|
Guide to the Application of Genotyping to Tuberculosis Prevention
and Control
Return to Genotyping Main Menu
Applying Genotyping Results to Tuberculosis
Control Practices
Evaluating Matching Genotypes
The first step in responding to new genotyping results is to identify
any new genotyping matches contained in the laboratory report. The
genotyping laboratory will flag all isolates with matching spoligotypes
and MIRU types by assigning them a PCR cluster designation. Except
in rare instances, two persons who are involved in the same chain
of recent transmission will have isolates with matching genotypes;
conversely, two persons with nonmatching isolates are rarely involved
in the same chain of transmission (See Chapter 4, Combining Genotyping
and Epidemiologic Data to Improve Our Understanding of Tuberculosis
Transmission, for an explanation of the rare exceptions to these
rules).
Figure 6.1. Flow diagram describing the evaluation
of genotyping results. This diagram describes the action steps
(shown in grey boxes) that might result from an analysis of new
genotyping data.
Could Genotyping Matches be Due to False-Positive Cultures?
When new genotyping matches are reported, the first question to
pose is whether one or more of the matching isolates might represent
false-positive cultures? Since the discovery of a false-positive
culture may require that a patient’s treatment be stopped, the TB
program must maintain a high index of suspicion for the possibility
of false-positive cultures, and there should be no delay between
receiving new genotyping results and determining if any matches
might need further investigation.
False-positive cultures occur when M. tuberculosis bacteria
from one specimen, instrument, or culture inadvertently contaminate
another specimen or culture, when clerical errors occur and specimens
are mislabeled or misreported, or when data entry errors occur.
Clinical equipment (e.g., bronchoscopes, sputum collection booths,
and ultrasonic nebulizers), if inadequately cleaned, can become
contaminated and be the source of false-positive cultures (as well
as the source of nosocomial transmission). Cross contamination can
occur in the laboratory during batch processing, pipetting, transfer
of bacilli from a broth-culture system, work in a faulty exhaust
hood, and species-identification procedures.
One of the most important advantages of routinely fingerprinting
all M. tuberculosis isolates is the ability to establish
an early warning system to identify suspected false-positive cultures.
Although this discussion is based on the assumption that the suspected
false-positive culture was identified through a genotyping laboratory
report, this suspicion can also be raised by health-care providers
who receive a questionable culture result from a clinical laboratory,
from the laboratory itself when more than one M. tuberculosis
culture that was processed during the same time period become positive,
or by health department staff members who investigate TB cases.
The following text box lists the factors to look for in evaluating
whether a cluster might involve one or more false-positive culture
results. If any one of the factors listed in the text box are identified,
a false-positive culture investigation should be conducted immediately
(see Suspected False-Positive Culture Investigations later
in this chapter for details). Note that to evaluate the factors
listed, the TB program needs access to data about how and when the
specimens were processed and whether particular patients have only
one or more than one positive culture result. If these data are
not readily available at the time the genotyping matches are reported,
the TB program should update their data collection and management
procedures.
If this initial evaluation determines that the genotyping matches
do not represent a false-positive culture, the next step in the
decision analysis depicted in Figure 6.1 is to decide if patients
in the cluster share known epidemiologic links.
Summing Up:
False-Positive Cultures
Suspect that a genotyping match might represent a false-positive
culture if any of the following are true:
- The health-care provider or the clinical laboratory suspects
a false-positive culture
- A patient had only one positive culture among multiple
specimens obtained
- A patient did not have symptoms of TB
- A patient’s chest radiograph did not show findings consistent
with TB
- A patient had another confirmed diagnosis to explain
symptoms
- The specimens were processed in the same laboratory on
the same day
- The isolates were collected in the same hospital or clinic
within 3 days
- The spoligotype and MIRU patterns match those of laboratory
control strains (H37rv or H37ra) or laboratory proficiency
specimens
|
Action Steps for Genotyping Clusters with Known Epidemiologic
Links Identified
Known epidemiologic links (see Chapter 4, Combining
Genotyping and Epidemiologic Data to Improve Our Understanding of
Tuberculosis Transmission, for definitions of epidemiologic
links) between at least some of the members of the same genotyping
cluster suggest that they are part of the same chain of recent TB
transmission. The evidence in favor of recent transmission is strong
enough at this point in the decision analysis that it is usually
not necessary to collect additional data by requesting RFLP analyses
of the isolates or by conducting a cluster investigation for the
purpose of deciding on appropriate action (see Chapter 5, Developing
a Tuberculosis Genotyping Program, for exceptions to this rule).
