was 41 years (range 1–78 y). Two-
hundred and one of the patients were male and 13 were
female. The injuries were most commonly caused by a farm
auger (64), followed closely by power take-offs and hay
balers (56 and 41, respectively). The most common month
of injury was October, corresponding to the harvest season
in the upper Midwest. Fifty-four of the agricultural injuries
in this study occurred during October.
STATISTICAL ANALYSIS
The statistical analysis focused primarily on the development
of infection. In order to properly account for the variability
 MICROBIOLOGY OF UPPER EXTREMITY FARM TRAUMA
TABLE 1: Classification Scheme of Open Agricultural Upper Extremity Injuries Based on Severity of the Injury and
Percentages of Each Wound Type Reported in This Series
Wound Type Injury Description
1 Laceration with minor soft tissue injury,
clean grade I open fracture
2 Deep laceration with tendon, nerve, or
blood vessel injury, crushing injury,
contaminated open fracture grade I or
clean II open fracture
3 Traumatic complete amputation proximal
to distal interphalangeal joint of more
than one digit, excessive skin and soft
tissue loss
in the timing and occurrence of the infections, as well as
patient follow-up evaluation, the risk of development of
subsequent wound infection was estimated and analyzed as a
time-to-event outcome. Specifically, the method of Kaplan
and Meier was used to estimate the risk of infection,9 and
the severity of injury was evaluated using log-rank tests.10
All statistical tests were two-sided, and the threshold of
statistical significance was set at p⫽.05.
RESULTS
Initial Injury Microbiology
Of the 214 patients, 37 had aerobic wound cultures
obtained within 24 hours of injury; 16 of these 37 patients’
aerobic cultures yielded at least 1 microorganism. Twenty-
nine of the 214 patients had anaerobic cultures obtained; 3
of these 29 patients’ anaerobic cultures yielded at least 1
microorganism. Eight of the 214 patients had fungal cultures
obtained; 4 of the 8 yielded fungal growth. Three of these
were type 3 injuries, and 1 was a type 2 injury.
Microbiology and Classification of Clinical
Infections
Of the 214 patients studied, 40 developed clinical signs and
symptoms of infection. Of these 40, 17 developed superficial
soft tissue infection, 16 developed additional deep soft tissue
infections, and 7 developed osteomyelitis. Fourteen of the
214 patients had culture evidence of bacteremia.
Twenty-six of these 40 patients were returned to the
operating suite for further debridement. At that time,
additional deep tissue cultures were obtained (Table 2) in all
of these patients. All patients with an infection had at least 1
microorganism isolated from aerobic, anaerobic, or fungal
cultures. Of the 26 patients, 14 patients’ aerobic,
intraoperative cultures yielded at least 1 microorganism, 7
patients’ anaerobic cultures yielded at least 1 microorganism,
and 8 patients’ fungal cultures were positive (8 of 22
cultures). Ten infections were polymicrobial.
JHS 䉬 Vol A, January 
89
Clinical Example Number
Distal phalanx fracture with nailbed 26
laceration
Avulsing ring finger amputation at 94
metacarpophalangeal joint
Mutilating upper extremity injury 94
Injury Severity Classification and Distribution
Of the 214 patients, there were 26 type 1 injuries, 94 type 2
injuries, and 94 type 3 injuries. The overall number of
patients who developed infection within the first 6 months
following injury was 40 (Fig. 2). The mean duration of
follow-up examination after injury was 6 weeks (range
10 d–9 mo). The majority of wound infections developed
within 1 month of injury and all within 6 months. The
infections that occurred after 1 month following injury
included no superficial ones, 3 deep tissue infections, and 2
cases of osteomyelitis.
Six of the 214 patients required an amputation to
manage their injury. Three of these patients needed a
below-elbow amputation. All of these were type 3 injuries.
Two patients were managed with digital amputations. These
were all type 2 injuries. Another patient required a digital
revision amputation due to recurrent infection. This was
also a type 3 injury. In this series, there was 1 soft tissue flap
failure due to infection of a total of 18 performed. This also
occurred in a patient with a type 3 injury.
Wound Severity and Subsequent Infections
There was a notable trend between the severity of the
injury and the likelihood of developing clinical infection that
did not reach statistical significance (Fig. 3). The number of
patients who developed infection at 6 months following
injury was 2, 14, and 24 for type 1, 2, and 3 injuries
respectively (p⫽.07).
