Infections caused by anaerobic bacteria are common, and may be serious and life-threatening. Anaerobes predominant in the bacterial flora of normal human skin and mucous membranes, and are a common cause of bacterial infections of endogenous origin. Infections due to anaerobes can evolve all body systems and sites. The predominate ones include: abdominal, pelvic, respiratory, and skin and soft tissues infections. Because of their fastidious nature, they are difficult to isolate and are often overlooked. Failure to direct therapy against these organisms often leads to clinical failures. Their isolation requires appropriate methods of collection, transportation and cultivation of specimens. Treatment of anaerobic bacterial infection is complicated by the slow growth of these organisms, which makes diagnosis in the laboratory only possible after several days, by their often polymicrobial nature and by the growing resistance of anaerobic bacteria to antimicrobial agents.

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Neonatal infections: conjunctivitis, dacryocystitis, parotitis, sialadenitis, cephalohematoma, pneumonia, ascending cholangitis, bacteremia


The incidence of infection in the fetus and newborn infant is high. As many as 2% of fetuses are infected in utero and up to 10% of infants are infected during delivery or in the first few months of life. The predominant microorganisms known to cause these infections are cytomegalovirus, herpes simplex virus, rubella virus, Toxoplasma gondii, Treponema pallidum, chlamydia, group B Streptococcus,  Enterococcus spp., Escherichia coli, and anaerobic bacteria. All of these agents can colonize or infect the mother and infect the fetus or newborn either intrauterinely or during the passage through the birth canal. Although anaerobic bacteria cause a small number of these infections, the conditions predisposing to anaerobic infections in newborns are similar to those associated with aerobic micro-organisms. Furthermore, the true incidence of anaerobic infections may be underestimated because techniques for the recovery and isolation of anaerobic bacteria are rarely used, or are inadequate. Several factors have been associated with acquisition of local or systemic infection in the newborn. Most of these factors are vague and difficult to define; however, most studies have described the presence of one or more risk factors in the pregnancy and delivery of these infants: premature and prolonged rupture of membranes (longer than 24 hours), maternal peripartum infection, premature delivery, low birth weight, depressed respiratory function of the infant at birth or fetal anoxia, and septic or traumatic delivery.1–3
Maternal infection at the time of delivery, can be associated with the development of infection in the newborn. Transplacental hematogenous infection that can spread before or during delivery is another way in which the infant can be infected.4 The acquisition of infection while the newborn passes through the birth canal is, however, the most frequent mode of transfer.
During pregnancy the fetus is shielded from the flora of the mother’s genital tract. Potentially pathogenic bacteria are found in the amniotic fluid (AF) even when the membranes are intact. Prevedourakis et al5 documented bacterial invasion of the intact amnion in nearly 8% of the pregnant women in their sample, but this was of no consequence to the mother or the newborn infant. It was suspected that the AF may have antibacterial properties, probably owing to lack of nutritional factors.5,6 The AF actively inhibited the growth of aerobic bacteria, through a phosphate-sensitive cationic protein that is regulated by zinc. 7 Its activity was independent of the muramidase and peroxidases and spermine. The pH of the amniotic fluid is the only variable predictive of bacterial growth in amniotic fluid in a laboratory model.8
The antimicrobial properties of the AF also vary with the period of gestation; it is the least inhibitory against E. coli and Bacteroides fragilis during the first trimester and most inhibitory during the third trimester.8,9 The relative scarcity of the B. fragilis population in the cervix at term labor and the added inhibitory effect of the AF at term may together explain the relatively low incidence of B. fragilis infections at full term as compared to postabortal sepsis.10–12
Following the rupture of the membranes, the colonization of the newborn is initiated4 by further exposure to the flora during the infant’s passage through the birth canal. When premature rupture of the membranes occurs, the ascending flora can cause infection of the amniotic fluid with involvement of the fetal membranes, placenta, and umbilical cord.13 Aspiration of the infected amniotic fluid can cause aspiration pneumonia. Since anaerobic bacteria are the predominant organisms in the mother’s genital flora,14 they become major pathogens in infections that follow early exposure of the newborn to that flora.
Genetic factors may be responsible for the predominance of sepsis in the newborn male.15 The immaturity of the immunologic system, which is manifested by decreased function of the phagocytes and decreased inflammatory reactions, may also contribute to the susceptibility of infants to microbial infection.16,17 The presence of anoxia and acidosis in the newborn may interfere also with the defense mechanisms.
The support systems and procedures used in regular nurseries and intensive care units can facilitate the acquisition of infections. Offending instruments include umbilical catheters, arterial lines, and intubation devices. Contamination of equipment such as humidifiers and supplies such as intravenous solutions and infant formulas and poor isolation techniques can result in outbreaks of bacterial or viral infections in nurseries. Such spread is thought to contribute to clustering of cases of necrotizing enterocolitis in newborns.