Two possible action steps are described in this situation in Figure
6.1: a) expanding the contact investigations or b) initiating (or
expanding) an outbreak investigation. The decision about which step
to take is based on what is known about the cluster from previous
investigations and whether the cluster of cases has grown to be
an outbreak.
Deciding when an epidemiologically conformed genotyping cluster
has become an outbreak is always a challenge. The following text
lists characteristics of outbreaks that may help in this decision-making
process; an outbreak is likely occurring if any one of the following
criteria is met.
Three criteria for defining an outbreak
1. An increase in the expected number of TB cases.
Although this is a standard epidemiologic definition, it is at
times a challenge to apply, since the expected number of TB cases
in a specific setting is often difficult to know. This criterion
is more useful if it is applied to specific subgroups of persons
who share demographic characteristics or specific exposures rather
than to the population as a whole.
For example, two unrelated children with TB who go to the same
school and are in the same classroom would arguably meet the “unexpected
increase” criterion for an outbreak, since under normal classroom
circumstances the expected number of children with TB would be
zero. Two homeless men with TB in the same city, on the other
hand, would probably not meet this criterion, since TB in homeless
men is more common than in school-age children.
Universal genotyping will help considerably in identifying outbreaks,
since it will help to provide an answer not only to the question
“is there an increase in the number of cases in a subgroup?” but
also to the question “is there an increase in cases that belong
to a specific genotyping cluster that involves recent transmission?”
Another helpful aspect of having genotyping results available
is that they will help define the scope of an outbreak, since
genotyping results can identify persons with genotyping links
to outbreak cases where no epidemiologic links were known.
2. Transmission continues despite adequate control
efforts by the TB program.
For example, two TB patients who work at the same job might not
be considered an outbreak. If each was well investigated, including
thorough contact investigations with appropriate screening and
treatment for LTBI, there might be little else to do. If, however,
an additional person with TB appeared a month later with an isolate
that was a genotype match to the isolates from the other two persons,
this might meet the criterion of ongoing transmission despite
an apparently adequate TB-program response.
3. The contact investigation has grown to a size
that requires additional outside help.
This often happens when a TB program is devoting most of its
resources to conducting a large contact investigation, but the
demand for resources continues to increase to the point that the
program cannot meet its routine obligations for basic TB control
practices. At this point, declaring the situation to be an outbreak
can lead to obtaining additional resources to conduct an outbreak
investigation from the state program or from CDC. If the decision
is made to conduct an expanded contact investigation or an outbreak
investigation, see the respective sections for guidance about
how to proceed.
Genotyping Clusters with Possible Epidemiologic Links Identified
The next decision point shown in Figure 6.1 focuses on genotyping
clusters where known epidemiologic links have not been established.
The next question to consider is whether previously collected data
from contact investigations and record reviews show that persons
in a genotyping cluster share possible epidemiologic links. If possible
epidemiologic links are identified (e.g., the TB patients live in
the same neighborhood or were homeless) (see Chapter 4,
Combining Genotyping and Epidemiologic Data to Improve
Our Understanding of Tuberculosis Transmission, for a definition
of possible epidemiologic links), the patients might be involved
in the same chain of recent transmission and further investigation
might be helpful, especially if the genotyping cluster has more
than two patients or if the patients are considered high-risk. If
the RFLP results show that the presumed cluster is, in fact, made
up of genetically distinct isolates (i.e., the isolates have non-matching
RFLP patterns), there is no need to conduct a cluster investigation.
If, on the other hand, the RFLP results confirm that the isolates
belong to the same PCR/RFLP cluster (i.e., if the RFLP patterns
match), the TB program should consider conducting a cluster investigation
Whether to Launch a Cluster Investigation
Cluster investigations should be launched only when needed, since
they can be labor intensive. If RFLP results confirm that the isolates
belong to a single PCR/RFLP cluster, it is helpful to compare the
characteristics of the cluster with the prioritization scheme described
in Table 6.1. This prioritized list should not be interpreted as
providing absolute instructions about when to conduct a cluster
investigation and when not to; rather, it provides helpful guidance
about when a cluster investigation is needed and when it might be
wise to wait to see if additional TB patients are identified as
belonging to the cluster. The information that this prioritization
scheme is based on comes from the NTGSN study, and parts of it may
have to be updated when our experience with the PCR genotyping methods
grows.