In the patients with type 1 injuries (26 of 214) there were 2
subsequent infections (Fig. 3). Both of these were superficial
soft tissue infections and developed within 1 month of injury.
In the patients with type 2 injuries (94 of 214) there were 14
clinical infections. Nine of these were diagnosed as superficial, 4
as deep soft tissue infections, and 1 was a case of osteomyelitis.
In the patients with type 3 wounds (94 of 214), there were 24
clinical infections. Six of these were superficial infections, 12
were deep soft tissue infections, and 6 patients were diagnosed
with osteomyelitis. The types of infections that were diagnosed
after 1 month from injury included 3 deep tissue infections and
90 MICROBIOLOGY OF UPPER EXTREMITY FARM TRAUMA

2 cases of osteomyelitis (Fig. 4). These data are summarized in TABLE 2: Microbes From 26 Infections Following
Table 3. Open, Upper Extremity Agricultural
Injuries That Had Surgical Debridement
Correlation of Spectrum of Antimicrobial
and Culture Acquisition
Prophylaxis and Initial Injury Microbiology
Seven patients had initial cultures taken and were treated Number of
with prophylactic antibiotics. Two of 7 patients were found Microorganism Patients
to have microorganisms resistant to the initial antibiotic
prophylaxis. The status of 4 patients was unable to be Aerobes
determined due to in vitro susceptibilities not being Coagulase negative Staphylococci 12
performed by the microbiology laboratory on the Enterobacter spp. 11
microorganism(s) isolated from the initial wound cultures.
Stenotrophomonas maltophilia 7
One patient had no growth from his initial cultures.
Staphylococcus aureus 6
Correlation of Spectrum of Antimicrobial Pseudomonas aeruginosa 6
Prophylaxis and Subsequent Infection
Serratia marcescens 5
Microbiology
Bacillus sp. 3
All 26 patients who had surgical management of their
infection had at least 1 microorganism identified as a Proteus mirabilis 2
pathogen. Ten of the 26 infections were polymicrobial, and Eikenella corrodens 1
7 had at least 1 species of fungus identified as a potential Viridans group streptococci 1
pathogen, although only 22 patients had fungal cultures
Other 8
obtained. Twenty-three of 26 patients who developed
infection and who had intraoperative cultures obtained as Anaerobes
part of the management of their infection had at least 1 Clostridium glycolicum 2
microorganism isolated that was resistant to the initial Peptostreptococcus sp. 2
prophylactic antibiotic regimen. No patients had positive
Propionibacterium sp. 2
fungal cultures in the absence of concomitant bacterial
growth. Gram positive rod (not identified 1
Twenty of the 26 patients who had deep tissue cultures further)
obtained for clinical wound infection had antimicrobial Fungi
susceptibilities obtained from these intraoperative cultures. Candida sp. 8
Nineteen of the 20 patients demonstrated growth of 1 or
Aspergillus sp. 7
more organisms that were resistant to cefazolin, a commonly
used first-line intravenous antibiotic. Absidia/Mucor sp. 6
Trichosporum sp. 2
DISCUSSION
Acremonium sp. 1
Little data is available concerning the modern microbiology
of infection resulting from open agricultural upper extremity Fusarium sp. 1
injuries. Fitzgerald and Cooney’s study in 1977 Geotrichum sp. 1
demonstrated that the organisms encountered in agricultural Penicillium sp. 1
infections differ from those found in other trauma Sporoblomyces sp. 1
situations.4 The organisms had a higher tendency to be
gram-negative and resistant to first-line antimicrobial agents Trichoderma sp. 1
such as penicillin. Moreover, these authors determined that Of the 40 patients who developed clinical infection, 26 had surgical
prophylactic antibiotics were not necessary, provided that debridement and acquisition of deep wound cultures managed with
surgical debridement (n ⫽ 26). For example, of the 26 patients in
the wound was managed appropriately with thorough whom intraoperative cultures were obtained, 12 separate patients grew
surgical irrigation and debridement. In a follow-up study, coagulase negative staphylococcus in culture. Of these patient cultures,
these authors also assessed the utility of trauma wound gram 10 were polymicrobial and 8 demonstrated fungal growth. Fungal
growth was not observed in isolation.