Conjunctivitis and Dacryocystitis

Conjunctivitis: Conjunctivitis in the newborn infant usually is due to chemical and mechanical irritation caused by the instillation of silver nitrate drops or ointment into the eye in order to prevent gonorrheal ophthalmia. Chemical conjunctivitis differs from infective forms in that it becomes apparent almost immediately after the instillation. The most common causes of infectious conjunctivitis in descending order of frequency are Chlamydia trachomatis, Neisseria gonorrhoeae, Staphylococcus, inclusion conjunctivitis caused by groups A and B Streptococcus, Enterococcus, Streptococcus pneumoniae, Haemophilus influenzae, Pseudomonas aeruginosa, Escherichia coli, Moraxella catarrhalis, Neisseria meningitidis, Corynebacterium diphtheriae, herpes simplex virus, echoviruses, and Mycoplasma hominis.. Clostridia and peptostreptococci were implicated as probable causes of neonatal conjunctivitis.18
The classical ophthalmia neonatorum caused by N. gonorrhoeae is an acute purulent conjunctivitis that appears from two to five days after birth. If untreated, the infection progresses rapidly until the eye becomes puffy and the conjunctiva is intensely red and swollen. The subsequent outcome would be corneal ulceration. Ophthalmia caused by organisms other than gonococcus, including Clostridium spp., occurs usually from 5 to 14 days following delivery, is indistinguishable clinically, and the conjunctival inflammatory reaction usually is milder than in ophthalmia caused by gonococci.
The conjunctiva of newborns acquires facultative and anaerobic bacteria during birth primarily from the mother’s cervical flora during passage through the birth canal. The role of anaerobes in neonatal conjunctivitis was investigated by obtaining conjunctival cultures from 35 babies prior to silver nitrate application and 48 hours later. 19  On initial culture, 46 facultative bacteria and 27 anaerobes were recovered. The organisms isolated in almost all of these cases were present also in the mother’s cervical cultures and in the baby’s gastric aspirates, taken concomitantly.
Isenberg et al20 who studied 106 infants, 50 delivered by cesarian section, and 56 delivered vaginally illustrated that those delivered by cesarean section had significantly fewer bacterial species and total number of organisms per subject than the infants delivered vaginally. The conjunctivae of infants delivered vaginally had significantly more bacteria characteristic of vaginal flora.
Clostridium spp. were recovered from two infants who developed conjunctivitis.14,18 Clostridium perfringens was recovered from one newborn, and Clostridium bifermentans with Peptostreptococcus spp. were recovered from the other infant with neonatal conjunctivitis. Similar organisms were recovered from the mother’s cervix immediately after delivery. These infections were noted on the second and third day postdelivery. The conjunctivitis was characterized by a profuse yellow-green discharge and the eyelids were edematous in both newborns, and there were no other abnormal findings. Local therapy was initiated with 2% penicillin eye drops (two drops every two hours). The conjunctivitis subsided within three days, and repeat cultures of the eyes after 10 days were sterile. The babies were followed for three months with no residual of infection noted.
Of interest is that the silver nitrate solution of 1% currently used in newborns was efficacious in preventing in vitro growth of clostridia. However, in a concentration of 0.1% or lower, it was only bacteriostatic or ineffective. The common practice of rinsing the eyes with distilled water after the addition of silver nitrate to prevent chemical conjunctivitis may alter the ability of this solution to effectively inhibit certain strains of Clostridium spp.
Because anaerobic bacteria have been recovered from children22 and adults23,24 suffering from bacterial conjunctivitis, their presence in neonatal conjunctivitis is not surprising. These organisms, however, are not the most prevalent cause of inflammation of the eye in these age groups. Their presence should be suspected in children whose aerobic and chlamydial cultures are negative, in those who do not respond to conventional antimicrobial therapy, and in those at high risk of developing anaerobic infection (i.e., the presence of maternal amnionitis or premature rupture of membranes).
The experience acquired from the documented cases of anaerobic conjunctivitis indicates that local therapy with appropriate antimicrobial agents is generally adequate.