Most commonly, clusters involve only two persons. One way to save
valuable TB program resources is to investigate only clusters that
involve at least three persons. Some programs will want to investigate
clusters of only two persons; if resources are available to do so,
this aggressive approach will identify episodes of recent transmission
sooner. If resources are scarce, however, conducting investigations
only of clusters with at least three persons is a reasonable policy.
In fact, if resources are really scarce, conducting a cluster investigation
only when the cluster grows to four persons may have to be adopted
as an interim policy until more resources are identified.
The decision as to what cluster size should be investigated is
influenced by whether the cluster contains high-risk persons. “High-risk”
in this setting refers to a) characteristics of the persons in the
cluster that might make them particularly infectious (e.g., having
cavities on chest radiographs), b) characteristics of the M.
tuberculosis strain that make it particularly dangerous (e.g.,
a multidrug-resistant strain), or c) characteristics of persons
in the cluster that, if shared by their exposed contacts, would
increase the risk of progression from LTBI to active TB (e.g., HIV
infection or other immunocompromising conditions) or would increase
transmission among a group (e.g., jail inmates, nursing home residents,
the homeless). A TB program that would otherwise decide to conduct
investigations only of clusters containing at least three persons
might decide to conduct an investigation of a two-person cluster
if one or the other persons with TB was considered “high-risk.”
Additional information that comes from future genotyping laboratory
reports may tip the balance in favor of conducting an investigation.
If one laboratory report identifies a two-person cluster, the TB
program might decide not to begin a cluster investigation if neither
of the two persons is “high-risk.” If the next laboratory report
identifies a third person with a matching genotype, the TB program
will probably want to initiate a cluster investigation of all involved
persons. In general, the decision whether to launch a cluster investigation
is a dynamic process, and a decision at an early stage not to do
one should not inhibit a TB program from changing its mind should
new information become available. If the decision is made to conduct
a cluster investigation, details on how to do so are provided later
in this chapter in the section titled, Cluster Investigations.
Table 6.1. Prioritizing genotyping cluster investigations.
Priority
(from high to low) |
Type of cluster |
Rationale for priority |
|
Suspected false-positive culture |
Need to determine which patients do not have
TB and stop treatment |
Cluster of three or more high-risk* patients
with possible epidemiologic links |
Need to confirm or exclude recent transmission
in large clusters of high-risk* patients |
Cluster of two high-risk* TB patients with possible
epidemiologic links |
Smaller clusters less likely to yield epidemiologic
links, but presence of high-risk patients deserves attention |
Cluster of three or more low-risk TB patients
with possible epidemiologic links |
Investigation of low-risk patients less urgent
than high-risk* patients, but larger clusters may deserve attention |
Cluster of two low-risk TB patients with possible
epidemiologic links |
Investigation of smaller clusters of low-risk
patients often does not yield helpful information
Investigations can, however, provide data for monitoring program
performance |
Cluster of high-risk* TB patients who have not
been found to have even possible epidemiologic links |
Low yield for establishing new epidemiologic
linksInvestigations can, however, provide data for monitoring
program performance Reserved for programs with sufficient resources |
Cluster of low-risk TB patients who have not
been found to have even possible epidemiologic links |
Very low yield for establishing new epidemiologic
links Investigations can, however, provide data for monitoring
program performanceReserved for programs with sufficient resources |
* "High risk" is defined as patients living in congregate settings
(e.g., correctional institutions and nursing homes), persons infected
with HIV or having other immunocompromising conditions, children,
patients with cavities on chest radiographs or with MDR TB, and
the homeless.
Genotyping Clusters with No Epidemiologic
Links
Not all genotyping clusters represent recent transmission, and
conducting a cluster investigation when the chance of gaining new
information is slim is often not a wise investment of resources.
If information from adequately conducted contact investigations
and case interviews does not reveal even possible epidemiologic
links between patients in a genotyping cluster, it is probably sufficient
for TB programs to simply ensure that standard TB control measures
are completed, such as ensuring that all cases are completely treated
and all infected contacts are identified and treated appropriately.
Of course, if future genotyping matches are identified and new patients
are added to a genotyping cluster, new epidemiologic links within
the cluster may become apparent, and at that point the TB program
may need to initiate a cluster or an outbreak investigation.
Last Reviewed: 05/18/2008 Content Source: Division of Tuberculosis Elimination
National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention
|