stains and cultures in predicting subsequent wound
infections.11 While the authors found cultures and gram
stains helpful, subsequent studies have been more
equivocal.12,13 improved outcomes when patients were treated with
Earlier studies showed no beneficial effects of antibiotics prior to surgery.16,17 The issue remains a
administering prophylactic antibiotics as part of routine controversial one with respect to orthopedic trauma.18
orthopaedic surgery.14,15 In the 1960s, however, studies in Regardless of etiology, antibiotic prophylaxis for open
orthopedic surgery and general surgery clearly demonstrated fractures is not nationally standardized. After the reports by

JHS 䉬 Vol A, January 


50
40
Percent (%)
30
20
20
18%
15
10
0
0 1 2 3
Months From Injury
FIGURE 2: Kaplan-Meier analysis of clinical infection for the 6-
month period following traumatic agricultural injury.
Cellulitis
12
Osteomyelitis
ents
9
6 Two patients experienced cellulitis
Number
3
0 2
FIGURE 3: Proportion of patients who developed any type of wound
infection, stratified by injury severity following open upper extremity
agricultural injury.
Gustilo et al in the 1970s,6 antibiotic prophylaxis for open
tibia fractures was recommended and encouraged. In upper
extremity trauma, the issue remains unresolved, largely due
to the heterogeneous nature of these injuries. With use of
antimicrobials becoming more widespread in society (as
evidenced by its inclusion in animal feeds19 and the
common use of antifungal and antibacterial medications and
cleansers20), however, we sought to reevaluate the
microbiology of wounds following open upper extremity
agricultural injury.
Although many wound cultures obtained within 24
hours of injury in our study demonstrated growth of
aerobic, anaerobic, and fungal organisms, the importance of
these initial culture results remains uncertain because only a
minority (37 of 214) of the patients in our study had wound
cultures performed within 24 hours of injury, and only 7
patients who had wound cultures obtained within 24 hours
of injury also received antimicrobial prophylaxis. Thus, we
cannot with any degree of certainty correlate the risk of
wound infection with the results of the initial wound
culture or the in vitro activity of the initial antimicrobial
prophylaxis with the development of wound infection based
on the data in this study. We recognize this limitation of
retrospective studies and recommend prospective studies
with protocols that standardize initial culture procurement at
the time of injury and standardize administration of
MICROBIOLOGY OF UPPER EXTREMITY FARM TRAUMA 91
50
40
p = .07
Percent (%)
30
Ty
20
Ty
10
Ty
22 22% 0
0 1 2 3 4 5 6
Months From Injury
FIGURE 4: Kaplan-Meier analysis of clinical infection for the 6-
4 5 6 month period following traumatic agricultural injury, subclassified
based on severity of injury.
TABLE 3: Clinical Infection Summary
Wound
Type Key Findings
1 Two patients experienced overall incidence
of clinical infection
No patients experienced deep tissue/bone
infections
Fourteen patients experienced overall
incidence of clinical infections
Nine patients experienced cellulitis
Four patients experienced deep soft tissue/1
patient experienced osteomyelitis
3 Twenty-four patients experienced overall
incidence of clinical infection
Six patients experienced cellulitis
Twelve patients experienced deep soft tissue/
6 patients experienced osteomyelitis
Increased risk of deep tissue infection and osteomyelitis correlates with
wound severity.
prophylactic antibiotics. Findings from these studies will help
determine whether initial cultures are useful in predicting
the subsequent risk of clinical infection and the most
effective method of antimicrobial prophylaxis.
Despite this limitation, there were several important
findings. In a majority of patients who developed wound
infection after injury and who had intraoperative cultures
obtained, there was at least 1 microorganism isolated that
was resistant to the initial antimicrobial prophylaxis regimen.
Based on the findings of this study, we recommend broad-
spectrum, empiric antibiotic therapy for open agricultural
injuries that develop clinical infection and require surgical
debridement. This scenario was present in 26 of the 40
infections in this study and 24 of type 3 injuries. The timing
of antibiotic administration should reflect the severity of the
wound. Patients with type 2 and 3 wounds that will require
some form of surgical debridement should receive antibiotics
on arrival in the emergency department; patients with type
1 wounds would possibly also benefit, but also may be
JHS 䉬 Vol A, January 
92 MICROBIOLOGY OF UPPER EXTREMITY FARM TRAUMA
followed up clinically and antibiotics continued only if signs
or symptoms of become apparent. The directed
antimicrobial regimen for the treatment of infection should
be based on culture and in vitro susceptibility data from the
tissue cultures obtained at the time of surgical debridement.