Conjuctivitis newborn


Dacryocystitis: The predominant bacteria causing acute dacryocystitis in neonates are aerobic organisms such as Streptococcus pneumoniae and Staphylococcus aureus,25,26 Anaerobic bacteria have been rarely recovered in these patients.27 We recently reported two newborns who developed acute dacryocystitis caused by anaerobic bacteria.28
Peptostreptococcus micros and Prevotella intermedia were recovered in one newborn, and Peptostreptococcus magnus and Fusobacterium nucleatum in the other. Parenteral therapy was given to both newborns and the first patient had surgical drainage. The anaerobes isolated are likely of endogenous origin because they are members of the normal oral and skin flora29 and normal conjunctival flora.30,31
The actual prevalence of these organisms in dacryocystitis in infants has yet to be investigated by prospective studies. This is of particular importance because these organisms are often resistant to the antimicrobials used for therapy of dacryocystitis. We elected to treat the patients for at least 21 days to achieve complete eradication of the infection. It is recommended that specimens of dacryocystitis be cultured for both aerobic and anaerobic bacteria so that proper antimicrobial therapy can be directed against the pathogens.





Dacryocystitis newborn



Suppurative parotitis and sialadenitis

Staphylococci are the usual bacterial etiology of suppurative parotitis and sialadenitis in newborns. Anaerobic bacteria from aspirates of the infected gland in two infants with suppurative parotitis. Peptostreptococcus intermedius and Prevotella melaninogenica were isolated from one child and Prevotella intermedia from the other patient. 31a   Complete recovery occurred after 4 weeks of antimicrobial therapy.
Anaerobes were recovered from aspirates of an infected salivary gland in 2 newborns with suppurative sialadenitis.  Peptostreptococcus magnus, Prevotella intermedia and Streptococcus pyogenes were isolated from one newborn and Prevotella melaninogenica and Fusobacterium nucleatum  from the other patient. 31b  Complete recovery occurred following surgical drainage and antimicrobial therapy.
  These reports illustrates the potential importance of anaerobes in acute suppurative sialadenitis in newborns. The isolation of anaerobes is not surprising since these bacteria are the predominant organisms in the oropharynx where they outnumber aerobes in the ratio of 10 to 1 to 100 to one in the neonate as well , and are important pathogens in other suppurative infection in and around the oropharynx. Prevotella spp. are the most common anaerobic Gram-negative bacilli found in oral flora and like Fusobactrium and  Peptostreptococcus spp., are frequently isolated from odontogenic orofacial infections.




Suppurative parotitis newborn



Suppurative sialadenitis newborn


Cephalohematoma

Cephalohematomas are rare complications that occur in less than 3% of all deliveries and are associated with instrumented delivery and prolonged labor. Six newborns with cephalohematoma infected by anaerobes were reported. 31c Polymicrobial infection was present in all instances, where the number of isolates varied from two to four. Two patients had anaerobes only and the other four had mixed flora of strict anaerobes and facultatives. There were 16 bacterial isolates (12 anaerobic, 4 aerobic). The anaerobic isolates were Peptostreptococcus spp. (5 isolates), Prevotella spp. (4), B. fragilis group (2), and Propionibacterium acnes (1). The aerobic isolates were E. coli (2), S. aureus (1) and group B streptococci (1). Blood cultures were positive for three patients.
The most common predisposing conditions were vacuum extraction and amnionitis (4 instances of each), instrumental delivery (3), electronic fetal monitoring (2), prolonged delivery (1), and premature rupture of membranes (1). All patients underwent drainage, and four also had surgical incision and drainage. Osteomyelitis developed in one instance and scalp abscess developed in two patients, both of whom had electronic fetal monitoring. All patients eventually recovered from infection after receiving parenteral and subsequent oral antibiotic therapy for a total of 14-38 days. This report highlights the polymicrobial nature and potential importance of anaerobic bacteria in infected cephalohematoma in newborns.