Based on the culture and the in vitro susceptibility results of
our intraoperative deep tissue cultures obtained from the
infections that were managed surgically at our institution,
we recommend that an initial, empiric antimicrobial
regimen for infection following agricultural injuries that
require surgical management be active against staphylococci,
Pseudomonas aeruginosa, Enterobacter, anaerobes, and
potentially, Stenotrophomonas maltophilia. The exact
antimicrobials used to achieve this spectrum of empiric
therapy should be tailored to the clinician’s institution based
on local resistance patterns and hospital formulary.
At this time, we do not believe that there are enough
data to recommend empiric antifungal therapy for all
infections following upper extremity agricultural injuries that
require surgical management. Although 4 of the 8 patients
who had initial fungal cultures obtained demonstrated fungal
microorganisms in culture, this is likely a biased subset of the
entire study population and the relevance of these findings
cannot be determined, especially because no patient
developed an infection known to be due to an isolated
fungus in the absence of bacteria. The possibility of fungal
contamination or colonization cannot be determined from
these limited data. Thus, these data cannot be used to give
definitive recommendations on antifungal therapy.
In addition, only 8 of the 26 patients with
subsequent infection demonstrated fungal organisms in
culture (8 of the 22 patients who had fungal cultures
obtained). Additional data and a larger sample size are
needed to determine the role of fungi in the
pathogenesis of infection following open, agricultural
upper extremity injury. Because fungal infection does
occur following these injuries, however, we currently
recommend a high suspicion for fungal infection in
patients with agricultural upper extremity injury who
have surgical debridement for subsequent infection.
We advocate obtaining both fungal cultures of infected
tissues and tissue specimens for pathological review to
look for evidence of infection. Empiric fungal therapy
pending these data should be based on the gross
appearance of the wound (ie, presence of obvious
fungal infection or invasion by surgical inspection,
evidence of tissue invasion by fungi on pathologic
examination of infected tissues, the ability of the
surgeon to do a thorough debridement, as well as local
and systemic host factors that would favor fungal
infection (ie, tissue hypoxia, diabetes mellitus, and
steroid use). Fortunately, there are now new antifungal
agents with activity against Aspergillus spp, Mucor, and
Candida spp other than amphotericin B deoxycholate
that may have some role in the treatment of these
JHS 䉬 Vol A, January 
infections, although data on the clinical efficacy in
these situations are extremely limited.21
This study also suggests that open, agricultural upper
extremity injuries have a likelihood of clinical infection
corresponding to the severity of the injury as classified by
our injury severity score. Type 3 injuries had a greater than
3-fold increased risk of infection compared to type 1
injuries, although the difference did not reach statistical
significance. This is a simple grading system that is easily
calculated by the treating surgeon. This correlation needs to
be further validated.
Recommendations
Based on the findings of this study, we recommend
broad-spectrum, empiric antibiotic therapy for open
agricultural injuries that develop clinical infection and
require surgical debridement. The directed
antimicrobial regimen for the treatment of infection
should be based on culture and in vitro susceptibility
data from the tissue cultures obtained at the time of
surgical debridement. We recommend an initial,
empiric antimicrobial regimen against staphylococci,
Pseudomonas aeruginosa, Enterobacter, anaerobes, and
potentially, Stenotrophomonas maltophilia. At this time,
we do not believe that there are enough data to
recommend empiric antifungal therapy for all
infections following upper extremity agricultural injury
that require surgical management, but we recommend
high suspicion for fungal infection in these injuries and
empiric treatment based on clinical examination or
laboratory testing (culture or pathology).
Management of open agricultural upper extremity
injuries can be complicated, and a multidisciplinary
approach, including infectious disease specialists and
surgeons, is often required, particularly when infection
develops. The microbiology of infections that result from
these injuries is often polymicrobial, and the risk of infection
can be predicted based on a simple classification scheme.
Prospective studies are needed to determine the optimal
prophylactic antimicrobial therapy for these injuries and
directed antibiotic regimens for the wound infections that
may develop.
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