Cephalohematoma in a newborn

Pneumonia

Pneumonia in the newborn can be classified according to the mode of acquiring the infection and the time when the infection takes place. The infection can be acquired in utero by transplacental route or following intrauterine infection. The pneumonia could be acquired during delivery by aspiration of bacteria that colonize the birth canal. The type of infection contracted after birth is acquired by contact with environmental objects (e.g., a tracheostomy tube) or by human contact. Aspiration can occur in up to 80% of intubated premature infants 32 and is common newborns with gastroesophageal reflux 33 or those who require general anesthesia 34 and have swallowing dysfunction. 35
Congenital and intrauterine pneumonia usually is caused by viruses such as herpes simplex, cytomegalovirus, or rubella, and can be caused also by intrauterine exposure to Treponema pallidum, Mycobacterium tuberculosis, or Listeria monocytogenes. Aspiration during delivery or after intubation can be caused by the mother’s vaginal flora, and the patient’s oral flora once that had developed. Early neonatal pneumonia is mainly caused by bacteria, group B streptococcus, Escherichia coli and listeria being the most frequently involved; 36 Herpes simplex is the main viral agent. These agents may also be responsible for late forms, as do Chlamydia trachomatis and the pathogen agents of community acquired pneumonia.
.
During vaginal delivery, the neonate is exposed to the cervical birth canal flora, which includes both aerobic and anaerobic bacteria. Almost every normal baby born by vaginal delivery swallows potentially pathogenic aerobic and anaerobic bacteria.19 These bacteria can be cultured in the infant's gastric contents. In a few instances, especially in high-risk infants, aspiration of, or exposure to, these organisms can lead to the development of infections. The diagnosis of bacterial pneumonia can be achieved by cultures of tracheal aspirate, pleural fluids, needle aspirates of the lungs, and blood cultures.
The major bacterial causes perinatal pneumonia are Enterobacteriacae, Staphylococcus aureus, group B beta-hemolytic streptococci,  group D streptococci, and alpha-hemolytic streptococci 36 In approximately 40% of the cases previously reported, no organisms were recovered at necropsy. Although the role of anaerobes as a cause of pulmonary infection in adults is well established 37 only two reports 38,39 described the isolation of Bacteroides fragilis from children with perinatal pneumonia.
Harrod and Stevens 38 described two newborns who presented with neonatal aspiration pneumonia that developed following maternal amnionitis. B. fragilis was recovered from the blood of these children.
Brook, et al.39 reported three newborns with neonatal pneumonia caused by B. fragilis group. The mothers of all three infants had premature rupture of their membranes and subsequent amnionitis. The maternal membranes ruptured more than 24 hours before delivery, and the amniotic fluid was foul smelling. Organisms identical to those recovered from the newborns were recovered from the amniotic fluid of two of the mothers. In all three instances, the organisms were recovered from tracheal aspirates and in two from blood cultures as well. Two of the newborns were treated with ampicillin and gentamicin but succumbed to their infections; one of these infants also had meningitis. The third baby, treated with clindamycin, recovered.
Anaerobic Gram negative bacilli (e.g. Prevotella, Porphyromonas and Bacteroides sp.) are part of the normal flora of the female genital tract.19 These organisms are involved frequently in ascending infections of the uterus and have been recognized as pathogens in septic complications of pregnancy, such as amnionitis, endometritis, and septic abortion, and from infection in other clinical settings.40 Amnionitis may develop prior to delivery resulting in an early exposure of the infant to the offending organism(s). Furthermore, the relative immaturity of the cellular and humoral immune systems of the newborn may permit localized infections to invade the blood stream.
Tracheal aspirates of infants who have recently had an endotracheal tube placed may be useful for diagnosing pneumonia and for identifying the causative agent.41 Repeated aspirates can reveal the presence of newly acquired organisms that may cause the pneumonia. 42
Pulmonary anaerobic infections tend to occur in association with aspiration, tissue anoxia, and trauma. Such circumstances usually are present in high-risk newborns, which make them more vulnerable to anaerobic pneumonia, especially in the presence of maternal amnionitis.
In most instances, a beta lactam antibiotic and one of the aminoglycosides are administered for treatment of infection or pneumonia in newborns. While most anaerobic organisms are susceptible to penicillins, members of the B. fragilis group and growing numbers of other anaerobic gram negative bacilli (e.g. pigmented Prevotella and Porphyromonas 43 can be resistant to these agents. The first two described newborns,29 who died of their infections, received the conventional antimicrobial therapy of a combination of ampicillin and gentamicin that was inappropriate for their infection. The third newborn, however, received a broader coverage that included therapy with clindamycin, a drug shown to be effective in the treatment of anaerobic infections in adults44 and children.45 Because clindamycin does not penetrate the blood-brain barrier in sufficient quantities, it is not recommended for treatment of meningitis. Other antimicrobial agents with better penetration to the central nervous system, such as chloramphenicol, a carbapenem (i.e. imipenem), a combination of a penicillin plus a beta lactamase inhibitor or metronidazole, should be administered in the presence of meningitis.


Pneumonia in a newborn 


Ascending cholangitis following porto-enterostomy 

Extrahepatic biliary atresia is an obliterative cholangiopathy that involves all or part of the extrahepatic biliary tree and, in many instances, the intrahepatic bile ducts. In the United States, from 400 to 600 new cases of biliary atresia are encountered annually.46 The diagnosis is usually suggested by the persistence of jaundice for 6 weeks or more after birth. Several factors have been considered for the pathogenesis of extrahepatic biliary atresia, including viral infection (e.g. cytomegalovirus), 47 metabolic insults, and abnormalities in bile duct morphogenesis. Although selected patients benefit from prompt diagnosis and Kasai portoenterostomy surgical intervention48,49 within the first 60 days of life, many ultimately require liver transplantation because of portal hypertension, recurrent cholangitis, and cirrhosis. 50
Infection of the biliary tract and rarely liver abscess are a known complication following Kasai’s procedure. About half of the patients who undergo the Kasai procedure develope post surgical cholangitis .51 Most episodes occurred within 3 months of the operation. Factors associated with cholangitis included good or partial restoration of bile flow, abnormal intrahepatic bile ducts or cavities at the porta hepatis, and routine postoperative use of antibiotics. External jejunostomy is not effective in preventing cholangitis. Fever decreased bile flow, increased erythrocyte sedimentation rate and signs of shock are frequently observed.
Early bacterial studies of cholangitis following Kasai’s procedure revealed coliform bacilli, Proteus species, and enterococci to be the predominant isolates recovered from these patients.52,53 However, adequate culture methods for anaerobic bacteria were not performed in most of these studies. The largest study reporting the bacterial growth within the biliary tract following the Kasai operation was done by Hitch and Lilly,52 who studied 19 patients over 23 months, obtaining 283 cultures. These investigators used methods for recovery of aerobic as well as anaerobic bacteria and reported the colonization of all the biloenteric conduits with colonic flora within the first postoperative month. Escherichia coli, and Klebsiella, Enterococcus , Pseudomonas, Proteus, and Enterobacter spp. were the predominant aerobic isolates. Bacteroides spp., including B. fragilis, were recovered in 11% of the cultures. These authors report the recovery of similar organisms during episodes of cholangitis.
Studies in adults demonstrated that E. coli, klebsiellae, Enterobacter organisms, enterococci, and anaerobes (B. fragilis group and Clostridium spp. ) are the main isolates recovered from patients with biliary tract infection. 53-57
Brook and Altman studied the aerobic and anaerobic microbiology of the bile duct system in six children with cholangitis following Kasai’s procedure.58 Fourteen aerobic bacteria were recovered from all six specimens, and 3 anaerobic organisms were recovered from three. The predominant aerobes were Klebsiella pneumoniae (4 isolates), Enterococcus spp. (3), and E. coli (2). The anaerobes recovered were B. fragilis (2) and C. perfringens (one). Since that report, we have isolated anaerobes in three more patients, which were two strains of C. perfringens and one B. fragilis. These findings demonstrate the role of anaerobic organisms in cholangitis following hepatic porto-enterostomy.
The mechanism by which both aerobic and anaerobic bacteria reach the bile ducts in patients who had undergone Kasai’s procedure is probably by an ascending mode from the gastrointestinal tract. This mode of spread is favored by the surgical procedure that approximates a part of the jejunum to the bile system, by the lack of the normal choledochal sphincter action, and by the stasis that can develop after the surgery. Other mechanisms of development of cholangitis are transhepatic filtration of bacteria from the portal venous blood into the cholangiole and periportal lymphatic infection.
The anaerobes recovered in children with ascending cholangitis5,58 are part of the normal gastrointestinal flora in infants. The initial sterile meconium becomes colonized within 24 hours with aerobic and anaerobic bacteria, predominantly E. coli, Clostridium species, B. fragilis, and streptococci.59 The isolation rate of B. fragilis and other anaerobic bacteria in the gastrointestinal tract of term babies approaches that of adults within one week.59
Although the number of infants studied so far is small, the data suggest that anaerobes play a major role in cholangitis following Kasai’s procedure, and that specimens obtained from these patients should be cultured routinely for anaerobic as well as aerobic bacteria. It is conceivable that some of the reported failures of conventional antimicrobial therapy to cure patients with postsurgical cholangitis60 could be due to failure to use antimicrobial agents effective against anaerobic bacteria, especially those belonging to the B. fragilis group.
While most anaerobic organisms are susceptible to penicillins, members of the B. fragilis group are known to be resistant to these agents.42 In administering therapy to infected patients, consideration should be given to the possible presence of anaerobic organisms. It is reasonable, therefore, to treat children with this infection with antimicrobial agents effective also against B. fragilis and Clostridium sp., at least until results of cultures are known.



Extrahepatic biliary atresia



Anaerobic bacteremia in newborns

The awareness of the role of anaerobic bacteria in neonatal bacteremia and sepsis has increased in recent years. The incidence of recovery of anaerobes in neonatal bacteremia varies between 1.8% and 12.5% [61]. Of the 179 cases reported in the literature and reviewed by Brook [61], 73 were due to Bacteroides spp. (69 were the B. fragilis group), 57 Clostridium spp. (mostly C. perfringens), 35 Peptostreptococcus spp., 5 P. acnes, 3 Veillonella spp., 3 Fusobacterium spp, and 2 Eubacterium spp. 
Multiple organisms, aerobic and anaerobic, were isolated from eight patients reported in one study [62], anaerobic co isolates from 6 (5 Peptostreptococcus spp., one Veillonella parvula) and aerobic co isolates from only two (Escherichia coli and alpha-hemolytic streptococcus). In one patient, reported by Noel et al. [63], Bacteroides vulgatus was isolated from a single blood culture along with 4 aerobic bacteria (Streptococcus faecalis, E. coli, Streptococcus faecium and Klebsiella pneumoniae).
Simultaneous isolation of the anaerobes from other sites was reported by several authors [62-69]. This was especially common with B. fragilis and Clostridium spp.
Chow and co-workers [62] reported the simultaneous isolation of Bacteroides spp. from gastric aspirate in four instances, from the amniotic fluid or uterus at cesarean section in two cases, and from the maternal and fetal placental surfaces and the external auditory canal in one instance each.
Brook et al. [70] reported the concomitant recovery of B. fragilis group from lung aspirates of two patients with pneumonitis; Harrod and Sevens [71] recovered B. fragilis from the inflamed placenta; Dysant and associates [67] and Brook et al. [65], Kasik et al. [66] and Webber and Tuohy [72] recovered B. fragilis from the cerebrospinal fluid of a total of four patients with meningitis. Brook [65] isolated B. fragilis from an occipital abscess that developed following neonatal monitoring with scalp electrodes. Ahonkhai et al. [73] described the concomitant isolation of C. perfringens in the placenta of a newborn.

Kosloske et al. [74] recovered Clostridium spp., B. fragilis, and Eubacterium spp. from the peritoneal cavity of four patients with necrotizing enterocolitis. Brook et al. [68] isolated Clostridium difficile from the peritoneal cavity and the blood of a newborn with necrotizing enterocolitis. Other cases of concomitant isolation include Spark and Wike [75] who reported four cases of isolation of Clostridium spp. from omphalitis, Heidemann et al. [69] who recovered a gas forming C. perfringens in the cerebrospinal fluid of a newborn with meningitis, and  Freedman and Hollander who isolated C. perfringens in the blood of a newborn after abdominal surgery [76].




Newborn in intensive care unite

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